Combined Lecture Notes

What is coalescence?

*Divergence viewed from the present* -Every allele has common ancestor -Random chance influences time of gene persisting (especially if neutral) -Always an underestimate because it is lessened by the extinction of species toward presence. We normally think of lineages diverging through time, but if we look back from the present day all extant lineages come together (coalesce) at some point in the past. Just like family geneologies, gene trees can be traced back to a common ancestor. The time at which that ancestor lived can be probabilistically estimated, and will vary for different alleles

Plate Tectonic Theory

- Earth's crust is divided into rigid plates that are supported by denser, more ductile rocks - On geological timescales these ductile rocks flow due to convection in the earth's mantle - Plates are dragged along and interact with one another at their margins, forming the most significant geological features on the planet • There are two major types of crust: oceanic (thin and dense) and continental (thick and less dense) • Three types of plate boundary: divergent, convergent, and transform

Unique homo erectus characteristics

- Increased requires brain size (got bigger over several million years) - Hunting becomes important to support brain nutrients (increased tool use and social cooperation) -Homos tend to be weaker in musculature and facial structure. We are good endurance runner. -No fur: running generated heat. -Long brain growth leads to decade of being under developed and dependent on tribes. -Concealed ovulation. It is not known when females are ready to mate. Thought to increased paternal investment (harder to be confident of fatherhood). Possibly helped prevent infanticide. -Menopause: thought to happen so that grandmothers can help participate in raising grandchildren

Solution to Signor Lipps Effect

- attempt to place confidence intervals on stratigraphic ranges based on preservation rate -If you have lots of appearances, there are short confidence intervals of when it went extinct -If you few appearances, there are large confidence intervals of when it went extinct

Hard fossils: Replacement

-A cast or mold that is a complete replacement -Can no longer see cell walls

Kill mechanism

-A kill mechanism may not cause instant mass death -Small changes in intrinsic population growth rate can cause it to crash to extinction -

Darwin's view on extinction

-A slow and a gradual process (it tends to be slower than origin) -Sudden extermination of species in fossil record is due to incompleteness of record -Organisms through time were becoming progressively more fit, this has driven older species an increased disadvantage over time that led to extinction

What is a vascular plant? (Synapomorphies)

-A vascular system (tubes) to provide support and transport substances -Cuticle: provides protection against dessication & UV. Protects from microorganism -Sporangia & spores: allows for propagation

Australopithecus afarensis ('Lucy') ~3.2 million years ago

-Afar Depression -More like humans that Ardipithecus -For sure bipedal gait (proven by footprints in ash bed)

Accommodation space

-Always accommodation space in ocean along continental shelf -Less common accommodation space in terrestrial place Accommodation space here = suitable environment You always have sediment deposition in the ocean, and much less in the terrestrial record.

Types of human evolution

-Anatomical -Ecological -Reproductive evolution -Cultural Evolution

Homo erectus (Nariokotome Boy or Turkana Boy) ~1.6 million years ago

-Best preserved homo fossil

Soft Fossils: carbonization

-Broad outline, not anatomy -carbon turns to graphite which is then preserved -Often happens to plants due to sturdy cell walls -Burgess shale

When might a (properly calibrated) molecular clock and the fossil record give very different estimates of the time of origin of a clade?

-Changes in generation time (changes in body size too) can cause issues -

Question 3:

-Comes from sediments and volcanic rocks. But specifically volcanic crust in oceanic rocks. -There is no oceanic crust older than mid Jurassic due to it getting subducted away

Soft Fossils: Original tissue preservation

-Completely drys out -Carbon dating possible -Green river formation?

theory of punctuated equilibrium

-Darwinian view of "phyletic gradualism" was wrong -There is actual a lack of morphological change throughout fossil record, unrelated to incompleteness -a theory that attributes most evolutionary changes to relatively rapid spurts of change followed by long periods of little or no change

Alfred Wegener's Evidence for continental drift

-Distribution of fossil species on separate continents -Very diagnostic "ice/glacier" sedimentary rocks (Tillite) could be found across most southern continents -Rocks of same age and configuration on a # of continents -Distribution of mountain ranges along past continent connections

Red Queens Hypothesis

-Explanation for law of constant extinctions, is that species are constantly competing with others around them in a serio-sum interactions such that no one get actually get ahead. Selective pressure on one group to another leads to adaptation that gets rid of that leverage. -Adaptations that increase absolute fitness in one species are countered by adaptations in its competitors, hence relative fitness remains roughly constant and extinction risk should be independent of prior evolutionary success -Posits a world in which extinction is ultimately driven by zero-sum interactions among species -Alt 1: In reference to an evolutionary system, continuing adaptation is needed in order for a species to maintain its relative fitness amongst the systems being co-evolved with. - Alt 2: Sexual reproduction persists because it enables host species to evolve new genetic defenses against parasites and other threats.

Darwin View on Rate of Extinction

-Extinction is a slow process -Viewed extinctions seen as imperfections of fossil record This is proven wrong by sudden drops of diversity across similar aged facies globally? Other reasons? -Mass extinctions that do conincide with gaps in the record, there is often more extinction than can be explained by a gap -There were big changes in climate -High extinction rates+Changes in environment

In what cases do concave survivorship curves indicate that extinction risk decreases with taxon age?

-For marine invertebrates usually -May imply that incumbents have a substantial ecological advantage, or may imply a greater role for the Court Jester: biota is 'hardened' through time as extinction-prone taxa are progressively removed by environmental fluctuations -Have had longer time to adapt to environment, evolved ways to dominate their interactions with other lineages

How does strong positive selection effect gene heterogozity?

-Genetic hitchhiking leads to massive drop in heterogzity of many genes -There is a small drop in heterogozity for a single independent allele right?

Hypothesis of Continental Drift

-Idea continents have moved around relative to one another through time -Continental drift theory came prior to plate tectonics -Coastlines on opposite sides of ocean seem to match up -Alfred Wegener (early 1900s) pushed theory through many lines of research

K-Pg boundary notable for

-Iridium anomaly: -a thin clay bed seemed to represent a fundamental divide: below it there were abundant Cretaceous foraminifera, and above it they were almost all gone. -Wanted to age the layer using the constant background rain of asteroid iridium. There was too much iridium to be explained by the length of time it represented; they hypothesized there was an asteroid impact.

How have continents grown progressively larger throughout geological time?

-Island arcs collide with continents at convergent boundaries. Because they include granitic rocks and are not easily subducted, they build up (accrete) around the continental margins -The oldest continental rocks on Earth are in the middle of continents, and the youngest tend to be at the margins -Younger wester coast of North America are accretionary island arcs added on to older portion of the continent 1. Collision of smaller continents which then become welded together to form one larger continent (which may later break into smaller pieces again). 2. Fragments of oceanic crust and micro-continents (like island arcs) may be added to the margin of much larger continents by plate collisions, making that continent larger still. 3. Prisms of sediment (derived from weathering of the continent), deposited in sedimentary basins along the margin of the continent, may become converted to granitic crustal rocks by metamorphism, melting, and igneous intrusions during collisions with other tectonic plates, and then welded to the margin of the continent.

Why might larger-bodied species be at greater risk of extinction?

-Larger home range sizes thus lower population densities -Slower reproduction -Ask for more examples

How was K-Pg asteroid crater found?

-Mapped out strength of gravitational field and found crater on Yucatán -Why did it lead to cenote creation?

Marine vs terrestrial sedimentation during K-Pg boundary

-Marine records tend to have continuous records -In terrestrial cases there is often not continuous record

Problems organisms need to solve to move from aquatic environment onto land?

-Mechanical support, movement & dispersal in fluid that is less dense than water -Avoid drying out (dessication). But still allow for gas exchange.

Hard fossils: Permineralization

-Minerals getting into pores of specimen and only some replacement occurs -Partial replacement leads to better resolution of internal structures

Uniformitarianism

-Modern depositional environments (places where sediments are being deposited) can be studied to understand ancient depositional environments -Present is key to the past

Cretaceous-Paleogene Mass Extinction

-Most recent mass extinction -K-T boundary or K-Pg mass extinction -Erobounding extinction: fundamental change in diversity at the boundary -Known for Dino extinction

Fungi do what for plants...

-Nitrogen fixer -Connection of root systems of fungi

Hard fossils: Recrystallization

-Occurs if specimen not energetically stable with environ -Dissolution and reprecipiation

Global diversity has 2 components:

-Origination (speciation) -Extinction

Why might biodiversity seem to increase towards present?

