Paleontology (GEOL 325) Final Exam Study Guide

Cenozoic Ocean Temperatures (δO18 Uses)

Oxygen isotopes used to assess climate change over the last 65 Mya using δO18 ratios recorded in deep sea cores that contain benthic forams. Ratios help reconstruct TEMP (see the glacial/interglacial system before). In the Cenozoic…

• Highest Temps at PETM (Paleocene-Eocene Thermal Maximum).

• Lowest Temps at Pleistocene Glacial Cycles (rapid change between glacials and interglacials).

• Fastest Changes at Eocene-Oligocene transition (massive cooling… mammalian extinction) and Late Oligocene (big warming → Antarctic thaws)

Annual Ocean Temperatures and Seasonality (δO18 Uses)

Seasonality can be recorded in bivalve shells and other bones/shells. Bivalves grow like how trees do (specific growth bandings). Age is recorded with growth in the shell → you can serially sample a shell from young to old ages (along the growth series) to determine growth rates, age, and climate (δO18). Bands indicate a YEAR of growth. You can do more fine-scale sampling within this yearly growth to get seasonal data and FINE-SCALE climate change.

Dinosaur Endothermy Case Study Using δO18 (Eagle et al. 2011)

Study System → looked at large sauropods from the Jurassic in Tanzania, Oklahoma, and Wyoming. Measured O and C isotope ratios in TEETH as a proxy for internal body temperatures (endothermy?).

Goal → they wanted to use various methods to analyze the possibility for whether dinosaurs were endotherms or not.

Result → compared O/C ratios to modern mammals and birds and with previous data built around growth rate analyses (as a proxy for dino body T). Compared growth rate T values w/ isotope data and body temp of crocodiles:

• Recorded 36-38 degrees C for the internal temp of 2 dinosaurs (similar to mammals and lower than birds). At SMALL body sizes (i.e., can use croc comparison; too large = not comparable), dinos have a normal internal T near modern crocs (based on growth rate body T estimates). LARGER sizes → T increases rapidly (confirmed by isotope data and growth rate body T estimates).

• Suggests that… high metabolic rates during ontogeny (small body size) and then a slowing of rates to prevent overheating as adults (ENDOTHERMIC → EXOTHERMIC).

δC13 System and Carbon Isotopes

δC13 compares ¹³C and ¹²C (refers to the ratio of C13 / C12). As organic material increases (higher productivity), there is an increase in C12 in the env = LOWER δC13 ratio!!

Used for… identifying hydrothermal vent communities, tracking evolution of grasslands, and measuring productivity bounce-back after mass extinctions.

CAMP/end-Triassic Extinction Case Study using δC13 (Yager et al. 2017)

Central Atlantic Magmatic Province (CAMP) = large eruption of flood basalts (covered a lot of land and ocean). Coincides with extinctions in the Triassic but OUTLASTS it by 86 Kya (via U-Pb dating).

Goal → interested in looking at when extinctions took place in Peru and how the extinction affected it there (i.e., looking at TIMING of changes in C isotopes for productivity changes).

Study System → focused on C isotope ratios across the Triassic-Jurassic boundary in Peru (δC13 through time) in sed samples (no organism)

Results → peak in δC13 (lower productivity) occurs BEFORE eruptions (predates CAMP eruptions dated in N. America/Morocco). Was there an earlier eruption? Another mechanism for increases in δC13???

Mohr et al. 2020 Paper - Clams and Catastrophes

Goal → wanted to reconstruct climate and environmental factors across the KPg in order to determine kill mechanisms and causes for extinction.

Study System → Lahillia larseni (infaunal bivalve species), collected individuals from Seymour Island, Antarctica (Lopez de Bertodano Fm). Maastrichtian to Danian in Age (Late Cretaceous to Early Paleocene).

Methods → specimens collected from the Fm across the KPg Boundary and used specimens from previous studies. Scanning electron microscopy - analyzed shell microstructure (for growth lines for subannual growth and env changes). High-resolution stable isotope schlerochronology (serial sampling) - for δC13 (anoxic/euxinic conditions) and δO18 (paleotemperatures… VSMOW standard).

Result/Interpretations → δC13 values yielded TWO lower-than-expected intervals occur (interval I/II) WITH low δO18 values (statistically significant). These intervals also correspond with INCREASED extinctions (increased LOs). 1st = Deccan Traps eruptions. 2nd = KPB (bolide impact). They interpreted the fluctuations and values in their isotopes as seasonal fluxes due to methanogenesis, which suggests an anoxic/euxinic env. Furthermore, low levels of both isotopes correlates with CLIMATE WARMING in the intervals. High T = low δO18 + methanogenesis (anoxia) = low δC13. Suggest that interval 1 (of extinctions) was caused by local methanogenesis/euxinic due to Deccan Traps. Interval 2 → less LOs of benthic mollusks suggest that euxinic conditions are NOT the kill mechanism.

Next Steps → increase sample size (better estimates), this does NOT address the kill mechanism for NON-benthic taxa (nektonic ammonites), not globally applicable (try sampling elsewhere… like Arctic), and expand research to look at kill mechanism for interval II. Evidence of anoxia?

Paleoecology

The study of relationships between organisms and their environment in the fossil record (extension of ecology to fossils). How does env (bio + geo) affect bio (opposite of geobiology)

Importance of Paleoecology

1) Contributes to understanding of MODERN ecological processes

2) Contributes to ability to reconstruct paleoenvironments (ex. biotic invasions, bio tolerances, diet, etc.).

Community

Formed by the interactions among populations of living organisms at a particular time and a particular place (NOT same species).

