BISC 2333 Exam 1

Phanerozoic Eon

-There was the Paleozoic first then the Mesozoic, then the Cenozoic. -The Mesozoic was the dinosaur period. -The Cenozoic was when dinosaurs except birds went extinct. Cenozoic is usually called the age of mammals. -Within the Mesozoic period there were 3 eras. --> Triassic, Jurassic, and lastly Cretaceous --> Before the Triassic there is the biggest extinction, one that is bigger than the dinosaur extinction. Modern things survive, and they evolve until eventually get dinosaurs, modern amphibians, and modern fauna's. -->In the Cretaceous, there were changes in fauna between early and late Cretaceous.

But which condition is primitive?

-To determine which condition of a character is primitive and which is derived we refer to an outgroup. -Species outside of the group we are investigating/the ingroup, should have the primitive condition. -This means we have to hypothesize which species are in the ingroup and which ones are outside it.

Simplest vs Most Likely

-Two main approaches to inferring phylogeny are parsimony and model-based approaches -->Parsimony finds the simplest arrangement of characters (the one maximizing homology and minimizing homoplasy) to find cladograms. -->Likelihood and Bayesian approaches use models of character change to find the most likely tree with branch lengths assuming those models.

Radioactive Decay

-Unstable elements (radionuclides), with excess nuclear energy, decay by ejecting particles -They generally change from isotopes or elements of higher atomic number to those of a lower atomic number. -For example, Uranium 238 decays to Lead 208, through a series of 12 intermediates of varying half-lives -Radioactive decay can be seen by placing an unstable element, such as the uranium above, in a cloud chamber. Alpha particles are composed of 2 protons and 2 neutrons, beta particles of electrons or positrons. As this happens, the atomic number is changing.

Dinosaurs are Vertebrates

-Vertebrates are deuterostome animals, closely related to other chordates and to echinoderms. -Vertebrates are distinguished by a well-developed head with a brain and vertebrae that form around the notochord. -Vertebrate embryos' neural crest tissue develops into the head skeleton and peripheral nervous system. Well developed head and nervous system.

Geologic Time, Precambrian:

-first the earth was molten (basically lava, probably nothing could live, nothing to preserve) -Next the time of the first fossils occurred (first life on earth, bacteria) Then oxygen in the atmosphere occurred (could tell this because iron turning red when oxidizing) -Then in the Phanerozoic time there was a cambrian "explosion" of fossils (at a certain point there was enough oxygen to fuel diversification of life on earth. Get a ton of fossils.)

What did Sir Richard Owen do?

-named the group Dinosauria. -recognized dinosaurs as a distinct group -Owen agreed with Darwin that evolution occurred, but thought it was more complex than outlined in Darwin's On the Origin of Species, opposed him.

Decaying can be

1) From one isotope of an element to another isotope of the same element. 2) From one element to another

What is fossilized?

1) Hard tissues (bones, teeth) via petrification 2) Soft Tissues via compressions, sometimes as mold and cast or petrification 3) Tracks and trackways via mold and cast 4) Eggs and coprolites via petrification

The requirements to become a fossil:

1) The organism must die in an area that accumulates sediment 2) Organism must be buried and remain buried 3) The burial environment must be conducive to preservation (some bacteria/fungi eat tissue)

Dinosaurs normally walked on __ legs, they evolved to walk on __ legs.

2, evolved to 4

Prospecting

Can find bits of bone streaming down hill can trace it back to where it is coming from. Can find a larger skeleton.

Compressions/Carbon films

Compressions of plant leaves, feathers and skin

Dates are for the time of crystallization of rocks, so dates of sedimentary rocks will be of the rocks from which the clasts were derived, not the age at which the sediments were deposited.

Ex: Erosion off of a mountain washes off rocks, rains, rivers pick up crystals and deposits farther down. Crystal ages are different to when they were deposited.

Only Derived Characters are Evidence of Relationships

Example: Can't group crocodiles, reptiles, turtles using scales because it's a primitive condition. Example: the similarities between humans and cats are primitive for mammals so they are not evidence that cats are more closely related to humans than are bats or whales (bats are closer to humans based on other characters).