-Perfect knowledge of modern biodiversity -More likely to discover fossils in recent rocks -More understanding of modern biota allows it to be easier to see modern day descendants of recent fossils. -Lithification bias

There is an increased number of Lazarus taxa around last extinctions. Why does the record get lousey?

-Periods of times that arent recorded -Facies bias. Facies are being altered by kill factors; alters changes in preservations. -Lineages are persisting in iscolated geographic event -Species being smaller would make them less likely to be found

Taphonomy

-Process of fossilization -Not always the case that the organism itself has been replaces by rock (lithification) -Fossilization requires a specimen to get away from biological processes through burying. Occurs most in oceans/rivers

Soft Fossils: Mineralization (coating/replacement)

-Replaced or coated with mineral -Amber (pulls out moisture and mummified) -Calcium phosphate common in burial environments, leads to high resolution replacement -Mineralization must occur soon after death

Three types of record bias to consider when considering fossil preservation potential in the context of the stratigraphic record:

-Sampling Bias: the correct environment preserved, but the species is simply missing from the record (jellyfish) -Facies Bias: the correct environment is not preserved (mostly affects environmental specialist species) -Animal is not represented in area of fossil record you're looking at -Hiatal Bias: no rock record to be sampled -No rock record recording period of time your are interested in

Plant taxa during K-Pg boundary

-Seem to be dropping our prior to boundary, could be backsmearing or gradual extinction

Mass extinctions event size selective?

-Some evidence for some extinctions -For climate hypothesis, you should see sized biased extinction for numerous fossil records. -Then end Pleistocene extinctions

Community definition

-Species that co-occur in space and time • A group of organisms representing multiple species living in a specified place and time (Vellend 2010) • Nested in nature, dependent on reference point/question • Other definitions: restrict community to a set of *interacting* species

How do we distinguish between species when all we have to work with is morphology?

-Species: set of individuals interbreeding -Relatively continuous morphological variations among a species. You can expect a normally distributed morphological spectrum. -Clusters in morphological spaces separated by gaps helps identify species. The clusters are species.

Surviorship

-Survivorship analysis: -Convex: increase mortality with age -Concave: decrease mortality with age -Lon linear: no change in probability of dying through time -the percentage of newborn individuals in a population that can be expected to survive to a given age

Things that let vertebrates get to land?

-Tetrapods originated from fleshy finned fishes (Sarcopterygians)

Relationships to spreading center and buoyancy

-The faster the spreading, the warmer the oceanic crust. The warmer crust makes it more buoyant -The slower the spreading, the steeper the ridge

Why do rock layers repeat on a non-annual scale? (Obliquity vs precession cycles)

-The orientation of Earth's spin axis relative to its orbital plane varies due to gravitational interactions with the Sun and Moon Obliquity cycle -axial tilt takes about 41k years to vary in extremes between annual angles Precession cycle -Direction of tilt varies with period of 23kya These cycles are driven by moon

sequence stratigraphy

-The study of rock relationships within a time-stratigraphic framework of related facies bounded by widespread unconformities. -recognizes that sediments occur in gap-bounded packages that reflect changes in accommodation space through time -Rising and falling sea levels creates gaps of deposition

Sedimentology

-The study of the components of sedimentary rocks -Reflects environment of deposition (grain size tells you about energy in environment) -Generally goes from sandstone, siltstone, to mudstone for nearshore to deep ocean -

Limitations of morphospace occupation methods:

-These patterns are confieren at low temporal resolution and without phylogenetic context. S -Features of outlines are not necessarily homologous (two arbitrary traits)

What causes variation in eccentricity of earths orbit?

-Variation in the eccentricity of Earth's orbit is driven by gravitational interactions with other planets, primarily Jupiter and Saturn -Jupiter & Saturn's gravity cause the ellipticity of Earth's orbit to change cyclically with periods of ~100,000 & ~400,000 yrs

Ardipithecus ramidus ~4.4 million years ago

-Volcanic ashes around this sequence allow for good dating -Mix of morphology suggests bipedalism and tree climbing -3ft tall -Afar Depression

What factors influence extinction during 'normal' (or background) intervals?

-We usually don't know things go extinct, but we can know general factors: -Most extinct species did not become extinct during major mass extinction events, but rather during the "background extinction" intervals between mass extinctions -With a few very interesting exceptions, in the great majority of cases the fossil record does not give us sufficient information to know specifically what caused the extinction of a given lineage (and it is rarely a single cause!) -However, by comparing the histories of many different lineages, we can try to learn something about the 'rules' of extinction and which factors are generally more or less important

Two hypothesis for most important causes of extinction:

-When you cant keep up with your competitors -Catastrophes

Sea Floor magnetic mapping + evidence for ocean ridges creating crust

-earths magnetic field switches polarity on ~10^5 to 10^6 yr timescales -Volcanic rocks record the polarity at the time they were formed. (They contain magnetic minerals) -Sea floor has a zebra like back and forth pattern of polarity. (Because of moving out from ridge line) -This along with radio-isotopes show how old the rocks were. -Showed that rocks along ridge were the youngest and were older as you moved out.

Principle of faunal succession

-fossils succeed each other in order of geological time ◦ Telling time via the distribution of fossils in the stratigraphic record ‣ William smith saw fossils were not randomly distributed

What clades have successfully moved from water to land?

-green algae/plants -Fungi -Vertebrates -Arthropods

Drivers of megafauna extinctions...

-human population growth -dramatic climate change. Greatly increasing temperature Which is it?

peripatric speciation

-occurs when peripheral populations become geographically isolated from the main population and undergo genetic divergence and speciation

zero-sum interactions

-one winner, one loser (pure competition) -If i get more of it, you less. Examples -You're my resource and if I don't get you then I don't get food -Getting light as a plant

Ratites

-ostrich, kiwi, emu; flightless birds -Member of the group of flightless birds. -A sister group of modern birds. -Found exclusively on southern continents (once part of Gondwana but separated by continental drift)

Haber-Bosch process

-production of fertilizers by combining nitrogen and hydrogen to synthesize ammonia -A process to synthesize ammonia on an industrial scale. Developed by German chemists Fritz Haber + Carl Bosch, the process has enabled humans to double the natural rate of nitrogen fixation on Earth and thereby increase agricultural productivity, but also altered the nitrogen cycle.

Density dependence

-regulation of population growth by mechanisms controlled by the size of the population; effect increases as population size increases -There is an effect of the standing population size at any given time on the mortality or on the fecundity -The larger the population size, the lower the pregnancy rate and the higher the mortality

Fossil definition

-remains or traces of prehistoric life. -Usually mineralized -Includes trace fossils -Also includes molecular fossils (like ancient DNA)

SNPs

-single nucleotide polymorphisms -variations in the DNA sequence that occur when a single nucleotide in the genome is altered

sediment accumulation is driven by...

...inputs but also by the availability of accommodation space, which in the oceans is controlled by changes in relative sea level Changes in relative sea level in a given spot can be caused by rise or fall of absolute (eustatic) sea level and/or by tectonically-driven local uplift or subsidence of the crust

Example question

1. A 2.B

Longterm Consequences of Mass Extinction

1.Mass extinctions may change adaptive landscapes, removing previously successful lineages 2.Recovery" intervals following mass extinctions may be characterized by unusual ecological and evolutionary dynamics in the new adaptive landscape 3.Mass extinction may result in lasting changes in ecological structure and macroevolutionary rates 4.By removing ecologically successful incumbents, mass extinctions ultimately create opportunities for other groups to diversify

Suppose that we buried 1000 shells of a single clam species on a Richmond mudflat next week. We return in 2061 and dig them up, and there are about 750 shells remaining. What is the taphonomic 'half-life' of the species in this environment?

100 years

Younger Dryas Event

12,000 BC. The shutdown of NADW resulted in ice age conditions A cold episode that took place about 11,000 years ago, when average temperatures dropped suddenly and portions of the Northern Hemisphere reverted back to glacial conditions. Triggered by what? Wouldn't it have effected Europe more

Earliest homo fossils

2.6 MYA and disperse from Africa 1.8 MYA

Oldest known ape?

25 MYA. Consistent with molecular clock estimate for divergence of old world monkeys and apes.

What percent of primary production does humanity take?

30% NPP

Homo Sapiens rise about...

300 kya

First evidence of animals

600ma rock records phosphatized animal embryos in Doushanto Formation What type of process leads to phosphatized fossils?

Rhynie Chert

A Scottish locality that has yielded some of thearliest vascular plants anywhere on Earth -Silicified lagerstatten formed by silicates saturated hydrothermal fluids that permineralized an entire community (dumps salts on plants) -Community permineralized IN PLACE so preservation is very good

Functional/Ecological diversity (phenotype?) NO

A measure of the ecological/functional range spanned by a set of taxa

Morphological disparity (Lifestyle?) NO Like bone cracking shown in teeth? Wouldn't that ultimately lead to change in ecological phenotype change?