5 Ways to Quantify Communities

1. Number of taxa = SPECIES RICHNESS (in a specific sample/area). Calculated via rarefaction (calculate richness while controlling for sample size → how does richness in each sample change as you increase/decrease the sample size/# of individuals; plateaus w/ enough sampling effort = “true” richness)

2. Number of individuals in each taxon = raw (raw numbers; SAMPLING BIAS), rank (what is most abundant, next, next…), and percent abundance (what percentage of an entire community does one taxon make up). Worry about PRESERVATIONAL BIAS.

3. Number of individuals between taxa = evenness (rare or dominant taxa?)

4. Density = average number of individuals in a give area of volume. Rare → organisms preserved in life position (determine density while living).

5. Spatial Distributions = uniform (individuals spread out evenly… ex. Skolithos), clumped (isolated groups), and random (no organization)

Symbiosis (Fossilized Behavior)

Can see MUTUALISM (both organisms benefit), COMMENSALISM (one benefits/one receives no effect), and PARASITISM (one benefits, one has a COST).

• Inoceramids w/ fish → very large clams preserved w/ fish inside them… considered COMMENSALISM!! Fish use clams as shelter

• Crinoids w/ gastropods → gastropods fossilize w/ the calyx of some crinoids (HAT). Appears to be eating crinoid poop (mutualism/commensalism?).

• Cambrian-aged bivalves w/ worm tubes → filter-feeding worms steal food from bivalves (PARASITISM).

Reproduction (Fossilized Behavior)

Seen in ichthyosaurs (dolphin-like reptiles during the Jurassic - evidence of live birth in fossil record), amber (insects mating), and Crepidula fornicata (gastropod that is preserved in life orientation as stacks that are copulating → top shell (male) fertilizes the rest underneath (female)).

Predation (Fossilized Behavior)

Seen in preserved fish (ex. Xiphactinus or Lagerstatten where fish are ingesting, digesting food), gastropod drillholes (in bivalves, blastozoans), dinosaurs, and coprolites (evidence of diet in fossilized poop).

• Evidence for… regurgitated belemnites (how - acid pitting on them in a massive pile)… possibly ichthyosaur/plesiosaur?

Competition

Interactions between organisms striving for the same resource (i.e., food, substrate, mates, etc.). Results in competition exclusion (two species that compete for the same resource CANNOT coexist… one is driven out) or niche partitioning (organisms competing for the same resource find compromise via spatial, tiering, temporal, etc. differences in consumption of a resource). HARD to test!

Bryozoan Competition Case Study (Sepkoski et al. 2000)

Goal → sought to quantify competition between cyclostome and cheilostome bryozoans from the Late Jurassic to Recent. Why bryozoans → encrusting organisms showcase competition more easily (for SPACE… competition between colonies for hard surfaces) + preserved in actual spatial orientation.

Study System → global, bryozoans, Late Jurassic to Recent! Compared diversity.

Results → CHEILOSTOME bryozoans heavily increased in diversity at ~100 Mya (before = similar diversities between groups). Still maintain larger diversity today. CANNOT just assume this is due to out-competition (could be predation/env change). So… determined if competitive advantage drove cheilostome diversity up:

• Fossil material containing colonies other either group → cheilostomes were in fact OUTCOMPETING cyclostomes (preserved in colonies) fighting for substrate/material.

Ecological Succession

Regular changes that take place in a community as it becomes established and matures to a stable endpoint (ex. after a forest fire, glacial retreat).

Reef Communities Succession Case Study (Walker & Alberstadt 1975)

Study System → looked at Ordovician-Devonian reefs in the American Southwest. In the fossil record… higher diversity in what built reefs (bryozoans, brachiopods, sponges, stromatoporoids, corals, bivalves). Looked at many diff communities across the time interval.

Goal → sought to see if succession can be preserved in the fossil record in reef ecosystems (b/c reefs preserve community structure through time).

Results → QUALITATIVELY argued for 4 different successional stages (note… big time discrepancy… order of Ma rather than months to years):

• Stabilization = a period in which soft sediment dominates the landscape. Organisms start to settle/provide hard surfaces for attachment. Examples: ramose bryozoans.

• Colonization = colonization of things that like hard surfaces, like corals, bryozoans, and stromatoporoids. Also sponges, encrusting/ramose bryo, algae, etc.

• Diversification = HIGHEST species richness. Taxa include bryozoans, algae, sponges, stromatoporoids, gastropods, etc.

• Domination = only one group of organisms LEFT - either laminate stromatoporoids OR encrusting bryozoans (depending on the community).

Improvement → QUANTIFY (species richness/evenness/percent abundance… does the diversification stage actually have highest diversity?), env stimulus for succession (could just be natural change), etc.

Food Webs/Trophic Levels

Notoriously HARD TO STUDY in the fossil record

Permo-Triassic Terrestrial Food Webs Case Study (Roopnarine et al. 2007)

Study System → looked at Permian-Triassic terrestrial communities in South Africa (includes Lystrosaurus - mammal-like reptile) in the Karoo Basin. Has good preservation of insects, amphibians, amnotes, freshwater fish, plants, etc.

Goals → sought to create simple food webs across the PT extinction (using morphology, tooth wear) and asses how food webs/communities change.

Results → using the food webs they created, they simulated disruptions to primary productivity (i.e., introduced diff extinction levels at diff levels of the food webs in the diff communities through time). EARLY TRIASSIC COMMUNITIES (after PT) = inherently LESS STABLE in disruption analyses (e.g., fewer extinctions led to whole collapse).

Evolutionary Paleoecology

The study of ecological phenomena that operate at long timescales. There are many approaches to evolutionary paleoecology: escalation, guild structures, tiering, and evolutionary faunas.

Escalation

Evolutionary arms races though to occur between predators and their prey.

