Macroevolution Test 2

List and describe the two kinds of extinction

Background extinction

• affecting lineages all the time

• occurs at stable rates across geologic time

Mass extinction

• extinction in one group very subtly

• interval during which extinction exceeds background rate

• a small number of really exceptional extinctions

Describe the general patterns in evolution though time

• Marked by increases and decreases through time

• Seem to have higher rates a long time ago, and seems to decrease over time

• extinction is also going down

• called turnover

  • origination of lots of things, then extinction of lots of things

• Maybe the decrease in extinction is because some phenotypes have become better?

  • increase in adaptation, and therefore less extinction?

Describe the origination of the Alvarez hypothesis

• noticed feraminefera

• great indicator fossil, very characteristic of deposit

• Rock made up 3 layers

  • oldest layer was super diverse with fossils

  • middle

  • most recent was more uniform

• Didnt know how to date

• looked for irriduim

• super rare, can use rate to quantify time (more irridium = more time has passed)

• found a stupid large amount of irridium (like, impossibly large amount)

• Something in the atmosphere (bc irridium comes from atmosphere) must have affected the earth around time of dinosaurs!

Describe the predictions of the impact hypothesis

• meteorite dust in rocks of end cretaceous (K) (eg. global iridium layer)

• impact crater contemporaneous with global iridium anomaly

• Debris from impact, dating to end-K

• Glass particles from heat of impact

• Impact models should predict large scale environmental  disturbance

Why is it that the signature of a mass extinction can be subtle?

the signature of discrete events can be blurred (eg. by all the problems w fossilization, that sort of stuff); Signor-Lipps effect

Describe the Signor-Lipps effect

• neither first nor last individual of a taxon will fossilize

• Therefore, youngest fossil of a species will likely predate actual time of extinction'

  • Imperfect fossilization > fossilization creates a jagged pattern, so not necessarily at true evolution

• Hollow distribution curve consistent with Signor Lipps effect

• Most species are rare, and therefore disappear way before actual extinction rate

  • Highest occurrence of rare species may be at extinction level or much earlier

  • Highest occurrence of common species likely will be at or near extinction level

Describe the end ordovician extinction

• after cambrian period

• ~44 million years ago

• ~85% species level extinction (marine)

• Major groups affected were:

  • graptolites

  • branchiopods

  • trilobytes

  • conodonts

Describe Late devonian extinction

• not quite as severe as ordov. extinction

• ~75% species level extinction (marine)

  • Little effect on terrestrial life

• ~375 mya

• Major groups effected:

  • trilobytes

  • branchiopods

  • reef builders (stromatoporoids. rughouse and tabulate corals)

  • graptolites (completely wiped out)

  • cystoid echinoderms (completely wiped out)

Describe the end permian mass extinction

• biggest mass extinction ever

• ~251 million years ago

• 96% species level extinction

• Major groups affected:

  • Tabulate corals (completely wiped out)

  • trilobites (completely wiped out)

  • eurypterids (completely wiped out)

  • branchiopods

  • bryzoans

  • blastoid enchioderms (completely wiped out)

  • crinoids

  • ammniotes

  • gastropods

  • forams

Describe the End Triassic extinction

• ~200 mya

• 80% species level extinction

• Major groups effected:

  • Conodonts (completely wiped out)

  • large amphibians

  • therapsids

  • archosaurs

Describe the end cretaceous extinction

• ~66 mya

• 76% species level extinction

• major groups affected:

  • Ammonoids (completely wiped out)

  • non avian dinosaurs (completely wiped out)

  • plesiosaurs (completely wiped out)

  • mosasaurs (completely wiped out)

  • sharks

  • plankton

List and briefly describe the three causes of extinction

• gamblers run

  • the only absorbing boundary is complete loss (ie. extinction)

  • Thus, the only “end possiblility” is complete loss

• Adaptation

  • May affect the probability of extinction, either via too much adaptation or not enough

• Catastrophe

  • Dramatic (and relatively rapid) environmental change

What is Van Valen’s law of extinction?

extinction probability is constant over time

• found in group after group after group

Describe Gambler’s Ruin as a cause of extinction

• Probabilistic expectation of resource “extinction”

• A gambler who continues to play a completely fair game will eventually lose all of their money, because the only absorbing boundary is complete loss

