Macroevolution

What were Darwins Main Ideas?

1. Life changes

2. Life branches (and has one origin)

3. Natural selection provides a mechanism for evolution

4. Evolution can explain lifes diversity at small and large timescales

What does Evolutionary Synthesis/Modern synthesis clarify?

the ultimate sources of heritable variation and the mechanisms by which such variation can lead to evolutionary change

What are the ultimate sources of heritable variation

• mutation

• migration

What are the mechanisms by which heritable variation can lead to evolutionary change?

• selection

• drift

What definition of macroevolution do we use in class?

• Evolution over large timescales

• the study of evolutionary patterns evident above the species level, and of the processes that create them

What are the three definitions of macroevolution?

• Evolution of taxa of supraspecific rank

• Evolution over large timescales

• Evolution that involves the differential birth and/or survival of species (as opposed to individuals)

how does macroevolution and microevolution differ?

• scale

  • Not all microevolutionary processes result in patterns that are detectable at macroevolutionary scales

• how we model them

  • Microevolution uses models of gene frequency or phenotypic change in/ among populations of individuals

  • Macroevolution uses models of species origination and extinction, and trait change, at the species level

• how we conduct empirical studies

  • Microevolution is amenable to direct observation, experimental manipulation

  • Macroevolution is comparative, retrospective, statistical, because were mostly interested in the past

What sources of evidence do we use to study macroevolution?

• the fossil record

• Phylogenic tree of life

• Information about living species (used in conjunction w paleontological or phylogenetic info)

What are the pros of using the fossil record?

• Detailed record of the past (what, where, when)

• Direct record of change through time

• preserves extinct species

• Contains information about historical environments, communities

What are some cons of using the fossil record?

• Woefully incomplete

• Biased (taxonomically, temporally, environmentally)

• Taxonomic challenges (no genetics)

• Unavailable for experimental study

What are the pros of using the molecular phylogenetic trees

• More robust estimation of relationships

• Taxa often also available for experimental study

• Can include any living organism

• Taxonomically straightforward (can identify species, sexes, life stages)

What are the cons of using the molecular phylogenetic trees

• Extinct species will be missing

• Lack information about historical environments, communities

• Biased (temporally)

• historical inferences is indirect

What are the problems with observational studies?

• Directionality

• Unconsidered (or uncontrolled) variables

• Chance association

What are the caveats about inferring macroevolutionary processes from a pattern

• A single pattern can often arise from many processes (so we need to be sure to test alternatives)

• Testing a hypothesis about a historical process is not the same as comin up with a post-hoc hypothesis to explain a pattern you’ve already observed in data

• Not all data sets can support rigorous hypothesis testing about process

• There will be some things we cant ever know with confidence

Arguments for the reality of species

• Common sense argument (nature organized into discrete groups)

• Concordance between folk and scientific species

• Statistical identification of clusters

Arguments against reality of species

• the gradual nature of speciation

• Asexual organisms

• Extensive hybridization in some groups

Describe the biological species concept

Species are groups of actually or potentially interbreeding populations, which are reproductively isolated from such other groups

What are the advantages of the biological species concept?

• Focuses on the process that gives rise to divergence of species

• Not misled by phenotypic variation unimportant for reproductive isolation of lineages

What are the disadvantages of the biological species concept?

• Restricted to sexual, outcrossing organisms

• Difficult to apply to incipient species, superspecies, other partially isolated lineages

• Difficult to apply, especially for allopatric populations

Describe the Phylogenetic Species concept

A species is an irreducible (basal) cluster of organisms diagnosably different from other such clusters, and within which there us a parental pattern of ancestry and descent

• diagnosable via synapomorphy (a trait only shared by the group)

What are the advantages of the Phylogenetic species concept?

• straightforward to apply

• can apply to asexual organisms

What are the disadvantages of the Phylogenetic species concept?