Example of Escalation → MMR

Mesozoic Marine Revolution → rapid adaptation to shell-crushing and drilling predation in benthic (often molluscan) organisms throughout the Mesozoic (ex. crab claws get larger, and shells get thicker in response… leads to even larger claws…). Natural selection favors snails with thicker shells. Natural selection favors crabs with stronger claws to pierce thick shells. POSITIVE feedback:

• Offense: marine predators - fish, rays, crabs, gastropods (acid secretion + radulla drilling), octopi (drilling), etc.

• Defense: marine prey - gastropods (apertural teeth (harder to peel back)) and bivalves (spines, thickened shells, ribs (large snails can’t drill between ribs), burrowing (long siphon allows for filter feeding), boring, swimming)

• Evidence of Predation: peeling (crabs peel snail shells backwards from the aperture), drilling, and chipping (use env materials to chip off/pry open prey).

Evolutionary Arms Race Activity

Hypothesis → Shallow burrowing taxa will be more frequently drilled than deeper burrowing taxa.

How to Test → sinus (divot in the pallial line that connects adductor muscles) is a good proxy for whether a bivalve is a deep or shallow burrower (indicates siphon length and thus burrowing depth). Then, you would compare drilling frequencies in bivalves with a LARGE sinus and those SMALL/W/O a sinus.

Data Collected → used a discrete condition: does the shell have a sinus (deep) or NO sinus (shallow)? Then, abundance counts were taken within both burrowing depth conditions based on the presence/absence of drillholes. Thus, occurrence of drillholes can be compared between shallow/deep. Restricted our study to WHITE CLAMS (like Mercenaria) to exclude scallops/oysters (not burrowers). Chose to analyze 50 deep-burrowing (had a sinus) and 50 shallow-burrowing (NO sinus) bivalves. Counted number of individuals with drillholes in each condition.

Stats/Analyses → use a Chi-Square test in PAST since we are comparing two groups (drilled vs undrilled) across a discrete variable (shallow OR deep).

Results → found that 15 (of 50) deep-burrowing individuals had drillholes. 34 (of 50) shallow-burrowing individuals had drillholes. Our Chi-Square test contained a statistically significant p-value (p <0.05), suggesting that our observed data is statistically significantly different from what would be expected if having a sinus (burrowing depth) was NOT a factor. This supports our hypothesis that burrowing depth affects drilling frequency.

Local Fossils to Know/Identify (Fieldtrip + Activity)

• Chesapecten = scallop

• Mercenaria = white clam. Generic - not circular in shape. Lots of ribbing/ornamentation. Generally large and thick.

• Glycymeris = white clam. More circular in shape. STRONG radial ornamentation (lighter concentric).

• Ostrea = oyster

• Turritella = snail in the shape of a rapidly-coiled spire

• Septastrea = coral. Scleractinian (white, has septa). Colonial!

• Balanus = barnacles. Hard outer shell in the shape of a cup. Usually found attached to shells, hard surfaces, etc.

• Fossil whale bone = very porous. Usually tan to black/dark brown in color.

Guild Structure Case Study (Bambach 1983… later Bambach et al. 2007)

Goal → wanted to QUANTIFY large-scale ecological patterns in the fossil record, looking at how the filling of ecological niches changes through time (niche = function of organism in env).

Study System → Study marine organisms (all) across the Phanerozoic globally.

Methods → based his niches on life habit (ex. pelagic, infaunal, epifaunal), diet (suspension, deposit, herb, carn), and tiering (within epifaunal and infaunal… ex. deep or shallow). Then, looked at how many taxonomic groups of organisms (phyla) existed in each category during the modern, Paleozoic, and Cambrian. Groups referred to as Bambachian megaguilds.

Results:

• Modern → nearly every major niche filled by at least one taxonomic group… quite a few have MANY. Pelagic dominated by mammals, Osteichthyes, and cephalopods. Epi/infaunal dominated by bivalves, polychaetes, and gastropods.

• Paleozoic → missing a LOT OF INFAUNA (why - burrowing kicks off only at the MMR). Missing herbivorous pelagic organisms (marine mammals). Also… less taxonomic groups per major niche.

• Cambrian → much fewer pelagic organisms (really only trilobites… no carnivores). Many missing infauna. A LOT LESS taxa per megaguild (missing many taxonomic groups… have not radiated).

In 2007 (quantify) → he created a 6-motility-6-tiering-6-feeding theoretical ecospace with 216 possible niches. Analyzed ow the number of niches/cubes occupied increased across geologic time using 5 intervals: Early Ediacaran, Late Ediacaran, Early/Mid Cambrian, Late Ordovician, and Recent. Global! Marine taxa!

• Found that modes of life for SKELETAL fauna increased by over 50% during the Ordovician radiation and has doubled since then. Soft-part fauna = even greater expansion!

Tiering Trends Case Study (Ausich & Bottjer 1982, 1985)

Tiering refers to the different levels above and below the sea bottom that organisms occupy (seen in intertidal, rainforests).

Goal/Study System → how do tiering trends change over time during the Phanerozoic in marine invertebrates globally? Analyzed suspension-feeding communities on soft substrates (coral reefs, mollusks, sponges, crinoids). Quantified where organisms were at which time interval and their magnitude (how infaunal or epifaunal)!

Results → infauna get deeper and deeper starting in the Carboniferous. Epifaunal taxa begin to extend further off substrate → diversification in Ordovician and Silurian = expansion of tiers (highest tier (tall crinoids) lost at the KPg). Tiers appear to break down around big MASS extinctions (PT/KPg).

Evolutionary Faunas Case Study (Sepkoski 1981)

Goal/Study System → examined diversity patterns in Phanerozoic marine taxa globally. Wanted to quantify extinction and origination and compile data on first/last occurrences for families/genera. Built a diversity curve through time.

Methods → used factor analysis to see if there was clustering of when originations/extinctions occur (do some organisms originate/go extinct together).