A measure of the morphological/phenotypic range spanned by a set of taxa -Really weird things that are very different morphological outliers, that make up small percent of diversity

Logistic population growth

A model describing population growth that levels off as population size approaches carrying capacity -Growth looks exponential at first but slows near carrying capacity. -K is set by the crossing of the birth rate and death rate functions

3 types of cladistic grouping: monophyletic

A monophyletic group is a true clade that contains all of the species above a given node (all the descendants of a common ancestor). The goal of cladistic systematics is to produce classifications based only on nested monophyletic groupings

3 types of cladistic grouping: paraphletic

A paraphletic group contains all only some of the species descended from a common ancestor. Because Linnean taxonomy predates cladistic thinking (and even evolutionary thinking), paraphyletic taxa are very common. -ex. Reptiles don't include birds

glide reflection symmetry

A pattern has glide reflection symmetry if it coincides with its image after a glide reflection.

ghost lineage

A phylogenetic lineage that is inferred to exist but has no fossil record We don't always know what characteristics to expect in ghost lineages that dont exist anymore

C4 plants

A plant that prefaces the Calvin cycle with reactions that incorporate CO2 into four-carbon compounds, the end product of which supplies CO2 for the Calvin cycle.

C3 plants

A plant that uses the Calvin cycle for the initial steps that incorporate CO2 into organic material, forming a three-carbon compound as the first stable intermediate.

3 types of cladistic grouping: polyphletic

A polyphletic group contains species from different lineages united only by homoplasic characters. Polyphyletic taxa are rare but can occur when only a few characters have been considered

Facies Analysis

A rigorous, scientific approach to the interpretation of strata -Depositional environments occur in a systematic and predictable order across the landscape so their associated facies do as well

Which of the following is NOT an example of a trace fossil?

A shell

Rarefaction

A way to analytically control for variation in sampling intensity Rarefaction suggests that species diversity differences are primarily a function of sample size differences

Question 8:

A) 5 million year time of observation: 10^-3.7 ____ year time of observation: 10^-4 2% when you divide them by each other A) + or - 50% B) Probably not because you only see 2% of all centuries that pass during that time interval. You do get 50% of eccentricity cycles, so you'd probably get a good idea of changes in community structure

Question 1: How many individuals of species A, B, C, D would we expect to find?

A) 200 remaining B) 75 remaining C) 37.5 (75% or so remaining) D) Can use half lives to get a handle on what original abundence were (missed this)

Question 5:

A) 22.9 MYA B) 22.1??? C) 7 total cycles (counting from deepest facies to deepest facies)

Changes in accommodation space based on rising/falling sea level?

Accommodation space=marine shelf? Wouldn't you have more marine shelf area/accommodation space with sea level rise? Shelf area is a kind of accommodation space. Also applys to a lake. Just think a depression. Sedimentation for shallow water: Sedimentation for deep water:

Upwelled waters tend to be

Acidic compared to surface waters.

Why have arthropods been able to go from water to land multiple times?

All crown arthropods have a chitinous exoskeleton that helps to limit desiccation and provides mechanical support

Fourier analysis

Allows us to replicate complex shapes by stacking trigonometric functions to model shape of interest. Quantification of deviation from a perfect circle: How D or theta angles change indicate shifts in morphology....

Combining two groups with different log linear decay rates creates a concave survivorship curve

Always? WhY?

Assuming that all species within the group actually went extinct at the same time, which of these groups would you expect to show the most gradual apparent extinction pattern? Trilobites Ammonites Amphibians Foraminifera

Amphibians because they are spatially disjointed and thus have lower preservation probability. Forams are more likely to show catastrophic extinction due to its high number of niches and global coverage?

Anagenesis vs. Cladogenesis

Anagenesis involves evolution within a single lineage. Cladogenesis, on the other hand, involves evolution in a branching pattern, with many new species evolving from a single parent species.

n-dimensional hypervolume

Analytical model that shows multiple dimensions to a species niche -n equals the number of environmental factors important to the survival and reproduction of the species. -This is the fundamental niche: what is theoretically possible

Use of aDNA: Reconstructing communities in the absence of fossils

Ancient Environmental DNA from sediments ("dirt DNA") opens up a new possibility: in some cases we can use DNA in ancient sediments, originally derived from skin cells, urine, feces, mucus, gametes, carcasses, hair, etc., to detect the presence of species without any macrofossils

Overall trend in hominid diet

Ardipithecine diet of leaves and fruit (C3 dominated) to Homo diet of grasses/herbivores (C4 dominated)

law of constant extinction

Are you at lower extinction risk when your species is older in age? the probability of extinction for a species is not dependent upon how long it has already existed. Everything is at equal rate of extinction now matter how long it has existed.

Characters that are found in only a singles species...

Autapomorphies (Not helpful for determining lineages among difference species because they exists in only a single species)

Which has highest equilibrium diversity?

B

When did eukaryotes evolve? When did they diverge from closest relatives? What are their synapomorphies?

Based on molecular clock estimates, last ancestor of crown eukaryotes was 1-2 billion years ago. There was stepwise synapomorphies that characterize modern day eukaryotes. They took in prokaryotes and incorporated them as organelles. Some synapomorphies of eukaryotes: Large size, true nucleus, membrane-enclosed organelles, complex flagella, plasma membrane with sterols, cytoskeleton, multiple linear chromosomes, mitosis

continental-continental collision

Because both are largely composed of low-density granitic rocks, neither plate can easily subduct into the mantle, so the result is head-on collision and consequent thickening of the crust Continental-continental collision between the Indo-Australian and Eurasian plates has drive the uplift of the Himalayan Mountains and the Tibetan Plateau

Question 7:

Boundary of J & A is also an angular unconformity

C13 reflects the ratio of

Burial flux of organic carbon that is made up of isotopically light plants

Origination or extinction rate can be indpendent of diversity...

But not both (where lines cross sets equilibrium diversity)

C3 vs C4 isotope fractionation

C4 is heavier. C3 is lighter. Many tropical grasses have a so-called 'C4' photosynthetic pathway that results in smaller δ13C fractionations compared to 'normal' ('C3') plants •δ13C values of carbonate minerals from paleosols (fossil soils) reflect the isotopic composition of CO2 from respired organics in the soil. Shifts to heavier δ13C values, suggest more C4-derived organic matter and less C3 derived organic matter

Calcium and carbonate are supersaturated in seawater, so they are cheap and easy. With ocean acidification...

Calcium carbonate creates have much harder time precipitating

You can combine morphological changes in the following plot...

Canonical variate charts

Eustatic sea level change

Changes in sea level caused by changes in the water volume of the world's oceans, such as those brought about by the formation or melting of mountain glaciers and polar ice caps. "Absolute" sea level

Occurrence-based diversity estimates

Collecting all occurrences allow for control of variation in sampling intensity

There are biases associated with sampling different regions at different times to assess global diversity changes. This can be overcome by...

Comparing similar samples drawn from similar habitats through time -Gamma diversity: diversity of the whole system (planet) -Alpha: diversity we find in any one spot (looking at plants in two different tropical areas in different times) -Beta: turnover in diversity between spots (plants in Berkeley vs Death Valley)

What is the driver of plate tectonic motions

Convection in the mantle & radioactive decay

Convergent boundary: oceanic crust vs. continental crust

Convergent boundaries are sites of the largest earthquakes & most explosive volcanism on Earth. -Partial melting of basaltic crust on convergent boundaries leads to low density minerals melting, rising, and contributing to continental crust formation. This crystallization leads to granitic rock. The sierras are the base on an ancient mountain range that had the granitic bottom contributed to by convergent subduction -As oceanic crust is subducted & subjected to greater heat & pressure it begin to partially melt -These melts are relatively low-density and buoyant, so they rise through the crust & cool to form granitic (continental) crust -Where the melts reach the surface, they make volcanoes

Where do deep sea trenches occur?

Convergent boundary where one tectonic plate is sinking beneath another, specifically ocean plates subducting under continental plates. Biggest earthquakes on earth occur here

Expansion of terrestrial biosphere did what to climate?

Cooling Pre plants -No stability for land so aquatic areas choked with sediment With Plants -Roots attack rock for stability and for nutrients -Plants increase weathering rate ??? -Rivers stabilize water sources -A massive carbon sink is created -Coal is created

Classification: crown groups vs. stem groups

Crown group: All present descendants of the most day recent common ancestor of all the living species of a group, including that ancestor. Crown groups can (and typically do) have extinct taxa in them. (The node that is the first divergence for all living members of that group) Stem group: All the taxa that lie between the crown group and the last common ancestor of that group living group and its living sister group. Total group: The crown and stem groups.

