Below are my notes from EPS SCI 17 (a.k.a., the “dinosaurs GE”) during the Winter 2015 quarter at UCLA. While few students taking it now are likely to use GitHub on a regular basis, a fan of dinosaurs may find them an amusing and informative read.

Donations are welcome via Venomo or Square Cash, and help support me in offering ongoing mentorship.

For a nice primer on dinosaurs, see Dinosaurs: A Concise Natural History and Dinosaur Odyssey. If your quench for all things dinosaurs goes even further, find a copy of The Dinosauria. (None of these are affiliate links).

Open a pull request if you find any errors, and I’ll gladly correct them. To read the notes offline, download this page’s Markdown version and open it in Sublime Text, with the MarkdownEditing package installed.

Happy finding out that dinosaurs are birds!

• Lecture #1: 6 January 2014
• Paleontology
• What is a dinosaur?
• What is NOT a dinosaur?
• So what IS a dinosaur?
• The History of Dinosaur Research
• Mary Ann and Gideon Mantell
• Willian Buckland
• Sir Richard Owen
• Bone Wars
• Charles Knight
• Dump
• Lecture #2: 8 January 2015
• The Dinosaur Renaissance
• The Nature and Importance of Science
• Paleontological Research
• Exploration
• Funding
• Permitting
• Collecting and Transport
• Preparation and Replication
• Research
• dump
• Lecture #3: 13 January 2015
• Geologic Dating and Plate Tectonics
• Rocks
• Igneous Rocks
• Sedimentary Rocks
• Metamorphic Rocks
• Relative Dating
• James Hutton
• Uniformitarianism
• Principle of Superposition
• Principle of Original Horizontality
• Principle of Cross-cutting Relations
• Principle of Included Fragments
• Uncomformities
• Index (Guide) Fossils
• Absolute Dating
• Geologic Timescale
• Plate Tectonics
• The Earth’s Crust
• Faults
• dump
• Lecture #4: 15 January 2015
• Pre-Plate Tectonics Ideas
• Harry H. Hess
• Plate Tectonics in Motion
• Plate Life Cycle
• Divergent Margins
• Subduction
• Transform Boundaries
• Intraplate Volcanism
• Geologic History
• Building Continents
• Plate Tectonics’ effects on life
• Lecture #5: 20 January 2015
• Origin of Life
• Origin of Eukaryotes
• The Burgess Shale
• Evolution of the Asshole
• Why so much diversity?
• Evolution of Vertebrates
• Fishes
• Agnathans
• Chondrichthyes
• Osteichthyes
• Sarcopterygii
• Invasion of Land
• Why?
• Plants
• Invertebrates
• Vertebrates
• End-Permian Extinction
• Dinosaur Anatomy
• Anatomical Directions
• Axial Skeleton
• Lecture #6: 22 January 2015
• Vertebral Column
• Appendicular Skeleton
• Pectoral Girdle
• Humerus
• Manus (hand)
• Pelvis
• Foot posture
• Metatarsals
• Dinosaur Origins
• Dinosaur Characteristics
• Marasuchus
• Early Dinosaurs
• Nyasasaurus
• Pisanosaurus
• Dinosaur Take-Over
• Evolution
• Fitness
• dump
• Lecture #7: 27 January 2015
• Sexual Selection
• Major Lines of Evidence for Evolution
• Direct observation
• Industrial Melanism
• Artifical Selection
• Lamarckian Evolution
• Comparative Anatomy
• Homology
• Analogy
• Embryology/Development
• Biogeography
• Convergence
• The Fossil Record
• Cope’s Rule
• Red Queen Hypothesis
• Classification/Taxonomy
• Biological species concept
• Paleontological species concept
• Comparative Genomics
• Homeotic Mutations
• dump
• Classification
• Phylogentic Taxonomy
• dump
• Lecture 8: 29 January 2015
• Analogous/Convergent Characters
• Homologous Characters
• Homology
• Shared Derived Characters
• Sister Groups
• Monophyletic vs. paraphyletic Groups
• Paraphyletic Group
• Uses of Phylogenetics
• Ecology and Physiology of Dinosaurs
• Lecture 9: 3 February 2015
• Modeling Ecosystems in the Past
• Inferring Diet from Dentition
• Toothy Terms
• Tough Plants
• Meat lovers have it easy
• Specialized Teeth - Piscivores
• Dinosaur Physiology
• Types of Metabolism
• No way is best
• Surface Area to Volume
• Gigantothermy
• Lines of Evidence
• Lecture 10: 10 February 2015
• Cardiopulmonary evidence
• Insulation
• Bone Growth
• Lines of Arrested Growth
• Growth Rates and Curves
• Encephalization Quotient
• Isotopes and Body Temperature
• Turbinates
• Posture
• Biogeographic Evidence
• Summary of Evidence
• The Goldilock’s Hypothesis
• Mesothermy
• Lecture 11: 12 February 2015
• Theropods
• Forelimb Characters
• Huge Diversity in Size
• Herrasaurids
• Ceolophysids
• Abelisaurs
• Ceratosaurs
• Tetanurae
• Spinosaurs
• Allosaurs
• Ceolurosaurs
• Compsognathus
• Tyrannosaurs
• Ornithomimosaurs
• Alvarezsaurids
• Maniraptors
• Oviraptors
• Therizinosaurs
• Deinonychosauria
• The Large Carnivore Macroevolutionary Ratchet
• Speed of theropods
• T. rex: predator or scavenger
• Tyrannosaur Diversification and Analysis
• Dermestid beetles
• Lecture 12: 17 February 2015
• Major Plant Groups
• Pteridophytes
• Gymnosperms
• Angiosperms
• Sauropods
• Skull Modification
• Snorkeling Sauropod
• Elongate Necks and Tails
• Neck Posture
• Sauropodomorphs
• Prosauropods
• Sauropods
• Brontosaurus
• Lecture 13: Ornithischians
• Sauropod Diets
• Factors Driving Gigantism
• Herbivore and Carnivore Diversity
• Ornithischians
• Thyreophorans
• Ankylosaurs
• Tail Spikes and Clubs
• dump
• Stegosaurs
• Stegosaur plates
• Marginocephlia
• Sexual Selection
• Stenopelix
• Pachycephalosaurs
• Ceratopsians
• Psittacosaurus
• Protoceratops
• The Species Pump
• dump
• dump
• Lecture 14: 24 February 2015
• Ornithopods
• Efficient Herbivory
• Heterodontosaurids
• Hypsilophodontids
• Iguanodontids
• Dinosaur Reproduction
• Steps
• Secondary Sexual Characteristics
• Sexual Dimorphism
• Why sexual selection?
• Mating Techniques
• Laying Eggs
• Dinosaur Embryos and Neonates
• Mesozoic Communities
• What is climate?
• dump
• Lecture 15: 26 February 2015
• Geologic Formations
• Petrified Forest National Park
• Major Insect Groups
• Dipetera
• Hymneoptera
• Coleoptera
• Specific Species Examples
• Effigia
• Revueltosaurus
• Coelophysis
• Triassic Dinosaurs
• Jurassic
• Morrison Formation
• Herbivores
• Carnivores
• Energetics
• Cretaceous
• Grand Staircase-Escalante National Monument
• Rise of the Angiosperms
• Latitudinal Variation
• The Rise of T. rex
• Overview of Mesozoic Communities
• Lecture 16: 3 March 2015
• Cretaceous Waters
• Marine reptile Characters
• Nothosaurs
• Plesiosaurs
• Pliosaurs
• Placodonts
• Ichthyosaurs
• Mosasaur
• Turtles
• Origin of the Turtle Shell
• Archosaurs
• Other Life in the Sea
• Xiphactinus audax
• Ginosu shark
• Ammonites
• dump
• Pterosauria
• Pterosaur Flight
• dump
• Lecture 17: 5 March 2015
• Order Aves: Birds
• Archaeopteryx
• Feathers
• Feathered Dinosaurs
• Longisquama
• The Origin of Flight
• Ground-up Hypothesis
• Trees-down Hypothesis
• False Dichotomy
• Wing-Assisted Inclined Running (WAIR) hypothesis
• Basal Birds
• Enatiorinthines
• Ornithurines
• Paeleognathae
• Lecture 18: 10 March 2015
• J. John “Jack” Sepkoski
• Pull of the Recent
• Ecological Diversification
• Mass Extinctions
• Permo-Triassic Mass Extinctions
• The Siberian Traps
• Cretaceous-Tertiary Extinction
• Deccan Traps
• Signor-Lipps Effect
• Fossils
• Taphonomy
• Lecture 19: 12 March 2015
• Rancho La Brea
• Entrapment Story
• Taphonomy
• Mammalian Evolution
• Jaw Transition
• Mammal-like Reptiles
• Pelycosaurs
• Cynodonts
• True Mammals
• Goals of this Class

## Lecture #1: 6 January 2014

Dr. Anthony Friscia, from Integrative Biology and Physiology

Friscia sees this class as a sneaky, fun way to teach biology and geology.

“If you’re thinking you’re going to come in and just watch Jurassic Park, find a different class. This is not a ‘rocks for jocks’ class.”

The lab portion: We get to play with casts of specimens, analyze them, etc. There even used to be a practical final portion, since removed. The labs do matter for this class, and should not be skipped. We cannot interchange between labs at-will.

Quizzes are online, multiple-choice or true/false, and about 10 of them. They are about the previous week and from the reading. He puts in a large set of questions, and the system generates a randomized quiz.

Slides will be posted after class.

The final is not cumulative (whaaat).

There will be a movie night, where we will watch Jurassic Park where Friscia will narrate the movie and tell us all the inaccuracies. There will also be an extra credit “exercise” to the Museum of Natural History near USC. Instructions to follow later.

Dr. Friscia is a mammalian paleontologist, specializing in mammalian carnivores.

// These modern little carnivores like meerkats and mongooses, are so cute!

// Showing pictures of dig locations “Mostly we just walk around and pick stuff up. The dino people have to dig.”

Locations he’s been:

Utah, near Salt Lake City Fayum, Egypt Northern Kenya, near the Sudan border

### Paleontology

The study of the remais of ancient life, including body, chemical, and trace fossils.

It sits at the nexus of other sciences: biology (genetics, ecology, etc.), geology (stratigraphy, etc.), chemistry (isotopic dating), physics (biomechanics).

He calls it the “bastard science”. There are actually very few paleontology departments across the US. It’s usually part of other departments. For UCLA, we have a paleo minor under Geology (who go on to dinosaurs, inverterbrates, microfossils). Also common: Biology (-> verterbrates), and Anthropology (-> primates & mammals). Dr. Friscia actually began in Anthro, with primate evolution, then got bored, and decided to study the things that eat the primates.

Archaeology is different: it studies the remains of human civilization. Indiana Jones is an archaeologist, not a paleontologist.

“Notice the very large beer bottles in our tent…Paleo is way cooler.”

### What is a dinosaur?

Not as simple a question as it seems.

#### What is NOT a dinosaur?

Dimetrodon (the one with the cool sail and the teeth) is not a dinosaur. It is more related to us than dinosaurs.

Post (behind) orbital (where the eye is) fenestra (window).

Stem reptiles
-> Synapsids (mammal-like reptiles) with one postorbital fenestra -> Dynapsids (reptiles) with two postorbital fenestras

Dimetrodon lived in the late Paelozoic, not in the Mesozoic.

NOT a dinosaur: Wooly mammatoths. “And they’re wrong! Tell little kids they’re wrong. Size does not matter.”

Most dinosaurs were also not large. Mammutus (the mammoth genus) lived in the Quaternary period, very distant from the dinosaurs.

What about alligators? Not dinosaurs. They have different posture from dinosaurs and mammals. They were upright like us, with their legs right beneath us. Lizards and crocodilians have their leg on their sides.

There were upright crocodilians before the dinosaurs though. “Imagine a crocodile running on its legs at you.”

Marine “reptiles” are not dinosaurs. There are no aquatic dinosaurs, but the aquatic beasts that did live were pretty awesome.

Pterosaurs are also not dinosaurs. “I’m blowing your preschool mindsets right now.” Dinosaurs don’t fly!

Some dinosaurs did eventually evolve flight: modern-day birds are all dinosuars, from hummingbirds to ostriches.

The two closest relatives to ancient dinosaurs are birds and crocodiles.

#### So what IS a dinosaur?

1. Dinosaurs were terrestrial diapsids that lived in the Mesozoic.

Organisms that lived on land during the Mesozoic with two holes behind their eye.

1. All the descendants of the common ancestor of the pigeon and Triceratops.

Look at the diagram: ornithischians and birds are on the outermost branches of the node pointed to by “dinosaurs”

Dinosaurs are divided into saurischians (lizard hips) and ornithischians (bird hips). It’s all about the orientation of the three bones in their pelvis, with whether the pubis is pointed backward (ornth). or forward (saur).

Ornithischia is the most numerous group, including the duck-billed, horned, dome heads, ankllysaurs, and stegosaurs.

Saurichians has the theropods (bipedal carnivores) and sauropods the quadrapel herbivores.

We have 600 dinosaur genera (plural genus) and about 720 dino species. We can estimate that there are 1800 total genera and 2200 species. Estimates show that dinosaurs got way more diverse throughout the Mesozoic.

For comparison: 10,000 bird species, 1 million insect species, 320,000 plants, etc.

In this class, we normally mean non-avian dinosaurs when we say “dinosaurs”. They weren’t particularly diverse, but dominated for 100-150 million years. We should not forget that there were many other species during that era.

Meanwhile, we keep finding more dinosaurs (more in the past 20 than in the past 100), and our finds are of better quality. New places have been opened up, explored better with refined techniques and tools, etc.

### The History of Dinosaur Research

// This is part of the next lecture

For a long time, dinosaur fossils weren’t recognized as fossils. There seen instead as evidence of monsters, like the hippogriff.

Picture of an elephant skull, with a large nostril for the trunk, but it was interpreted as a cyclops. There’s a book about this, on the evidence in ancient literature and records where they misidentified fossils, like “The earliest fossil hunters or something”

#### Mary Ann and Gideon Mantell

Mary Ann actually did most of the work of describing and collecting. In typical science history stupidity, she wasn’t credited for much of it . Gideon, a physician, published a monograph in 1822 on his discoveries. He named the first dinosaur, Iguanodon. This was done in the Tilgate Quarry in England. They were the first to recognize dinosaurs as such.

#### Willian Buckland

William Buckland was the first to name a dinosaur (Megalosaurus, though he thought it was a giant lizard), coined “paleontology”, and taught Charles Lyell (father of modern geology). He’s of Oxford.

#### Sir Richard Owen

Sir Richard Owen (1804-1892) headed the British Museum of Natural History, a brilliant anatomist who coined the term dinosauria (“the thunder lizards”), and he was the first to think that dinosaurs were endothermic (warm-blooded). This idea was later lost. He believed in evolution, but not of man, and helped with some of Darwin’s specimens. Later, he clashed with Darwin.

In 1851, there was a world’s fair, the Crystal Palace held reconstructions of dinosaurs. Though inaccurate, they are still there.

Endothermy returned with the return of archaeopteryx in 1861 in Germany. It’s a transitional form between dinosaurs and birds (late Jurassic), and later added to Darwin’s Origin of Species as an example of evolution.

#### Bone Wars

In the late 1800s, late 1900s, Othniel Charles Marsh, and Edward Drinker Cope had the bone wars. They worked for museums on the East Coast and competed to find and collect bones. OC Marsh was with the USGS and president of the National Academy of Sciences. Cope was with the Academy of Natural Sciences, and named more than 1,000 verterbrate species. The fossils were put on display, and attraced large crowds.

#### Charles Knight

1874-1953, one of the first dinosaurs’ illustrators. His artwork shows the popular conception of dinosaurs at the time as large, lumbering, slow lizard-like things.

Major discoveries in the early 1900s:

• Gastroliths (stomach stones)
• Dinosaur eggs
• Dinosaur National Monument
• Cleveland-Llyod Dinosaur Quarry
• Mongolian expeditions by Roy Chapman Andrews
• Ceolophysis mass burial in New Mexico

## Lecture #2: 8 January 2015

Gertie the Dinosaur, one of the first cartoons ever made.

### The Dinosaur Renaissance

John Ostrom and his study of Deinonychus kicked off the modern view of dinosaurs.

(Velociraptor is actually small, but Deinonychus is the one that’s actually near our height.)

Ostrom solidified dinosaur ancestry of birds, w with the wrist bones, especially.

Jack Horner (dino mamas) found dinosaur embryos, but most importantly, he found a nesting ground, similar to modern birds, and the first to show dinosaur childcard.

Bob Bakker (known as a sort of asshole) popularized dinosaur endothermy. He was also a great artist, who illustrated his own books. He showed them to be active and more bird-like.

Both of them were Ostrom’s students.

This dinosaur renaissance brought about paleobiology. We’ve found more species in the last 25 years than in all previous years, include Antarctic dinosaurs, and ones with feathers. And of course, we got the asteroid impact theory, and modern tech for investigating fossils, including CT scan and computer models, etc.

Questions remain: How “warm-blooded” were dinosaurs? How smart were they? What are their origins? What are the details of bird origins? How fast did they move? Did they care for their young? Why did large size evolve multiple times?