Results → 3 major evolutionary faunas (diverse at specific intervals): Cambrian (diverse in Cambrian and then less important after; includes trilobites, Lingulata, primitive crinoids), Paleozoic (increase in diversity during the Ordovician Radiation but were hit hard by the PT; ex. Rhynchonellata, rugose/tabulate corals, cephalopods, graptolites, crinoids), and Modern (increase in diversity after the PT; make up ocean diversity today; ex. bivalves, gastropods, modern bryozoans, fish (bony and cart), mammals, crustaceans, echinoids).

Evolution

"“Descent with modification.” A change in allele frequencies in a population over time (organisms have changed through time and are related by descent from a common ancestor).

Microevolution

Small-scale changes usually below the species level

Macroevolution

Large-scale changes usually above the species level (ex. evolution of different dino groups across time)

Why care about evolution?

1. Medical Applications = AIDS, cholesterol (cholesterol differences due to evolutionary differences in peoples that originate from Africa and migrated earlier or later), antibiotics (indiscriminate use = evolution of resistant strains of bacteria QUICKLY), Influenza, and TB

2. Agricultural Applications = pesticides (evolution of pest resistance - only the resistant pests survive to reproduce, passing on resistant alleles), herbicides, etc.

Theory of Evolution by Natural Selection by Charles Darwin

Darwin did NOT invent evolution (studied and hypothesized long before him)… he came up with a MECHANISM for the pattern of evolution (= natural selection) and provided overwhelming EVIDENCE for evolution (e.g., finches). He came up with ONE DRIVER out of many.

Natural Selection

One of MANY evolutionary drivers (mutation, gene flow, genetic drift, artificial selection, sexual selection).

1. Individuals within a species vary.

2. Some of these variations are passed on to offspring (mechanism NOT known by Darwin… genetics discovered later).

3. In every generation, more offspring are produced than survive.

4. The survival and reproduction of individuals are NOT random. Those who survive/reproduce the most are those with the most favorable variation.

How does natural selection work - Example

Peppered moths live in England and have a light/dark morph. During the Industrial Revolution, lighter morph was dominant; however, over time, the trees became covered in black soot from all the factories. Thus, it was easier for predators to spot the lighter morph on the trees they lived on. This provided a selection pressure in which the darker color morphs survived more (better camouflage), lived to spread their genes, and expanded the proportion they make up in the population until dominant (why - better survival/reproduction).

6 Major Contributions of the Fossil Record Supporting Evolution

1. Phyletic Gradualism vs. Punctuated Equilibrium

2. Direct Evidence for Change Through Time

3. Direct Evidence for Relationships Among Species

4. Fact of Extinction

5. Direct Evidence of Transitional Forms

6. Species Selection/Sorting

Punctuated Equilibrium (PE)

A hypothesis that species change very rapidly during episodes of speciation then remain stable for long periods of time between speciation events. Proposed by Eldredge and Gould (1972). Evidence of PE AND PG in the fossil record.

Organisms experience DRASTIC morphological change associated with branching event (new species in relatively short time; maybe due to allopatric/sympatric speciation). Times of no morph change = stasis! Change is EPISODIC. Speciation ALWAYS involves branching and thus morph change is limited to branching (cladogenetic).

Phyletic Gradualism (PG)

Gradual transformation from one species to the next. Morphological change gradually through time (diagonal lines where x-axis = morph change). Change is GRADUAL. Speciation sometimes involves branching (not limited to that). Shows anagenetic change. Morphological change is NOT limited to branching.

Anagenesis

Morphological change within one branch through time… i.e., species formation without branching

Cladogenesis

Morphological change with the splitting of branches… i.e., species formation with branching

Testing PG vs PE

1. Does change occur in conjunction with speciation events or INDEPENDENTLY?

2. Is rapid change followed by stasis or continued change?

Problem with paleo → if we define species on the basis of morphology, then speciation and morphology MUST be correlated (circular reasoning)! So… we have to make sure to use SEPARATE morph characters when determining different species vs. morph change through time.

PE Case Study (Cheetham and Jackson 1996)

Goal → wanted to test for the presence of punctuated equilibrium in the fossil record.

Study System → studied Caribbean bryozoans from the Miocene to Recent. Bryozoans b/c control for genetic variability (clonal = same genome).

Methods → established 19 morphospecies on the basis of morph traits. Check the genetic validity of some of the living morphospecies = WERE genetically different from each other (actually diff species). Constructed an evolutionary tree of morphospecies based on OTHER morphological characters (NO circularity). Y-axis = time. X-axis = morph change in tree.

Results → within each species lineage, NO morph change through time. LOTS of morph change in short amount of time (ex. species 9, 8, 7, and 6 branch off 5 at same time). Morph change associated with SPECIATION → evidence for PE.

Direct Evidence for Change Through Time

Trilobites → see evidence for changes in the number of ribs through time in MULTIPLE families/genera. Often INCREASES in the number of ribs.

Chesapecten → differ in the number of ribs they have and micro-ornamentation (threads) through time (ex. C. jeffersonius (few ribs) → C. madisonius (MANY more ribs)).

Direct Evidence for Relationships Among Species

THROUGH fossils being incorporated into evolutionary trees. Have found that birds and raptor dinosaurs are closely related (when/where and how similar they look in the fossil record). Would NOT have known if we did not start building trees with fossils.

Fact of Extinction

The presence of taxa in the fossil record and absence of those same taxa in the modern day provide EVIDENCE of evolution (ex. trilobites, blatozoans, graptolites, Giant Moa, etc.).

Direct Evidence of Transitional Forms

Archaeopteryx = means “ancient wing.” Oldest fossil bird! Has bird-like traits (furcula (wish bone) and feathers… now known that dinos had these) and dinosaur-like traits (teeth, long bony tail, claws).