Crown meta pans must have evolved in a ____ world

Crown metazoans must have evolved in an O2-rich world Why? -O2 level is a strong control of the maximum size of diffusion-limited organisms (there was just not enough O2 in atmosphere before Cambrian) -O2 is used extensively in the construction of metazoan collagen

measuring evolution

Darwin (d)

Denisovans _____ with expansions of archaic humans

Declined

As timespan of observation increase, net sedimentation... & why?

Decreases -We incorporate more hiatus over longer timespans -Unsteady accumulation of sediment -the magnitude of episodic (or quasi- episodic) fluctuations in both sedimentation and erosion increases with their recurrence interval. On average, you have to wait longer for larger depositional or erosional events -There is a hierarchy of timescales that control sedimentation, including tectonic processes at longer time scales and Milankovitch-driven climate changes at shorter time scales

Why at an outgroup when building a tree and what does it determine?

Designating an outgroup determines character polarity (what is the ancestral state for the species of interest?)

Does time averaging make the fossil record useless?

Despite time-averaging, changes in living communities are reflected in changes in death assemblages When we ignore very small specimens that are often missed, there is typically good agreement between live and > 1 MM ONLY dead (indicated by low correlation p-values in the green region), even when sample sizes are relatively small

Cladogram

Diagrams that depict the relative degree of relatedness among taxa by showing the inferred sequence of divergence/branching events

Dickinsonia

Dickinsonia and several other Ediacaran forms appear to be "quilted", like an air mattress -no evidence of a coelom (body cavity) Enriched in cholesteroids (which only is made by animals). Thus they are somewhere on animal stem. Can you assume photosynthesis if there is not body cavity? NO, usually unknown in animals. Heterotrophy? Unlikely. No evidence of mouth, gut, anus, movement, predation scars (in most cases) Photosynthesis? Unlikely. At least some Ediacarans clearly lived below the photic zone, and photosynthesis occurs only secondarily in very derived modern animals Chemosymbionts? Possible. Ediacarans may have lived in close association with microbial mats that could have supplied nutrients Osmotrophy? Possible. Late Neoproterozoic seas may have been very rich in dissolved organic compounds -could have been absorbed directly through the body wall

How to reconstruct diet in hominids?

Differences in dietary proportion of C3 vs. C4 plants are recorded (with an offset of about 10‰) in mammal bones and tooth enamel -C3 plants: fruits and nuts -C4: tropical grasses, grains, corn, etc.

Cladisitcs implications

Direct ancestors are relatively rare in the fossil record (because most species are not preserved). Rather, most fossil species are not ancestors but cousins —lineages that branched off, or diverged, from extant lineages at some point in the past

Diversity vs disparity

Disparity: morphological outliers that occupy new niche Diversity: speciation within that new niche/accompanying morphology This is true, but morphological diversity can be part of disparity. Disparity: a measurement of how significant that morphology (shapes) is, or what the range of shapes is and how important that is, as opposed to pure diversity (sheer number of taxa) So disparity includes outliers but isn't limited to them.

So when shells get fossilized they turn from Aragonite to calcite due to being ergetically being more stable?

Do living calcite shells preserve better & faster than aragonite shells? Calcite is harder and more dense. Aragonite is fundamentally unstable. Stable on organism timespans. Inflated numbers of calcitic shells because of better preservation? Scallops preserve better because they use both types Why are calcite shells heavier? Other than denser atomic structure? Sediment Calcium carbonate is more soluble in cold water than warm water, thus shell designs require higher efficiency in cold water and there is a resulting less diversity in shape -Calcium efficient shells are characteristic of cold waters and calcium inefficient shells are confined to warms seas -Calcite is harder than araginite -why is drilling more common in tropical waters if shell dissolution occurs more easily in cold water? -Softer aragantic shells are more prone to boring -Why are organic rich shells stronger than heavily mineralized ones? (They are less hard though). Organic rich shells common in cold water, mineralized ones in warm.

The principle of furstraiton

Drives increases in the morphological disparity of "evolved" plant shapes

What is the earliest evidence of life?

Earliest claimed evidence for life comes from stable isotope ratios in organic carbon found within metamorphic rocks dated at ~3.8 Ga Stable isotopes of carbon (12C and 13C) are fractionated by carboxylating enzymes during biological carbon fixation (more on this later!) Biologically fixed C is on average about 25 parts per thousand (‰) less enriched in 13C than atmospheric CO2 -Rubisco in calvin cycle tends to take lighter carbon, thus air has enrished C13 -Thus if there are high levels of atmospheric C13 you can assume lots of terrestrial vegetation 2nd example of early life evidence: Stromatolites

Diversity of small shellys increases gradually through the

Early Cambrian. first trilobites appear by 521 million years ago

Lithification bias

Easier of extract/identify fossils from unlithified sediments; these are more common in younger record

Clementsian view of communities

Ecosystems are tightly connected, synergistic systems of closely co-evolved species plus environment

Splading Finnegan fisher

Energetic shell building costs

Carcinization

Everything turning into a crab

If species do not compete with each other for some limiting resource, we expect...

Exponential diversification

In the absence of limiting resource, as long as birth rate exceeds death rate, populations will exhibit

Exponential growth

Environment during evolution of hominins and hominids?

Fall atmospheric CO2 and consequent global cooling and acidification (drying)

Stratigraphic range

First and last appearance in the fossil record (Will always be an underestimate of the actual time range of existence)

When did trees appear?

Forests with trees >6m by the late Devonian

Ediacaran fauna

Fossils of multicellular, varied organisms lacking a mouth, anus, and gut that were widely distributed in the shallow oceans of the late Proterozoic and flourished between 570 and 670 million years ago. Found in Ediacara Hills of Australia Ediacaran synonymous with Proterozoic?

Best preserved material..

From caves and permafrost

Genetic structure of human populations reflects

Geographic structure & national delineations

Carbon sink created with spread of forests decreased greenhouse effect and caused

Glaciations

Solubility of oxygen in water decreases with temperature so marine mammals...

Have tightened metabolic constraint on habitat availability Extinction rates were high at all latitudes, but especially high among species in high-latitude areas Why are they so high for high latitude when tropical species live in higher temperature water and have faster metabolic rates?

The timing of megafaunal extinction is correlated to

Human arrival. Extinctions occurred often prior to climate change.

Density independent checks on population growth

Hurricanes, floods, etc. Exponential growth flattened with these "checks" reoccurring

Snowball Earth

Hypothesis that proposes that the Earth was entirely covered by ice in part of the Cryogenian period of the Proterozoic eon, and perhaps at other times in the history of Earth IF sea ice extends to low latitudes, you get runaway cooling because ice has a high albedo (it reflects most incoming sunlight) After a few million years, volcanic outgassing of CO2 causes sufficient greenhouse warming to melt the ice, leading to very rapid warming

How to differentiate morphological steps from overall trajectory of morphological change?

If you take every one of these time series (trajectory): you reduce it to a series of steps and magnitudes, you get distributions on top left. Shows distribution is centered on zero. Shows there's no selections occurring. The right graph is not centered on zero. Maximum likelihood framework: Allows you to quantify amount of directionality Morphological change of a whole population TRACKS environmental change, it goes in different directions all the time.

Gradual change of species change in fossil record is eliminated by...

Incomplete fossil record makes gradual morphological trends look like abrupt shifts

Evolutions of roots ____ silicate weather rate

Increases. Exposure of silicate rock draws down CO2 how? Erosion is a carbon sink, but other than burying plants, how? Silicate weather feedback: acts to regulate earths surface temperature and keeps it in confined range. Rain water precipitates. More CO2 in air more in water that become carbonic acid. When it falls on silicate rocks, reacts with it, breaks it down to clay. Biocarboate is the byproducts of the reaction. Goes into ocean and become alkalinity. More CO2 in atmosphere, lower the PH of rainwater, the faster the reaction rates. The more CO2 there is the higher the silicate weathering. Rocks draw down CO2. It's a feedback loop. The warmer it is, the higher the silicate weather rate, the higher it is the more quickly you draw it out of atmosphere and turn it into ___. It regulates the temperature.

Changes in C13 caused by...