All of this means dinosaurs are immensely popular these days too, like Land Before Time, Land of the Lost, etc. “A Nypmphoid Barbarian in Dinosaur Hell” (WTF), Dinosaurs (a sit-com), Barney, “I Am a Paleontologist” music video

So many videos, haha. He’ll post links to them all.

### The Nature and Importance of Science

In 2006, we found two-thirds of American suck at understanding science.

Carl Sagan: “Most newspapers in America have a daily syndicated astrology column. How many have daily syndicated astronomy column, or even a science column?”

The U.S. public is out-of-sync with the rest of world on science.

Science is a process for finding out things about the natural world.

// The scientific method always seemed self-evident to me // When they laid out the diagrams to me, it seemed lame // The diagrams didn’t mesh with my thinking and experience // Dr. Friscia’s diagram showing all the messiness is much more like it

The best question we can ask is, “How do they [the scientists] know that?” when it comes to dinosaurs and everything else we learn.

Our theories/paradigms/laws are always at risk being replaced by being more inclusive, more sophisticated description of nature. That’s the principle of correspondence. All scientific ideas are subject to challenge and modification.

Science is self-correcting and progressive via open debate until a strong consensus is reached. Results must be replicable, and research is peer-reviewed. Science builds on itself and its previous work. It asks more questions than it answers.

It is not a democracy; it’s a rigid meritocracy. There is no “centrist” view; most debate happens at the edges.

There are two main methods: inductive (where we form hypotheses to explain observations [and then test them through further observations]–“The present is the key to the past”) and deductive (we use experiments to confirm/deny a hypothesis).

Science is part of–and influenced by and an influence–on culture: “You don’t get to have your own facts”

### Paleontological Research

#### Exploration

To know where to find fossils, paleontologists examine geology, especially geologic maps that should where certain rock types of certain ages are, etc. Also handy is where fossils were previously found. They’re also known for their superstition on where to go. A lot of work happens in deserts because there’s not a lot of vegetation in the way. There’s also less erosion and less geological activity.

#### Funding

Hit up the National Science Foundation (NSF), the National Geographic Society, the Society of Vertebrate Paleontology (SVP), the Geological Society of America (GSA), and even the petroleum industry. They’re required to mitigate their impact on the environment sometimes to avoid fossil destruction. Universities may also have funding.

All the money received has to be accounted for. The NSF has less than one-half of one percent of the national budget.

• Overhead (up to 1/3 or 1/2 of it): the university takes this for university upkeep
• Students’ tuition can be paid for with some grants
• Equipment
• Travel

#### Permitting

A permit is required for fossil-finding on federal land manged by the bureau or one of the services. Any fossils found on these lands must be given to a public museum after study (via an accession agreement setup beforehand with a museum).

Private lands just require permission of the landowner. The fossils start off as the property of the landowner.

Foreign expeditions vary in rules and regulations.

The story of “Sue” (the largest and most complete T. Rex fossil) is an interesting case study. Found by the Black Hills Institute on the Cheyenne River Indian Reservation in South Dakota in 1990.

Found on private, leased land, the owner was part of the Sioux tribe, but the land was in a trust held by the US DOI. So there were many claims on the fossil. Seized by the FBI in 1992, the courts found in favor of the land ownder. The Field Museum in Chicago bought it, for \$7.6 million, with help from Disney and McDonald’s. Museums don’t like paying for fossils; it’s a bad precedent. It’s the position of the paleontology association that fossils should never be bought/sold.

#### Collecting and Transport

Pull out a topo map and walk around in an area for prospecting.

Most stuff is found via surface-collection, i.e. pick stuff up from the ground. Quarrying is sometimes used for a rich area or for a big fossil. Screen-washing is where we put sediment in the water, and washing it, which gets little rocks and fossils. Life in the field is much like extended camping with lots of work. Everyone’s restless and itching to go.

#### Preparation and Replication

Fossils are preserved (via a thin glue), and removed from their matrix (the rock surrounding a fossil), then fossils are molded and cast (in plaster, fiberglass, etc.). Casts are what are usually on display.

#### Research

The museum work happens mostly in backrooms. The research collections are full of specimens for researchers. Only a small amount is on public display. Researchers get to measure and compare them.

GIS (Geographic Information Systems) let paleontologists do things like model the location of fossils in the La Brea tar pit in 3D. CT scanning lets them get 3D scans too via many x-rays. Finally, computer modeling lets them create physical models.

## Lecture #3: 13 January 2015

### Geologic Dating and Plate Tectonics

Three main rocks: sedimentary, metamorphic, and igneous rocks.

Sedimentary rocks were built up from little bits packed together. Igneous rocks were recently melted. Metamorphic rocks are igneous or sedimentary rocks transformed under heat and pressure.

Rocks are made from a mix of minerals, which in turn are chemical combinations of some common elements (oxygen, iron, carbon, etc.).

### Rocks

#### Igneous Rocks

These are solidified molten rocks, and either intrusive (plutonic) or extrusive (magmatic). They have many crystals of various sizes, varying based on how long it took for the rock to solidfied. Longer solidification means larger crystals.

Intrusive rocks solidified beneath the crust, i.e. not exposed to the atmosphere, vs. extrusive rocks solidified in air.

Batholiths are intrusive igneous rock structures, e.g. walls of granite in Yosemite. They’re the roots of volcanoes. The magma under the volcanoes solidified, and later erosion exposed them.

Basalt flows (solidified lava flows) are an extrusive igneous structure.

#### Sedimentary Rocks

They’re made of eroded clasts from other rocks. They’re deposited by water, air (aeolian), glaciers, etc. They’re normally classified by grain size, running from coarse conglomerates to fin mudstone. You can use the taste test to see if it’s sand/silt-like or mudstone-like.

Chemical sediments are called evaporites. The water evaporated from a body of water that had dissolved minerals. Example: salty water that evaporates and leaves behind the salt. and biogenic (“made by life”) sedimentary rocks includes limestones, which are actually made of chemicals deposited by living things, often calcium carbonate.

Aeolian deposition (a-oh-lee-un) is deposition by air. The Great Sief Dune in Egypt is a nice example. Over time, pressure can solidify the sand into sandstone, like at Zion National Park.

Fluvial deposition is deposition by water, and exemplified by badlands, as in South Dakota. A river on occasion overflows and deposits sediments.

#### Metamorphic Rocks

This is rock formed from solid state changes in the the textures of other rocks. WE begin with protolith (unaltered rock). Under pressure and high temperature, we get something else.

Limestone -> Marble Shale -> Slate/schist/gneiss

Death Valley has some great examples of metamorphosed limestone. The canyons there show rock that was deep before and then lifed to the surface.

All the rocks can eventually become each other.

Now, we only really get fossils in sedimentary rock, as the other rocks only form under pressure and heat. Low-grade metamorphic (not much depth or heat) rocks sometimes have fossils. Igneous rocks are useful for dating though.

### Relative Dating

“No, I don’t mean incest.”

This means we don’t know a year on something, but we are able to determine that it’s older or younger than something else.

#### James Hutton

The father of modern geology, including the concept so deep time (the Earth is old, and there has been plenty of time for stuff to happen) and uniformitarianism (the processes that happen today happened in the past too, and there’s not a lot of catastrophe driving change). Catastrophism, previously popular, posited a young Earth shaped by sudden changes, e.g. the Biblical flood. His ideas were popularized by Charles Lyell

#### Uniformitarianism

Deep time: Large amounts of time and recurring processes that have small changes can account for the observations we make today.

“The present is the key to the past.”

Opposed to catastrophism/Neptunism, which has a large event accounting for the features we see.

Modern geology stands in-between, closer to uniformitarianism, as we do have large catastrophes sometimes, the idea of punctuated equilibrium.

Hutton was wondering how layers ended up at near-right angles to each other. He posited that events inclined one set of sediments, and then another new (flat) layer of sediments was laid atop it.

#### Principle of Superposition

Older rocks are under younger rocks, at least at first.

#### Principle of Original Horizontality

Rock layers, called strata or beds were originally deposited horizontally, i.e. gravity.

The folded layers near Lulworth Cove, England have cool-looking folds.

#### Principle of Cross-cutting Relations

Older rocks may be cut by younger rocks or other geological features, typical of igneous intrusions. Something had to be there first (in solid form) for it to be cut through.

#### Principle of Included Fragments

If fragments of one material are included in another, then the included material must be older. All clasts are in a sedimentary rock must be older than the rock in which they are now found.

This is why it’s hard to date sedimentary rock, as isotopic dating would be dating the clasts, which were actually formed at a different time from when the sedimentary rock solidified.

#### Uncomformities

There are sometimes gaps in time in the sedimentary record, as when no beds are deposited or part of the rock record is removed by erosion.

Sedimentation -> deformation -> uplight & erosion -> subsidence -> uplight & erosion

To solve this, events usually don’t affect the whole Earth at once, so we can look at rock elsewhere from the same time period.

We’ll have relative rock-dating diagrams on our exams.

#### Index (Guide) Fossils

Easily distinguishable, widespread, around for short periods of geologic time, and abundant, we can correlate the strata using these fossils.

This is fossil correlation, known as biostratigraphy.

Probems: In one area, there may be a missing nearby strata because of the ancient environment, animal migration, etc.

Using everything we’ve discussed, we created the Geologic Time Scale with our eras, periods, and epochs. These are defined by assemblages by fossils.

### Absolute Dating

Now, we want to put a time on everything, and we need something that tells time, e.g. we measure by something that happens with regular periodicity: Earth’s rotation or revolution, pendulums, the vibrations of crystals and atoms, etc.

Radiometric dating is what we’ll use. Radioactive decay occurs at a constant rate, with parent atoms decaying into daughter atoms.

We know the half-life of various elements, how long it takes for half of the element to decay.

To measure half-life, we can measure over shorter periods of time, and measure the amount present after some time, and we fix our time t = 0 when we begin.

// Friscia is doing a simulation. The TA is handing out pennies. // This is interesting…

// Ah, he had us flip the pennies. Anyone who got heads sat down. // We got variation, of course, but we saw the number of people // standing up halving each time.

Here, the standing people are parent element. The sitting people are daughter element. And the time between flips was the half-life.

Overall, about half of the element will still decay with each half life.

We have the graphs 2^x and 2^{-x} here.

Some common parent/daugthers:

Uranium 238 -> lead 206 has a half-life of 4.5 billion years

Carbon 14 -> Nitrogen has a half-life of 5730 years

By knowing what the half-life is, and the current percentages of the parent/daugther, we can the rock’s age, when it formed with its 100% parents.

Crystallization of the rock resets the clock, so igneous rocks are used for dating, not sedimentary rocks or actual fossils.

We have to assume: There is no daughter isotope at the time of crystallization, and that no parent or daughter has entered or left the same since crystallization, but there are methods to correct for any exceptions to them.

It is not possible to date all rocks by radioactive isotopes. We can’t directly date sedimentary rocks and their fossils, so we date the igneous rocks cross-cutting them to get brackets on the the fossil’s ages.

### Geologic Timescale

The last 500 million years has most of the fossils, due to the hard parts from the Cambrian Explosion.

Dates we should know:

• Oldest minerals on Earth: 4.5Ga
• Oldest rocks on Earth: 4 Ga
• Oldest record of life: 3.5 Ga
• Beginning of the Phanerozoic Eon/Paleozoic Era: 550 Ma
• Beginning of Mesozoic Era/Triassic Period: 245 Ma
• Beginning of Jurassic Period: 210 Ma
• Beginning of Cretaceous Period: 150 Ma
• Beginning of Cenozoic Era/Tertiary Period: 65 Ma

Thus dinosaurs were around for for ~150 million years. Humans have only been around for ~1 million years. The time between Stegosaurus and Tyrannosaurus Rex is more than the time between us and T. Rex.

Dinosaurs were around longer than they’ve been gone.

### Plate Tectonics

“Broken plates, just like a Greek wedding - OOPAH!”

// OMG

The layers of the Earth have different densities and thicknesses. How do we know about this? From earthquakes. We can examine the refraction of pressure waves of earthquakes on different sides of the planet and when we received those waves.

#### The Earth’s Crust

Continental crust is thicker, less dense, and a lot older than oceanic crust, and so it floats just a bit higher than the oceanic crust.

The crust itself is not constant; it breaks.

#### Faults

Faults are fractures in the crustal rocks, from stress. A normal fault is when two pieces of crust are pulled apart. A reverse/thrust fault has them being pushed together where one set of rocks starts to pile atop the other. Sunset Blvd. is a reverse fault. Finally, strike-slip/transform faults is where pieces of crust are sliding past each other, like with the San Andreas.

We can date again, knowing that the fault must have happened after the layers formed, and must be younger than the layers they cut across.

## Lecture #4: 15 January 2015

### Pre-Plate Tectonics Ideas

The Deluvian Flood (Biblical flood).

Uniformitarianism (Lyell and Charles Darwin [Chuck D.]) as well as land bridges as the hand-waving explanation for how animals spread around the globe.

Upheaval theory (early 20th century).

Continental drift (by Wegener) in 1915. He said that the continents fit together like a puzzle. He came up with the name Pangaea (“all the Earth”), and later came “Laurasia” (northern group of continents) and “Gondwana” (southern group).

He showed biographic evidence: terrestrial organisms (that could not have crossed oceans) that were spread across modern continents. Put the continents together, and their ranges matched up.

There was also glacial and rock evidence. By looking at the rocks moved by glaciers and the striations they scratched out, the direction of glacial movement could be inferred.

With the modern map, it looks random, but as a supercontinent, it becomes apparent that they spread out from a central region.

Rocks in the Appalachians match up with rocks in Scotland, Greenland, and Norway. At the time though, Wegener’s explanation was rejected for lack of a mechanism. The continents couldn’t have possibly moved through the ocean floor’s dense basalt.

Another line of evidence: paleomagnetism. Magnetic rocks record the magnetic field’s inclination (parallel near the equator, and near-vertical near the poles) and its reversals (every tens of thousands of years). The magnetic bits are crystallized and locked into position toward what was North at the time. Why the periodic flips? Not a fully resolved question; turbulence in outer core?

Thus, we can get the latitute from where the rocks are, or where the poole was at that time.

### Harry H. Hess

A naval sonar operator and geologist, he worked to map the topography and magnetism of the ocean floor. He found things like:

• The world’s longest mountain range
• Volcanoes and heat output at the crest of the mountains
• Gradation of sediment thickness outward
• Magnetic “stripes”, the same on both sides (the reversals of the Earth’s MF)

Farther away from the crests of the mountains, the sediment was probably older.

New crust is being formed at those underwater volcanoes, pushed out on both sides, recording the magnetic field at the time, then solidifying. The further away from the mountain range, the older the crust.

Crucially, the magnetic stripes matched what we had already found on land.

Problem: The Earth isn’t getting bigger. If we’re making new crust, we have to be destroyed.

Answer: crust is destroyed in trenches. It’s like a circular conveyor. The mechanism? Convection!

We heat something up, it rises, cools off, and falls back down, where it heats up again, goes up again, etc. It’s a circulation. The mantle convects, and so the crust is pulled apart at the bulge, and then dragged down into the trenches with it. As for the continental plates, they’re thicker and stuck between the oceanic plates.

Spreading and sinking happen all the over world, and they form the lifecycle of a plate.

This phenomenon explains the “Ring of Fire”, where we have active volcanoes.

### Plate Tectonics in Motion

QUESTION: How do we identify where the continental plates are?

#### Plate Life Cycle

##### Divergent Margins
1. At a divergent margin, a rift opens and spreads to make passive margins. A lot of normal faults emerge, and new oceanic plates may be formed.

Example: East Africa, where a new ocean could form.

A passive (intraplate) margin is one where the continental plates has moved far away from where the current spreading is happening.

In the middle of continental plates, little geologic activity occurs. They’re sometimes called shields, or cratons, the stable center of continental plates.

“When I go to national parks, I find the safety barriers to be more of a suggestion.”

##### Subduction
1. Subduction (convergent boundaries) and mountain-building

Here, the oceanic plate is subducting beneath a continental plate. It does so irregularly, giving rise to earthquakes and volcanoes.

Types:

• Oceanic-oceanic

Gives rise to things like island arcs; Caribbean

• Oceanic-continental

Example: The Andes, or the Northwest US

• Continental-continental

Example: The Himalayas, with the Indian and Eurasian Plate, which are still growing.

Density determines which one subducts; the denser one descends. Continents are less dense than the oceanic ones. For the oceanic case, it gets denser and cooler with age, and will subduct. However, continental plates tend to just ram together

The crust going down, melts and that magma melts upward to cause volcanoes.

Evidence of old subduction is batholiths.

The main boundary thrust is the meeting place of two plates (verify this).

##### Transform Boundaries

Plates can slide past each other with strike-slip faults.

This is either between continents, or linking spreading There may also be mountain-building here.

Example: The San Andreas fault running through California. LA is on the Pacific plate. Eventually, we’ll get to San Francisco. How quickly do plates move? On the order of the growth rate of our fingernails, meaning centimeters over a year

#### Intraplate Volcanism

We can get volcanics in the mdidle of plates, called hot spots. Magma from the mantle burns through the oceanic crust and builds a volcano. Then, a second volcano is built as the oceanic plate rolls over the hot spot. The first island eventually erodes into an atoll, and eventually goes beneath the waves altogether.