• Speciation is not always a strictly branching process

• Evolution of fixed population differences may have little bearing on reproductive isolation (eg. upon secondary contact)

Describe the evolutionary species concept

Species is a single lineage that maintains identity separate from other such lineages, and has own evolutionary tendencies and historical fate

Describe genealogical species concept

species are exclusive groups of organisms, where all members are more closely related to one another than to any organisms outside of the group

Describe recognition species concept

species is the most inclusive population of individual organisms that share a common fertilization system

Describe cohesion species concept

species is most inclusive population of individuals having potential for phenotypic cohesion via intrinsic cohesion mechanisms

What are the 2 components of the general lineage concept?

1. Species are separately evolving metapopulation lineages

2. The former is the only necessary property of species

What is a lineage?

a single continuous line of descent from an ancestor

A lineage can refer to ancestor-descendant sequences of what?

• individuals

• populations

• species

What do phylogenic trees represent?

historical patterns of lineage splitting

What is the assumption that is typically expected for most methods of estimating phylogenies?

The genealogical history of lineages way strictly bifurcating

When is the bifurcating history assumption for phylogenies violated?

• When there is horizontal gene transfer

• Introgression (sexual transfer from one group to another, like in hybridization)

• Lineage fusion (reasonably common in species that have very recently diverged)

What can a tip in a phylogenic tree represent?

• Individuals

• Species

• Clades

Describe the root in a phylogenic tree

• A node representing the earliest time point in the diagram

• Often represented by an unlabeled branch

Describe the MRCA on a phylogenic tree

the youngest ode that is ancestral to all lineages in a group of taxa

Describe a crown group on a phylogenic tree

Includes all living members of a clade, the MRCA of those species, and all descendants of the MRCA (living and extinct)

Describe a pan group on a phylogenic tree

Includes the crown group, plus any lineages more closely related to the crown group than any other extant species

Describe a stem group on a phylogenic tree

• Includes all lineages of a pan group that are not included in the crown group

• Contains only extinct species- those that are more closely related to the focal crown group than to its sister crown group

Describe sister groups on a phylogenic tree

those that are the immediate descendants of the same ancestor

Why do we sort fossils into their own branch/node, rather than putting them at the node where known living species diverge?

• very rare to find fossils overall- sampling bias

• Even MORE rare to find a direct ancestor, so better science to assume we didn’t unless we have hard proof

Describe monophyly

• describes a group made up of an ancestor and all its descendants

• ex. a clade

• Uses one snip of scissors to separate

Describe paraphyly

• describes a group made up of an ancestor and some (but not all) of its descendants

• ex. paraphyletic group

• Sort of like how you don’t consider a black sheep of the family to be actually part of the family, even if they share blood

  • Disown!!!!!!!! Disown the species you dont like!!!!!!

Describe polyphyly

• describes a group that does not contain the most recent common ancestor of all members

• ex. a polyphyletic group

• Like how you don’t count your weird cousin Phil as part of the family despite bein related but you DO count the friends of the family, even though they ARENT related (or, at least, closely)

• Doesn’t include MRCA

Describe what, if anything, the branch lengths mean in a cladogram

Don’t mean jack

Describe what, if anything, the branch lengths mean in a phylogram

Reflects units of numbers of substitutions (basically the amount of character change)

Describe what, if anything, the branch lengths mean in a chronogram

Reflects time (made using phylogram AND some evolutionary model of time)

Describe a polytomy

• multifurcation in a phylogeny

• can be hard or soft

Describe a hard polytomy

Reflects an actual case where three or more lineages branched simultaneously

Describe a soft polytomy

Reflects a multifurcation that is likely the result of a lack of data

Describe homology

when structures observed in different taxa can be traced to a single structure present in a shared evolutionary ancestor

Describe homoplasy

When a character or state arises more than once on a phylogenic tree (convergence is one kind)

Compare ancestral vs. derived traits

• refer to the inheritance of traits for a given group of species

• do not describe species themselves

• for the species in a clade, a trait is ancestral if it was inherited in its present form from the MCRA of the clade

• a trait is derived for that clade if it originated within the clade

• the same trait can be ancestral for a clade, but derived within a larger clade

Describe a synapomorphy

• a shared, derived trait for a clade

• a trait that all species in the clade share, and that evolved on the branch leading to the clade

Describe a symplesiomorphy

A shared, ancestral trait for a group of two or more taxa

how do we estimate phylogenies

we analyze traits that evolved during the phylogenic history of the species of interest

What makes a good phylogenetic character?