• Same thing goes for species

• Smaller population is mDescribe the ore susceptible to extinction (closer to extinction)

• positive relationship between pop size and survival time

Describe the overspecialization hypothesis

predicts that extinction probability will increase with time (as organisims become too specialized)

• adapt/specialize so much that they become super dependent

Describe the incumbancy hypothesis

predicts that extinction probability will decrease with time (as organisims become better adapted to their niche)

• basically, the longer a species is around, the better it is at being on earth

Describe the Red Queen Hypothesis

• predicts that extinction probability will be constant over time because selection  selection is always changing (eg. due to coevolution) and a species must constantly adapt or face extinction

• background extinctions are a failure to adapt

• ever changing selection can explain why clades don’t become “extinction resistant”

• extinction is due to a lineage wide failure to adapt to ever changing conditions

Describe catastrophe as a cause of extinction

Dramatic (and relatively rapid) environmental change

• Rapid but not instantaneous

  • may take years for things to get wiped out

• Multiple causes often implicated

• some extinctions due directly to catastrophic event; many more likely due indirectly to transformations of earths systems

List candidate causes for mass extinctions

• flood basalts

• extraterrestrial impact

• sea level fall

• climate change

• methane clathrates

• Oceanic O2 decline

• Oceanic hydrogen sulfide3 emission

Describe flood basalts as a candidate cause for mass extinction

• massive sustained igneous extrusions

• emit particulates that can inhibit photosynthesis, disrupt food chains

• emit Sulphur oxides, causing acid rain

• emit carbon dioxide, causing later global warming

• before meteor was known about, people thought this was what killed the dinosaurs

Describe extraterrestrial impact as a candidate cause for mass extinction

• violent impact by large asteroid or comet

• emit particulates that inhibit photosynthesis, disrupt food chains

• can cause megatsunamis, global forest fires

describe sea level fall as a candidate cause for mass extinction

• reduce (highly productive) continental shelf area

• Restructure ocean currents, disrupting terrestrial climates

Describe climate change as a candidate cause for mass extinction

• global cooling reduces habitable area for tropical species, causes shifts towards equator > leads to global terrestrial drying (as freshwater sequestered in ice/snow)

• Global warming reduces area for temperate/polar species, causes shifts towards poles > leads to wetter periods (as freshwater released in ice/snow)

Describe methate clathrates as a candidate cause for mass extinction

• clathrates are when a lattice of one substance encases another substance

• H2O entraps methane in methane clathrates in ice

• rapid changes in temperature or pressure can trigger release of methane from stored continental shelf clathrates

• has been suggested for end permean extinction

Describe oceanic O2 decline as a candidate cause for mass extinction

• anoxia occurs when middle or upper layers of ocean become deficient in oxygen

• typically associated with periods of global warming (usually triggered by volcanism)

• can trigger oceanic mass extinctions, and restructure global food webs

Describe oceanic hydrogen sulfide emission as a candidate cause for mass extinction

• proposed that the end permian warming disturbed balance between photosynthesizing plankton and sulfate reducing bacteria, triggering massive hydrogen sulfide emissions

• hydrogen sulfide poisons both marine and terrestrial life, and depletes the ozone layer

How do background and mass extinctions differ in selectivity?

Background extinction is proposed to be darwinian (the unfit species are the ones that die) while mass extinction i proposed to be wanton and random, with survivors no better adapted to the environment

What traits predict survival of a species through a mass extinction?

• abundance

  • basically numerical insurance- the more individuals, the harder it is to wipe them all out

• larval dispersal mode

  • the farther the species can colonize, the less likely it is that there will be a disaster that will affect all individuals in a species

• habitat (infaunal vs. epifaunal)

  • animals in soil may be protected in a way

• species range size

  • vast spatial expanse > more likely you can hide/avoid extinction

how do we recognize adaptations

• evidence from design

  • architecture of the phenotype

  • adaptation for a particular function

• complexity

• Performance (or, ideally, fitness experiments

Describe natural selection

any consistent difference in fitness among phenotypically different classes of biological entities

Describe fitness

• reproductive success

  • how many copies are being passed to the next generation (sometimes in terms of alleles or traits)

• the average per capita rate of increase in numbers for a class of biological entities