Whale Evolution = occurred over 10-20 mya (short time) in which terrestrial mammals went back into the ocean. Evidence through Ambulocetus (“walking whale” - looks like a mammal crocodile). Also… Indohyus = an artiodactyl (hooved mammals) that had a specialized thickened ear bone (LIKE modern whales and Ambulocetus) but was terrestrial-based (4 legs, hooved, etc.). Represent artiodactyl to whale transition (Indohyus) and terrestrial to marine transition (Ambulocetus).

Species Selection/Sorting

Analogous to natural selection but acts on SPECIES instead of individuals. Looks at extinction/speciation that correlates to species-level traits (selection on HIGHER levels.) Species may survive b/c they possess characters that give them an evolutionary advantage. Characters must be “IRREDUCIBLE” (can’t go below species level), such as size of species geographic range (greater range = lower extinction), sexual dimorphism (more dimorphic = more likely to go extinct), etc.

Species Selection for Gastropods Case Study (Jablonski 1986 / Duda and Palumbi 1999)

Jablonski → wanted to look at whether species selection evidence is found! Wanted to determine whether molluscan species with narrower geographic ranges are more likely to speciate. Geo range = NOT reducible, and geo ranges are probably heritable b/c LARVAL TYPE IS HERITABLE:

• Planktotrophic larvae = large geo ranges

• Non-planktotrophic larvae = small geo ranges

Measured speciation rate during the Cretaceous of molluscan faunas with these larval forms globally (can determine geo range of each species based on larval shell preserved (shows whether plank or not)! Also looked at diet for correlation.

Results → non-planktotrophic mollusks (small geo range) SPECIATED MORE. Possibly b/c they become hyperspecific to env to outcompete planktonic larval generalists. Env change = new adaptations and speciation. Also… LITTLE GENE FLOW (plank = gene flow across world).

Duda and Palumbi → are larval types (and thus geo range size) actually “heritable”? Studied Conus (a specific genus; limitation) and used DNA-sequencing (characters on tree) of many species within the genus to create a phylogeny. He then distributed larval forms of each species across the phylogeny to asses whether new species are more likely to inherit the larval type of an ancestor species:

• If you are non-plank, you are NOT more likely to produce a non-plank descendent than a plank descendent (i.e., random distribution of larval types). NOT heritable.

Tetrapod

“Four feet” (includes amphibians, reptiles, birds, and mammals). They originated during the transition from fish to amphibians/AQUATIC TO TERRESTRIAL. Occurred during the Devonian (bacteria/viruses likely moved during the Proterozoic and plants during the Silurian). Why…

Major Challenges of Moving Onto Land

Moisture (how to retain it), thermoregulation (maintaining body T), diet (finding food), defense (against pred), respiration (how to breathe…), mobility (how to go from swimming to walking), reproduction (can’t broadcast spawn anymore), dealing with gravity (support), etc.

How Do Verts Deal With These Challenges/What is Preserved

Laying eggs in water/amniotic egg/staying near water (MOISTURE), development of new teeth/snout shape (DIET), developing lungs/cutaneous respiration (BREATHING), hardier legs with improved strength (MOBILITY/BODY SUPPORT), etc.

What is preserved?

• Changes in Skull Shape - head first becomes flat and eyes move towards top of head (like a croc - shallow-water habitats w/ aquatic and terrestrial life). It later becomes more triangular (when predominantly terrestrial).

• Stronger Limbs - development in pelvis (pelvic girdle), wrist, ribcage, and neck bones for better movement and support of body.

• Digits Evolve - the evolution of digits (8 at first… decreases to 5/6) for movement and body support.

Evolution of Flight

Evolved OVER 30 times in verts (including gliding). Seen in birds, pterosaurs, bats, frogs, lizards, snakes, and squirrels. Best known…

• Pterosaurs, birds, and bats

Pterosaur Flight and Wings

Originated in the Triassic and divided into two groups: Rhamphorhynchoids (arboreal, smaller, long tails with kite shape) and Pterodactyloids (large sizes, desert/marine, headgears). Both went extinct during the KPg.

Have a humerus, radius, and ulna (conserved in birds and bats as well due to common ancestor that had these bones). Different wing structure → fingers on the midwing with the 4th finger extending to the end of the wing. SKIN MEMBRANE w/ thickened fibers make up the wing and connect the 4th finger to the body.

Bat Flight and Wings

Originated in the Eocene. Do not live in env conducive to fossilization… thus no transitional forms!

Have humerus, radius, ulna. The fingers are ALL present and are COMPLETELY SPREAD OUT w/ skin membranes present between EACH finger. NO thickened fibers. Wings connect to feet.

Bird Flight and Wings

Evolved during the Jurassic. There are TWO MAIN HYPOTHESES for origin of flight in dinosaurs (see next).

Have radius, humerus, ulna. The wrist and finger bones are fused. Feathers attach to the bones and have filaments in them to stick to each other (barbed structure). Feathers = used to fly (help them withstand drag due to sticky filament structure).

Arboreal Hypothesis (For Dinos → Birds)

From the trees down!

• Pro = makes sense from an aerodynamic POV, vertebrate flight most likely originated via a gliding stage, etc.

• Con = scarcity of arboreal dinosaurs (could be PRESERVATIONAL BIAS → forests are not conducive to fossilization)

Xu et al. 2000 → evidence of Microraptor (a small arboreal theropod that is NOT ancestral to Archaeopteryx… suggests evolution of wings SEPARATELY/MANY TIMES IN DINOS). Other finds support multiple evolutions of flight in dinos as well (some evidence of even membranous wings).

Cursorial Hypothesis (Dinos → Birds)

From the ground up!