Burlap and plaster

Flipping and adding a top jacket: -Usually fossils contain some dirt from pedestalling to prevent fossil damage when removing the plaster

What places are good for dinosaur bone deposits?

Floodplain rivers

How do isotopes occur in rocks?

For example: a small percentage of Potassium atoms are radioactive, and decay to Argon gas captured in the crystal. Can measure how much argon was produced.

You do not really carbon date dinosaurs, not much left in fossils. Why?

Half life is short.

Linnaean Classification =

Kingdom Phylum Class Order Family Genus Species (always combined with genus)

Separator

Makes it easier to separate the fossils from the wrapping after plaster is put on top

Many large extinct reptiles are NOT dinosaurs.

Marine reptiles -->Maintained tetrapod features but NOT dinosaurs. -->Mammoths, finbacks are also NOT dinosaurs.

The first dinosaur to receive a scientific name was

Megalosaurus

"Chimps are more closely related to us than are gorillas"

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Adding supports

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After digging fossils, need some kind of glue (NOT white glue, often resin).

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Asilisaurus is the closest relative to dinosaurs.

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Dating of fossils is most accurate when volcanic rocks, such as tufts (volcanic ash), above and below the fossils bracket their age; fossils are almost never found within volcanic rocks.

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EVOLUTION IS A BRANCHING PROCESS!

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If you only have 2 taxa, you are not really saying anything.

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Radioactive decay is exponential.

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Character Optimization

--Once a tree or cladogram is found, the character state changes can be mapped/optimized onto them. --The derived character states for each group are optimized at the node for that group. --Character optimization, at its simplest, is the act of looking at two choices when building a character and choosing the option which will make your character more mechanically effective.

(Mesozoic) Jurassic Climate

-A lot of warm wet regions. -Triassic is dry.

Comparative Biology

-Animals and other groups of organisms share similarities -->All mammals have hair -->All birds have feathers -Comparisons among different types of organisms depend upon these similarities-we look at the hand of humans and the hand of chimpanzees and recognize that they are in many ways "the same". -It is impossible to discuss organismal diversity without referring to shared features and groups of organisms. -->Example: experiments on lab rats rely on similarities to humans to test and apply to humans. Implicit.

Dinosaur Relatives - Fossil Archosaurs

-Antorbital fenestra present in most, along with several other skeletal features -The oldest archosaurs are Early Triassic Some are related to birds, some to crocodilians, some to birds + crocodilians -Archosaurs can be closer to dinosaurs, closer to crocodilians, or outside of crocodilians and dinosaurs. -Some crocodiles now can gallop which they evolved from animals that could gallop/walk. -Terrestrisuchus were long legged, fast, non-aquatic animals -Ornithodira tells us what the primitive conditions of dinosaurs were.

Cladograms & Trees

-Cladograms only show how species are related to one another. -They reflect the branching pattern of evolution but not time. -They do not show ancestral-descendant relationships which are difficult to identify. -The branches of trees are proportional to time and ancestors may be indicated.

Collecting dinosaurs, planning the field work:

-Collaborators (need permission of government unless private land in US) -Permits -Arrange for equipment, food, transport, medical contingencies, shipping, etc. -Find money to fund the field work and fossil preparation -Repository for fossils (determine where the fossils will be given)

Finding Phylogenies

-Compare similarities to find the set of relationships (phylogeny) that requires the least conflict (homoplasy). -These relationships are usually shown in a tree or cladogram to show the patterns.

How are Groups identified?

-Current practice is for taxonomic groups to include only groups of closely related (monophyletic) taxa that include all the descendants of a common ancestor. -These are the groups on a phylogeny that form a natural hierarchy, and are testable with phylogenetic analysis. -Non-monophyletic groups are polyphyletic and paraphyletic (VIEW PICTURE IN LECTURE 3 SLIDES PAGE 49)

How does isotopic decay help us date the mineral?

-Decay rate, half lives, can help determine the amount of time that has passed. -For example, Rubidium to Strontium takes billions of years vs Fluorine to Neon takes seconds. -Like the parent isotopes, the daughter isotopes are locked into the mineral crystals: they exist side by side.

