bsc2010 - exam 3

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what is evolution?
\- change in the genetic composition of populations over time

\- change in population allele frequency across generations

\- evolutionary theory represents a vast field describing how and why evolutionary change occurs
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variation
differences in physical traits of an individual from the group to which it belongs
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natural selection
phenotypic variation influences survival and reproduction
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heritability
phenotypes are passed down from parents to offspring
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genetic drift
more variation that arises through mutations
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common ancestors - species share these and diverge over time
Common ancestors are extinct organisms from which multiple species evolved. They are identified through fossils and genetics. This principle is important in evolutionary biology for understanding species relationships.
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endemic species
exist only in one location
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darwin conducted studies on which islands?
Galapagos
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descent with modification
Descent with modification is a phrase used to describe the process of evolution by natural selection, as proposed by Charles Darwin. It refers to the idea that species change over time through the passing down of traits from parent to offspring, with modifications occurring through the accumulation of small changes over many generations. This process leads to the development of new species and the diversity of life on Earth.
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alfred wallace
another researcher trying to publish w/ Darwin, he rushes to publish and each had independent origins of evolutionary theory
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biogeography
alfred wallace is best known for this;

**Biogeography** is the study of the distribution of living organisms and the patterns and processes that shape their geographic ranges. It involves understanding how historical events, such as continental drift and glaciation, have influenced the evolution and distribution of species across the planet. Biogeography also examines the factors that determine the boundaries of species' ranges, such as climate, topography, and biotic interactions.
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philosphical origins prior to darwin/wallace
9th-century Islamic scholar al-Jahiz in “Book of Animals” discusses natural selection and the placement of humans among other life forms

darwin and wallace most famously initiated evolutionary theory, not the first to consider biodiversity arising through changes over time
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is evolutionary theory complete?
no! more research papers are being published every year

modern applications of evolutionary theory:

* medicine/epidemiology
* virology, microbiology
* conservation biology

modern misapplications of evolutionary theory

* adaptationist viewpoints
* social darwinism
* eugenics
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evolutionary synthesis
combines evolutionary theory and genetics
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fitness
the relative success of a phenotype regarding __survival and reproductive capability__, relative to other phenotypes
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adaptation
a beneficial trait that spreads through a population by __natural selection__. also describes the process that produces the trait
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mutation (genetic drift)

mutation (gene flow)
generate variation
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selection

nonrandom mating
reduce variation (sometimes)
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mutations
changes in nucleotide sequences that occur in individuals regardless of the organism’s need, can be deleterious, beneficial, or neutral
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gene flow
Gene flow is the transfer of genetic material from one population to another. This can occur through the migration of individuals or through the movement of gametes (such as pollen or sperm) between populations. Gene flow can introduce new genetic variation into a population, and can also help to prevent genetic divergence between populations.
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genetic drift
occurs in populations over time; random small changes in allele frequencies from one generation to the next, can produce large changes over time; most effective with ***neutral mutations*** in ***small populations***
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allele frequency
the proportion of each allele in the gene pool

* 1.0 - everyone has this allele (fixation)
* 0.5 - half of individuals have this allele
* 0 - no one has this allele
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population bottlenecks
caused by extreme declines in population size, reducing genetic variation in the surviving population
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founder effects
initiation of a new population with fewer individuals from a larger group, reducing genetic variation in the surviving population
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migration
movement of individuals (alleles) from one population to another, can increase variation, from a genetic perspective, this is called **gene flow**
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selection
natural selection increases the frequency of beneficial alleles in populations by removing individuals with deleterious alleles

* often represented by frequency distributions
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frequency distributions
* visualize count data
* can show absolute frequencies or relative frequencies, such as proportions or percentages
* wider distributions represent a greater amount of variation, peaks represent the most common traits
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non-random mating (sexual selection)
when individuals choose partners based on their characteristics, can generate exaggerated traits like antlers, long tails, coloration, etc, or when one sex competes for access to reproductive opportunities

* can be trade-offs between attracting mates (more likely to reproduce) and attracting predators (less likely to survive)
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modes of selection
how subsequent generations differ from original populations
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directional selection
individuals at one side of a trait distribution contribute more offspring to the next generation, over many generations an evolutionary trend can be seen