  • statistical property of groups of organisms, not individuals

• groups can differ in fitness due to chance (ie. drift), but chance fitness will not be consistent through time

• natural selection describes consistent fitness differences

What kind of fitness differences does natural selection describe?

consistent fitness

Describe the Panglossian paradigm

People were prescribing functions to things that didn’t necessarily have that function (basically saying the equivalent of things like our noses being made for glasses and saying that that’s why we wear them instead of it just being a convenient way of completing some other function)

List and describe the criticisms of the adaptationist research program

• studies partition organism into traits, and environment into problems that have no biological basis

  • atomizing organisms rather than looking at the whole

• Characters are studied in isolation from one another, when they need to be studied together

• All characters are assumed adaptive (studies focus on “how” traits are adaptive, rather than considering non adaptive alternate hypothesis)

When might a trait NOT be an adaptation?

• drift

• Necessary consequence of physics or chemistry

• Constraints due to development

• Correlation with other adaptive traits

Describe exaptation

• a trait that is inherited from an ancestor and coopted for a new use

• may or may not have been an adaptation for a different purpose in the ancestor

An adaptation is a characteristic that:

1. enhances the fitness of the organisms that bear it

2. evolved via natural selection for its current function

Describe phylogenic effect

for many traits, closely related species are more similar to one another than distantly related species, due to recent common ancestry

• NO statistical independence :((((

Describe the problem posed to data collection by phylogenic effect

• phylogenic effect means that species data will not be independent

• bc they are not drawn independently from same distribution

• violates assumption of standard statistical models

Describe phylogenically independent contrasts

• rather than asking whether two variables are correlated for a set of species, asks whether the independent evolutionary change in the two variables is correlated

  • is one change associated with the other?

  • involves analysis of evolutionary differences (“contrasts”) not raw species data

What are the key assumptions of Ordinary Least Squares

Errors must be

1. independent

2. identically distributed

What 2 common violations of normal statistical assumptions do Generalized Least Squares accommodate?

1. heteroscedastic errors (not identically distributed)

2. correlated errors (not independent)

• with species, we expect to have phylogenicaly correlated errors

Do we always have to account for phylogenic non independence in species data, and if not, explain.

• No, not always

• only when species data doesnt exhibit phylogenic signal (ie. when a trait evolves slowly and thus not a lot of relatedness)

What are the two solutions to the phylogenic nonindependence problem

• independent contrasts

• phylogenic generalized least squares

What are the key features of Brownian motion?

• direction of change at each step is random (equally likely to go in either direction)

• Memory less (direction of NEXT) change independent of direction of last change)

• expected (ie. most likely) value over time interval is the starting value

• Variance about this expectation increases with time

  • the longer the time, the greater the difference from the expected value

In terms of Brownian Motion on a single branch, what is the relationship between the rate of change and the variance of the expected distribution of individual changes?

The rate of change is proportional to the variance of the expected distribution of individual changes

• when sigma is high, theres higher variance, and thus higher rate of trait change (looks wider on a histogram)

• lower sigma means lower variance and thus lower rate of trait change (skinnier histogram and flatter line on a plot)

In terms of Brownian motion on multiple branches, if you have multiple lineages evolving independently from a common starting point, the expected variance at a given time will be a function of what?

rate evolution and time

Describe disparity

• the variance of the trait values for a set of taxa

• basically just trait diversity; how much variation is exhibited

Under Brownian Motion evolution on a phylogeny, disparity is a function of

• the rate of evolution

• time

• differential patterns of shared ancestry among species

What are the uses of Brownian motion model in macroevolution

• used to test hypotheses about evolutionary rate (and disparity)

• used to “reconstruct” ancestral trait values

• can be used to estimate phylogeny (from continuous phenotypic traits)

• Used as a basis for more complex models of continuous trait evolution

What are the 3 key components of natural selection?

• phenotypic variation

• differential fitness

• heritability

describe unit of selection

• any replicating entity that is subject to natural selection

• can include a unit at any level of biological organization

  • replicating molecule

  • gene

  • cell

  • organism

  • species

    • eg. birds with smaller beaks dying off due to selection

Describe species selection in a broad sense

a consistent difference in fitness among phenotypically different classes of species

What are the two kinds of phenotypic variation

• aggregate traits

• emergent traits

Describe aggregate traits

• aggregate of individual traits

• organism level traits shared by the members of a species

  • eg. body size, fur colour, number of teeth, shell thickness, reproductive age, etc.