Example: Hawaii, which is part of a whole chain. This kind of volcanic activity tends to produce rather “calm”, shield volcanoes.

An interesting case is when a hot spot burns through continental crust. As that’s thick, it takes longer, and produces large, explosive volcanoes.

Example: Yellowstone

The last time it blew, it covered the plain states in meters of ash. There goes our breadbasket.

“And between this and now is…600,000 years.”

“suturing” – continents ran into each other and closed the oceans between them.

### Geologic History

The Appalachians used to be much taller but have since eroded.

#### Building Continents

Ocean-ocean boundaries can change to ocean-continent. The island arc gets sutured to the continent. The western US has lots of terranes, island chains, etc. that got added on.

We used to have a massive Western Interor Seaway, a book called the Oceans of Kansas.

### Plate Tectonics’ effects on life

• Dispersal routes

It determines where animals can move.

• Isolates groups so they evolve independently

Example: Ceratopsians (horned dinosaurs) are only found in Laurasia

• Affects climates

Example: Dinosaurs in Antarctica (recent development)

## Lecture #5: 20 January 2015

“Life Before the Dinosaurs” is the theme of today’s lecture. Earth is 4.5 billion years old; see the fascinating Cosmos episode for how that was determined.

### Origin of Life

Modern life traces back to 3.5-8 Ga, right after the end of the Late Heavy Bombardment.

Primordial Earth was an interesting mix of gases like CH4, NH4, H20, N2, H2, H2S, CO2, O2, with lightning, volcanoes, vents, and a lot of UV light, as the ozone layer hadn’t formed yet.

(Methane; ammonia, hydrogen sulfide, and maybe oxygen)

It’s theorized that many of these compounds and molecules came from interstellar space, brought on comets and asteroids. The extent of this is still a debated point.

“There are no aliens coming for our water, so don’t worry.”

There’s the Miller-Urey (uri) experiment, which simulated the early Earth. I want to repeat this experiment, but with different configurations!

They didn’t find life, but they did find a lot of complex molecules, the building blocks of life. The earliest fossils are in very old sedimentary rock, often partially metamorphosed. To find them, they slice up thin layers of rock, and then look for them via microscopes.

For macrofossils from this period, see the stromatolites, from 3.5 Ga. They’re mounds made by one-celled, photosynthetic organisms. Sediment settled, and the bacteria kept moving up, so layers of sediment and bacteria form into a fairly large structure at ~1 m in height.

There are modern examples of this, in shallow oceans.

These photosynthetic bacteria changed the atmosphere, as they released oxygen as a waste product.

Banded iron formations from 3-1.5 Ga are evidence of increased oxygen in the atmosphere.

### Origin of Eukaryotes

Previously, we had simple, one-celled organisms.

The symbiosis of bacteria-like organisms resulted in the formation of organelles like mitochondria, chloroplasts, and possibly also the nucleus.

Ediacaran Period fauna: just before the end of the Precambrian, we get the evidence of the first multicellular life.

We found it in Australia, dated to 600-700 Ma. Interestingly, they’re so old, and so different from modern life, that we don’t know what they were.

We also find burrows, tracks in the ground made by animals with at least a mouth and anus to dig into the ground. Eat at one end; blast out at the other. This shows life growing in complexity.

At this point, all life is in the oceans.

### The Burgess Shale

Found in Canada, found by Walcott (spelling?) is one of the best records for the beginning of the Phanerozoic, with phenomenal preservation, even soft parts.

Now, we see shrimp-like things, and copepods (which are small and shrimp-like). We also see old worms, which look similar to modern fire worms.

Some of these are old, oceanic equivalents of what we find on land now. Hallucigenia is like a worm, with spikes.

Trilobites: they go extinct in Paleozoic, but we find many of them in the Shale. One of the most interesting finds is Pikaia, a primitive vertebrate, which looks similar to the modern Amphioxus.

Predators: We see weird predators like Opabinia, with a mouth on the end of the trunk and 5 eyes, like Anomalocaris, which got up to 2 meters.

We also have many things we don’t understand.

The main points:

1. A lot of diversity
2. A lot of experimentation

The big question: Why this sudden “explosion” of diversity?

### Evolution of the Asshole

Primitive examples like anemones, have but one hole; everything goes in/out of that one hole. With two, we can have more complex body plans.

#### Why so much diversity?

Another possibility: there was a large mass extinction, which would leave a gap to fill.

Also possible: a positive feedback loop. Complex animals reshape the environment, e.g. left-over burrows that can be reused; more niches emerge.

One good driver: the arms race between predator/prey.

Finally, we have had a Snowball Earth, where we had complete, global glaciation, right before the Cambrian; it may have caused/contributed to extinction.

We will now trace the vertebrates.

### Evolution of Vertebrates

Key events:

• Evolution of bone
• Evolution of jaws
• Moving onto land; lungs and limbs
• Evolution of endothermy (constant body temperature)

Bones probably first evolved for mineral storage, rather than structural support. Endothermy will come later, as that’s a big question for dinosaurs.

### Fishes

4 main groups:

• Agnathans (jawless fishes)
• Chondrichthyes (cartilaginous fishes)
• Osteicthyes (bony fishes)
• Sarcopterygii (the lobe-finned fishes)

#### Agnathans

Jawless, the extinct groups of these were quite diverse, but we only have 2 living groups: lampreys, and hagfishes (scavengers, often found in dead whales; they can make slime to protect themselves).

“They’re disgusting, gross animals” – woooow, professor

#### Chondrichthyes

They have cartilaginous skeletons, and are the first group to have jaws, which allows for predation.

Examples: chimeras, sharks, skates, and rays

They have oil-filled liver for buoyancy. We have a comparative anatomy class, where they actually dissect sharks.

#### Osteichthyes

“Nemo and everything else.”

Bony fishes, they have fins which are thin rays supporting a membrane.

Most have a lung, modified into a swim bladder.

They are the most diverse of vertebrate groups, with ~25,000 specides.

#### Sarcopterygii

“The meaty wings”; they have more muscular fins with small bones for support, homologous to the bones in early tetrapods. We have two living examples: lungfish, and coelacanths.

These are the ancestors of the early tetrapods.

In fact, the transition from fins to limbs is well-documented. Example: Tiktallik (375 Ma).

### Invasion of Land

This happened in the middle ot late Paleozoic:

• Plants (~420 Ma)
• Invertebrates (~410 Ma), esp. arthropods, including insects
• Vertebrates (~360 Ma)

#### Why?

• Escape predation
• Less competition (not a lot of organisms on land)
• More resources (sunlight, oxygen, and later the plants, etc.)
• Easier to move around

A predator example: Dunkleosteus was up to 6 meters long! Jaws first arose in the mid-Paleozoic.

Less competition:

• Especially apparent for founder species

More resources:

• Oxygen is more plentiful in air
• Sunlight is less diffused in air than in water

Easier to move around:

• No fluid friction

#### Plants

Mosses were the first to invade land. They had little protection against desiccation (drying out), and a weak cuticle.

Ferns evolved later, and had a strong cuticle, support, regulated gas exchange via stomata, and transport tissues.

Both of these need water for reproduction.

Seed plants evolved later, and are independent of water for reproduction.

#### Invertebrates

These were the first animals to inhabit land, and there probably many independent colonizations.

Insects goes crazy, with an especially large number of beetles.

Quote from evolutionary ecologist: “If evolution isn’t true, then God had an inordinate fondess for beetles”

#### Vertebrates

Endoskeletons are developed for support against gravity, get scales for anti-desiccation, gas exchange via lungs (air is easier to move, and has more oxygen).

Sight and hearing become more important.

Some vertebrates, like amphibians, still have issues with desiccation. Reproduction requires water or eggs/larvae will dry out.

We have three groups: salamanders/newts, Caecilians (snake-like), and frogs/toads. They have a permeable skin, which have a permeable skins

We get the amniotes, which develop a hard egg to prevent desiccation. They are the first group to become independent of water.

They split into two groups, which lead to mammals, and birds/dinosaurs/”reptiles”

### End-Permian Extinction

The Paleozoic Era ends with the biggest mass extinction in Earth’s history. 90-95% of life is wiped out.

Possible examples:

• Formation of Pangaea
• Marine anoxia: oxygen levels drop from no mixing of

49% of all marine families. 63% of all terrestrial families

New groups replace the formerly dominant forms.

### Dinosaur Anatomy

“Dinosaur” is a taxon (plural, “taxa”) is a grouping of organisms, e.g., a species, a genus, etc., defined on the basis of characters that all the members share.

For fossil taxa, these characters are usually parts of the bony anatomy:

• Medially open acetabulum
• Astragalus with ascending process
• No postfrontal bone
• Humerus with long deltopectoral crest

• 3 or more sacral vertebrae
• Cnemial crest on tibiba,
• etc.

#### Anatomical Directions

Anterior (cranial) vs posterior (caudal) (for humans)

Dorsal vs. ventral

Medial vs. lateral

CREATE ANKI flashcards with pictures!

Proximal vs. distal

The standard anatomical direction in medicine so the person standing, palms-forward looking at us.

Axial vs. appendicular skeleton.

The axial akeleton includes the stuff on the midline: skull, vertebrae, etc.

The appendicular skeleton has all the limbs and the parts that attach the limbs to the body.

### Axial Skeleton

Includes: Skull, vertebral column, ribs, and sternum

Dinosaurs have an antorbital fenestra in front of the orbit (where the eye is) and they have 2 post-orbital foramen.

Dinosaurs (and us too) are missing a post-frontal bone in their skulls.

They are two types of skull:

• Kinetic (multiple joints)
• Akinetic (1 joint)

We have two, which allows our mandible to work, and which allows a stronger jaw and bite.

Kinetic skulls allow flexibility to widen the jaw, as seen in snakes (which can move the sides of their jaws [which are actually dislocated] independently)

Most dinosaurs had kinetic skulls, which allowed chewing.

## Lecture #6: 22 January 2015

### Vertebral Column

“Ver-tee-bruhl”

The vertebrae form the vertebral column. The spinal cord travels inside of here; it’s part of the nervous system, and is protected by the column.

Vertebrae have a body, and above that an arch. Between is a hole through which the spinal cord travels.

The different regions of the column:

• Cervical vertebrae (neck)
• Dorsal (thorax with ribs)
• Sacral (pelvic) [dinosaurs have at least 3 of these]
• Caudal (tail)

Those arches are where many muscles attach. Dinosaurs (many of them) have ossified tendons on their vertebral column, meaning that the tendons became bone.

### Appendicular Skeleton

The arms (forelimbs) and legs (hindlimbs) and any attachments.

#### Pectoral Girdle

This attaches the forelimb (arm) to the axial skeleton.

It’s not a very strong connction, common in many
tetrapods; most attachment is with muscles and little or no bony connections. Compared to humans, dinosaurs have a separate coracoid.

Where the humerus (upper arm bone) meets the pectoral girdle, we have the glenoid fossa. In dinosaurs, this distinctly faces caudally (toward the tail).

#### Humerus

The upper arm bone, we have a big ridge where we have the deltoid muscle attach, the deltopectoral crest. In general, large ridges/bumps on bones correlate with large muscles.

#### Manus (hand)

We have the carpals (wrist bones), then the metacarpals (palm bones), and finally the phalanges (digits, as “thumb” distinct from “fingers”), numbered from 1 from thumbward direction. Singular “phalanx”.

The phalangeal formula is the number of phalanges of phalanges on each finger. For humans: 2-3-3-3-3 (notice 1 joint on thumb, and 2 on the others).

Dinosaurs had an asymmetrical 123-hand, as digits 4 and 5 are reduced in them.

#### Pelvis

This attaches the hindlimb to the axial skeleton. We have three bone: illium, pubis, and ischium.

We have the acetabulum, the hip socket.

“ass-suh-tah-boo-luhm”

This is where our hip joint goes. In dinosaurs, they have a defining hole in it.

This is partly because of their upright posture.

We also have an in-turned head, but that was separate and convergently evolved.

#### Foot posture

Plantigrade: We walk with the sole of our foot on the ground

Digitigrade: Many animal on all-fours walk on their digits

Best seen as when we’re in heels

Unguligrade: Always walking on the very tips of their toes

The ankle is up in the air.

“Dinosaurs are always wearing heels.”

Being digitigrade is a characteristic of fast runners, alongside:

• Elongated lower leg bones
• Fused leg elements (lighter)
• Reduced toes

This means longer strides and lighter legs. Theropod dinosaurs had all these traits.

Other defining hindlimb characterics:

• Cnemial (“nee-mee-ahl”) crest on tibia, where the quads attach.

• Ascending process of the astragalus, where fusion of bones makes for stronger, lighter joints

In the hindfoot, dinosaurs tend to have a 234-foot, with reductions in digits 1 and 5.

#### Metatarsals

Dinosaurs have a sigmoid (s-shaped) metatarsal III. An s-shaped middle metatarsal, letting the bones be packed together more tightly.

The combination of all the aforementioned characteristics is unique to dinosaurs, and point to dinosaurs being (primitively) fast runners.

### Dinosaur Origins

Amniotes are the animals that evolved the amniotic egg, freeing them from water.

Cladograms come in detail next week.

The definiing characteristics of dinosaurs:

Dinosaurs are diapsids: two holes behind the orbit (where the eye is). (Early, mammal-like reptiles did lay eggs; only later did we evolve away from them)

Turtles are sort of special, and there’s theories on where they fit. They’re anapsids (no holes), and are thought to have lost their holes secondarily, and our best guesses are based mostly on DNA.

We can divide the diapsids into the lepidosaurs (the “true” reptiles) and the archosaurs (“ark-oh-soar”; the name means “ruling”) The latter have the antorbital fenestra and dentary fenestra (a hole in the jaw). The antorbital fenestra is a hole in front of the orbit.

Euparkeria is an early archosaur from the early Triassic and around a meter long or less.

Up another node, we have the ornithodirans which have a specialized ankle joint.

Just below this node is “crurotarsi/pseudosucia”, plural “curorotarsans”.

Smok wawelski was the biggest land predator in Europe through the early Jurassic, including dinosaurs. Crurotarsans were the biggest predators for a while. and hugely diverse then. They filled the dinosaur niche before the dinosaurs arrived.

That special ankle joint actually unites Dinosauria and the pterosaurs.

It’s called a mesotarsal ankle joint, meaning the middle one.

Pterosaurs come later for origin of flight.

#### Dinosaur Characteristics

Based on the anatomy we’ve seen so far, we can see that the earliest dinosaurs were probably primitivelt bipedal (which may have hlepd with running), and had modified skulls and arms.

#### Marasuchus

From the middle Triassic: It’s possibly a “silesaurid”, a mixed bag of early “dinosauromorphs” (hard to tell if dinosaur, as so early).

### Early Dinosaurs

Most were small, bipedal, and saurischian, and originated in the mid-late Triassic (~230 Ma).

#### Nyasasaurus

Possibly the oldest dinosaur from the middle Triassic, found in Tanzania. Previously, we dated back to the late Triassi, as seen with Eoraptor, a small bipedal that may have been an early sauropod.

#### Pisanosaurus

Onne of the earliest Ornisthicians, for which we have few fossils until the Jurassic.

#### Dinosaur Take-Over

Two theories compete to explain why the dinosaurs came to dominate:

• Competitive displacement

Dinosaurs may have out-competed everyone else around them

• Opportunistic

Perhaps most of the earlier life was wiped out by a massive extinction, and then the dinosaurs got lucky and filled the ecological niches left behind. A recent study suggests the latter, as the dinosaurs may not have been in direct competition with the synapsids and archosaurs

This is historical contingency, where the dinosaurs won by chance. This is passive replacement, rather than active replacement.

Some scientists suggest that the synapsids (big mammal-like reptiles) and Crurotarasns were evolved as big plant eaters and eaters of the big plant eaters, whereas the dinosaurs were better adapted for eating small invertebrates, e.g. insects.

E.C. Olson was the main driver behind this idea, and had the idea of community change driving evolution.

Community evolution drives the evolution of major groups.

The evolution of dinosaurs may be been driven by evolution of new plant-eaters: the insects, which out-competed the big herbivores, which in turn collapsed the food supply for those previous predators. By the Late Triassic, dinosaurs had spread globally.

### Evolution

What is evolution? It is:

• Change though time (generally)
• Change in gene frequencies (microevolution)
• Descent with modificaiton (macroevolution)

The main mechanism for evolution is natural selection:

1. Invididuals in a population naturally vary (randomly)
2. More individuals are produced than can survive
3. The variations influences the survival and reproduction of individuals (some will do better than others; this is selective, and determined by the environment)
4. If the variations in features is heritable, there will be evolution.

Key points:

• Evolution work on populations, not individuals
• All evolution is genetic at the most basic level, with changes in the gene pool.

• Macroevolution is microevolution writ large, the synthesis of genetic inheritance and evolution by natural selection.

• Evolution has both random and selective components. The characters that are selected for in a particular environment are adaptations. There’s no drive toward “perfect” form.

Ecology is the interactions of organisms with each other and their environment. Evolution is a reaction to ecology.

#### Fitness

This is the relative ability to survive, reproduce, and propagate genes.

Selection acts on the fitness of individuals to cause changes in the average fitness of a population. Selection can be natural or sexual.