Intensity of weather of continental silicate rocks, marine productivity, sea floor oxygen levels, volcanism,etc

As you near carrying capacity, exponential growth levels off and you start to see the effect of diversity more and more on

Intrinsic diversification rate (birth rate-death rate)

Observed rates of morphological change are ____ ______ on the timescale over which they are observed

Inversely dependent -Average amount of morphological change you see decreases when you look at larger and larger time bins - -Net rate of change decreases over time. -Incompleteness of fossil record leads to under estimation of rates of morphological change (it vary a lot on short time scales and less on long)

During times of glaciations, ocean water is...

Isotopically light more positive δ18O values in carbonate shells grown from seawater indicate cool temperatures and/or large glacial ice sheets

Which of the following kinds of animals would you guess has the worst fossil record?

Jellyfish

Lagerstatten: konzentrat or konservat

Lagerstatten: exceptional German word for deposits that are exceptional because of either the concentration (konzentrat) or preservation (konservat) of fossils. Lagerstätten preserve exquisite details of morphology and ecology otherwise absent in the fossil record, and typically form under unusual conditions that inhibit the physical, chemical, and biological processes that normally attack and destroy tissues and hart parts.

Photosynetically fixed carbon is ______ than the pool of carbon that exist in the environment

Lighter

If they do compete, we expect...

Logistic diversification (leveling off at carrying capacity)

If either birth rate or death rate are density dependent, we will observe...

Logistic population growth

What % of species are fossilizable?

Lots in Burgess Shale, only 15% in normal fossil record

Where did lungs come about?

Lungs ancestral to all bony fish. Ray finned fishes have detached esophagus from head and turned it into a swim bladder.

'trigger mechanism' vs. 'kill mechanism'

Major perturbations such as asteroid impacts or large volcanic eruptions have relatively localized direct effects, but they can initiate cascades of environmental changes that affect much larger areas and play out over much longer timescales. The impact is the 'trigger' mechanism, but the downstream effects may be the 'kill' mechanisms

Cuviers view of extinction

Major unheavals, unlike anything witnessed in modern times, were responsible for extinction

Why build phylogenetic trees based on morphology?

Make sense of history of life we dont have DNA for.

What makes neutral mutations neutral?

Many neutral mutations involve silent (or synonymous) substitutions in the 3rd position of codons -they have no phenotypic expression Many others are conservative missense substitutions that cause only minor changes in protein structure and function

Ancestral State Reconstruction

Mapping features on a phylogenetic tree to determine what features were present in an ancestor Phylogenetic trees can help us infer what ancestors looked like, even when we do not have fossils of them, via ancestral state reconstruction

Ediacaran fauna are ___ ________ to each other than the Cambrian

More similar

Corals are made out of aragonite, a kind of limestone mineral. Groundwater typically has a pH of about 5.5. If there is groundwater flowing through rocks, would you expect corals in those rocks to be well preserved?

No

Does the demonstrable incompleteness of the fossil record necessarily inhibit our ability to draw conclusions about the biodiversity histories of specific groups? Why or why not?

No, because although adding new species changes our perception of the absolute numbers it often does not change our perception of the relative highs and lows

Cambrian explosion is the beginning of life?

No, only change of biomineralization, ecological complexity, and morphological disparity. No single trigger of this event

Is Megafaunal biomass lower now?

No. Diversity is lower but with livestock production it is higher biomass.

Earthquakes are random or non random?

Non random, usually fall along ocean ridges

Ecological interactions roughen fitness landscapes

Non-additive interactions among different organismal functions roughen fitness landscapes. This has been called "the principle of frustration" (Marshall, 2006) Optimizing any one function is a simple cost-benefit curve —for example speed and armor both reduce predation and thus increase fitness up to a point, but they are also energetically costly In an imaginary purely additive world in which you could be both very fast and very heavily armored, there is a single peak on the speed vs. armor fitness landscape

Binning Bias

Not all taxa in an interval coexisted. Interval based methods likely oversestimate diversity (an effect exacerbated by uneven interval lengths)

Observed stratigraphic ranges

Number of levels between first and last appearances Sp. A=1 Sp B= Try

How to calculate preservation potential?

Number of stratigraphic units and fossil appearances (look up formula from last lecture)

How is the oxygen isotopes between water & carbonate minerals precipitated from that water is a function of temperature?

O18 bonds stronger than O16 -The colder it is, the more likely you will incorporate heavier O18 -The warmer it is, the less likely you will incorporate a strongly fractionated O ration (due to higher vibrations of bonds)

What are molecular fossils made of?

ONLY CARBON STRUCTURE (it is stripped away of functional groups)

Logistic diversity growth

Occurs if origination and/or extinction rates are diversity dependent: if extinction rate (q) increases and/or origination rate (p) decreases as diversity increases

Most clades still confined to...

Oceans

When did primates diverge?

Oldest crown groups about 56 million years. Diverged in late Cretaceous.

Example where presence and loss of a trait is what is more likely to take place than the simplest route:

Ornamentation

Human Driven Extinction

Overkill hypothesis: human population growth led to hunting/disruption of other species. Most extreme version of this is "blitzkreig" hypothesis. Issues with this: -Possibly not plausible that humans at low population levels with low tech to make so many species go extinct

What caused rise of oxygen in atmosphere? Conditions before and after this event?

Oxygentetic photosynthesis created oxygen, but respiration would have canceled out the effects of that. Great oxygenation event over around 1.2mya. Oxygentic photosynthesis could have occurred in small areas with Cyanobacteria prior to great oxygenation event. Likely that oxygen was still low and challenging for many organisms.

Archea are ____phyletic relative Eukaryotes?

Paraphyletic

Selecting the "best" tree: parsimony. Define Occam's Razor.

Parsimony is an algorithmic implementation of Occam's Razor, the philosophical principle that, when confronted with multiple alternative models of reality, if all else is equal we should prefer the simplest one

Why are evolutionary changes concentrated at speciation?

Peripatric Speciation

How Darwin thought evolution occurred:

Phenotypic changes accumulate gradually within species. Rates of morphological change occurring during speciation occurs at same rate as in between speciation.

How do we know the ancient atmosphere was reducing?

Phyrites existed in South African rivers without being rusted from oxygen; today pyrite rusts immediately

Has there been diversity dependent changes in origination or speciation pr extinction rate through time? On a global scale, island biogeography suggests...

Pic. If so, we should see a logistic increase.

Assign meaning of negative and positive O18 and C13

Positive O18 indicated cooling and negative indicated warming Positive C13 indicated increase organic C burial and negative indicated decrease in burial

Homologous character traits

Presence of absence of a particular gene or morphological feature (eyes or particular gene)

Convection

Process by which, in a fluid being heated, the warmer part of the mass will rise and the cooler portions will sink.

Half life

Rate at which fossils are destroyed in a given environment

Early earths atmosphere was reducing or oxidizing?

Reducing A reducing atmosphere is an atmospheric condition in which oxidation is prevented by removal of oxygen and other oxidizing gases or vapours, and which may contain actively reducing gases such as hydrogen, carbon monoxide, and gases such as hydrogen sulfide that would be oxidized by any present oxygen.

fractal geometry in plants. What use?

Results in high surface area to volume ratio for oxygen availability purposes

Why did arthropods get so big?

Rising oxygen is one possible cause of Devonian-Permian gigantism in a variety of terrestrial arthropod lineages? If O2 levels were higher today would animals be larger? Did change in global O2 levels lead to decrease in megafauna? IDK. We don't know how much of it is oxygen or other things. How evolution occurs in oxygen states is pretty interesting.

Taxonomic durations

Same as stratigraphic range, time between first and last occurrence. Always underestimate of actual species number. Species with low preservation potential, it could be a substantial underestimate.

HCL destroys....

Silicates but not organics. What to use for silicate fossils?

Equilibrium Diversity

Similar to carrying capacity On an isolated island diversity can increase rapidly and then level off, confirms presence of an equilibrium diversity. Reflecting the balance between immigration and extinction Holding area constant, Islands closer to mainland maintain higher number of species

Similarities & Differences of Ediacaran organisms with extant organisms

Similarities to animals: - Bilateral symmetry? - Segmentation? - Anterior-posterior body axis? - Cholesteroids Differences: - No evidence of mouth, gut, or anus - No appendages - Limited evidence of movement - Little evidence of predation - No apparent sense organs - 'Bilateral' symmetry is ...weird - 'Quilted' structure - 'Fractal' structure

Chromospecies

Single species, but there is a time component that take into account. Doesn't take into account specieation event, but does take into account physical change.

Why do you remove "singletons" from Seposki's Marine Animal diversity curve?

Singletons are taxa known only from one time interval. A taxon that you sample only once in time bin. The number of singletons can be altered by numerous other factors (proximity to university, preservation state, etc) Getting rid of them reduces impacts of variation in fossil preservation & collection from the following: accessibility, overly good preservation, & duration of existence

What is the most basal organism?