Summary of Lecture 4

-Dinosaurs (monophyletic group) are archosaurian amniote tetrapod sarcopterygian osteichthyan gnathostome vertebrates. -Birds are dinosaurs, and the closest living relative of the group is crocodilians. -The closest fossil relatives of dinosaurs are silesaurids -There are many other extinct archosaurs that are not dinosaurs (they do not have the homologies of dinosaurs)

Dinosaur Skeleton

-Dinosaurs are known mainly from skeletal remains (similarities with birds, lizards, and crocodilians) -To understand dinosaurs you need to know the bones of the skeleton. -Tetrapod skeletons are conservative and mainly comprise homologous bones recognizable in all tetrapods, including humans.

Dinosaur Relationships

-Dinosaurs are members of the following nested sets of monophyletic taxonomic groups: -->Vertebrata - animals with backbone -->Tetrapoda - four-limbed land animals -->Amniota - land animals with modified eggs -->Archosauria - birds, crocodilians and their fossil relatives

Lecture 1 Summary:

-Dinosaurs are preserved in fine to medium-grained clastic sedimentary rocks: river, lake, soil, ash, catastrophic deposits. -Both body and trace fossils of dinosaurs are preserved. By far, bones and teeth are the easiest, most likely to be preserved. -Preservation is primarily by permineralization/petrification, but compressions and mold and casts also occur. Permineralization/petrification can preserve organic materials down to the molecular level.

Dinosaur Features

-Dinosaurs form a monophyletic group (including birds) with several homologies -->Fully erect stance -->Head of femur is inturned, opening in pelvis for limbs to stand erectly -->Crocodilians do not have inturned heads on femurs because they crawl and can move their legs all around. -DINOSAURS ARE PARAPHYLETIC IF THEY DO NOT INCLUDE BIRDS

Summary of Lecture 2 part 1:

-Dinosaurs lived from the Late Triassic through the entire Jurassic and Cretaceous and on to the recent in the form of birds. -Climate in the Triassic through Cretaceous was generally warm with low pole-to-pole temperature gradients. There were no polar ice caps. Pangaea broke apart through the Jurassic and Cretaceous (begin with one super continent with similar fossils everywhere but then begin to split, fossils differentiate from area to area). -Radiometric dating provides a numerical age for minerals and rocks using the natural decay of isotopes. Most sedimentary rocks cannot be directly dated, but volcanic rocks can, including those within sedimentary rocks.

Cretaceous: 80 million years

-End of Maastrichtian extinction occurs in the late Cretaceous, and dinosaurs die off. -Mammals could not compete with dinosaurs so they were very tiny at the time. -After dinosaurs became extinct, mammals and birds evolved to be larger and increased. -Dinosaurs lived for over 163 million years.

Summary of Lecture 3:

-Evolutionary relationships are inferred from features shared among groups. -Features shared due to evolutionary relationships are homologies, features that are similar for other reasons are homoplasies. -Dinosaurs are archosaurian reptiles, if Reptilia is considered to include birds. -Birds are dinosaurs, because some dinosaurs are more closely related to birds than to other dinosaurs.

Example: Scales

-Feathers are modified reptilian scales -Scales are the primitive condition for sauropsids -Scales are not a derived character of a group of "reptiles" that doesn't include birds.

Primitive/Derived Conditions

-For every feature, there is a comparable feature from which it evolved. -The original feature is called the primitive state. -The modified feature is called the derived state. -->Example: Feathers in birds are derived and the primitive condition is a scale covering like that of crocodilians, turtles, and lizards.

In the lab after collecting fossils:

-Fossils from the field are taken to a preparation laboratory to have the sediment removed from them -There are numerous methods for doing this, depending on what kind of rock they are preserved in -Most methods are mechanical, involving chisels, needles, and air-powered tools.

Phylogenies of Fossils

-Fossils typically consist only of hard (skeletal) and occasionally soft (non-skeletal) tissues, and DNA is rarely preserved (except in recently fossilized specimens). -Phylogenies of fossils are therefore typically based on analysis of their anatomy (morphology). -Because most fossils are more fragmentary than living animals and lack DNA, there is not as much data to use in inferring their phylogeny.

Why do we need phylogenies?

-Framework for biology -It is not possible to study evolution between different species without having an idea (hypothesis) of how organisms are related to each other.