## Lecture #7: 27 January 2015

### Sexual Selection

Competition for mates between individuals can lead to characters not necessarily good for survival can end up being selected for. (Also by Darwin)

While they may not help with or even detract from survival, these traits affect their ability to pass on their genes to the next generation.

// The interaction or discord between these two effects // would be fascinating to study.

Classic example: Peacock feathers, big beetle horns, etc.

### Major Lines of Evidence for Evolution

1. Direct observation
2. Comparative anatomy
3. Embryological development
4. Biogeography
5. Fossil record (paleontology)
6. Classification
7. Comparative genomics

### Direct observation

#### Industrial Melanism

Two examples: industrial melanism, and artificial selection.

The first: the peppered moth. It has versions: black and white.

Historically, the white form was more common. Then, the darker one spread more from 1870-1920. The second Industrial Revolution was covering trees with soot, as well as killing off white lichen. The environment had changed, as did the selective pressures.

In 1950, Bernard Kettlewell, released moths into urban and rural areas, and compared how many he recaptured afterward. In the urban area, far more of the darker form remained, and vice versa in the rural areas.

Then, we saw the opposite effect,, as in 1958, the UK passed a clean air act. The experiment was run backwards, a nice line of evidence for the converse when the conditions had been switched.

Similarly, the US had its Clear Air Act in 1963, and an experiment in the US in Michigan showed the same effect.

All four of Darwin’s premises are met:

1. The moths vary in their color pattern
2. They’re subject to predation
3. The different color patterns vary in their probability of survival
4. This variation in color is heritable

#### Artifical Selection

The deliberate elimination or cultivation of particular individuals with desirable traits by humans.

Darwin used artificial selection as an analogy for natural selection. He experimented with pigeons, creating wild-looking ones from natural pigeons.

The classic example: the domestication of the dog, and all the varieties of breeds. These all came from the gray wolf, canis lupis. Why/when wolves became domesticated is still under debate. Fascinating how quickly we pulled this off: most dog breeds were created in the last 200 years.

Sometimes, evolution (including artificial selection) is about trade-offs: speed, size, strength, cuteness, etc.

Another example: oil content in corn has been increased. Similarly, modern corn looks nothing like the maize from which we developed it.

Again, the premises are met:

1. Individuals vary in some character desirable to humans
2. More are produced than are allowed to survive reproduce
3. They vary in a character that is used as a basis for selection by humans.
4. The differences are inheritable

More examples: antibiotic resistance in bacteria, lizards on isolated islands, etc.

The main obstacle to direct observation is time between generations.

#### Lamarckian Evolution

Giraffes: necks don’t stretch to get that long length.

Classic, cruel experiment: Some guy cut off rats’ tails, and did so for all their offspring. He never got tail-less rats.

The Darwin-Wallace explanation is far more logical: The giraffe population varies naturally, and the longer neck is more favorable for survival.

#### Comparative Anatomy

The study of the similarities and differences in morphology (animal and plant form).

Example: the limbs of tetrapods are very similar in bone structure/plan.

##### Homology

Homologous features are derived from a common ancestor. They’re not necessarily similar in form or function.

##### Analogy

Similar in form/function, but not derived from a common ancestor; they’re due to convergent evolution. The similar form is just due to similar function.

Example: butterflies and bats.

They have very different wing structures, but they both have wings for flight.

Another example: convergence in fusiform (spindle/torpedo-like) body plan: sharks, purpoises, etc.

Differences reveal differing ancestry: e.g., the different planes in which sharks and dolphins flip their tails

Vestigial structures (our appendix, wisdom teeth, etc.), are another thing that only make sense in light of evolution. They were fully functional in ancestors, and are now reduced in size relative to closely-rated species. They persist in reduced size “if they’re not harmful. Example: the flightless Galapagos cormorant, which still have wings, despite being flightless, or the hindlimbs in whales.

Would we ever lose our appendix or wisdom teeth? Sure: if there was a selective pressure for it, but our medical care prevents that. That said, mutations might cause us to just lose them, and the lack of selection for them might mean their gradual disappearance.

#### Embryology/Development

1. Strongly supports descent with modificaiton

2. The development of homologous structures within embryos follow a similar sequence.

// I once had gills and atail!

1. Structures may appear early in embryos and then disappear.

2. These are best understood in the context of evolution.

Compare how embryos look so similar at first.

The pictures are so damned hard to tell apart without training.

Ernst Haeckel studied this. He had the The Biogenetic Law:

“Ontogeny recapitulates phlyogeny.”

Ontogeny = development Recapitulate = repeat in concise form; summarize Phylogeny = the evolutionary history of species

This is sorta right. It suggests that evolution can only occur by adding on to ontogenies, and not by shortening them, and a strict interpretation is clearly wrong.

#### Biogeography

This is the study of the geographical distributions of animals. Before Darwin, it was accepted that the geographical distributions of animals were non-random. No one knew why.

Also, people noticed how different niches were filled by different animals.

##### Convergence

Similarity in form between distantly related species is the result of adaptation to similar environments. We used to have a marsupial wolf, the Tasmanian wolf.

When a taxon invades a new area, it diverges to fill unfilled niches. Example: the finches of the Galapagos with all their different beaks.

Another example: South American canids.

When the Panamanian land bridge formed between N. and S. America, dogs arrived in S. America, and diverged into many different species. They’re similar to coyotes, foxes, wolves, etc. that came from N. America.

#### The Fossil Record

1. Most fossils of extinct organisms can be classified into groups of existing organisms (they share similarities due to descent with modification).

2. Observed differences between living and extinct forms become greater as you go back in time.

3. Flora/fauna living during any one period, tend to be intermediate in form between those that come before and those that come after.

// I wonder if anyone has applied graph theory // to evolutionary trees.

The transition from fins to limbs is well documented (fish to amphibians), and similarly from limbs to fins (the development of whales). We’ve found transitional fossils.

Archaeopteryx is the transitional fossil between non-avian dinosaurs and modern birds.

##### Cope’s Rule

Lineages tend to evolve larger average body sizes over time. This is not true for all groups. Why might this be so?

##### Red Queen Hypothesis

Predator and prey evolve in tandem just to keep up with each other. The sauropods and theropods get bigger to keep up with each other. Prey becomes too large to eat -> Predator grows bigger -> etc.

#### Classification/Taxonomy

1. Before Darwin, organized organisms into a hierarchy of forms, and explained this as evidence of God’s wisdom. Carl Linnaeus (1707-1778) created his system based on the similarity of form.

The classification system is called the taxonomic hierarchy.

Darwin realized that this similarity in forms could be explained by evolution from a common ancestor.

##### Biological species concept

A species is a group of organisms that can potentially mate and have viable, fertile offspring.

##### Paleontological species concept

But how do determine species for things that are just fossils now?

“I’ve played some very romantic music, but I’ve never gotten fossils to mate.”

This is based on morphological differences observed in living groups and applied to fossil groups. Similar levels of differences, etc.

#### Comparative Genomics

1. DNA is identical to all organisms
2. Closely related organisms share more genes
3. Genes that control the development of body parts, like limbs, are similar among all animals that have those body parts. E.g., flies and humans.

DNA is the ultimate shared primitive character. All living things have it, with the same structure and the same code.

##### Homeotic Mutations

Strange, wild mutations happen sometimes. They occur when we have mutations in the HOX genes.

These genes set up the basic axes of body orientation, and they are highly conserved, meaning that similar species are very similar for them. They’re also colinear, meaning that the genes for thorax might be rigtht next to the ones for the head, etc.

### Classification

We want to build the family tree for dinosaurs.

Darwin surmised that speciation was a fission process, that linage branch makes another, and deduced that everything had a common ancestor, eventually getting us the ultimate common ancestor.

Things that are more closely related will be closer on the tree, and look more similar.

This tree-like structure lends itself to a method of classification, a taxonomy. We don’t need evolution for building a system, but nowaday we use homology for:

#### Phylogentic Taxonomy

Uses homologies to generate a tree that shows relations of organisms, the trees are cladograms.

Group similar things together using characters. Then, we can build a nested tree structure, where the characters (traits) used for classification let us split up things into smaller and smaller groups.

## Lecture 8: 29 January 2015

### Analogous/Convergent Characters

Features that are similar but that are NOT inherited from a common ancestor. They are analogous. Example: Bat wings and bird wings. Wings evolved twice, independently of each other.

### Homologous Characters

These are featuers that are similar because they were inherited from a common ancestor.

Example: Feathers are homologous in eagles and ducks.

However, features can be both.

For example: the forelimbs of tetrapods are homologous, but the wings of bats and birds are analogous. It depends on how we’re examining them.

For cladograms, we use traits that are shared organisms whose common ancestor all had that trait.

These diagrams communicate relationships, not time. We can have dinosaurs right alongside modern birds. The only sense of time is when we go bottom-up. It’s relative, however.

We’re not showing lineages, e.g., who evolved into who. Rather, we’re saying who’s related. The main power of them is showing how traits have been acquired by different groups.

### Homology

A homology is a trait that two taxa shared that was present in their last common ancestor.

#### Shared Derived Characters

We want shared derived characters, shared only between those taxa derived from their last common ancestor, i.e., the clade derived from the LCA. We’re looking for shared characters that are specific to a group.

Shared primitive characters are also shared by taxa outside of the clade.

We use shared derived traits to classify organisms in our taxonomies, and build our cladograms.

Example: Pokémon!

Both of these are homologous, the difference is in the unique presence in a clade, i.e., “What is unique to a group?”

Examples: Nursing young in mammals -> Derived

Nursing young in humans -> Primitive

The same characters can be derived primitive, depending on the taxon.

Not only that, sometimes characters are lost. The loss of a character can be a derived character for a clade, e.g., snakes are also tetrapods. It can be tricky to figure out if a trait was loss, or never evolved in the first place.

Only use evolutionary novelties to determine relationships.

We want to find a character that unifies all of the Pokémon, except one. This makes our first branch. Then, we look for a character that does the same for the remaining subset.

At the end, the cladogram is fully resolved, with only two branches from any particular point. Tic marks label the diagnostic characters or loss thereof.

We can use different characters to define our clades, but we use parsimony to prefer the cladogram with fewer character changes.

Ocam’s Razor: The simplest solution is the best. This isn’t always right, but it gives us a hypothesis to test.

Cladograms themselves are hypotheses for how evolution proceeded. There may have been a lot of losses, reappearances, etc., but we begin with the simpler hypothesis.

To test our cladograms, we examine other taxa, and attempt to add them to our diagram. When there are too many characters or taxa, we turn to computers to do the work for us.

// I wonder how to implement this as a program // I wonder how many combinations are possible // for n taxa?

Nowadays, we use DNA sequences too.

Clade: All of the organisms derived from one common ancestor. They all share unique homologous characters.

Note that “shared” and “primitive” are relative.

The taxa are at the end of branches. The branches themselves are called lineages.

The common ancestor sits at the branching point. Cladistics predicts that we will never find “the” common ancestor, just ones close to it. They’re considered hypothetical.

Only the nestedness of groups matters, we can swivel branches. Even with missing taxa, we still see the same relationships.

Who is more closely related to whom? -> Who shares the more recent common ancestor?

Trace the branches back up the tree, and find their earliest intersection. We can also have equally related organisms. We’re going down the tree.

#### Sister Groups

Taxa that share a common ancestor. Go back to the ancestor node, and see who is on the other branch going up the tree.

### Monophyletic vs. paraphyletic Groups

“One-branch” vs. “part-branch”

A group defined by the presence of unique derived characteristics.

It’s an ancestor and all of its descendants; they are each other’s closest relatives. We only name clades.

#### Paraphyletic Group

A group defined by the absenece of some derived character.

It’s an ancestor and NOT necessarily all of its descendants.

The popular usage of “reptiles” and “dinosaurs” epitomize the problems with overusing this.

We name clades only for monophyletic groups.

Examples: binomial nomenclature for species: genus + specific name -> species name

The old-fashioned Linnaean system runs from Kingdom to Species, but this doesn’t work well for modern phylogenies. It’s too easy to run out of names.

The new system just calls everything a clade, with only genus and species still kept specific.

Humans don’t need to be at the top of a cladogram. We’re interested in the relationships displayed, not our species’ ego. Are we evolved from chimpanzees? No, we shared a common ancestor that was neither a chimpanzee nor a human.

Having computerized methods turns relationships-studying into a science, and they made it clear that birds are derived from small, carnivorous dinosaurs. Tony doesn’t like how some paleontologists spend most of their time on this. He thinks the goal is to figure out what life was like in the past, and cladistics should be used as a first step. Finding out relationships lets us know what modern life is most closely related to the extinct creature we’re studying.

### Uses of Phylogenetics

We can use phylogenetic bracketing, e.g. crocodiles and birds have color vision, and dinosaurs evolved between the two. The parsimonious explanation is that dinosaurs had color vision too, but it’s possible that it was evolved, lost, and then evolved again.

We don’t know if dinosaurs had color vision, but we can guess. Another example: determinign the placement of T. rex’s fleshy nostril.

### Ecology and Physiology of Dinosaurs

Consider the modern grassland food web. Who eats whom? This leads to the trophic pyramid. Energy and carbon are being recycled. Note that moving up a level induces an efficiency cost: only ~10% is retained from level to level. All the energy comes from the Sun, but it’s lost all the time to heat. That’s why there are usually ~10 times more herbivores than carnivores.

So something like the La Brea Tar Pits is interesting: there are many more carnivores there. What does this mean? It was probably a carnivore trap: herbivore got trapped, and then the carnivores got trapped themselves while going after them.

When it comes modeling ancient ecosystems, we assume that they had a similar structure to modern ecosystems. This is a relatively good assumption to make, as it’s all energy conservation at the end of the day.

## Lecture 9: 3 February 2015

// “Uhh, what is the format of the exam?” // “Really?!” It’s right on the slide in front of us, haha.

### Modeling Ecosystems in the Past

We assume past ecosystems are similar to modern ones:

• Interconnected
• Inefficient -> More herbivores than carnivores

This is a relatively good assumption to make.

### Inferring Diet from Dentition

The shape of teeth tells us something about how animals ate and processed their food. Teeth handle the physical digestion (breaking things into smaller pieces), and chemical digestion happens in the gut.

#### Toothy Terms

Dinosaurs have a thecodont dentition, meaning the teeth sit in sockets and have roots. The other types are pleurodont (some lizards), and acrodont (fish, other reptiles). One of the old terms for archosaurs is “thecodonts”.

Another tooth term is homodont, with “homo” meaning “same”. The teeth are of the same shape, true for most vertebrates.

Most dinosaurs were homodonts.

Most mammals are heterodont; we have canines, molars, incisors, premolars, etc. They’re all of different shapes.

There are some heterodont dinosaurs, e.g. heterodontosaurus. Typically, being a heterodont means a varied diet.

Polyphyodont means tooth replacement occurs constantly throughout life.

(All) dinosaurs were polyphyodont. Scans show a conveyor belt of replacement teeth on the way.

Diphyodont means only 2 generations of teeth: juvenile and adult. Typically, we have more adult teeth than baby teeth, as our jaw grows.

This helps with chewing in mammals, as we can have precise occlusion (bringing opposing surfaces of teeth in contact, i.e. upper and lower teeth interlock and meet). Being a diphyodont helps with this, as we’re not constantly having new teeth pop into place–or rather, out of place.

Most animals don’t chew, but this was a key adaptation in mammals for processing plant matter. Most reptiles are not herbivorous, in fact.

#### Tough Plants

The cuticle on plants in tough to break down, and grit/dirt from grass wears teeth down. Not only that, leaves are nutritionally poor, so we have to eat a lot. Mammals solved this with hypsodonty (tall teeth), which gives them margin for wearing down their teeth.

Herbivore teeth also tends to be flat, with lots of ridges. This allows for grinding/scraping.

To solve this, dinosaurs had their own solutions. Sauropods had gastroliths. A muscular part of the gut was filled with rocks they ate. When food came in, they squeezed, letting the rocks do the crushing for them. Thyreophorans and certaopsians had gut fermentation, i.e., they left it there like a compost pile. That’s why gorillas have big bellies.

Hadrosaurs and ceratopsians had the innovation of dental batteries. The teeth grow in a row upward, and we grind at the top, which wear down and are replace from below. We get a grinding/slicing surface between them. This is a way of chewing.

Humans can chew side-to-side like a cow. But hadrosaurs did something different.

They took advantage of their cranial kinesis, with their lower teeth pushing up, pushing their upper teeth out, which then come back. Their cheeks pumped laterally like an air pump for a fireplace. This gives a grinding motion.

Another thing that helps is the presence of a predentary bone, especially in Ornithischians. Ceratopsians also had an extra rostral (nose) bone. This is basically like a little beak that helps them nip off plants

Another thing about chewing: We need cheeks. Otherwise, the food spills out the sides. Looking for the presence of cheeks can let us know.

#### Meat lovers have it easy

As for eating meat:

• Just tear off a chunk and swallow
• Meat is relatively easy to digest
• Requires blade-like teeth for tearing and cutting flesh
• Simple conical teeth helps for puncturing/killing

Cats kill with their front teeth, and use their side teeth to slice up the meat before swallowing. Their raspy tongue cleans meat from bone. This is why cats have that weird scratch tongue.

“So when your cat’s licking you, it’s trying to take all of the meat off of you. “

Serrations are a jagged, saw-like surface. They help hold what is being cut in place, and also keep the edge sharp. They can also hold bacteria, as a bit of rotting flesh with disgusting bacteria might get it sick. This point is disputed.