* positive directional selection: antibiotic resistance to gonorrhea
* individuals with phenotypes at one end of distribution do best, mean changes, sometimes changes variation
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stabilizing selection
reduces variation in populations but does not change the mean; also called **purifying selection**, meaning selection “purifies” the gene pool by removing deleterious mutations

* individuals at the mean of the distribution do best, mean changes and sometimes changes variation
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disruptive selection
extremes in populations survive, bimodal patterns may result; can increase variation although selection often reduces variation

* can generate polymorphisms: stable, discrete categories of phenotypes, bimodal or multimodal distributions of traits, sometimes a basis for speciation
* individuals at both extremes outperform those in the middle, increases variation
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heteroozygote advantage
in changing conditions, heterozygous individuals often outperform homosygotes; different alleles of a gene may be advantageous under different environmental conditions
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geographic variation in selection
genetic variation is maintained in populations in different geographic regions with different selective pressures

* tradeoffs result in differences across geographic space, example being white clover plants producing cyanide to deter herbivores but being more likely to be killed by frost
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frequency-dependent selection
maintains genetic variation - a polymorhpism can be maintained when fitness depends on its frequency in the population

* results in oscillations of relative abundance
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artificial selection
cornerstone of human civilization (agriculture, domestication, selective breeding); purposefully guided by humans, often with a goal in mind

* selective breeding of animals and plants with desired traits
* natural selection, however, has no “goal”
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heritability
estimates the proportion of trait variation that is driven by genetic variation
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the breeder’s equation
predicts evolutionary change in a trait; a foundational tool in quantitative genetics, can be used to predict evolutionary change

* S = selection differential (parents selected + base parents)
* R = response to selection (offspring)
* h2 = heritability

R=h2S

assumes the trait of interest is not correlated with other traits affecting fitness
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domestication
provides strong evidence for “descent with modification”
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history of domestication/artificial selection
crops were likely domesticated where their closest wild relatives were more diverse, first began about 10,000 years ago
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agricultural research
long-term selection experiments showed that selection can result in strong phenotypic differences, and that trait can be reversed
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artificial selection, just like natural selection, can only operate on
existing genetic variation
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quantitative traits
the same genotype having different phenotypes
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heritability estimates
the proportion of variation in a trait determined by inherited genes vs the environment; ranges from 0 to 1

* if H2=1, all variation in a population is due to genetic differences
* if H2=0, no genetic variation, all variation in the population comes from differences in the environments experienced by individuals

not necessarily constant, can be influenced by many factors

* precision of measurement
* environmental change
* migration/gene flow
* inbreeding (changes to allele frequency)

does not mean genetic determination; it is an estimate of the proportion of phenotypic variation due to genetic variation, specific to that study

* higher heritability and stronger selection differentials will generate stronger responses to selection
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reproductive isolation
a fundamental step in the process of speciation (when one species splits in two), has been achieved through artificial selection and lab populations
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population genetic structures
can be described by frequencies of alleles and genotypes; an allele’s frequency is calculated using the following formula

* p = (2NAA + NAa) / 2N
* q = (2Naa + NAa) / 2N
* p + q = 1
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null model
generates predictions that you can compare against to assess whether some other process is taking place
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hardy-weinberg equilibrium
a null model in which allele frequencies do not change across generations

several conditions must be met for a sexually-reproducing population to be at hardy-weinberg equilibrium

* __**no mutation**__ - allele frequency does not change, and no new alleles are added
* __**no selection**__ - different genotypes have equal survival and reproduction
* __**no gene flow**__ - no movement into or out of the population
* __**population size is infinite**__ - the larger a population, the smaller will be the effect of genetic drift
* __**mating is random**__ - individuals do not preferentially choose mates with certain genotypes
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if hwe conditions are met, then
* the frequencies of alleles remain constant across generations
* we can predict genotype frequencies from allele frequencies
* deviations from hwe show evolution is occurring and that nonrandom mating is really important
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two main forms of sexual selection
* intrasexual competition
* mate choice
* historically viewed as “male-male competition” and “female choice for males”, now lots of data for female-female competition and male mate choice
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secondary sex trait characteristics
* good genes hypothesis: sometimes traits are honest signals of mate quality
* runaway sexual selection: offspring will inherit their parents’ ornamental traits and preferences for that trait
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genetic (sexual) conflict
can occur when genes that govern male and female traits are antagonistic
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novel gene combinations…
arise during “mistakes” in DNA replication when organisms make gametes; changes to nucleotide sequences, gene location, gene repeats, and expression
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nucleotide substitutions
changes in one nucleotide in a DNA sequence
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synonymous substitutions (silent)
do not affect the functioning of a protein; always neutral
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nonsynonymous substitutions (missense/nonsense)
affect protein function, can be deleterious, neutral, or advantageous