• must vary more among species than within species

• individuals may vary; just take average

Describe emergent traits

• Traits that cannot be reduced to the individual level

• traits that arise as statistical properties of sets of individuals

• eg. range size, range complexity, sex ratio, population size, intraspecific variation, etc.

  • doesn’t make sense for individual to have sex ratio

Describe differential fitness

to have as many descendants as possible (a lot of speciation)

• goes extinct = low fitness

• more diversity at the end = high fitness bc less likely to go extinct

Describe heritable fitness

• lineage has high speciation rate, descendant likely to have high speciation rate

What are the components of species selection

• phenotypic variation

• differential fitness

• heritable fitness

How do we distinguish if a trait is good for an individual versus if it leads to success in a species

• greater isolated reproduction

• reduced extinction rate

Describe Gould’s Paradox of the first tier

• the failure to observe macroevolutionary “progress” despite expectation of progress from microevolutionary theory

• less evidence in long time scales

• Basically, according to evolutionary theory, we expect that genes are essentially what control evolution, but then we see all sorts of weird patterns on a macroevolutionary scale that shouldnt give the individual itself an advantage and yet seems to help the species succeed

Describe Gould’s first tier

• evolution across generations

• <1MYA

• selection among individuals, within species (ie. microevolution)

• Darwinian adaptive evolution occurs at this tier

Describe Gould’s second tier

• if species are fit or not (eg. sex ratio, ranges, etc)

• 1-26 MYA

• selection is among species, within clades (ie. sorting, species selection)

• contradicts/erases evolutionary progress from Tier 1

Describe Gould’s tier 3

• >26MYA

• selection is among species or clades (but unrelated to tier 2 selection)

• Contradicts/erases evolutionary progress from tiers 1 and 2

What are the consequences of species selection on macroevolution

• shapes evolution of biodiversity

• shapes distribution of traits within clades

Describe the controversy over species selection

• dominant view in evolutionary biology was that selection among individual organisms and among genes were the most important modes of selection

• Long accepted that selection among species could occur in theory, and on occasion (eg. selective mass extinctions)

• difficult (until recently) to test for consistent species selection

Describe the paleontological approaches to empirically studying species selection

• Score clades or ancestor descendant pairs for trait of interest

• estimate origination rates, extinction rates, and/or durations using standard methods (eg. interval, boundary, crosser)

• Statistically compare rates/durations for taxa with and without traits of interest

What are the pros to the sister group approach to testing for species selection

• Easy to implement

• Doesn’t require fully resolved phylogenies (or branch lengths)

  • don’t need every single species

• test is conservative (detected diversification differences are real)

• age doesn’t matter (sisters are the same age, has control for time)

What are the cons to the sister group approach to testing for species selection

• doesn’t distinguish speciation, extinction

• low power

• trait change must be rare enough that all clades have the same trait

Describe the phylogenic nonindependence problem

• when data points, such as species traits, aren’t truly independent bc the species are closely related

• Sort of like if aliens abducted a family of redheads and concluded that all humans on earth must be redheads bc these humans are

• closely related species are more similar to one another than distantly related species, due to recent common ancestry

• for traits exhibiting a phylogenetic effect, species data are not independent and thus violates statistical assumption that the data points are independent

Describe phylogenetically independent contrasts

• rather than asking whether two variables are correlated for a set of species, asks if the independent evolutionary change in two variables is correlated

  • is one change correlated with the other?

• involves analysis of evolutionary differences not raw species data

Describe how to do an independent contrast

1. subtract the trait value in one tip from the other

2. Add the branch lengths of the tips (eg. 1+1) and then take the standard variance (square root the sum of the branch lengths)

3. Divide the difference in trait value from step 1 by the variance in step 2- this gives you the contrast

4. Repeat steps 1-3 for all tips you have

5. Do the same for the branch nodes to get the ancestral state (eg. add the trait values in descendent tips, divide by two tips to get ancestral trait value) then do steps 1-3 again

Describe what we would expect to see under an individual level species hypothesis for the following question: Does photosymbiosis affect diversification (speciation and/or extinction) in corals?