Sponge

Mammal extinctions in late Pleistocene were...

Strongly size selective. Larger species experiences higher extinction rate (for all continents)

Cladograms are based on shared derived characters called..

Synapomorphies

Range-through assumption

Taxa must have been extant between their first and last appearances, even if absent from the fossil record in between

ductile deformation

The bending and flowing of a material (without cracking and breaking) subjected to stress.

divergent boundary

The boundary between two tectonic plates that are moving away from each other. -Forms from rising plume of magma that stretches and breaks continental crust. -In the portion of ripping then oceanic basalt in pumped out. This is how ocean basins are formed.

Community Assembly

The creation of an ecological community through a sequence of invasions of species. -Why are there those species and not other species?

neutral theory of molecular evolution

The hypothesis that most mutations that become fixed do not significantly alter fitness and have become fixed by genetic drift. Kimura (1968) proposed that most molecular evolution occurred through accumulation of mutations that are neutral (e.g., have no fitness consequences) If so, then the rate of neutral molecular divergence between two groups is a simple function of: -Mutation rate -The number of generations since the groups diverged (i.e. time to last common ancestor)

(P-Q)

The intrinsic net diversification rate, analogous to intrinsic population growth rate

Signor-Lipps effect

The lag between the last observed fossil of an extinct species and the actual date of extinction. This effect can cause paleontologists to date an extinction earlier than it actually occurred • Consideration of this pattern led to recognition of the 'Signor-Lipps Effect' (named after the scientists who first pointed it out): because of incomplete preservation, species that go extinct at a given time will last appear in the fossil record at some time prior to that. This "backsmearing" of last appearances can reach back millions of years, even with a well-sampled fossil record • How then can we evaluate whether observed stratigraphic ranges are consistent or inconsistent with a sudden mass extinction?

theory of island biogeography

The number of species found on an island is determined by a balance between two factors: the immigration rate (of species new to the island) from other inhabited areas and the extinction rate (of species established on the island). The model predicts that at some point the rates of immigration and extinction will reach an equilibrium point that determines the island's average number of different species (species diversity).

Taxonomic diversity

The number of taxa

continental crust

The portion of the earth's crust that primarily contains granite, is less dense than oceanic crust, and is 20-50 km thick Continental crust is dominantly granitic (density ~2.6 g/cm3 ), forms from partial melting of basalt. Because it is typically thick and because of its relatively low density, it floats higher on the mantle than oceanic crust Timing and drivers of continental crust formation? It's all older than oceanic crust? Always more oceanic crust that continental, so there is little chance of continental crust sinking and melting. What is the decay process? If there is continued rising of this crust does elevation of land on average rise through time?

Empirical (descriptive) morphospaces

The size of an empirical morphospace is determined by what is known, so we are limited by our experience.

Morphospace

The space of all measured morphologies a quantitative depiction of similarity/dissimilarity between species for a given set of anatomical traits

Stratigraphy

The study of how sediments are packaged together at different spatial and temporal scales

Great Oxygenation Event & Evidence

The time in Earth's history, about 2.4 Ga, when the concentration of oxygen in the atmosphere increased dramatically. -There are no more River deposits with pyrite -Banded iron formations appear. Fe is soluble in anoxic waters bit rusts in presence of oxygen; can't form today -Global age distribution of banded iron formations indicates that a vast amount of iron was oxidized and titrated out of seawater around this time. Requires huge amount of oxygen from oxygenation photosynthesis

What is an issue with early eukaryotic divergence?

There is a lot of horizontal gene transfer. How do you identify this?

Which statement about the relationship between species' preservation potential and the degree of time-averaging of their fossil records do you think is generally true?

There is no consistent general relationship between preservation potential and degree of time-averaging

Is extinction risk actually increasing with body size?

There is no negative relationship between body sizes and durations of mammal genera throughout the Neogene, as would be expected if extinction risk increased with body size No inverse relationship as would be expected

Why does the presence of photosynthesis oxygenation not necessarily increase atmospheric CO2 in the past?

There is respiration. You have to have a carbon sink to accumulate oxygenation.

As morphospace and eco space increases, we expect

To see less significant morphological change

Cambrian is defined biostratigraphically by...

Trepnichnus pedum First appearance of the complex trace fossil Trepnichnus pedum defines the base of the Cambrian globally. Sediment-displasive trace fossils such as T. pedum imply a bilaterian with a muscular body wall and a coelom for hydrostatic support Have to be bilaterians because? Why is that significant?

Question 2:

Two groups ideal for bio stratigraphy (avoid preservation preservation factors): -Wide geographic change -High rates of morphological evolution - Not fecundity (lots of groups with lots of offspring but low evolution)

How does the punctuated equilibrium model change our understanding of evolution?

Uncontroversial: if most evolution is occurring rapidly in small populations inhabiting peripheral environments, we should not expect to capture intermediate forms in the fossil record very often • More controversial: most species, most of the time, are not undergoing directional selection • Most controversial: macroevolution is not simply accumulation of microevolutionary changes; macroevolution exhibits emergent patterns that cannot be predicted from microevolutionary dynamics; the role of adaptation in driving evolutionary patterns has been overestimated

Solution to binning bias

Use only boundary cross (all the taxa that are found both before and after a given boundary had to co-exist at that time)

Milankovitch Cycles

Variation in insolation (intensity of solar radiation hitting different parts of Earth's surface at different times of year) is a major driver of natural climate cycles Things this cycle effects: A. The size of the polar ice caps B. The temperature of the oceans C. Absolute (eustatic) sea level D. The amount of rainfall in the Sahara Desert E. The rate of erosion of the Himalayan Mountains F. The geographic distributions of species Are milankovitch cycles just the direct outcomes of obliquity & precession variations? YES and eccentricity

Relative abundence of species in fossil record

Varies with size, conditions, etc. But carbonates are the most abundant.

What causes rhythmic sedimentation patterns in rock layers?

Varves (annual sedimentary layers), below formed in a glacial lake (sediment derived from rock ground to a fine dust by the glacier in winter is washed into the lake during spring melts)

A monophyletic group with 2 lineages: Chlorophyta/Streptophyta

Viridiplantae. Includes green algae and such/

How do we figure out last common ancestor of crown bilaterians?

We can get some sense from Hox genes, which are highly conserved across extant bilaterians and involved in fundamental body-pattering during development

CO2 inputs CO2 outputs

Weathering, volcanism, fossil fuels Organic and inorganic C burials is

The reason there can be large increase in disparity, no change in diversity is because of extinction solely right?

When there is a few lineages starting out (high disparity), but not lots of speciation yet. Eventually increase in disparity will be followed but an uptick in diversity.

Question 6:

Y, D, F, B, S, Z, J, A, L, M, K, R

Do different genes for different proteins exhibit different rates of change?

Yes, These rates can be shown to be approximately clocklike, in that they happen at a rate that is stochastically constant

factor analysis

a statistical technique that explains a large number of correlations in terms of a small number of underlying factors Looking for groups with similar temporal family diversity trends

Character matrix

an array of taxa (at left) and characters (at top) that contains the character states for the taxa

Divergence time estimates based on molecular clocks are

best interpreted with caution, since they depend on assumptions that are difficult to test.

Hiatal bias

can cause last occurrences of species to cluster below hiatuses and first appearances to cluster above them, distorting our perception of macroevolutionary patterns -Some species going extinct during gaps, could mislead you to believe there was an extinction event -You see bunch of new species after gap, that could be considered wrongly as speciation following extinction

In CaCO3, C13/C12 tells you about _____ O18/O16 tells you about ______

carbon cycling Climate

Disparity

degree to which organisms are taxonomically diverse from each other

oceanic-oceanic convergence

denser plate is subducted, deep trenches generated, volcanic island arcs generated happens where 2 oceanic plates push against one another, causing the colder, denser, older plate to buckle up and sink into the mantle. Hot magma comes from where the plate sank, creating new crust.