* higher rate is strong evidence for directional selection
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hybrid incombatibility
offspring of individuals from different populations or even species are worse off
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mutation rates
rate of substitutions (mutations) is higher at synonymous sites than non-synonymous sites; substitution rate is even higher in introns (pseudogenes), the space between exons that do not transcribe RNA

* reflects stronger stabilizing selection in functional genes than in pseudogenes
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neutral theory of molecular evolution
* majority of evolutionary change occurs at the molecular level, and most genetic variation is due to random genetic drift of alleles that are selectively neutral
* provides another null model for molecular evolutions, the rate of fixation of new neutral mutations is independent of population size
* m = u
* u = neutral mutation rate
* m = rate of fixation of neutral mutations
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molecular clocks
* uses the average rate at which a given gene region/protein accumulates changes to gauge the time of divergence between species
* mutation can be used as this to calculate evolutionary divergence times between species
* must be calibrated using independent data
* the fossil record
* known times of divergenve
* biogeographic data
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molecular evidence of selection (ds/ds ratio)
ratio of number of nonsynonymous substitutions per nonsynonymous site (dn) to the number of synonymous substitutions per synonymous site (ds)

* if dn/ds = 1: neutral, no selection
* if dn/ds > 1: positive directional selection (rate of change higher than expected, that DNA sequence is “moving”)
* if dn/ds < 1: stabilizing selection (rate of change lower than expected, that DNA sequence is staying put
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gene expression
changes might account for much of the evolution of diverse body forms we observe across living organisms - evolutionary developmental biology
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homeotic mutation
replaces one structure with another
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genetic switches
can turn genes on or off, regulate the amount and timing of gene expression

* multiple switches control each gene, creating different expression patterns in different locations
* major changes in phenotypes can be driven by amount, timing, and location of gene expression
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heterometry
different amount of gene expression
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heterochromy
different timing of gene expression
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heterotropy
spatial differences in gene experssion
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shared ancestry
general principles of biology apply to all organisms because all life is related through a common ancestor
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phylogeny
the evolutionary history of genetic relationships
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phylogenetic tree
a visual reconstruction of shared history, may portray evolutionary theory of

* all life forms
* major evolutionary groups
* small groups of closely relates species
* individuals
* populations
* genes
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lineage
series of ancestor and descendant populations
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components of phylogenetic tree
* common ancestor: shared by all organisms; in the tree, it forms the root of the tree
* vertical distances between branches have no meaning
* the vertical order of lineages after a node is arbitrary - you can rotate branches, but you cannot switch branches from different nodes
* nodes indicate the timing of splitting events
* a speciation event
* a gene duplication event
* a transmission event
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homologous features
compared in phylogenetic trees, are shared by two or more species and are inherited from a common ancestor

* can be any heritable traits, such as DNA sequences, protein structures, anatomical structures, and behavior patterns
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traits in phylogenetic trees
every trait evolves from one condition (ancestral) to another condition (derived)
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ingroup on a phylogenetic tree
the group of organisms of primary interest
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outgroup on a phylogenetic tree
species/group known to be closely related to but phylogenetically outside of the group of interest
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parsimony
the preferred explanation of observed data is the simplest explanation; minimizing the number of evolutionary changes that need to be assumed over all characters in all groups in the tree

* a trait that is present in both the ingroup and outgroup most likely evolved before the origin of the ingroup and this is ancestral for the ingroup
* traits present in only some members of the ingroup must be derived trait
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convergent evolution
different selective pressures on different taxa let to similar solutions, so they converged on similar traits
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taxa
expected to be monophyletic, meaning the taxon contains an ancestor and all descendants of that ancestor, and no other organisms