• Pro = dinosaurs are ground-dwelling, and those most related to birds are highly cursorial (running) organisms (ex. Deinonychus).

• Con = aerodynamically difficult to evolve flight from the ground.

Dial 2003 → possible evidence for Cursorial through Wing-Assisted Incline Running (WAIR). Worked with juvenile birds from Montana and observed that juveniles of some species of bird, when presented with an incline, pump their wings in a figure-eight fashion to assist in running up the incline (NOT flying… push them towards wood/surface). Shows how wings might first be used as a juvenile and suggests a possible mechanism of flight evolution if cursorial!

Systematics

Scientific study of the kinds and diversity of organisms and relationships among them. Phylogeny is a method of studying the relationships between organisms. I.e., systematics = umbrella term (includes phylogeny and taxonomy)

Phylogeny

Evolutionary history of a group. A phylogenetic tree is a GRAPHICAL summary of an evolutionary history (graph of a phylogeny) and is a hypothesis about how organisms are related to each other.

How to Read a Phylogenetic Tree

• Organisms = at the top of the tree at different TIPS (ends of branches).

• Root = base of the tree (part of the tree that evolved earliest in geologic time)

• Branches = evolutionary pathways that led to organisms

• Node = where two branches diverge/split from each other… represent a COMMON ANCESTOR

  • Can rotate them in space → MEAN THE EXACT SAME THING

  • Organisms are MORE closely-related to other organisms that SHARE A COMMON ORIGINAL NODE. Example: frogs are more closely related to cows than sharks b/c frogs/cows share a common ancestor w/ the branch that leads to cows.

• Character State Changes = represented as black dashes across branches

• Sister Taxa = two branches that are MOST closely-related (most recent common ancestor/node).

Evolutionary Tree

A phylogenetic tree (relationships between organisms) WITH rates of evolution (i.e., time on an axis) WITH information about ancestors.

Characters

Traits like morphological features that are the raw material for phylogenetic trees (paleo = almost exclusively morphological).

Two Types of Characters

• Discrete = represent different categories. Are QUALITATIVE and compose of “states” (ex. number of limbs or “presence/absence” characters).

• Continuous = QUANTITIVE. Includes things like size, length, width, etc. Everything that changes along a CONTINUUM

Convergent Character State

A state that arises independently in 2 independent evolutionary lineages (e.g., wings in birds, bats, and pterosaurs). NOT arising through a common ancestor. Seen when a character state evolves AT LEAST TWICE in a tree.

Homologous Character State

A state that arises in 2 lineages because these lineages SHARE A COMMON ANCESTOR possessing this character (ex. fur in mammals, bones in the vertebrate limb (humerus, radius, ulna… highly conserved b/c present in common ancestor).

Cladistics

A phylogenetic technique that determines relationships based on SHARED, DERIVED characters. Cladograms = hypotheses about evolutionary relationships (graphical).

Cladistic Characters - Primitive vs. Derived

Usually DISCRETE characters.

Based on primitive/ancestral (relatively primitive character that is present EARLY in the evolutionary history of a group) or derived (relatively derived character that is present LATE in the evolutionary history of a group; most helpful characters for a tree). This is RELATIVE → depends on organisms in the tree and may be ancestral at one level (e.g., fur in mammals) or derived at another level (e.g., fur in vertebrates only evolved with mammals).

• Plesiomorphy = a primitive character state

• Apomorphy = a derived character state

Cladistic Characters - Shared vs. Unique

Shared traits = more than one organism on the tree has those traits (THESE help you group organisms together). Unique trait = ONE organism has it. Can combined with earlier terms…

• Symplesiomorphy = shared, primitive character state.

• Synapomorphy = shared, derived character state (IMPORTANT)

• Autapomorphy = unique, derived character state (e.g., present on one organism at the top of a branch)

Determining Polarity (whether traits are ancestral/derived)

1. Outgroup Method = examine character states in distant relatives (OUTGROUPS). Outgroups are assumed to represent primitive state.

2. Paleontological Method = examining the order in which character states appear in the fossil record (only works well for organisms with a GOOD fossil record).

Constructing a Cladogram/Fun with Phylogeny (Review Activity)

First, determine what character states are derived for EACH character (compare with outgroup - if it is a different state from the outgroup, it is derived).

Second, determine what character states are derived and SHARED for each character. Compare each state across multiple taxa (if multiple taxa have it… circle them to include them in that trait). Note - EXCLUDE a derived state of a character if it is UNIQUE to only one taxa.

Third, create a row of the taxa, and circle different taxa to group them together based on shared, derived character states from the most inclusive to least inclusive. The outgroup will be at the BASE of the tree (outside of the circles).

Fourth, create a tree based on the circles w/ taxa at tips. Then, add to your tree only the SYNAPOMORPHIC CHARACTER STATE CHANGES (shared, derived states) → do not draw losses, autapomorphies, etc. Aka the number of EVOLUTIONARY STEPS! Written as “Character: Character State” (like “Limbs: 4” for 4 limbs) at the NODES to which it is common to all taxa above the node (unless state is later lost).

Fifth, determine convergence (if a synapomorphy appeared twice or more) or homologous (all other synapomorphies) character states.

How to Choose Between Trees

1. Parsimony

2. Maximum Likelihood

3. Stratocladistics

Parsimony

Choosing the tree with the FEWEST changes (i.e., minimizes the number of evolutionary steps). Follows the idea of simplicity and that a trait evolving once seems more likely than evolving twice. Most common method… BUT assumes evolution is parsimonious!