Gleasonian view of ecosystems

ecosystems are haphazard, loosely structure assemblage of species, temporarily sharing a region -species interact, but often weakly -widely accepted by ecologists -evidence -species geographic distributions moved independently of each other -species geographic distributions presently independent, non-coincident *this view makes it harder to acknowledge intrinsic view of ecosystems if they're transient* *difficulty of protecting ecosystems legally*

Walthers laws

facies that are horizontally adjacent in space will be vertically stacked in the rock record

Basin and range

fault-block bounded mountain ranges with valleys in between -This extreme landscape of short, parallel mountain ranges and desert basins extends along the eastern border of California ---The northern section is part of a lava plateau ---The southern section is generally dry. The Mojave Desert is the major geographical feature in the south. -The Northwest and Southwest Great Basin, the Northwestern Sonoran Desert, and the Salton Sea Trough are significant areas in this region -Death Valley (in the Mojave Desert), the lowest point in the U.S., was formed by faulting (not erosion) -The system extends in to Nevada and Utah -Irrigation with water from the Colorado River has allowed large-scale farming in the Imperial and Coachella valleys

Cooksonia

first known vascular land plant -No leaves -No vasculature

K-Pg kill mechanism: atmospheric one?

injection of massive amounts of vaporized rock into atmosphere and space -Lots of carbon in area where asteroid hit, lots of CO2 goes in atmosphere -Dust in atmosphere blocks light -Lots of sulfur in rock, leads to good reflection of radiation from sun and decrease in temperature (In this case there was very sharp cooling, followed by longer term warming)

character transition

introduction of new trait in offspring that wasn't visible in immediate common ancestor -gain, loss, or change in state

Mass extinction events are associated with...

large and rapid changes in the shapes of fitness landscapes

Cause of stasis: Ephemeral Local Divergence

local populations of a species may change, but most often they die out or are re-absorbed into the rest of the species (also consistent with the peripatric speciation model) -Random spin offs of main populations. Barriers between populations break down and they can be reabsorbed. They could go extinct. etc.

evolutionary systematics: (pre-cladistics)

many fossil species are interpreted as being directly ancestral to modern species

Wide ranging genera just as vulnerable as narrowly distributed ones during....

mass extinctions. Why? All populations across wide range are selected upon with HUGE extinctions.

Modern Human Emergence: Multiregional

modern humans arose gradually across the full range of H. erectus, with lots of interbreeding among different populations

Modern Human Emergence: Out of Africa

modern humans arose in Africa, then dispersed to other regions and 'replaced' H. erectus (which was already widespread outside Africa)

Relative to Ediacaran faunas, the Cambrian fauna is striking for its degree of...

morphological diversity, also called disparity

Removal of incumbents leads to...

new opportunities and niches for other groups. There are bursts in subsequent evolution.

Cause of stasis: Stabilizing Selection

once a species has a morphology that places it at a peak on the adaptive landscape, selection tends to maintain that morphology with little change. Facilitated by habitat tracking (species following optimal environment through time) -Phenotype already occupies a "fitness peaks". Thus there is stabilizing morphological selection. -

eccentricity of orbit

one of the forces behind climate cycles; sometimes the orbit is nearly circular, sometimes eliptical

Characters that are found in all species...

plesiomorphies

Concluding in paleo are always...

probabilistic (not which model of nature is right or wrong, but which is best supported by available evidence) Our conclusions are always provisional and subject to change when new evidence becomes available

Proportion of originations vs time plots help show...

rate of extinction over time

Extrinsic values

related to the physical environment Changes in the physical environment that affect the ecosystems in which organisms are evolving and diversifying -Meteor -originate outside the individual, and are not necessary for the maintenance of life (e.g., holism, humanism)

intrinsic values

related to traits of the individuals & populations themselves -Generation time -Mutation rate -Species interactions -Way niches are created in organisms -Related to the maintenance of life (e.g., food and water)

Hox genes

series of genes that controls the differentiation of cells and tissues in an embryo

Cause of stasis: Fluctuating Directional Selection

species experience directional selection as the environment changes, but if the environment switches back and forth between states there may be no sustained trend -Finch beak size changing over Decadal cycle based on La Niña and El Niño. Directional selection doesn't go anywhere.

Cause of stasis: 'Constraint'

species simply lack the variation required to move to a different fitness peak (this never garnered much support and we won't discuss it further in this lecture)

Lilliput effect

survivors of extinction events are often markedly smaller than the pre-extinction populations

Taxa in a cladogram are grouped by:

synapomorphies: Taxa are grouped based on the shared presence of evolutionary innovations, termed synapomorphies (here feathers, fur, limbs, etc.)

Biostatigraphy

the branch of stratigraphy concerned with fossils and their use in dating rock formations. ‣ Most useful groups for timing are fast evolving and widespread ‣ High phenotypic plasticity or fastest speciation? ‣ PHENYOTYPIC PLASTICITY is bad. More changes, speciation, is better. And rapid extinction. Helps constrain time intervals.

Intrinsic growth rate

the maximum potential for growth of a population under ideal conditions with unlimited resources The birth rate minus the death rate

Biomineralization

the precipitation of minerals by organisms, as in the formation of skeletons

Realized Niche

the range of abiotic and biotic conditions under which a species actually lives Factors that cause realized niches to be less than fundamental niches: -Dispersal limits, etc -Species interactions (predation or competition) -Not all parts of the fundamental niche are equally good (gradient)

Sister groups

the two lineages that emerge from a node on a cladogram

oceanic crust

thinner, more dense, younger crust making ocean floor Oceanic crust is dominantly basaltic. Basalt is relatively dense (~2.9 g/cm3), forms from melting of mantle rock. Because it is typically thin and dense, oceanic crust sinks lower into mantle than continental crust

Stratigraphic completeness depends on..

timescale of analysis -Thus we have to be particular about what timescale of sedimentation "rate" we are talking about

Amniote

vertebrate whose embryo or fetus is enclosed by a thin, tough membranous sac -Breaks you dependence on water environments -Encloses embryo in a dessication proof area

How to ask why certain morphologies have evolved and other theoretically possible morphologies have not?

we will need a generative (theoretical) morphospace that generates shapes based on underlying developmental rules Guess the variety of shapes that could appear, and understand why they didn't appear

Range extension

when a species extends its area of distribution or range until it meets barriers to its further spread

Major issues with molecular clocks

• "Strict" molecular clocks assuming constant rates of molecular evolution are rarely supported by data -rates can vary significantly across even closely related lineages • "Relaxed clock" approaches are more sophisticated statistical analyses that allow rates to vary on different branches, now used for most molecular clock analyses • Choice of fossil calibrations is key- careful paleontology and geochronology are essential

Prediction potential: Clementsian vs. Gleasonian

• 'Clementsian' prediction: individual species' niches are less important than interspecific interactions, so as the climate changes communities will remain coherent; species in the community will shift in lockstep • 'Gleasonian' prediction: individual species' niches are much more Important than interspecific interactions, so as the climate changes species will respond individualistically; existing communities will disintegrate and new communities will arise

Using trees to compensate for the incompleteness of the fossil record

• Can only correct diversity below observed stratigraphic ranges, not above • Cannot correct diversity below stratigraphic range of oldest lineage of a sister pair

Why does Africa still have megafauna?

• Did their long evolutionary history with hominins instill African mammals with more of an aversion to humans compared to "naive" mammals in other areas? If so why wasn't this true in Eurasia? • Did tropical diseases and high parasite loads keep human population densities lower in Africa than in other areas? • Were there cultural differences that led to less intensive hunting and habitat destruction? • Occupying a large continent centered on the tropics, were African species less strongly impacted by climate changes?

How do you identify a selective sweep?

• EPAS1 gene is a transcription factor where expression is induced by low oxygen levels • The version of EPAS1 in the Tibetans decreases the hemoglobin count, reducing the viscosity of the blood, which is important at high altitude. This allele is also known to increase athletic performance in some people, and has been called the "super athlete gene"

What might explain the long gap between the inferred basal metazoan divergence events and the first appearance of clear crown group fossils?

• Failure of preservation? Maybe, but we have beautiful preservation of soft-bodied algae from the Ediacaran • Animal groups were around but represented by difficult-to-recognize stem group taxa? Possibly, but only gets you back to the late Ediacaran. • Animal groups were around but living in environments that are not preserved? No good reason to think this was true. • Stem animals were around but were small, morphologically unlike crown animalls, and lacked mineralized skeletons? - Large size is difficult to evolve in an O2-poor world - Skeletons may have evolved for defensive purposes once O2 levels were high enough to support predation

All K-Pg kill mechanisms from asteroid:

• Global cooling from ejecta and aerosols blocking sunlight • Marine and terrestrial primary productivity collapse • Acid rain from sulphates injected into atmosphere • Massive heat pulse from ejecta re-entering atmosphere and burning up, global wildfires • Massive global earthquakes and tsunamis • Ocean acidification from CO2 ejected into atmosphere

Nice concepts

• Grinnell (1910s): What environment does a species occupy? Abiotic requirements, habitat, food, and (to some extent) interactions with other species. • Elton (1920s): What role does a species play in the food chain? How does a species impact other species and the environment? • Hutchinson (1940s): Provided a quantitative framework. Introduced the concepts of 'n-dimensional hypervolume', fundamental vs realized niche.