• vertical inheritance

• lack of horizontal inheritance

• species level traits

• unbiased

• variable enough

• not too variable

Describe phenotypic characters

• includes morphology, physiology, behavior

• can be continuous or discrete

• state space often large (potentially less homoplasy)

• Only source of data for most fossils

• Rarely neutral (can be biased by selection)

describe genetic/molecular characters as a type of phylogenetic data

• includes nucleotides, amino acids, proteins, etc.

• Discrete

• State space often small (very hih potential for homoplasy)

• Not available for most fossils

• Often neutral

• Extremely abundant

• Sophisticated evolutionary models

how do we evaluate whether a phylogenetic tree is supported by evidence?

Establish an optimality criterion, deduce from there

Describe an optimality criterion

the establishment of an objective measure by which a given hypothesis will be evaluated against potential alternatives

List the primary methods of phylogenetic inference

• Distance (ie. phenetics)

• Maximum parsimony

• Maximum likelihood

• Bayesian inference

What is the optimality criterion of distance

minimize overall dissimilarity

Describe maximum parsimony and its optimality criterion

• lookin for synapomorphies

• criterion is to minimize inferred evolutionary changes

Describe maximum likelihood and its optimality criterion

• model based

• comin up w algorithm

• criterion is the likelihood of the observed data

What are the common pitfalls of using the fossil record as a source of information?

• assuming that the fossil record is so complete that it can always be taken at face value

• the assumption that the fossil record is so biased or incomplete that it is of little scientific use

List the factors that affect the likelihood of fossilization

• tissue composition

  • harder tissues will be more likely to fossilize, but this applies to the materials in hard AND soft parts

• Environmental chemistry

  • the more acidic the environment is, the less likely you are to find fossils from that period

• habitat

  • is it a depositional zone or an erosional zone?

List commonly fossilized tissue types, from most decent (more likely to fossilize) to least decent

Silica > phosphates > carbonates > keratin > lignin > cellulose > chitin

List modes of fossilization

• freezing

• preservation in amber

• Carbonization (distillation)

• permineralization

  • original skeleton material permeated and hardened by materials in solution

• recrystallization

  • skeletal material converted under heat and pressure to more stable form

• replacement

  • skeletal material replaced by permeating aqueous minerals

• mold and cast formation

  • mold is the negative impression of a fossil in rock

  • a cast is made if a mold later fills in with rock

• Trace fossils

  • records of behaviour

how do fossils vary?

• What tissues (if any) are preserved

• how preserved matter has been altered

What is taphonomy

The study of processes of preservation and how they affect information in the fossil record

Biostratinomy

study of material before long term burial

Diagenesis

study of material after long term burial

Describe the sansom study

• studied the decay of lampreys at various stages

• With no decay, the lamprey could be easily classified in a phylogenic tree

• At stage 1 of decay, could only place it in the crown group based on the characteristics it hadnt lost yet

• the more the lamprey decayed, the more classifying characteristics were lost

  • stage 5- could only identify it as a stem chordate

• TLDR- the fossils we rely on are probably really rotten, so how reliable are they, really?