The location of the jaw joint gives us another clue. If the joint is in-line with the tooth row, we have a scissor-like structure, perfect for carnivores. On the other hand, herbivores have the jaw joint above the row, which lets them have the teeth come together for a flat, grinding action. Sometimes, it’s below the tooth row, but the effect is the same.

The two also emphasize different muscle groups. Sometimes, herbivores have big pointy teeth, like in warthogs. These are usually a result of sexual selection, and are irrelevant to eating.

#### Specialized Teeth - Piscivores

Fish-eaters have long, thing snouts with homodont, pointer teeth for catching fast prey.

Some dinosaurs were fish-eaters too, lik e spinosaurs. Many pterosaurs (not dinosaurs) also seem to have been fish-eaters. Similarly, insect-eating animals tend to have no teeth, and instead just have long snouts and tongues.

Remember that our goal is to figure out where an animal fit into the ecosystem.

### Dinosaur Physiology

How animals get and use energy.

This comes up with the “cold-blooded” vs “hot-blooded” debate.

#### Types of Metabolism

There are two major axes:

Endotherms (generate heat internally) vs ectotherms (need external sources of heat).

Homeotherms (maintain constant internal body temperature) vs. Poikiloterms (body temperature varies with the environment).

Most mammals and birds: endothermic homeotherms. (This is what most people mean by “warm-blooded”)

Most modern “reptiles”: ectothermic poikilotherms. E.g., when Friscia ran into rattlesnakes while hiking in the earlr morning.

Exceptions:

Bats and some birds are endothermic poikilotherms, as well as hibernating mammals. They can drop body tmeperature and metabolic rate,etc.

Some fish and insects are endothermic homeotherms. Some large reptiles are ecothermic homeotherms.

#### No way is best

Pros of endothermy:

• Sustained activity
• Active at night

Cons:

• Requires A LOT of food, 10-30x similarly-sized ectotherms.
• Not efficient at small body sizes

Pros of ectothermy (which is the primitive condition):

• Need little food

Cons:

• Capable of only short bursts of activity
• Limited ability to be active at night

The key to catching lizards: Tire them out. We can keep going for miles; they cannot.

#### Surface Area to Volume

Imagine two spheresn and compare their surface/volume to volume ratio. Note that the smaller the sphere, the closer a surface is to the the center.

We dcan model animals as shapes, and larger animals tend to have lower SA/V ratios.

Small endoterhms have a problem with retaining heat (because they have high SA/V), and large endotherms have a problem with dumping excess heat (because they have SA/V). They need radiators to stay gool, e.g., elphnat’s surface area.

The problems with retaining limits on endotherms gives ua a minimum bound on mammal’s size, as they lose too much heat otherwise.

#### Gigantothermy

Large animals retain heat, and large ecoterms can be homeothermic too, like large turtoises.

To infer things about dinosurs, we can again use phylogenetic bracketing, but this doesn’t work very well for metabolism. It’s not clear who evolved what when.

### Lines of Evidence

• Cardiopulmonary evidence: hearts and lungs
• Insulation
• Bone and growth rates
• Neurophysiology (relative brain size)
• Isotopic evidence
• Skull features: turbinates
• Postire: bipedality and running
• Biogeographic distribution: Do we find animals in cold places

## Lecture 10: 10 February 2015

Phylogenetic bracketing doesn’t help us between birds and crocs for dinosurs.

### Cardiopulmonary evidence

Looking at some fossils, some people think that some dinosaurs may have a 4-chambered heart. This is an adaptation common among endotherms.

Except crocs also have 4-chambered hearts. (Though there is some debate over whether this is homologous or analogous; crocs have a slightly different heart that’s more useful for diving)

Bird lungs are interesting. Unlike ours, which branch off as dense trees, birds also have air sacs connected to their respi ratory pathway. They have lungs, but also all these air sacs. This allows for one-way airflow while breathing. The air goes into a sac, then across the lungs, and then out. This prevents dead space. Air is always moving across the lungs.

This is counter-current flow of blood and air. Birds need it, as flight is costly on oxygen.

Another guiding hint: endotherms have higher respiration rates than ecotherms.

It turns out some dinosaurs also had air sacs. But, a study that came out in the past few years showed that crocodiles have their own version of one-way air flow. Again, used more for diving.

Thus, our evidence point is still equivocal.

### Insulation

Only modern endotherms have insulation:

• Feathers in birds
• Fur for mammals

// I love feathered raptors. They look so cute

Many, many dinosaurs had feathers too. We’ll look at the evolution of birds and flight later.

### Bone Growth

Bones are not solid. There’s a solid wrapping of compact bone and then the inside is either hollow (birds) or we have cancellous bone (spongy bone). Marrow is found within the spongy bone.

Bones grow in a particular way. They start off as a piece of cartilage that gets replaced with bone. It happens systematically. We can look at the bone from the growth plate and figure out how tall we’ll be as a little kid.

Mammals and birds have determinate growth. “Reptiles” have indeterminate growth. The growth is still in a similar fashion, but it just keeps growing, laying on more layers. The growth rate does slow down though. Growth keeps going. With humans, we eventually stop growing.

Another thing to look at: mammalian bone is highly vascular. Even the compact bone has blood vessels running through it. Every 5-10 years, our bones are replaced. That reworking is unorganized though, and called woven.

We get an osteon, and a Haversian canal for the blood vessel. The dark spots are bone cells.

Bird bone turns out to be similar to mammalian bone.

#### Lines of Arrested Growth

Contrastedly, we see lines of arrested growth in ectotherms. Continuous growth in ectotherm happens in fits and starts. Times where there was slowed/stopped growth result in these lines, which often formed on an annual cycle. This is similar to tree things.

So how do dinosaur bones look?

They’re also woven,like mammalian bone,–but they have some lines of arrested growth. Another twist: some mammals get LAGS too, often ones that live in climates vary greatly.

#### Growth Rates and Curves

Mammals and birds have a 3-part growth curve:

• Slow growth as infants and toddlers
• Fast growth as juveniles and adolescents
• Slow growth (or stopping) as adults

• Ecotherms tend to have a relatively constant growth curve.

In dinosaurs, we see 3-part growth curve, esp. among the biggest ones, and grew at rates faster than birds or mammals, on the order of 20 kg/day for sauropods (like whales), or 2 kg/day for theropods (birds and mammals).

That growth rate is similar modern endotherms.

Life spans: 50 years for sauropods, 30 for large thropods, 7-15 for medium ones, and < 5 for small ones.

### Encephalization Quotient

This is the ratio of brain size to body size.

Endotherms have EQ, because brains are expensive. Dinosaurs have a range, with some similar to modern birds.

E.g., the Diplodocus skull would have held a grapefruit brain, with a body that would barely squeeze into this lecture hall.

### Isotopes and Body Temperature

Different isotopes have the same name of electrons and protons, and so act the same chemically, but their weight is different due to number of neutrons.

Lighter isotopes are preferred for most reactions though, as they’re easier to move around via heat. At higher temperatures, this difference becomes less, as then there’s enough heat to move everything around.

Extremities on the body (like limbs and tails) will be colder in ectotherms. Our cold hands are nothing the limbs of a lizard. So, in ecotherms, we’d expect a larger difference in isotope distribution between bones in the core regions and those in extremities.

From these isotopic comparisons, we can see that dinosaurs show extremity-core temperature differences comparable to mammals.

This is relative work, but we can get absolute measures of temperature too, though clumping of isotopes at different temperatures. Finding the absolute body temperature of dinosaurs, we see rather high body temps.

### Turbinates

Mammals and birds have unique structures in their nose. They’re scroll-like, and help make breathing more efficient. We have them too.

Upon inhalation, cool dry air passes over moist, warm turbinates and is heated and saturated with water. This is easier for the lungs for absorbing oxygen.

Upon exhalation, the air passes over cooler, dryer turbinates, and the heat/moisture is dumped back onto the turbinates. This helps conserve heat and moisture. Pursuit predators that run prey down tend to have more complex turbinates.

To summarize, turbinates:

• Condition incoming wter
• Conserve heat
• Conserve water

This is important as high ventilation rates create a ehat/water conservation problem.

Sadly, nasal turbinates rarely fossilize well. We use nasal volume as a proxy. Birds also have these, but they’re cartilaginous.

However, a more recent study suggests that dinosaurs did have turbinates.

### Posture

Dinosaurs and mammals have an upright posture, unlike the sprawling posture of lizards. Crocodiles and mammal-like reptiles have a semi-sprawled posture.

Upright posture allows breathing while running. We can time our inhalation/exhalation with the compressions.

That dinosaurs were upright is suggestive of endothermy.

### Biogeographic Evidence

There were dinosaurs that lived near the Poles. But, the Mesozoic were a much warmer time. Also, dinosaurs may have migrated. We can see this from the isotopes in the tooth. There may have been annual migrations like modern mammals.

Some dinosaurs lived at the poles year-round.

### Summary of Evidence

Ecology: predator-prey ratios among dinosaurs are similar to modern mammals

Cardiopulmonary: Tends toward endo

Insulation: Had insulating featers -> edno

Bone and growth rates: Leans endo, but could be ecto too

Neurophysiology: Reflects ecto based on small brain size for most

Isotopic evidence: Endo, with little termpeatures difference

Skull features: May have had turbinates -> Endo or ecto

Posture: Non-sprawling -> Endo

Biogeographic distribution: endo

### The Goldilock’s Hypothesis

Animals can put energy into

Maintenance: renewing cells, generating heat, finding food Production: growth, reproduction, fat storage

Endotherms put a lot (97:3) of energy into maintenance, but ecotherms apportion more evenly (60:40). Being an endotherm is very costly.

### Mesothermy

Dinosaurs were somewhere in between. They burned energy like ecotherms (more energy into growth). They were probably gigantothermic. (due to low SA/V ratio).

Thus, they’re in the middle, they have a large pool of energy, and can spend more on growth.

Ectotherms: Can put more energy into production, but with a smaller pool of energy

Endotherms: Have a larger energy pool, but their maintenance is costly.

They raise their body temperature, but don’t “defend” it. They don’t use energy to actively maintain it. Evidence for this comes from growth rates vs metabolic rates. They fell into the middle for metabolic rates, like tuna, echidna (egg-laying mammals), and sea turtles.

But there is a breaking point. Increasing metabolic rate, we eventually become endothermic. Some theropods may have become fully endothermic.

Thus, dinosaurs were probably a mix of eco/endotherms, and may have changed as they grew, e.g. diplodocus babies vs. adults. Some taxa were probably more to one end or the other.

// Midterm scores will be posted right after class // Outside of lab room, an answer key will be posted, // plus a sheet with ID numbers, scores, and answers

Mean was 74.5%, with a large leanign toward the right. The high score was 61 (out of 64, as one question was removed).

Friscia scales according to the highest score. He will also take improvement into account. There’s a magic formula: the difference between midterm and final percentages, with some added to final score. If we’re at the mean or above it, we’re fine.

## Lecture 11: 12 February 2015

It’s Charles Darwin’s birthday today, same day and year as Abraham Lincoln.

He apparently had some antislavery views, and was originally training to become a doctor, then a parson.

[On becoming a parson] “Kids who don’t have anything to do, that’s what they do, like being a psych major–yeah, I went there!”

On the HMS Beagle, Darwin chilled with the captain, who didn’t consort with the lowerclass crew. He was actually deathly seasick most of the time. He married his first cousin. In 1840, he developed some mysterious illness, and spent most of his later life infirmed. He did get buried in Westminster Abbery, near Newton.

Origin of Species doesn’t discuss human evolution, but Descent of Man does. Prolific author overall.

Recent article just showed evolution of Darwin’s finches controlled by a gene named ALX1. This links macro and micro evolution. We have it too, and it may contribute to our facial expresion diversity.

### Theropods

We’re now going to begin our march through the dinosaur taxa.

Theropods and sauropods fall under saurischians.

Each group will be used as examples for talking about previous general concepts.

Theropods in general are:

• 40% of all species named (popular with paleontologists), despite only being in 10-20% of finds
• Most debated group in studies
• Very diverse taxonomically and ecologically
• Widely distributed: present at every dinosaur fossil locality

They used to be considered the only dinosaur with feathers (modern research has shown otherwise).

They are carnivores, with an intramandibular joint, and sharped, recurved teeth, sometimes with serrations.

Their skulls are pneumatized, with air spaces to lighten the skull. They’re between and even within bones. Think of human sinuses.

They trend toward larger brains, higher EQs, and have enhanced hearing, smell, and stereoscopic vision.

to wear an eyepatch and try to catch a baseball.”

They’re the only group to retain full obligate bipedality. Dinosaurs were primitively bipedal, but only theropods remained only walking on two legs.

They have 234-feet, 5 sacral vertebrae, stiffened tails, and are digitigrade. These are all adaptations useful for cursoriality (runnning).

#### Forelimb Characters

Loss/reduction of digits IV, V, and sometimes III. They sometimes had opposability of digit I. Their forelimbs were sometimes quite dinky though, but still strong. They weren’t vestigial.

#### Huge Diversity in Size

We have 6000 kg for T. rex to 1 kg for Microraptor. Including the hummingbird, we have a 5,000,000x range. T. Rex is the largest (in terms of weight) terrestrial predator ever.

Not all were big, and they weren’t the only predators around.

Theropod classification is crazy.

### Herrasaurids

They’re South American from the mid-late Triassic (230 Ma), and are possibly theropods/dinosaurs. They’re defined by lack of characters.

### Ceolophysids

They’re mainly small, from North America and Africa, from the late Triassic and Jurassic. It’s the most numerous dinosaur fossil, due mainly to the Ghost Ranch Site in New Mexico, which has a mass burial of them.

It was probably a big “flock” of them when a mass flood happened.

They were originally thought to be cannibals, but recent analysis showed the content of stomachs to be archosaurs.

### Abelisaurs

They’re mainly Gondwanan and Cretaceous. Some have headgear (horns), and may have had paddles for hands rather than fingers.

### Ceratosaurs

The horned lizards. They have horns or ridges (like Dilophosaurus). We have no evidence for spitting poison. They’re mainly Gondwanan and Cretaceous as well.

### Tetanurae

One of the clades we’re looking at.

They’re characterized by:

• A stiff tail
• Further reduced digits (IV, V, and III reduced/lost)
• Pubic foot (probably for muscle attachment)

They also have a maxillary fenestra in front of the antoorbital.

#### Spinosaurs

Mainly Cretaceous.

Large, but lightly built, and sometiems with large sailbacks. It’s not clear what they’re for.

Some were probably piscivorous and semiacquatic. This clade includes Megalosaurus, one of the first dinosaurs named.

As for the spines, some suggested purposes:

• Thermoregulation: cooling or heat storage
• Display (mating)

### Allosaurs

Middle Jurassic to late Cretaceous.

They’re Laurasian, and mostly medium sized.

The Cleveland-Lloyd Dinosaur Quarry shows a bunch of allosaurs specimens. The lopsided carnivore-herbivore ratio shows a likely predator trap, like sticky mud near a river bank.

### Ceolurosaurs

“see-lo-soars”

They’re convergent on the Allosaurs and Ceratosaurs, and are characterized by:

• Arctometararsals
• Semilunate carpal

### Compsognathus

Late Jurassic, turkey sized, probably feathered, and were in Europe was which was mostly near-shore islands.

### Tyrannosaurs

Late Cretaceous, mostly Asia and North America, and possibly also Australia. They had robust skulls, and Dilong was a feathered example. Some species may have feathers as juvenuiles too.

### Ornithomimosaurs

“bird-mimicking lizards”

They’re Cretaceous of Laurasia, and omnivorous or herbivorous. Some have bizarre osteological (skeletal) adaptations: include duck-like beaks.

Example: Deinocheirus, the largest of this clade.

### Alvarezsaurids

These have one single digit, and may have been anteaters. These stout digits are useful for breaking into colonies of social insects.

### Maniraptors

They learned how to fly, but are not considered birds. They may have been gliders, and some had two sets of wings. There is debate over their relationship to birds.

Microraptor gui is the smallest dinosaur and belongs to this group.

### Oviraptors

The “egg-stealers”, and we misidentified eggs near them as eggs stolen from other species.

They have toothless jaws, useful for crushing things like clams.

### Therizinosaurs

They have hyper-specialized forelimbs (Edward Scissorhands). They are possibly analogous to giant ground sloths (now extinct) for pulling down branches and leaves.

### Deinonychosauria

They’re the “terrible claw” dinosaurs. Late Jurassic to Cretaceous.

This is the group that birds are derived from. Some were possibly arboreal and/or omnivorous.

General trend of theropod development is increasing diversity, including geographic diversity. There’s also an increase in size.

This increase in tooth size and skull robustness suggests a different approach to biting. Allosaurus was probably a nipper that wore down prey. Otoh, T. Rex could just crush with its bites. Its biomechanical models have it with more crushing power than anything else ever.

Analogously: Dogs which attack in packs and wear down the prey. Cats tend to be solitary (exception: lions) and kill with powerful “killing bites”. We see this mirrored in small vs. large theropods. Cats also had much more use of their limbs.