Choosing characters: homology and homoplasy

• Homology is any similarity between characters that is due to their shared ancestry • Homoplasy (convergent evolution) occurs when characters are similar, but are not derived from a common ancestor. Ex. Presence of wings in dinos and bats and such -Homoplasy results from convergent or parallel evolution -To produce trees that accurately reflect evolutionary relationships, critical to recognize and avoid homoplasic characters

Other evidence of K-Pg boundary layer

• Impact-shocked quartz grains worldwide • Microtektites and spherules formed from melted rock worldwide especially near the impact • Tsunami-deposited sediments below the Ir layer on the Gulf of Mexico coastal plain (HUGE) • Charcoal-rich layers associated with boundary in terrestrial settings, implying widespread wildfires (after impact fires) -Progressively smaller iridium layers with distance from Yucatán

Basics of carbon geochemistry

• Isotopes of a given element vary in number of neutrons, but have a fixed number of protons and electrons • Isotopes have (mostly) identical chemical interactions • Unstable isotopes decay at a constant rate and can therefore be used for geochronology • Stable isotopes are often differentially sorted (fractionated) by natural processes according to their mass

Explain Mitochondrial tree for modern humans

• Mitochondria are effectively haploid and inherited only from the mother • The mitochondrial tree of all living non-Africans forms a monophyletic clade nested within the diversity of living Africans. The estimated coalescent time is ~200,000 years (with large uncertainty) - The oldest H. sapiens fossils (in Morocco) are about 300,000 years old, thus the fossil record in misleading

Why biomineralize?

• Movement —mechanical support, muscle attachment • Dispose of Ca2+ ions to avoid calcium poisoning? • Protection from predators

Summary

• Permissive environmental conditions had to be in place (e.g., sufficient oxygen) • The genes and developmental systems required to build bilaterians must already have been in place (they did not evolve during the Cambrian) • With the evolution of behaviors required for interactions, especially predation, fitness landscapes became much more complex & latent potential for innovation was realized as a relatively rapid "explosion" of morphological disparity and ecological diversity • In this new fitness landscape Ediacaran taxa either rapidly evolved new, very different morphologies, or (more likely) went extinct

Importance of plate tectonics for paleobiology

• Terrestrial sediments accumulate in rifts • Marine flooding of continents controlled by interaction of tectonic processes & sea level • Deep-sea sediments are destroyed by subduction • etc. • Plate tectonic processes are major influence on the evolution and distribution of earth's biota • Plate tectonic processes are first-order controls on global climate because they influence the amount of CO2 produced by volcanism & consumed by weathering, & the amount of carbon buried in sediments & subducted into the mantle. They also influence atmospheric oxygen levels and ocean chemistry

eDNA shows that Elephant birds are more related to Kiwis than any other bird, thus...

• That the current distribution of ratites is due to dispersal rather than continental drift. • Thus, the ancestral ratite flew, and large flightless ratites evolved convergently at least 5 times! (the blue arrows)

Which group would you expect to have the highest fossilization potential? Which would you expect to have the lowest?

• clam > sea star > squid

Cladistic Methodology

•Determine character state polarity by reference to outgroup or fossil record •Construct all possible trees for the taxa in the ingroup •Map evolutionary transitions in character states onto each tree •Find the most parsimonious tree — the one with the fewest implied character state transitions (the simplest one is always more likely?) •Only synapomorphies (shared, derived characters) are informative •Critical that the characters used be homologous

Best preserved species

‣ Carbonates! ‣ Graph shows on right that plants would have different fossil records than mollusks • Plants don't mineralize well whereas mollusks do

Which ranking of environments, from lowest to highest potential for preserving fossils, do you think is correct?

‣ Coastal marsh>rainforest>mountain ◦ Best preservations area (high to low) ‣ Fluvial (where most sedimentation occurs on continent) ‣ Lacustrine ‣ Karst(caves, fissures, etc) ‣ Amber

What factors influence probability of preservation?

‣ Evaluate preservation potential of extinct species: gap analysis of stratigraphic ranges ‣ Tabulate opportunities to sample a species between first and last occurrence • Observed sampling events/possible sampling events • Don't calculate first and last occurrences, you don't get information about preservation potential ◦ End points leads to distortion of estimates ◦ We only use frame where we KNOW them to be present

◦ Time averaging

‣ How much cumulative time is represented by the fossils in a given bed? ‣ Lots of organisms can exist in one deposit from a number of times ‣ Amount of time averaging in a deposit limits ability and resolution of identifying changes ‣ TAZ varies based on oxygen level in sediment ‣ Different depositional environments exhibit different degrees of time averaging • Deeper water with low sedimentation has much much older shells

Uniformitarianism

‣ Hutton/Lyell ‣ Many features of geological record explained via processes today that have been happening throughout geological time ‣ Predicted/Found a Angular unconformity: • Based on uniformitarianism, there would have to be deposition, uplifting, erosion, and then additional deposition to get this feature. It would take a LONG time.

Basic Observations for recognizing deep time

‣ Rocks stratified ‣ Rocks folded and deformed ‣ Rocks also faulted ‣ Rocks can intrude into or cross cut other rocks

4 principles used for interpreting rock relationships

‣ Superposition: that young beds are on top of old ‣ Original horizontal: beds depositied horizontally always ‣ Original lateral continuity: beds are continuously deposited but gaps are caused by erosion ‣ Cross cutting realtionships: when one rock cuts through another, the one cutting across is younger

How was age of earth determined?

◦ Determining age of earth ‣ William Thompson • Based on physics timing of cooling of molten rock led to earth age of 100mya ‣ Darwin ‣ Marie Curie • Discovered isotopes that decayed • Thompsons calculations wrong ◦ Radioactivity could heat earth interior long after cooling ◦ Carbon 14 ‣ Only goes back to about 50 kya ???(Becasue of too rapid of a half life) And isn't useful for measuring in deep time prior to Cambrian ‣ We use a variety of isotope fractions to determine ages ‣ Earth of age assigned using zircon crystals or meteorites ◦ Sedimentary rocks are commonly cross cut by intrusive igneous rocks that can be directly dated ‣ Dikes give a minimum age of how old fossils area ◦ Ash from explosive volcanic erruptions ‣ Constrains rock age to very precise age

How to correlate rock layers?

◦ Info from multiple areas can be combined to produce a single composite record ◦ Chemostratigraphy: uses patterns of chemical changes in rock to correlate them ‣ There is a decreasing linear trend in strontium throughout all fossils over time, then we can better date and group stratigraphic records ◦ Magnetostratigraphy: ‣ There are magnetic polarity reversals ‣ The polarity of the earths magnetic field flip flops ever few 100k years

How are fossils preserved?

◦ Need to be in sediments ◦ Other process (but not as good) ‣ Tanning, amber, etc ◦ Environments with good fossils record ‣ Look at balance of erosion and sedimentation

Not a lot of modern biogeography makes sense without historical context

◦ Not a lot of modern biogeography makes sense without historical context ‣ Most big mammals are gone everywhere on earth over the past 50k year ‣ Wallaces line: two very close geographic areas have entirely different species compositions • separates an Asian fauna which includes primates, carnivores, elephants, and ungulates from the marsupial fauna of Australia and New Guinea. • Glacier interglacial cycles also cause historical land connections; there is a deep water channel where Wallace line is ◦ Extinction means that any understanding of the history and diversity of life on earth could end with disappearance of species ‣ Horses started in North America, went extinct, and then were reintroduced! ◦ Earths physical environment has changed radically throughout its history, and this allows us to see how different climates/conditions have impacted earth

Trace Fossils

◦ Remains of animal life outside of body: tracks or burrows ◦ Marine tracks are more common than terrestrial ◦ Attack marks ‣ Evidence for behavior of organisms ‣ Moon snail drill holes

Atmospheric CO2

◦ We've have measurements from Manoa Loa since 1958 ◦ There are seasonal cycles to CO2 in atmosphere ‣ Northern hemisphere in summer and winter fluctuating ‣ Biomass mostly in Northern atmosphere ‣ CO2 levels drawn down during spring when leaves are made ‣ In fall, leaves drop and CO2 goes back in atmosphere ◦ On 10k year time span, there is a large trend up in CO2 ◦ On 800k year time span, there is a 100k year timespan of glacial interglacial cycles ‣ CO2 regulated on this timespan due to interaction with other planets ‣ Mila Koch cycles ◦ 600 mya, we rely on proxies to measure CO2 ‣ There are even longer term cycles here (300mya or so) are driven by plate tectonics