Maximum Likelihood

Choose the tree that has the highest statistical likelihood based on a particular model of character change. E.g., the rate of molecular substitution can be modeled (e.g., A to T). Can test this likelihood of substitutions against different phylogenies using e-DNA, a-DNA, sed-DNA, etc. Gives you the likelihood (out of 100%) that the tree existed. Note - need MOLECULAR data (harder to do with morph data). Asks “given a phylogeny, how likely am I to obtain this particular set of DNA sequences”

Stratocladistics

Choose the tree that minimizes “stratigraphic debt” (discrepancies between the order of branching on the tree and order of appearance in the fossil record). I.e., comparing trees to stratigraphy/order of appearance in fossil record. Dashes lines created by the phylogeny = what you would EXPECT to see in the fossil record if the phylogeny were true. MINIMIZING the amount of dashed lines.

Crassatellid Bivalves Case Study (Guardado and Lockwood 2021)

Goal/Study System → wanted to test the effect of mass extinction on a group of taxa (were some more resilient). to reconstruct the phylogeny for crassatellid bivalves from the U.S. Coastal Plain across the KPg boundary (Cretaceous into the Miocene/Pliocene).

Results → collected data on 54 shell characters and reconstructed a PARSIMONY phylogeny, Discovered which taxa made it across the KPg boundary (some live until Miocene/Pliocene and others only into Eocene/Oligocene) and which did not. One side of the tree pretty much died at the KPg.

Measuring/Quantifying Extinction

• Total Extinction (TE) = number of taxa that goes extinct during t (E/t; aka… extinction/time interval)

• % Extinction = TE / number of extant taxa during t (magnitude of extinction depends on how much is there)

• Total Extinction Rate (TER) = TE / duration of t (a RATE)

• Per-taxon Extinction Rate = TER / number of extant taxa during t

Issues → SAMPLING bias (in Oligocene/Silurian) and PRESERVATIONAL bias (further back in time).

Extinction Rates (Raup 1994)

Trying to distinguish between regular extinction (regular turnover of species composition) with periods of heightened MASS extinction. Raup calculated the frequency of brackets of percent extinctions (0% = no extinction; 100% = everything dead) per 1 million yrs based on PER-TAXON extinction rate. I.e., he compared large vs. small extinction events across the Phanerozoic for marine species:

• LARGER frequency of smaller extinctions (5-20%) with FEWER larger extinction events (50-80%). One outlier → PT extinction (~85-90% extinction).

The Big 5 Mass Extinctions (Raup and Sepkoski 1986)

Looking at Phanerozoic marine families, they wanted to test for background extinction rates and intervals of HEIGHTENED extinction. Plotted the per-taxon extinction rates of marine families over time:

• Saw that the background extinction rates are slowly declining over time from the Paleozoic to the Paleogene (5% of families during the Cambrian to smaller %s). Possible due to “pull of the recent” (better sampling closer to the modern day leads to more accurate extinction estimates).

• Saw 5 BIG OUTLIERS (1 myr-intervals) ABOVE background extinction…

Mass Extinction Qualitative → a large decrease in biodiversity rapidly on Earth.

Mass Extinction Quantitative → 1) statistically significant higher extinction than background rates, 2) be global in size, 33) be a taxonomically-broad event, and 4) be geologically-short in duration (< 1 myr). Note - only summate to 4% of all Phanerozoic extinctions in total…

The Big 6 - End-Cretaceous (K/Pg)

Occurred 66 Ma. 76% of species went extinct, including all non-avian dinosaurs, pterosaurs, mosasaurs, plesiosaurs, ammonites, etc. Many shell-building species (mollusks), plants, and mammals went extinct (but these groups survived).

Two Main Causes → eruptions at the Deccan Traps (pre-impact) and the meteor impact at the Yucatan Peninsula. Large volcanic province eruptions caused ocean acidification, changes in T, lowered pH, and low O levels before the impact; the impact of the meteor exacerbated many issues by creating a massive impact, large tsunamis, and expansive cloud of ash/dust across the world, blocking out the suns. Plants died and food webs wit them. This caused cooling with eventually warming due to increased GHG levels.

Background Intervals/Extinction

Intervals that do not include a mass extinction / natural rates of extinction due to normal evolutionary processes.

Survivorship Curves (Van Valen 1973)

Wanted to look at background extinction, so he plotted survivorship curves for 24,000 fossil taxa… = the number of an original sample that survives for a particular amount of time. X-axis = duration that a fossil family/genus lived in the fossil record. Y-axis = the number of organisms remaining in a lineage.

• E.g., 100 genera of ammonites live for at least 1 Ma, while only 7 genera of ammonites live for 100 Ma.

You get an exponential curve → there is an exponential decrease in duration lived by organisms (only a few live very long). Shows DURATION OF TAXONOMIC GROUPS. If you LOG the y-axis… the slope becomes the PROBABILITY of going extinct at a given time. Constant slope = OLD and YOUNG lineages are just as likely to go extinct as the other! Created the idea of….

Red Queen Hypothesis

The probability that a species will become extinct is INDEPENDENT of how long it has survived. It is NEITHER more or less likely for long-lived organisms to go extinct based on survivorship curves. Why aren’t species getting better at avoiding extinction (if evolution = better adapted for env)?

• Species must CONSTANTLY evolve to keep up with competing species. Cannot keep up with extinction b/c competitors and prey are constantly evolving. You must keep evolving, which may lead to “getting rid” of a beneficial gene. The context is constantly changing, and it has to evolve with that (no constant env to “master”).

Speciation

The gain of new species (above species level = origination). Speciation is driven by the stoppage of GENE FLOW (flow of genes from population to population)… cohesion of a species occurs via gene flow.

Species

A population of closely-related and similar organisms (fundamental unit of evolution). There are many different species concepts:

• Biological

• Evolutionary/Phylogenetic

• Morphological

Biological Species Concept

Group of individuals capable of interbreeding and producing fertile offspring in the WILD.

• Advantages = makes intuitive sense. Follows the idea of stopping gene flow, leading to speciation/lack of reproduction between two populations (reproductive isolation → speciation).