Photosymbiosis should expand niche rate, increasing mean fitness

• so, basically, the individuals should generally do better

• the niche the individuals access is getting bigger

Describe what we would expect to see under an species level species hypothesis for the following question: Does photosymbiosis affect diversification (speciation and/or extinction) in corals?

Photosymbiosis may reduce extinction rate

• eg. through increased individual niche width, or increased range size

• the species as a whole is showing more success

• Maybe the individuals don’t live as long, but the range where the organisms can be found increases > better species survival, even if the individual suffers

Describe a sister group comparison as a phylogenetic approach to the empirical study of species selection

• split at the exact same time (sister has trait, other sister lacks it) > does the trait that has it diversify more than the other?

  • good control comparisons

• sister clades are the same age

• diversity differences necessarily reflect differences in the net diversification rate

• can use simple statistical tests to assess whether evolution of a phenotype leads to increased net diversification

Describe what we would expect to see under an individual level selection hypothesis under a sister group test for whether or not zygomorphic (symmetric) flowers increase diversification

Symmetry increases pollinator efficiency

Describe what we would expect to see under a species level selection hypothesis under a sister group test for whether or not zygomorphic (symmetric) flowers increase diversification

• symmetry increases pollinator efficiency (increasing speciation rate)

  • having a more accurate pollinator would increase reproductive isolation

Describe trait dependent diversification models

• does the trend depend on speciation/extinction rate

  • eg. does having this trait increase speciation?

• Obtain time calibrated phylogeny (chronogram)

• score all tips for binary character of interest

• Use maximum likelihood to fit joint model of speciation, extinction, and character state transition

.What are the parameters estimated in a BiSSE model

• lambda 0 > speciation rate, lineages in state 0

• mu 0 > extinction rate, lineages in state 0

• lambda 1 >speciation rate, lineages in state 1

• mu 1 > extinction rate, lineages in state 1

• q 0→1 > transition rate from state 0 to 1

• q 1→ 0 > transition rate from state 1 to 0

What does state 0 mean in a BiSSE model?

The lack of a trait

What does state 1 mean n a BiSSE model

the presence of the trait

What would we expect to see under an individual level selection hypothesis for the following question: Is self compatibility (the ability to self fertilize) an evolutionary dead end?

Self compatibility increasing fitness if pollen from other plants is unavailable (favouring selfing)

What would we expect to see under a species level selection hypothesis for the following question: Is self compatibility (the ability to self fertilize) an evolutionary dead end?

self compatibility leads to inbreeding depression (increasing extinction rate)

• comprises ability to adapt further

Describe the meiotic drive in Drosophilia as gamete level selection

• cheat process off meiosis

• one copy of chromosome is overrepresented (sperm w this copy, XSR, only gives rise to females)

  • XSR competing with Y sperm (Y sperm die)

    • phenotypic variation

    • differential fitness (between the Y and the XSR bc the Y dies)

    • heritable

• Thus, example of natural selection acting on the gamete level

Describe cancer as an example of cell level selection

• cells divide via mitosis

  • no genetic variation

• Want cells to be evolution-proof (not completely each other)

  • but nothing can stop mutation

• In cancer lineages, selection favours fast dividing, death-resistant cells

  • slow apoptosis

  • increasing in frequency in tissue

  • Therefore, successful and selected for (yoikes)

What is the formula used for Ordinary least squares (OLS)? Describe what it does.

y=XB+E

• basically creates a really fancy line of best fit

How does PGLS adjust OLS for correlated errors

• In OLS, variance = O²I

• In PGLS, variance = O² C

• O is rate of evolution in both

• I is identity matrix  for INDEPENDENT  variables

• C is a matrix for shared phylogenetic history (Off diagonal covariances in this matrix represent shared evolutionary history)

What is the formula for Brownian motion?

dX(t) = O²dB(t)

What does dX(t) represent in Brownian Motion?

the change in trait (x) over time (t)

What does O² represent in Brownian motrion?

• its a scaling parameter for random normal distribution

• makes distribution really skinny or wide (small value makes it skinny and means less variance and thus slower evolution, while a larger value means faster evolution)

What does dB(t) mean in Brownian motion?

random normal distribution with variance dt and mean 0