Summary of Lecture 2 part 2:

-Geological maps and satellite images help paleontologists find areas to search for fossils -Techniques for searching for and collecting dinosaur fossils haven't changed much over the past 100 years. -It still involves travelling to the location, walking the ground, and excavating using hand tools and occasionally power tools. It is hard work. -Once back to the lab, fossils are extracted from the rock matrix using a variety of techniques. This is precision work requiring knowledge of both the fossil and the matrix.

Naming Names

-In Linnaean taxonomy every species is within a genus, so Tyrannosaurus rex cannot be referred to as rex. Only the genus is capitalized, and it is sometimes abbreviated (e.g., T. rex) -All species must be represented by a specimen (the type specimen), the genus is based on a type species, the family on a type genus.

Cretaceous

-India was moving fast throughout the Cretaceous era. -Cretaceous climate paralleled that of the Jurassic. -Lots of coal deposits, still have deserts. In general have warm wet conditions. Cooling event occurs at the end of Cretaceous.

Relative Dating of Fossils

-Lower rocks and fossils are older than those closer to the surface. -The same concept of relative dating applied everywhere. Allows to find age on a relative time scale. Where we get our geological time scale. -Generally don't date fossils besides dating recent fossils with radiocarbon dating. -Other techniques are dating crystals in rocks. Can date rocks fossils are positioned between and determine time. Can determine the fossils are between so-and-so time & so-and-so time.

Mold and Cast

-Negative and positive molds -Casts of footprints, skin, etc.

Biases in the Fossil Record

-Not all areas where dinosaurs lived accumulated sediments. -Not all burial sediments were conducive to fossil preservation.

I. Skull Openings

-Openings in nares (nose) -Openings in antorbital fenestra, upper temporal fenestra, and lower temporal fenestra, orbit, external mandibular fenestra, and foramen magnum.

(Mesozoic) Early Jurassic

-Pangea begins to break up. -India migrated up, slammed into Asia and formed the Himalayan mountains. -In Jurassic, get a fissure where the Atlantic Ocean will be. -Series of volcanoes in mid oceanic ridges create lava which ends up pushing continents aside. Rocks nearest is youngest, oldest is farthest.

Are Dinosaurs Reptiles?

-Reptilia should include birds. -Crocodilians are more closely related to birds than to any other living animals; if Reptilia were a monophyletic group crocodilians would be more closely related to turtles and lizards than to birds. -"Reptilia" is not a valid taxonomic group unless birds are included in it. -Birds are more closely related to dinosaurs than they are to crocodilians. -Both birds and dinosaurs are reptiles, so Reptilia now refers to this group, and Sauropsida is a group that is almost the same but includes a few more extinct forms. PIC ON SLIDE 54.

Screen washing (usually with water) sediment for small fossils

-Smaller fossils/bones usually require screen washing. Usually just bits and pieces. -Bones can erode into bits and pieces

Homologies in Groups

-The homologies of a group are not necessarily found in all members of the group, they may be modified or lost in some. -Example: snakes are related to tetrapods (four limbed land animals) but have lost their arms and legs; loss of limbs is the derived condition in snakes. Does not mean they aren't tetrapods! They are, they just lost limbs.

Classification and Evidence

-The taxonomic classification of organisms is based on phylogenetic analysis. -The evidence for the existence of each group is the derived characters (homologies) identified in the analyses.

Linnaean hierarchy =

The pattern of groups within groups formed the basis of a formal taxonomy (groups of similar organisms).

II. Postcranial Skeleton

The postcranial skeleton is composed of the axial skeleton (vertebrae, ribs, and sternum), forelimb and shoulder girdle, and hindlimb and pelvis.

What are some environments for fossil preservation?

Tuffs, strata, formation, and sedimentary environments. Lake and river deposits. Landslides and dune collapses.

What is an isotope?

Unstable, shoots electrons and protons, rate is measurable and can be measured in laboratory.

Are birds dinosaurs?

YES

Dinosaur to fossil a) vs b)

a) quick burial, dismemberment before burial, scavenging by other animals and other natural processes (decomposition, etc), mineral deposits entering forming internal casts of bones (permineralization), isolated bones exposed. b) quick burial, mineral deposits entering forming internal casts of bones (permineralization), nearly complete specimen exposed.