T. Rex (2-5 metric tons) could probably kill ceratopsians and ankylosaurs (which were more like 8 tons).

### The Large Carnivore Macroevolutionary Ratchet

A selection for larger body sizes to the evolution of hypercarnivory, where we favor larger prey, (as we can’t eat little things fast enough).

But, this decreases population size and and increases vulnerability to extinction. What’s good for the individual may not be best for the species. It’s a ratchet because it only goes in one direction.

• Predator avoidance
• Can kill wider range of prey species
• Improved thermal efficiency
• Body size wins

We do know that theropods ate other theropods.

Thus the increase in size leads to a decline in evolutionary versatility as we lose: dental versatility,

Evolution is not prescient.

Selection at the individual level leading to the extinction at the species level.

### Speed of theropods

// Actually at start of following lecture

One estimate for T. rex’s speed is 9-25 mph based on computer models, and “Tyrannosaurus was not a fast runner” more or less the current general result. Much faster speeds for smaller taxa are found though.

### T. rex: predator or scavenger

Evidence for scavenging:

• Relatively small eyes
• Enhanced smell (very common among modern scavengers)
• Relatively slow speed
• Tiny forelimbs
• Piercing teeth

Evidence for predator:

• Large, absolute eyes
• Smell is usable for live prey too
• Prey were slow too
• Some modern predators don’t have useful arms either
• Teeth smilar to crocodiles
• Obligate scavengers need to be soaring vertebrates (e.g., vultures) due to energy costs of constantly roaming with high-speed vector to food before it’s goen

Image on slide is a scan of a Hadrosaur vertebrae with a T. rex tooth embedded, but the wound is healed over. So, the animal was attacked by a T. rex while alive.

Answer: Probably in the middle, where T. rex actively hunted, but wouldn’t mind eating something dead that it came across.

Behavior probably changed during growth, as younger ones were smaller and faster. They also had high mortality rates among neonates. Don’t forget that there were plenty of young dinosaurs around too.

The older ones were slower and probably ate bigger prey.

### Tyrannosaur Diversification and Analysis

This may have tracked changes in sea level, as that can cause isolation and migrations => speciation.

Tooth wear patterns, coprolites, skull stress pattern simulations, etc. let us infer more information.

### Dermestid beetles

These beetles are flesh-eating and remove all soft tissues, perfect for skeletons for display. They’re also used for forensic work, as counting lifecycles of these beetles lets us know how long the body has been out. There are “body farms” where human donors bodies are placed in different environmental conditions and then observed as they decay.

Look up “forensic studies” in the literature.

Friscia took some bobcat legs and observed the decay time of bobcat legs in tar.

Interestingly, some dinosaur bones show boreholes from dermestid beetle-like activity.

## Lecture 12: 17 February 2015

### Major Plant Groups

#### Pteridophytes

Characterized by vascular tissue and spores (need water for reproduction).

Modern examples:

• Horsetails

They have fruiting bodies that releases spores which require water to germinate. Modern taxa are small, but Mesozoic taxa reached 10 m in height.

• Ferns

These have a two-stage lifecycle:

- Sporophyte: gives off spores
- Gametophytes: a developing spore


Think of gametes going out on their own and then coming together.

They still need water to germinate, but we do have large tree ferns (even larger in the past).

#### Gymnosperms

These are naked seed plants (and don’t need water to germinate).

Example:

Also called “sego palms”.

They are dioecious (“die-eee-shus”; “two houses”):

- Male plants give off pollen
- Female plants have seeds


They have very tough, thick leaves to resist predation. They were much more diverse in the Mesozoic.

• Gingkos

These are the first woody plants, and are also dioecious. Their seeds are stinky and attract “reptiles”.

• Conifers

Examples: cedars, cypresses, firs, junipers, pines, redwoods, etc. Not all of them have a Christmas tree shape: monkey puzzle trees for example, have a “lollipop” morphology that focuses the leaves all in a bunch high up. This was likely an adaptation to deter predation by herbivorous dinosaurs.

Some are monoecious (having male and female reproductive parts), and some dioecious.

#### Angiosperms

These are flowering plants that become fruit. The seeds are encased in fruit rather than naked.

The first ones don’t emerge until the early Cretaceous. They have often have male and female reproduction organs in the same flower. Many grow faster than gymnosperms, and they go on to dominate.

Their rise coincides with a rise in insect pollinators and herbivores, an arms race.

To reconstruct previous forests, we can see ones preservedin fossil record, and also examine climatic variation. For example, deserts are mostly long the the 30 degree latitude lines north and south, which has to do with air circulation patterns.

In the Jurassic: most plant diversity is in the mid-latitudes. Hot-house conditions meant that the the Mesozoic in general was hotter.

### Sauropods

Originally from the South America in the Triassic, they were the largest vertebrates to walk the Earth, and the first adaptive radiation of dinosaurian herbivores.

With them, we have the first extinction of a major dinosuar linege: the prosauropods.

Sauropod subgroup Titanosaurs were the largest ever animals on land.

Some early forms were still theropod-like.

Later, they got small heads, which just ingested food, with hastroliths and fermnatation taking care of digestion.

#### Skull Modification

• Large ares (nostrils) moves postererioyly during evolution

// TODO: FINSH

#### Snorkeling Sauropod

Some proposed thay their long necks and high-up nostril and had a trunk, like alaphant.

Problem: Water pressure would have been too much

Another problem: They wouldn’t have sunk (due to airsacs), which negates the buoyancy benefit.

#### Elongate Necks and Tails

They had longer cervical veb, and they also have more vertebrate. Giraffes actually have the same number of vertebrae, but they’re longer.

Why have such large necks and tails? Could be

• Dumping heat for thermoregulation

#### Neck Posture

MOdels that it’s probably side-to-side than than up/down to reach branchces. Their vertebrae are pneumatized, meaning filled with empty space. This gets us flexbility and libgndxx.

A ligament helped hold up the long neck, like a suspesion bridge.

Note that all sauropods had long necks.

Graviportal posture: pillar-shaped legs to support massive weight.

Short hind limbs and some taxa have longer forelimbs.

Shorter distal elements: humerus > radius/ulna

They were still digitigrade though and probably had a big fat pad beheind and the foot, which gives a nice flat surface for shock absorption.

Some had clawed feet, on digit 1 in forelimb, and some on 1-3 in hindlimb (in later forms). Possible claw uses? To defend themselves against carnviroes, perhaps rearing up on its tail. Answer, they probably could not do this, or least only for sex, with the claws for holding on. The hindlimb claws were probably for digging out nests.

Their trackways reveal a close-together stance and movement in groups.

### Sauropodomorphs

Two major groups:

Prosauropods and sauropods.

#### Prosauropods

Late Triassic to Early Juarassic, and are the first exxample of an exctinction in a major dinosaur lineage. They had long, narrow skulls, and serrated, leaf-like teeth. They were probably facultative bipeds, meaning they had an option between four limbs and two.

#### Sauropods

Mainly Jurassic, and few groups last till Jurassic. Titanorsaurs lasted through Cretaceous.

Two subgroups: the diplodocoids and Macronarians

Some go on to development of dermal armor.

### Brontosaurus

Orignally caled Apatosaurus, we messed up and the wrong skull on it and named it a different dinosaur: “brontosaurus”. ‘

## Lecture 13: Ornithischians

### Sauropod Diets

Recall that angiosperms weren’t around for most of the Mesozoic with all their nutritious bits. Sauropods had to make do with conifers and cycads. Their large size probably helped with digesting this lower quality material, as their stomachs could act as massive fementing vats.

This may have prevented overgrazing, as they had to keep moving to get higher quality plants, which prevents total devegetation, which would be disastrous for them in the long run. Plants adapted to sauropods, growing in size to get out of reach, a Red Queen race.

### Factors Driving Gigantism

See slide for examples of factors that drive high body mass. There were factors besides theropod predation pressure.

### Herbivore and Carnivore Diversity

Note that herbivore diveristy spikes in the Cretaceous, when we get angiosperms. Not only that, the herbivore community changes. The large sauropods constantly knocked down coniferous forests, selecting for plants that can enter the newly cleared area and grow quickly. This favored angiosperms, and so sauropods helped drive their evolution. Elephants do this today in Africa. More herbivores, which are low browsers like ankylosaurs, evolve.

### Ornithischians

Three major groups:

• Thyreophorans: armored
• Marginocephalians: horned and domed
• Ornithopods: duck-billed

Derived characters to ornithischians:

1. Bird hips (reverse pubis), perhaps to make room for bigger stomachs
2. Leaf-shaped teeth
3. Lower jaw with predentary bone
4. Network of bony ligaments (ossified tendons), all across their back, not just in tail

These are the thyreophorans and marginocephalians.

#### Thyreophorans

These have the ankylosaurs and stegosaurs.

These are characterized by osteoderms, or scutes, which are bones embedded in the connective tissue of their skin. This is probably the result of another arms race with theropods to avoid being eaten. They are all herbivorous (only theropods are carnivorous), and also have post orbital processes.

Osteoderms form in the connective tissue layers of the skin and have multiple purposes:

• Defense
• Display
• Thermoregulation

These are also found in titanosaurs (the large sauropods), other diapsids (crocodiles, etc.), and edentate mammals (armadillos, etc.)

Small, leaf-like teeth, inset for probable cheeks. Thes have beaks on the lower jaw for nipping off plants, and possibly had long tongues, as they have well-developed hyoid bones. Their thoracic regions are wide, perfect for fermentation vats, rather barrel-shaped.

They were quadrapedal and had a large forelimb to hindlimb ratio (1:2), with thickened limbs.

They had a wide stance and slow gait, with possibly semi-sprawling forelimbs, and were low browsers. We never see trail dragging in fossilized trackways, and so their tail was held up.

They were pobably mostly solitary, as we find no mass graves for thyreophorans.

First found in the Early Jurassic of Laurasia, they were possibly bipedal (facultative or obligate), ane eventually becoming quadrapedal as they grew in size.

##### Ankylosaurs

These from the mid-Jurassic to the end of the Cretaceous. Found in Laurasia and Australia, they had a conservative body plan that didn’t change much over time, except in size.

Teeth have cingula: ridges around the base of teethe Osteoderms cover their heads and fuse to cover temporal fenestra. These were massive skulls, with small brains.

They have strange air passages in their head that may have been used for vocalization, temperature regulation (like turbinates), or smelling.

Their pelvises (Pelves) are modified to bear the weight of their armor. Their synsacrum (fused vertebrae and pelvis) with horizontal ilium. We see this in modern birds for absrobing the shock. of landing.

###### Tail Spikes and Clubs

These are made of enlarge osteoderms and linked tail vertebrae, and use possibly for display. Computer models show that they were swingable, especially the smaller ones. Could have been used for defense or sexual selction, for intermale competition.

#### Stegosaurs

Found in Laurasia, Africa, and Australia, these lived in the mid-Jurassic to the mid-Cretaceous; they were gone before T. rex emerged.

3-9 meters long, they had parasagittal plate-like osteoderms that rose up along their backs. They had tiny skulls and brains, like sauropods. They also had horizontal tail spikes.

Interestingly, the stegosaurs and ankylosaurs flip in which dominats. Only one really filled this niche at a time. Stegosaurs then replaced by ankylosaurs. Why? Unclear.

##### Stegosaur plates

These had an alternating arragement, and could have been use for thermoregulation or display.

#### Marginocephlia

These are the “margin heads” and relatively numerous (at least ceratopsians (Triceratops, etc.)), and are very endemic to Laurasian Cretaceous.

They are taxonomically complex, and probably over-split,
e.g., not actually so many species as named.

Still some debate over Triceratops/Torosaurus.

Their heads are huge, with the largest head/body ratio of any terrestrial animal, with huge frilles.

Pachycephalosaurs: had heterodont dentition and were also bipedal, the only group besides theroposd to remain so.

Ceratopsians: Had dental batteries (used more for slicing than grinding) and gastroliths. They began as facultative bipeds and ended as obligate quadrapedals. Detailed trackway analysis shows an upright stance.

##### Sexual Selection

Increases fitness by increasing the number of mates and therefore offspring and genes in the enxt generation.

Artiodactyls (horned, hoofed animals) are the classic example today: deer, cows, sheep, antelopes, elk, moose, etc.

Horns and antlers are often used for competition over mates.

##### Stenopelix

This is an early marginocephalian, found in Germany during the late Cretaceous.

#### Pachycephalosaurs

These have huge domed skulls, all solid bone.

Evidence for head butting shows these were likely used head butting or pushing for male competition over females. There is evidence of sexual dimorphism.

The flatter-headed ones were probably pushers, whereas the domed ones were probably full-blown head butters. They may also have engaged in flank butting.

#### Ceratopsians

Late Jurassic to Late Cretaceous of North America and China, they were 5-9 meters long.

• Rostral bone (the top beak-like bone)
• Dental batteries
• Powerful jaws
• Expanded cheek bones

Analysis of fossils shows injuries in-line with horns interlocking.

They later split into the centrosaurines and chasmosaurines.

Pretty darn diverse overall, and they were social too, with lots of mass burial sites.

##### Psittacosaurus

One of the earliest, it was from the early Cretaceous, small (< 2 meters), bipedal, and we do have a mass grave of them, with evidence for tail “feathers” or “quills”.

##### Protoceratops

May have been a facultative biped, and evidence for sexual dimorphism. Mass burial sites including juveniles mean exceptional knowledge of it.

We even have a specimen dead in its tracks, confirming its trackway.

##### The Species Pump

The repeated rise and fall of the Western Interior Seaway would have fragmented populations leading to speciation. It didn’t open/close, but rather its seas levels went up and down, pushing into and out of the continents.

This effect has been seen for modern animals and glacial advances. We thus get new species. Modern example: warbler birds, and the effect of glacial retreat/advance into/out-of North America.

## Lecture 14: 24 February 2015

// CHECK lecture number // The notes up to and including the // Mesozoic Communities lecture were taken // on Ba’s laptop

### Ornithopods

They are part of the ornithischians, which included the thyreophorans and the marginocephalians.

These are teh duck-billed dinosaurs, but the name means “bird feet”. They are teh herding herbivores, and similar to modern bovids (cows, etc.), zebras, and so on.

They have the best record of social structure in dinosaurs, as well as possibly the most efficient chewing system in vertebrates.

They were all bipeds of facultative quadrapeds, and some have hoofed fingers in forelimbs, and all have ossified tail tendons.

They were 1-12 meters long.

### Efficient Herbivory

The jaw joint joint is below the tooth row, indicating herbivory. They also have dental batteries, cranial kinesis, and later forms have a duck bill. Tooth wear is similar to modern ungulates.

Diversity in the Late Cretaceous increases diveristy, as the continents are breaking up, leading to new ecosystems and population fragmentation.

Why be in flocks/herds? There’s safety in numbers.

### Heterodontosaurids

They’re from the early Jurassic of Africa, and are characterized by heterodont dentition. Their canines are smilar to mouse deer.

Also bipedal, they have really long tails with fused distal elements, and some people think they’re not ornithopods but primitive to ornithischians overall.

This is the smallest known ornithischian, at 65-75 cm.

Examples can be found in our LA County Natural History Museum.

### Hypsilophodontids

Mid Jurassic to late Cretaceous, they show the first adaptations for efficient herbivory. Old reconstructions thought them to be arboreal, but this is no longer the popular view.

### Iguanodontids

includes most of the ornithopod taxa, including Igaunodon and Hadrosaurs and Lambeosaurs.

From the late Jurassic to end Cretaceous, some had elongate neural spines, like spinosaurs. Many were probably facultative quadrapds with a dagger thumb on forelimb, and an opposable “pinky”.

The Hadrosaurs were teh duck-billed ones with the most developed dental batteries. The Lambeosaurs were the “hollow-crested” ones with large head ornaments.

### Dinosaur Reproduction

#### Steps

• Attracting/finding a mate; this is where sexual selection comes in
• Mating
• Building nests and laying eggs
• Parental care (if present)
• Growth

We have evidence for every one of these steps in dinosaurs, with much of it from ornithopods.

#### Secondary Sexual Characteristics

Often, these are maladaptaptive structures, ones that make it harder to survive on a pragmatic basis (e.g., running away harder).

If we want to say that something is used exclusively for sexual selection, we have to eliminate the possibilities of other uses, like offense/defense. Some ceratopsians have crests that were hollow with just thin skin coverings.

Another possibility is thermoregulation.

Also note that species recognition is technically different. Features used for this let individuals recognizes ones with which they can mate.

Finally, absence of evidence is not evidence for anything. We need to look for affirmative evidence that the features are used for sexual selection.

Some signs:

• The features don’t develop until the animals are adults, i.e., sexually mature and ready to mate. We see this from fossils of individuals at different ages. Example: cassowary and lambeosaur.
##### Sexual Dimorphism

Another sign is the presence of different forms in the same population. Sometimes, it can be difficult to tell apart genders from species. We’re helped when we discover mass graves of the same species.

We also see this dimorphism in theropods (like with T. rex size).

#### Why sexual selection?

Why male-male competition or female choice?

• Unequal investment in resources

Eggs are much more costly than sperm. Many species’ females also usually care for the young, and invest more resources in that processes.

Sexual selection push things too far, like with peacocks or the Irish elk.

Dewlaps (inflating sacs) and head sacs (also inflated, and popped in competition; pretty brutal) are features in modern diapsids and may have existed in ornithopods too, but these would not fossilize well.