* a true monophyletic group can easily be removed from a tree in a single cut
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hierarchy of biological taxa
kingdom > phylum > class > order > family > genus > species
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monophyletic groups
include all descendents of a common ancestor as well as the common ancestor itself
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polyphyletic groups
do not include its common ancestor
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paraphyletic groups
do not include all the descendants of a common ancestor but does include the common ancestor itself
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species
groups of organisms that share a suite of genetic and morphological attributes, and are reproductively isolated from other such groups

* over 20 species concepts have been developed
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speciation
divergence of biological lineages and emergence of reproductive isolation between lineages (when one species splits in two)
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carolus linnaeus
developed the binomial system of nomenclature we still use today, species were based on their appearance

complications:

* polymorphisms: multiple phenotypes within one species
* cryptic species: two or more species that are indistinguishable but cannot interbreed
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ernst mayor
biological species concept: species are groups of actually or potentially interbreeding natural populations that are reproductively isolated from other such groups

complications:

* asexual reproduction (bacteria)
* extinct groups only known from fossils
* hybridization between closely-related species
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reproductive isolation
two groups of organisms can no longer make viable offspring
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phylognetic/lineage species concept
proposes a species is a branch on a phylogeny, which has a history that starts at a speciation event (node) and ends either at extinction or another speciation

complication:

* speciation is almost always a gradual process
* difficult to determine when the split actually occurs, or what the outcome will be at a single point in time
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various species concepts
can all be applied at once, each emphasize different aspects of species or speciation and have different benefits/costs

* __morphological species concept__: convenient for categorizing species but often over/underestimates
* __biological species concept__: focuses on the process by which species split and remain distinct, but fails to explain asexual/hybridizing species
* __lineage species concept__: accommodates asexually reproducing species and extends to the patterns of relationships over evolutionary time
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reproductive isolation
an allele that causes reprouctive incompatibility could not spread through a population because individuals with that allele cannot reproduce
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dobzhanky-muller model
assumes that ancestral population is divided into two descendant lineages; in each lineage, new alleles arise and become fixed at different loci

* may combine to produce hybrid incompatibility
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reproductive incompatibility
often a gradual process, incompatible gene combinations accumulate slowly in each lineage; in some cases, compelte reproductive isoltaion may take millions of years; in others, it can develop in just a few generations
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hybrid zones
if reproductive isolation is incomplete, hybrid zones may form where population ranges overlap; may persist for long periods.

* suffer from a range of defects and do worse than either parental species
* zones are narrow b/c there is strong selection pressure against hybrids
* reinforces/maintains species barriers
* not all reinforce species barriers, some can relax reproductive barriers between species, can act as bridges and move alleles between species, also serve as bridges for parasites
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allopatric speciation
speciation that results when a population is divided by a physical barrier; populations are separated by a physical or geographic barrier, thought to be the dominant mode of speciation

* genetic divergence between populations caused by mutation, drift, and adaption to different environments
* pairs of sister species (species that are each other’s closest relatives) can arise on opposite sides of the barrier
* galapagos finches are famous examples of this
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sympatric speciation
no physical isoltaion, occurs within the same “population”; speciation without physical isolation, may occur via disruptive selection where different genotypes have preference for distinct microhabitats for mating

* ecological speciation - divergent natural selection between contrasting ecological environments
* another common form is polyploidy - duplication of sets of chromosomes within individuals, can result in complete reproductive isolation in two generations
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temporal isolation
subtle changes in breeding season can cause reproductive isolation
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behavioral isolation
a lot of overlap in courtship characteristics between closely related species; mating calls of male frogs from closely related species are more distinct in sympatric populations due to stronger selective pressures for recognizing your own species
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speciation rates
* usually higher in groups with poor dispersal abilities than in highly mobile groups because even narrow barriers can effectively divide species
* lineages with strong sexual selection are often associated with high rates of speciation
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adaptive radiation
rapid diversification of a large number of descendant species from a single ancestor species that now inhabit a variety of environments