Trace fossils =

fossils that are not of the organism itself but provide evidence about that organism.

Permineralization/Petrifaction

mineral rich water seeps into the void spaces of an organism, leaving deposits of minerals behind that slowly build up, creating a cast of the organism. In some cases, the entire plant or animal may be turned to stone this way, in which case the resulting fossil is said to be petrified.

Parsimonious

most optimal cladogram. Parsimony chooses the relationships supported by the argument that minimizes the homoplasious characters (least conflict).

Darwin argued

that patterns in living organisms was evolution and that shared similarities are due to common descent. These shared similarities are called homologies.

Nodes =

the place where two branches meet. -Nodes on cladograms and trees can be rotated without changing the relationships.

Geochronology =

the process of discovering the numerical age of rocks using radiometric dating.

Exploration of ________ in the late 1800s skyrocketed dinosaur discoveries

western North America

(Mesozoic) Triassic "Hothouse Climate"

During the Triassic, some dinosaurs in the south never made it to the north due to climate.

Taxonomy

Biological taxonomy is the practice of giving names to groups of organisms (taxa) organized into the Linnean hierarchy.

Pedestalling

Dig around the fossils, put them on a pedestal

Dinosaur Relationships 6

Dinosaurs are amniotes, including mammals and sauropsids. -->Calcareous eggs are primitive. -->Along with amniotic eggs, animals began to get faster and more active. ----->Enlarged ankle bone ----->Ribs attach to pelvis

Dinosaur Relationships 8

Dinosaurs are archosaurs, including crocodilians and birds -->Skull opening by the eye socket (air sac) -->Air sacs in living crocs and birds and inferred in the T-rex.

Dinosaur Relationships 1

Dinosaurs are gnathostomes, the group including all jawed vertebrates.

Dinosaur Relationships 2

Dinosaurs are osteichthyans, the group including ray-finned "fish '' and sarcopterygians.

Dinosaur Relationships 7

Dinosaurs are reptiles, including lizards, tuataras, snakes, turtles, and archosaurs. -->Scales -->Diapsid Skull -->Molecular evidence shows turtles being closer to archosaurs. -->Forebrains of dinosaurs are enlarged in the same area as in living reptiles.

Dinosaur Relationships 3

Dinosaurs are sarcopterygians, the group including lobe-finned "fish" and tetrapods (note that "fish" are a paraphyletic group.

Dinosaur Relationships 5

Dinosaurs are tetrapods, the group including amphibians and amniotes.

Triassic: 52 million years (When in the Triassic did Dinosaurs exist?)

Dinosaurs only existed in the late Triassic so about the last 29 million years.

Jurassic: 54 million years

Dinosaurs took off in Jurassic.

People in the past who found dinosaur fossils made up animals they thought the fossils belonged to. This was the origin of what?

Myths

Mesozoic World:

Pangea

I. Skull Bones

Premaxilla, Maxilla, nasals, frontals, lacrimal & prefrontal, jugal (zygomatic in humans), postorbital, parietal, squamosal, quadrate, quadratojugal, sclerotic ring (they show the dinosaur of the pupil, helped show size of eye if nocturnal etc.), occipital condyle (back of skull), paroccipital process (exoccipital), dentary, angular, surangular, articular, KNOW HOW TO LABEL THEM ON A PICTURE.

How do isotopes behave once they are locked into a mineral crystal?

Some isotopes are unstable and radioactive. They convert to other more stable isotopes over time by the loss of neutrons and/or protons.

PTEROSAURS ARE NOT DINOSAURS. THEY WERE FLYING REPTILES.

They had specialized forelimbs, 1 finger holding their wing UNLIKE bats/birds

Dinosaur Relationships 4

Tiktaalik is a very transitional animal in many ways. Develops stronger arms as it evolves to flop on land. Had fish characters and tetrapod characters.

What are some types of sedimentary rock?

sandstones, mudstones

Homology =

similarity due to common descent (common ancestry). Homology is identified by phylogenies.

Homoplasy =

similarity that is not due to common descent.