Parasaurolophid head gear has been modeled for sound, and they may used these for mating calls.

### Mating Techniques

The closest we see for this magnitude of mating, it’s elephants.

In most non-amniotes, there’s one hole, the cloaca (“sewer”), used for everything: bodily waste and gametes. The female lays eggs in water, the male comes and fertilizes them. Somethimes this is done simultaneously, as with frogs, but rarely is it internal. Sharks are an exception.

We even have fossils of animals that died in the throes of love. Turtles back into each other.

In amniotes though, fertilization must occur internally. Sperms is sometimes stored in female after mating, and eggs grow inside female in oviducts.

They still have cloaca; they’re just brought together for mating. Some males have protuberances, primitive penises, like the hemipenes (“half penes”) in snakes.

Mammals are the first to divide up the the cloaca.

Cloacal kiss, like modern birds. A museum in Europe has two T. rex’s mounted (haha) in the midst of sex.

“Apposition” means bringing together apparently.

Males in T. rex had an extra bone for more muscles to help with everting their penis.

#### Laying Eggs

One strategy: r-selection, where lots of offspring are outputted with little parental investment. Example: frogs

Another: k-selection, with few offspring and lots of parental investment. Example: large mammals like elephants

The names come from the graph of population growth.

Which strategy is chosen affects things like:

• Clutch size
• Parental care level
• Growth rates

Dinosaurs clutches had 2-30 eggs, similar to modern birds. Contrast this with modern large reptiles, which have >100 eggs. Modern birds in general are more k-selectedc than r-selected. We do know that eggs were produced in two oviducts. We actually have fossils that include eggs in the oviducts.

Sexual dimorphism is also seen with bone structure. Females tend to have more spongy bone, as the minerals normally used for bones are diverted to eggs.

Jack Horner’s work on Maiasauria showed:

• Eggs were laid in shallow depression and covered with vegetation, like with modern crococdiles. Decomposition produces heat, speeding up embryo devlopment. Female crocodiles do guard their nests.
• Egg-laying sites were reused
• The young were able to walk when young
• Also konwn for sauropods and other taxa

Claws on sauropod feet may have been used for nest digging, as with modern turtles.

In addition, some dinosaurs (like oviraptors from the theropods) engaged in brooding behavior, warming eggs with their bodies.

Again, why nest together? Protection. Seen in elephants, for example.

#### Dinosaur Embryos and Neonates

Many dinosaur embryos and newborns are known. One fossil is a sauropod buried and killed just as it emerged from its shell.

Herbivores tended to be altricial, vulnerable and helpless for a while.

Carnivores tended to be precocial, able to hunt soon after birth, though they filled a different niche when it came to hunting.

Both are born small, with quick growth and allometric change (changes in shape). We also see evidence of an egg tooth, a little bump used for breaking out of their egg, and lost soon afterward.

There is evidence in some nest sites that young stayed in nests after birth: larger young and broken egg shells from being trampled by them. the level of parental care probably differed in different taxa.

Lactation in birds/reptiles means partially digested food being thrown up to feed their young. A recent sensational paper explored this in dinosaurs. We do see evidence of nest predation too, like a snake fossil nest to eggs.

### Mesozoic Communities

Some important reminders:

• Animals don’t live in a biological vacuum
• Not all interactiosn are predator/prey

Dinosaurs are the charismatic megafauna of the Mesozoic, They’re popular, but ecosystems have many other actors too, plus the fact that ecosystems are embedded in climates.

#### What is climate?

What is weather? It is the short-term changes in wind, pressure, temperatures, cloud cover, precipitation, etc.

Climate is the long-term average of weather. Deserts are always deserts, but it may rain once in a while.

How do we investigate paleoclimates? Via proxy data:

• Glacial deposits
• Leaf shape
• Tree rings
• Oxygen isotopes
• Others…

## Lecture 15: 26 February 2015

It’s centered on the Four Corners, and has been geologically stable since the Mesozoic, and upraised in the Cenozoic. It has little precipitation and erosion with a daramatic geology produced by the Colorado River. All of this means that this is one of the best North American dinosaur sites.

The geography: highlands to the east and west.

In between, it’s wet with lakes and rivers draining to the northwest.

We see the Chinle Formation deposited at this time.

### Geologic Formations

These are the fundamental units of stratigraphy, as applied to cohesive units of sedimentary rocks. They’re subdivided into members and grouped into groups.

#### Petrified Forest National Park

Found in east-central Arizona, it’s a badlands exposing the Chinle Formation with many tree fossils (especially large conifers) from the Late Jurassic.

Some fossils:

Metaposaurs: large, carnivorous salamanders (1-2 m long) living like crocs.

Therapsids: Large, herbivorous synapsids leftover from the Paleozoic, at 3.5 m long, the largest herbibore of the time, and one of the few survivors of the P/T extinction.

Sphenodontans: Relatives of modern tuatara. They look like lizards, but they’re a separate group unto themselves. They’re small, insectivorous and carnivorous.

Procolophonids: These are some true lizards, and also small and insectivorous. They’re possibly related to turtles.

### Major Insect Groups

Not yet diverse yet.

#### Dipetera

Flies and mosquitos

#### Hymneoptera

Hornets, bees, wasps, and ants

#### Coleoptera

Beetles

We also see fleas, which don’t live on scales, but they do attach to feathers, so there may have been Triassic animals with feathers.

Recall that the crurotarsans (croc relatives) are the dominant group at the time.

### Specific Species Examples

#### Effigia

This is a convergent crurotarsan, similar to later to ornithomimid dinosaurs.

#### Revueltosaurus

Originally though to be a ornithischian, but now thought to be crurortarsan.

### Triassic Dinosaurs

Three big waves of diversification:

• Prosauropods (none in NA, but elsewhere)
• Small theropods
• Ornithischians (SA only)

What was the key winning adaptation? Not clear, and it may not have been direct competition to win. Current evidence points toward an opportunistic win-out, due to a large climate change during the middle Triassic.

### Jurassic

Pangea nows begins to break up, with subduction continuing off the West Coast of NA.

Now, the Colorado Plateau is more arid, with rain shadows from the western mountains growning taller.

There are still some wetlands, draining to an inland sea forming. The Four corners has sand dunes. A nice model today is the serengeti, which is relatively arid grasslands.

Recall that grass is an angiosperm, so it didn’t exist yet, but ferns and horsetails would have been around.

#### Morrison Formation

146-156 Ma

Deposited in braided streams, flood plains, swamplands, and similar in age to Solnhofen Limestone. It’s found throughout Colorado Plateu and into Canada.

The Cleveland-Lloyd dinosaur quarry: There may have been a drought assemblage, where a bunch of animals trying to get water were suddenly buried.

#### Herbivores

Sauropods were high browswers, and we can identify low-browsers like stegosaurs too.

#### Carnivores

The small ones are like lions: deinonycosaurids, etc.

The largest ones are still half the size of T. rex

#### Energetics

Studies on amount of food and land needed show that large animals need more of both.

Not only that, sauropods may have changed the climate, due to their methane gas.

### Cretaceous

By the mid-Cretaceous, we have a teh western US as an island continent with an interior seaway. By the late Cretaceous, it’s receded. The seaway in genera

#### Grand Staircase-Escalante National Monument

South-central Utah, with deposits of the Kaiparowits Formation from the mid-Cretaceous

There’s a record of near-continuous deposition on the Colorado Plateay from the Paleozoic to the Mesozoic, extending from the Grand Cayon to southern Utah.

#### Rise of the Angiosperms

Advantages: They occupy many habitats and grow relatively quickly.

Many representatives of modern trees.

#### Latitudinal Variation

Comparing north to south of the same age, we see differences in teh taxa present in each area. We would expect them to be spread out if they needed so much space.

Some explanations:

• The plant communities vary between north and south
• As mesotherms, dinosaurs probably need less space than similarly sized endotherms
• Migration into the highlands

Also, remember that different taxa from different times and places often fill the same niches: pack pursuit predator, pounce predator, scavanger, etc.

#### The Rise of T. rex

By the end of the Cretaceous, it is the ONLY large predatory dinosaur.

Don’t forget that dinosaurs weren’t the only predators.

### Overview of Mesozoic Communities

Triassic: Limited diversity of dinosaurs

Jurassic: Increasing diversity

Cretaceous: Most diverse.

## Lecture 16: 3 March 2015

// Final is ecology/physiology up to the end of the class // and is not cumulative. We’ll reuse concepts but don’t // need to remember details.

Everything we’ve done so far has been on land. Now, let’s enter the wter.

### Cretaceous Waters

Remember we had a lot of abundant, warm, shallow seas, like the interior seaway in North America. I would have loved to vacation in the Cretaceous–whilst accompanied by heavy guard.

Recall that terrestrial life went from the sea onto the land. During the Mesozoic, some reptiles return to the sea. We are fairly certain they lived in the sea because:

• They’re in marine sediments
• They have adaptations for aquatic life

### Marine reptile Characters

Their skulls are modified: anapsids or euryapsids.

Large forms may been endothermic homeotherms, like with large dinosaurs. This would have helped with sea-faring domination.

Recall: synapids (where mammals are), diapsids (where dinosaurs and reptiles are). Anapsids have no holes. Euryapsids have one hole like synapsids, but in a different place, between different bones. We belived that euryapsids are derived from diapsids.

// I wanna play Battlefield 3/4 right now…

Triassic:

• Ichthyosaurs, placodonts, nothosaurs, and plesiosaurs, and pliosaurs. All were euryapsids. The latter 3 were sauropterygians. These were probably happening over multiple invasions, as with marine mammals. All died out by K/T, and they may or may not be closely related, as they’re highly modified.

• Seas turtles. The’re anapsids, and are a separate invasion. Originated in Triassic, but not common till Cret.

Jurassic:

• Crocodiles (diapsid archosaurs). Mostly terrestrial during Triassic, but then completely marine (in saltwater) during Jurassic

Cretaceous:

• Mosasaurs (diapsid lizard side). Died out at K/T.

#### Nothosaurs

They’re not fully modified for life in the water. They had (probably) webbed digits, not paddles. They’re possibly analagous to seals, sea lions, walruses.

Some are quite large, up to 4 m long. Their temporal fenestra are huge, and the muscle strength is proportional to cross section of them. Their jaw strength must have been immense.

A nostril moved back is an aquatic adaptation, and they have piscivorous dentition.

Their shoulder blades and hips are beneath body. Many of the marine reptile groups move their shoulders and hips to their anterior surface, to the front to face down, which helps with swimming. The hips are also detached from the backbone (no attachment between illium and backbone). There’s no need for weight support anymore.

#### Plesiosaurs

2-20 m long marine predators.

They’re probably evolved from nothosaurs, and better suited for life in the water. Their paddles could be used for forward propulsion and also lift (like penguins).

Their necks were strong, flexible, and allowed side-to-side motion.

They also have large gastralia, belly ribs, probably for balance.

Extra phalanges plus the uniformity of the other bones result in a strong paddle.

We also see evidence for stone swallowing and thick gastralia (belly ribs) allowing them to dive down (all serving as ballast).

Some may have come to land to lay eggs

#### Pliosaurs

Also derived from nothosaurs, but with short necks and huge heads. These were also huge: one 15 m long with a 3 m long skull. The Jurassic World sea show predator is either one of these or a mosasaur.

#### Placodonts

They look like turtles, but it’s convergent evolution.

They’re 3 m long, with armor, with webbed feet, large, plate-like teeth (probably for crushing shells) that also’s on the roof of their mouth. Their limbs are webbed, but not paddles, plus a tail.

#### Ichthyosaurs

These are the best-adapted reptile swimmers, and convergent on the shark/dolphin sort of body plan.

2-4 m long, they may have been cephalopod prey specialists, e.g., they ate squid, octopuses, and ammonites, among other things. The largest forms have been similar to modern orcas (killer whales), and may been macropredatory, i.e., they kill and eat things bigger than them.

Their eyes are huge, probably for light gathering at deep depths. Their eye has a sclerotic ring for bony support against water pressure.

The shape of their fins are known from carbonaceous outlines preserved well. Almost every specimen found had a bend in the tail. Better specimens show forming the leading edge of one side of the tail.

Fossil shows a live birth in-progress. It was tail-first, as in whales. They probably never visited land. Some debate over whether they were being born or the unborn juvenile bloated during death and was pushed out. It’s still live birth though, as they were fully developed before being born.

Large, barrel-shaped bodies allowed for muscle to hold oxygen (they were air-breathers, not fish with gills). They may had dived as deep as 600 m or more, and some show decompression injuries. Their bodies overall look very similar to dolphin. Notice that their tail fluke is side-to-side like sharks though, not up-down like dolphins. Their vertebrae changes over time, holding their head steady while their tail pushes hard. This let swim faster. Over time, they go from lizard-like to dolphin-like, and become the best marine reptile swimmer, as well as probably the fastest.

#### Mosasaur

They’re the gigantic (up to 12 m) marine lizards, and are closely related to lizards/snakes. They were the dominant marine reptile in the Cretaceous, and some smaller ones may also have lived in freshwater in addition to their worldwide pelagic reach.

We know they ate ammonites thanks to nice matches between teeth and marks on ammonite shells. They were large enough to eat anything: sharks, ocean-diving pterosaurs and birds, etc. They also fought or preyed on each other. They too had live birth, which is something that evolves over 100 times in reptiles.

#### Turtles

The larget turtle ever was Archelon ischyros, similar to modern snapping turtles, and from the Cret. We also see an example of a suction-feeding turtle.

##### Origin of the Turtle Shell

The shell is ribs broadened around till they joined. Scapula moved inside of the rib cage, and it’s a bizarre process.

#### Archosaurs

While no aquatic dinosaurs (Spinosaurus was semi at best).

Deinosuchus, was an aquatic crocodile from the Cretaceous and 50 ft long. Supercroc (Sarcosuchus imperator) was the size of a freaking bus, and probably ate dinosaurs, e.g., hadrosaurs. Spinosaurus may have competed with it.

There were other large predators: large fish and sharks.

#### Other Life in the Sea

##### Xiphactinus audax

The largest non-shark fish eever (7 m long), from the Cretaceous.

##### Ginosu shark

Its mouth was like a cookie-cutter. Not clear if they were scavengers or hunters.

##### Ammonites

Large cephalopods that went extinct at K/T. Modern Nautilus is unrelated, but it took pumped gas into their shells to control buoyancy at different depths. There’s a tube connecting the chambers.

The marine ecosystems overall were quite complex.

### Pterosauria

Birds come around in the Jurassic, and shared the skies with flying reptiles, the pterosaurs, a sister group of the dinosaurs. Together, Pterosauria and Dinosauria make up the Ornithodirans.

They are around for almost the whole Mesozoic: late Triassic to K/T. Over 100 species are known.

Unique features:

• Short trunk
• LArge head with pointed jaws and teeth
• Wings supported by an elongate 4th digit (wing hung over pinky finger)
• Hollow bones
• Large brains big optic lobes (eyesight), cerebellum (for balance), but reduced olfactory lobes (not at as great for smell)

They could fold their wings like modern birds. It’s an analogous structure built atop a homologous one.

Pterosaurs, bats, and birds have the same basic forelimb bones structure, but their wings are structured totally different.

#### Pterosaur Flight

Their flight was powered (flapping), with flight muscles located ventrally, as in birds. This again helps with balance, so that weight isn’t on top and back, which would make balance harder.

Their sternums and crests on humerus were as robust as that of birsd.

Most were superb fliers, as good as birds.

• Massive flight muscles
• Lightest skeleton of any vertebrate ever
• Larger pterosaurs probably soared (soared > glided) rather than flapped all the time

Two groups:

• Rhamphorynchoids (smaller, and gone by late Jurassic)

• Pterodactyloids (larger, and gone at end of Mesozoic)

Many were probably insectivorous, some insectivorous, and some may have been planktivorous, like modern flamingos. Some may have speared fish. Others may have speared fish.

We even see evidence of gastroliths, like some modern birds.

Finally, we see a lot of diversity in crests, possibly for sexual selection (with evidence of sexual dimorphism and change in size over time).

They probably walked on all fours, and not upright, with their forelimbs vaulting them into the air.

## Lecture 17: 5 March 2015

### Order Aves: Birds

Birds are extant archosaurs, and so their closest living relatives are crocdiles. Dinosaurs fell between crocodiles and birds, and note that birds are dinosaurs too.

They are endothermic, and their origins are in the Jurassic, 200-150 Ma.

We’ll check for novelties for in birds that make them distinguishable from non-avian dinosaurs.

• Loss of teeth
• Enlarged brain (high EQ, though seen also in some theropods)
• Carpometacarpus: Carpals and metacarpals are fused together Some debate over which are fused/reduced
• Furcula: the “wishbone”, the clavicles (collar bones) are fused (“clavicle” in diagram)

In the axial skeleton:

• Keeled sternum (chest bone, which is freaking huge)
• Pygostyle: Only a few caudal vertebrae remain, and they’re reduced and fused together

Their flight muscles (the ones that move the wings) are attached to the sternum on the front. The trioseal foramen is a little hole for where one of the muscles’ tendons go through and wrap in, making a sort of pulley system.