Describe the Western and Behrensmeyer study

• looked at how representative the dead community is of the live community (live dead comparison)

• Some species were okay, but most kind of sucked

  • some species had features that made the bones/remains less likely to stay together, and others had features that were harder to break down

• Wasn’t really a helpful estimate of population size > fossils may be the same, may be unreliable for population size and characteristics

Describe Stenos principle of superposition

In undeformed rock layers, rocks at the top will be earliest and rocks at bottom will be oldest

Describe Stenos principle of lateral continuity

The same layer of rock will continue across a gap 

Describe Stenos principle of original horizontality

Rock layers are distributed horizontally, so any deformation of layers must have happened after the rock was deposited

What are the two ways that deposition is episodic ADD INFORMATION

• transgression

• regression 

Describe time averaging

• when one fossil layer preserves organisms that accumulated over a lengthy period of time

• Function of rate of production of skeletal material vs. rate of sedimentation

• Can also occur due to reworking of sediment prior to lithification (ex. Bioturbation)

• Affects estimates of community composition, mask evolutionary trends

What issues do we need to consider if we do decide to sample the fossil record?

• Is our fossil sample random (unbiased)?

  • taphonomic control

• Are measurements of our sample sensitive to sampling effects?

  • deposits vary in fossil abundance > affects richness comparisons

  • Rarefaction

Describe rarefaction

• compares samples that differ in size

• an after the fact standardization to control for biased sampling

• Randomly draw individuals from the sample without replacement

• Plot number of species against number of individuals

• Curve will depict expected species richness for smaller sample sizes

Describe completeness in the context of the fossil record for a fossil lineage 

• probability of sampling a given taxon within a specified interval of time

  • Break time period into intervals of equal length

  • assume species truly occurs in all intervals between first and last observed occurrences

  • calculate sampling probability from that (ex. if 3 occurrences between first and last, within 10 intervals > 3/10 = 0.3)

  • To calculate first future interval, do that but backwards (likelihood of it bein there but not sampled > 10-3/10 = 7/10= 0.7)

Describe temporal biases in the fossil record

• rock availability

• Distribution of habitats

• Bioturbation

Describe net diversification rate of a clade

• the rate of lineage splitting (ie.  speciation rate/birth rate/origination rate) minus its rate of lineage extinction (ie extinction rate/death rate)

• b - d

• OR lambda - mu

  • positive net diversification rates = clade growing

  • negative net diversification rate = clade shrinking

Marshalls first law of paleobiology 

all species go extinct eventually

• most only last ~1 million years on average 

how is diversification modelled?

• as a birth-death process, via a continuous- time Markov process

  • poission distribution (how often discrete events happen- exponentially distributed)

  • probabilities (instantaneous rates) of change constant, memoryless

• Waiting times for speciation or extinction follow exponential distributions

• depends on birth-death parameters

What kind of growth do we see in the birth death process when modeling diversification

exponential growth or decline of lineages

When we model diversification, what trends do we expect to see in waiting times for a growing clade, and why?

waiting times to events should get shorter over time, despite constant per-lineage rates, because of exponential growth of lineages 

True or false: a growing or declining clade is mathematically similar to a growing or declining population of individuals 

• True

• birth- death diversification models are analogous to exponential population growth models in population ecology

• Over a given period of time (delta t) a lineage has a probability of producing a daughter lineage (birth or speciation) =lambda, or b

  • also has probability of extinction (= mu or d)

• As diversification proceeds, b and d events become more frequent due to the buildup of lineages (the per lineage probabilities are constant) 

What kind of process is diversification? Does this ever change due to extinction? Explain.

• exponential

• does not change even with extinction

  • compounding branches balance it out

What is N(t) in diversification models?

number of species at time t

What is N(t) in diversification models?

Number of species at time 0

What is b (or lambda) in diversification models?

birth rate

What is d (or mu) in diversification models?

death rate

What is t in diversification models?

time interval length 

What is the formula for the pure birth diversification model

N(t) = N(0)e^(bt)

What is the formula for the birth death diversification model

N(t) - N(0)e^((b-d)t)

Why do researchers typically plot lineages through time using a semi log plot

Makes exponential far easier to interpret

What are the issues with modeling diversification

• high expected variance in outcomes

• outcome strongly dependent on early events 

What are the two principal approaches for studying macroevolutionary diversification

• the fossil record

• molecular phylogenies