• Disadvantages = difficult to observe, not widely applicable (ex. to plants, fossils, asexual taxa), and less quantitative!

Note - can BREAK DOWN with hybridization (coywolves… same species?)

Evolutionary/Phylogenetic Species Concept

A lineage evolving separately from others (mostly used in vert paleo). Determined via MONOPHYLETIC groups in phylogenies (monophyletic group = a species).

• Advantages = quantitative! Takes evolution into account (evolutionary history)!

• Disadvantages = few phylogenies are available with living and fossil species. What is the hierarchical level that there are species? You can choose ANY node going back to further ancestors (how close/far should you go).

Monophyletic Group

Include a NODE and all its descendants (clades that contain tips). Used to determine species in the phylogenetic species concept.

Paraphyletic Group

Include a NODE and only SOME of its descendants (ex. Reptilia does not include Aves even though birds evolved from reptiles (dinosaurs)).

Polyphyletic Group

Combining two separate branches/nodes together while ignoring the more ancestral common ancestor.

Morphological Species Concept

Diagnosis of a species based on morphological differences (used in invertebrates and plants).

• Advantages = widely applicable and very quantitative (can test statistically for likelihood of the phylogeny occurring).

• Disadvantages = the choice of traits you use is SUBJECTIVE. Many traits are NOT fossilized.

Measuring/Quantifying Origination

• Total Origination (TO) = number of taxa that originate during t (O/t; aka… origination/time interval)

• % Origination = TO / number of extant taxa during t (magnitude of origination depends on how much is there)

• Total Origination Rate (TOR) = TO / duration of t (a RATE)

• Per-taxon Origination Rate = TOR / number of extant taxa during t

Issues → SAMPLING bias (in Oligocene/Silurian) and PRESERVATIONAL bias (further back in time).

Evolutionary Radiations

Rapid diversification of clades into a variety of ecological niches (rapid production of species/clades). Examples include…

• Cambrian Explosion

• Dinosaur Radiation (after the PT, which heavily harmed the ancestors of mammals, paving the way for dinosaurs)

• Mammal radiation (after the KPg, which decimated the dinosaurs, allowing for niche gaps that mammals could diversify into and fill)

Cambrian Explosion

An evolutionary radiation in which 34/35 metazoan phyla appeared in the fossil record over a period of 40 million years. This Cambrian Explosion was predated by…

The Ediacaran Fauna

Occur around 550 Ma. Fossils are found in Australia and N. America. Consist of ENTIRELY soft-bodied organisms that have a double-layered body structure with offset symmetry (NOT bilateral or radial). No organs. Though to directly absorb nutrients from water.

What replaced the Ediacaran fauna?

Seen in the BURGESS SHALE - occurred 510 Ma and found in British Columbia. Showcases many new animal innovations (that occurred during the Cambrian Explosion), such as hard parts (skeletons), most forms of symmetry, predation, first limbs, first burrows, etc. There is LITTLE connection between the Burgess Shale and Ediacaran faunas, but the Burgess Shale can be connected with modern organisms.

Possible Causes of the Cambrian Explosion

1. Environmental Factors = increased oxygen (perhaps too low O2 levels for animals to survive before the Cambrian), increased ozone (DISCREDITED), increased Ca concentrations in oceans, snowball earth (melting could release nutrients that would support the growth of photosynthesizers; problem - occurred 90 myr before explosion…)

2. Ecological factors = skeletons tied to increased predation, evolution of complex eyes/nervous systems (better sense prey, leading to coevolution (prey develop better defense) - selection pressure on hard parts, shields, spines, faster locomotion), disappearance of Ediacaran fauna (ecological niche gap filling)

3. Developmental factors = homeotic genes (DISCREDITED… existed 100 myr before Cambrian Explosion)

4. Preservational factors = preservational bias (DISCREDITED… studies have accounted for this)

Cambrian Explosion Case Study (Peters and Gaines 2012)

Goal → sought to determine the cause of the Cambrian Explosion through geology.

Study System/Methods → compiled 21,521 rock units from 830 locations in N. America for geochemical info through time across the Proterozoic and Phanerozoic → strontium isotopes (vary based on continental weathering and chemical alteration of seafloor) and neodymium ratios (differences in weathering between young volcanic arcs and old continental crust). Time is on the x-axis.

Results → increase in Sr ratios before and into the Cambrian. Neodymium levels at that time suggest weathering of old continental crust. Argued that an expansion of shallow seas, increased oceanic alkalinity, and enhance chemical weathering of crust drove the Cambrian Explosion (e.g., GEO FACTORS).

Growth Strategies

1. Accretion = organisms that add discrete GROWTH LAYERS to skeleton (similar to tree growth rings). Records an organism’s lifetime! Example - bivalves, gastropods

2. Addition = adding discrete new parts, such as entirely new segments. Example - trilobites, other arthropods

3. Molting = shedding entire exoskeleton periodically. Example - arthropods (crabs, etc.)

4. Modification = continually modifying existing skeletal structures as an organism grows. Example - vertebrates. Note - has a MAX size.

Ontogeny

Embryonic and post-embryonic history of an organism. Ontogenetic changes involve all changes that occur during an organism’s lifespan (morphological, behavioral, chem). Development = ontogeny!!

How is ontogeny reconstructed in the fossil record?

1. Growth Series = measure populations of specimens thought to represent different stages of growth of the same organism (e.g., fossils of embryos, hatchlings, juveniles, adults).

2. Preserved Ontogeny = measure ontogeny directly from the specimen (an entire lifespan in ONE specimen). Works well for accretion/addition! Example - gastropod.

Isometry

NO change in shape during growth. Seen in bivalves. Most organisms are NOT isometric.