In the hindlimb:

• Tibiotarsus: Tibia and tarsals are fused together
• Tarsometatarsus: Tarsals and metatarsals are fused together
• Digit 1 is reversed, which allows for perching
• Pubis is reversed, like ornithischians, even though birds are Saurischian
• Synsacrum: The pelvis and sacral vertebrae are fused

Birds also have:

• Feathers (wonderfully complex structure)
• Pneumatic bones (bones with air spaces in them)

All of these mentioned characters are found in various (non-avian) dinosaur groups, including possibly feathers throughout all of Dinosauria.

Birds are Maniraptorian dinosaurs. This dinosaur-bird connection has been suggested since Darwin, but was only recently consensus since the dinosaur renaissance with Ostrom.

“There are a few holdouts, but those people are crazy.”

Some bird-like dinosaurs: Velociraptor, Dromeosaurids, etc. This group actually shrinks in size over time. This is possibly due to their move toward endothermy, where large size makes it easy to overheat.

### Archaeopteryx

This is the earliest definitive bird. Recent fossil finds may have found earlier ones, but it can be treated as a model for early ones. It’s of similar size to Compys or a very large raven. The Solnhofen specimens have feather impressions.

It serves as a near-perfect transitional fossil between dinosaurs and birds:

• Tail still long
• Still has claws
• Arms are modified for wings

It has a mix of traditionally avian:

• Feathers
• Wishbone
• Reverted big toe

and dinosaurian characters:

• Teeth
• Bony tail
• Vertical pubis
• Separate fingers with claws
• Less fusion in claws

But recent research has shown dinosaurs to have more “avian” characters than we thought.

This is mosaic evolution: Birds’ characters evolved piecemeal over time, rather independently of each other. Birds weren’t fully formed from the outset; they changed over time into their present form. Also common: features evolve for a different purpose and are later co-opted for something else later, e.g. feathers for insulation becoming a tool for flight.

Archaeopteryx has forelimb claws, not something found among modern adult birds, but the hoatzin from South America, in its juvenile form, has claws for climbing trees.

It was definitely capable of powered flight, and its claws definitely look good for perching and arboreal life.

How well could it fly? Well, one clue is that it lacked the large, keeled sternum of modern birds. However, its deltopectoral crest was enlarged even more behind the diagonostic level for Dinosauria. It’s possible its sternum was cartilaginous and didn’t preserve during fossilizaiton, etc.

Another clue: the flight feathers of birds have a central barb (rachis) that is off-center, as does Archaeopteryx. This makes it more like like an airfoil shape.

### Feathers

Feathers are clearly derived from scales, being made of the same material and so they are homologous in relationship. There is excellent developmental evidence for this.

#### Feathered Dinosaurs

Dinosaurs may have evolved multiple times in different dinosaur lineages, which implies that they did not originally evolve for flight. Possible alternatives: sexual display, thermoregulation (insulation), gliding, etc.

Microraptor was interesting: It was a glider, but unrelated on the way to birds.

Another piece of evidence for nonflight: the feathers were symmetrical (similar to non-flight feathers in birds). Across most theropods, we have evidence for feathers, but we also have evidence in other dinosaur groups too.

To determine feather color, we can check the melanosome-like structures in fossils. These impart color to modern feathers, and different colors have different shapes.

Maniraptorian theropods had a lot of adaptations already before they evolved into birds. It was an easy “pivot”.

#### Longisquama

This is a Triassic diapsid reptiles with feather-like structures. As feathers are more common than we thought, it’s unwise to use feathers in general to probe bird origins.

### The Origin of Flight

Ground-up or trees-down? This is the cursorial vs. arboreal hypothesis.

#### Ground-up Hypothesis

Birds came from theropods and may have evolved wings to catch insects

Primary evidence: No theropods could climb

#### Trees-down Hypothesis

Climbed trees to escape predation, and wings for gliding.

### False Dichotomy

Wings are useful for running up steep inclines too, seen with modern ground birds.

#### Wing-Assisted Inclined Running (WAIR) hypothesis

Univerisity of Montana Flight Laboratory video

Once you’ve evolved wings for getting up inclines, you can get up into trees. From there, gliding is useful for getting down safely.

Another possible use: Roadrunners use their wings for rapid banking to catch prey.

WAIR is the current best argument.

// Why does science always fall into dichotomies?

We can also see how maniraptorans look like modern juvenile birds.

The early birds could run away into trees and glide away, but weren’t good enough yet at flying to catch insects while flying.

### Basal Birds

There are birds around during the Cretaceous.

These begin to evolve toward modern birds in features, but retain some primitive featrues.

### Enatiorinthines

Almost all were perching birds, but one may have been a wader.

### Ornithurines

They’re the only birds to survive the K/T boundary. This clade includes all modern birds.

### Paeleognathae

Mostly flightless birds. All modern examples on the southern continents? Why? Plate tectonics, where they were once together, then split up apart.

For a while, before mammals grew larger, we had large predatory birds.

“This is a giant chicken that ate horses.” This is basically converging toward theropods.

Later, other mammalian predators pushed them out.

There was also a giant hawk on Maddagascar (10-ft wingspang) that could eat the now-extinct elephant birds. There were also large condor-like birds.

The biggest bird ever? From South America, with a 12-ft wingspan, from the early Cenozoic.

Bats and pterosaurs are all totally different in their wing structure. Sadly, the fossil record for bats is terrible.

## Lecture 18: 10 March 2015

### J. John “Jack” Sepkoski

At U Chicago, he was the first to analyze large-scale trends in marine communities across time.

“Sep-cow-ski”

The darkened line is the number of marine families (vertebrates and invertebrates).

What we see is diversity increasing over the entire Phanerozoic (time since beginning of Cambrian). Two reasons:

• Pull of the recent
• Ecological diversification

#### Pull of the Recent

This is an artifactual bias: paleontologists tend to more interested in more recent things, and erosion kills off older rocks and the fossils in them. This is a sampling bias. This is part of the larger problem of taphonomy, the study of how fossils become fossils.

#### Ecological Diversification

There was an undeniable increase in diversity though, a result of diversity begetting diversity. Predator-prey interactions also drive this.

Vermeij, a blind paelontologist who can identify snail shells by touch.

#### Mass Extinctions

But we also see 5 major drops: those are extinction events:

• End Ordivician
• End Devonian
• End Permian
• End Triassic
• End Cretaceous

Don’t forget: biostratigraphy used. We define geological times based on the start/end of chronological ranges of species. We set geological boundaries based on them.

We see a bunch of species die out, and new ones emerge to take their place.

Definition for mass extinction:

• Global in extent
• Affected marine and terrestrial organisms
• Relatively brief in duration

Possible causes:

• Major climatic change
• Sea level changes
• Volcanism
• Plate tectonics
• Extraterrestrial

### Permo-Triassic Mass Extinctions

~250 Ma, the biggest one of all time (thus far).

Possible causes:

• Formation of Pangaea
• Marine anoxia (oxygen levels greatly depleted due
to lack of mixing by nonexistent current)
• Sea level falls about 100 meters
• Volcanic activity: huge basalt flow in Siberia about 251 Ma

Answer: Probably combination of these causes

80-95% of all marine species were lost.

Bioturbation: The disturfance of sedimentary deposits by living organisms.

How quickly did the PTr extinction happen? In marine realm, very fast: < 1 million years. There may have been several smaller extinctions happening together.

Based on oxygen isotopic evidence, we see a 6 degrees C rise in global temps. We also see a serious decline in plant productivity based on based on ratio of C13:C12. Plants prefer C12, and less of it indicates a major biotic crisis.

Possible explanations:

• Bolide impact (something slamming into Earth)

No definitive evidence for this at PTr boundary. Possible crater in Australia.

• Marine regression

Unlikely. Does not explain terrestrial extinctions and slowness in sea level change doesn’t explain rapidity of extinction.

A sudden drop would remove extensive area of shallow nearshore environements, increasing competition and extinctions

• Volcanism

Maybe:

#### The Siberian Traps

The largest known volcanic eruption in Earth’s history.

They spanned over 1 million years, and covered 2 million square kilometers to a depth of 400-3000 meters. These are igneous rocks, and so precisely dateable. They’re flood basalts, emerging from huge hot spots.

Effects come from all the gases and things spewed out into the atmosphere. There’s cooling effects (10^3), but they last shorter than global warming effects (10^6).

We’ve seen cooling effects before (Krakatoa).

Problem: Models show they can’t account for sudden large increase in C12. What killed all the plants?

Another contributing factor: melting of methane hydrates, formed under pressure in the sea (> 300 meters deep). If sea temperature rises enough, then these deposits are melted and bubble up into the atmosphere, where a positive feedback cycle releases more and more CO2. A runaway release of gas would also increase the acidity of the water, killing off the shelled organisms.

This is a runaway greenhouse effect:

Massive volcanic eruptions -> Atmospheric CO2 increase –> Global warming on land and sea —> Melting of methane hydrates

A similar effect could happen now, with human-caused global warming. Fossil evidence shows desertification of environments.

Probably multiple causes.

It takes 100 myr for marine biodiveristy to regain pre-Triassic levels.

Diversities are rebuilt.

We see refugia: Lazarus taxa that disppaer and then reappear.

### Cretaceous-Tertiary Extinction

Some groups march right through K/T like nothing, e.g. turtles. Percentage extinctions is not something you want 100% on.

Cause: Extraterrestrial impact, first posposed in 1980 by Luis Alvarez et al.

The main line of evidence for this: an iridium spike right at the K/T boundary, which they found in Italy. Iridium is uncommon on Earth, but it’s common in meteors. After Italy, they found it around the world.

Next thing needed was smoking gun: a crater, discovered in 1990, the Chicxulub Crater. 200 km in diameter, it’s big enough. We also see shocked quartz, glass spherules (melted and resolidified droplets of ground spewed up), evidence for massive tidal waves around the impact area, and increased acidity in fluvial deposits. Finally, we see continental-scale global fires.

But did it kill the dinosaurs? Let’s evaluate the basic consequences:

• Dust, smoke, and debris that would end photosynthesis for several months (decrease in pollen seen, plus weedier fast growth strategies)
• Fires started by thermal pulse

Extraterrestial Cause for the Cretaceous-Tertiary Extinction

This discovery means we now have a Neo-Catastrophist/Uniformitarian view, where we accept the possibility of unique events in the past and future.

At the same time:

#### Deccan Traps

Similar to the Siberina Traps, they’re dated to a little earlier than the K/T boundary, and probably contributed to decrease in diversity. One hypothesis says that the bolide impact was the last straw to life already in decline.

But more recent evidence supports rapid extinction, based on detailed biostratigraphic analysis.

#### Signor-Lipps Effect

They may have only appeared to be in decline due to Signor-Lipps Effect, which says that larger animals are rarer in the fossil record, so they just seem to go extinct earlier. Simulations bear this out, showing how a rapid extinction can look like a gradual one, due to an incomplete fossil record.

### Fossils

Fossils are evidence of past life, including body, chemical, and trace fossils.

Diagenesis: The physical and chemical processes that lead to fossilization

• Whole Body Fossils

These are rare, and include mummification, frozen, bog specimens, and amber. We do have a few mummified dinosaurs, and some humans from bogs.

• Hard Parts

Petrification: actual subtance turned into rock. Permineralization: spaces filled with rock

• Casts and molds

Impressions of the fossils; the original was eaten away by acid, say, and rock filled the space.

### Taphonomy

The study of the processes by which animals become fossilized.

Steps

• Consumption and decomposition
• Exposure and weathering
• Transport and burial
• Fossilization and exhumation

Sometimes, we find a lagerstätte, a fossil locality with exceptional preservation. Examples: Solnhofen Limestone, La Brea Tar Pits, Burgess Shale, Messel Pit

## Lecture 19: 12 March 2015

Ackerman grand Ballroom, Thursday MArch 19, 8-11 am. No leaving during the exam.

100 questions, multiple-choice, true/false, matching.

3 full hours, for lectures “Ecology” through today’s.

Scantron provided!

### Rancho La Brea

It’s from the Pleistocene (~4-44 thousand years ago). No dinosuars, of course, but we do see: bison, horses, dire wolves, short-faced/running bears, sabre tooth cats, and even a lion.

The geography: broad plains, with rivers from nearby mountains, but most useful to us is the petroleum seeping out (it continues to do so), which trapped animals and preserved them.

Petroleum tends to flow to the surface as its density is less.

LA actually used to have a lot of oil, and so in 1914, we had a lot of stacks.

The tar pits that formed are a natural trap for large animals, and the specimens are now sub-fossils, with some original material still present. They’re not petrified, but the bone is permeated with asphalt. We believe that herbivores got caught, and then carnivores came by and got caught themselves.

We’ve never been able to get DNA out of things in the tar pits, as the chemicals for getting rid of the tar also destroy the DNA.

Friscia did part of his dissertation work at Pit 91. The tar pits were not big pools; they were thin layers that trapped animals, got mixed up with sediments, etc. In 1969, this pit was reopened from crude collection work earlier in the century, and fine collection work were done. Data like bone distribution and angle were recorded.

Based on this, we saw that the entrapment rate was something like 1 every 50-70 years (over tens of thousands). Radiometric dating was usable, and it mostly shows the Law of Superposition, though there is some mixing.

What we also see that few of the skeletons are articulated; most are a bunch of pieces everywhere. It’s not clear what causes the mixing. Proposed: trampling, multiple combining deposits, etc.

Recall also that we had a inverted food web distribution of the specimens in the La Brea Tar Pits.

“Juveniles are kind of stupid and naïve.”

#### Entrapment Story

Herbivores, mostly juveniles, get trapped in the tar.

This attracted carnivores, many of which got trapped themselves.

Carnivores that didn’t get trapped dragged off of the carcasses.

What we left got buried quickly

After burial, fossils were compacted, and some mixing occurred.

Some questions remain:

• Why do we find articulated skeletons at all?
• How long does it take for the skeletons to fall apart in tar?
• What causes the mixing: trampling, settling, churning?

Friscia recently did an experiment. He took some bobcats that had been used for genetic work but died. He took their logs and put them in tar to see how they rotted and fell apart over time.

The legs were placed in a cage-like apparatus and then stuck in the tar. The flesh disappeared quickly. Mixing thus could have could happened early on the surface.

### Taphonomy

This is the study of how fossils form, and it’s based on the study of modern processes.

### Mammalian Evolution

Mammals are modified reptiles evolved to be endotherms.

Three main groups:

• Monotremes (egg-laying)
• Marsupials (have pouches)
• Placentals

Shared characteritics:

• Hair
• Mammary glands
• Endothermic, etc.

Which pretty much don’t fossilize!

• Monotremes

Platypus, echidnas, etc. They’re probably evolutionary holdovers from the Mesozoic, and are only in Australia and New Zealand.

• Maruspials

Opossums are the only ones in North America.

All their young are born like bean-size which crawl into a pouch, and then develop inside of there.

• Placentals

All the mammals with which we are familiar.

### Jaw Transition

As for identifying mammals in the fossil record, we look at their skeletons, especially in a lower jaw made of one bone, not many. On the other hand, reptiles have many bones making up their lower jaw.

Our earbones vibrate our inner ear fluids. Air vibrations become liquid vibrations.

In mammals, those reptilian jaw bones (quadrate and articular) become our ear bones. This is why our jaw and ears are so close together.

There’s a great fossil record for this transition. Effects: our jaw joint strengthened, which got us chewing and stronger bite. Our hearing also got better.

Our stationary tube links the back of our throat to the ear chamber. Without the eardrum, there’d be a canal between the ear and our throat. Go back far enough, and we’d find that this is our old gill slit.

PBS: “Your Inner Fish” is a show.

So why this transition?

• Better hearing
• Better teeth occlusion for better chewing
• More powerful bites
• Suckling

Most of these things probably had to do with endothermy, which means homeothermy, the ability to keep a constant body temperature. We need more food, which leads to the need for better food processing, e.g., chewing.

This also drives diphyodont dentition, as it makes chewing easier. Reptiles have polyphyodont dentition, and constantly replace their teeth. In addition, having baby teeth means relying on Momma for nutrition for a while, which may have led to lactation.

### Mammal-like Reptiles

Therapsids: mammal-like reptiles, which leads to true mammals.

The late Permian was the “Age of Ugliness”.

#### Pelycosaurs

Earlier mammal-like reptiles, many carnivorous.

Furry carnivores

#### True Mammals

Earliest known mammal: 220 Ma, from the Triassic: Megazostrodon, which was small. There were Mesozoic mammals, with the old model for them being small, and non-diverse. New studies show a lot more diversity than we thought. Warthoh-size ones that ate small dinosaurs! A few gliders! And even one that looked modern beavers, with an aquatic life.

Once the dinosaurs died out, mammals took over, diversifying quickly. We see convergent evolution, e.g., marsupials in Australia evolved into similar niches as placental mammals elsewhere. There was even a sabertooth marsupial! There was marsupial wolf, the Tasmanian wolf, which went extinct early last century.

Recall that marsupials got stuck in Australia on their own, and placentals evolved separately, due to plate tectonics.

### Goals of this Class

That’s it for class material!

• Dinosaurs were biological entities and not just plot devices (This is why he didn’t talk about fossils till the end)

• Understand how science gets done (paleontologists as a serious science)

• Understand the basics of biology, ecology, and evolution

• Understand the basics of geology, plate tectonics, and dating

• Understand the interaction between the biotic and abiotic world (Environment can drive evolution and vice versa)