bsc2010 - exam 3

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

variation

differences in physical traits of an individual from the group to which it belongs

natural selection

phenotypic variation influences survival and reproduction

heritability

phenotypes are passed down from parents to offspring

genetic drift

more variation that arises through mutations

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.

endemic species

exist only in one location

darwin conducted studies on which islands?

Galapagos

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.

alfred wallace

another researcher trying to publish w/ Darwin, he rushes to publish and each had independent origins of evolutionary theory

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.

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

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

evolutionary synthesis

combines evolutionary theory and genetics

fitness

the relative success of a phenotype regarding __survival and reproductive capability__, relative to other phenotypes

adaptation

a beneficial trait that spreads through a population by __natural selection__. also describes the process that produces the trait

mutation (genetic drift)

mutation (gene flow)

generate variation

selection

nonrandom mating

reduce variation (sometimes)

mutations

changes in nucleotide sequences that occur in individuals regardless of the organism’s need, can be deleterious, beneficial, or neutral

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.

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***

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

population bottlenecks

caused by extreme declines in population size, reducing genetic variation in the surviving population

founder effects

initiation of a new population with fewer individuals from a larger group, reducing genetic variation in the surviving population

migration

movement of individuals (alleles) from one population to another, can increase variation, from a genetic perspective, this is called **gene flow**

selection

natural selection increases the frequency of beneficial alleles in populations by removing individuals with deleterious alleles

* often represented by frequency distributions

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

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)

modes of selection

how subsequent generations differ from original populations

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

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

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

heteroozygote advantage

in changing conditions, heterozygous individuals often outperform homosygotes; different alleles of a gene may be advantageous under different environmental conditions

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

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

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”

heritability

estimates the proportion of trait variation that is driven by genetic variation

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

domestication

provides strong evidence for “descent with modification”

history of domestication/artificial selection

crops were likely domesticated where their closest wild relatives were more diverse, first began about 10,000 years ago

agricultural research

long-term selection experiments showed that selection can result in strong phenotypic differences, and that trait can be reversed

artificial selection, just like natural selection, can only operate on

existing genetic variation

quantitative traits

the same genotype having different phenotypes

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

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

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

null model

generates predictions that you can compare against to assess whether some other process is taking place

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

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

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

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

genetic (sexual) conflict

can occur when genes that govern male and female traits are antagonistic

novel gene combinations…

arise during “mistakes” in DNA replication when organisms make gametes; changes to nucleotide sequences, gene location, gene repeats, and expression

nucleotide substitutions

changes in one nucleotide in a DNA sequence

synonymous substitutions (silent)

do not affect the functioning of a protein; always neutral

nonsynonymous substitutions (missense/nonsense)

affect protein function, can be deleterious, neutral, or advantageous

* higher rate is strong evidence for directional selection

hybrid incombatibility

offspring of individuals from different populations or even species are worse off

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

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

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

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

gene expression

changes might account for much of the evolution of diverse body forms we observe across living organisms - evolutionary developmental biology

homeotic mutation

replaces one structure with another

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

heterometry

different amount of gene expression

heterochromy

different timing of gene expression

heterotropy

spatial differences in gene experssion

shared ancestry

general principles of biology apply to all organisms because all life is related through a common ancestor

phylogeny

the evolutionary history of genetic relationships

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

lineage

series of ancestor and descendant populations

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

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

traits in phylogenetic trees

every trait evolves from one condition (ancestral) to another condition (derived)

ingroup on a phylogenetic tree

the group of organisms of primary interest

outgroup on a phylogenetic tree

species/group known to be closely related to but phylogenetically outside of the group of interest

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

convergent evolution

different selective pressures on different taxa let to similar solutions, so they converged on similar traits

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

hierarchy of biological taxa

kingdom > phylum > class > order > family > genus > species

monophyletic groups

include all descendents of a common ancestor as well as the common ancestor itself

polyphyletic groups

do not include its common ancestor

paraphyletic groups

do not include all the descendants of a common ancestor but does include the common ancestor itself

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

speciation

divergence of biological lineages and emergence of reproductive isolation between lineages (when one species splits in two)

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

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

reproductive isolation

two groups of organisms can no longer make viable offspring

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

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

reproductive isolation

an allele that causes reprouctive incompatibility could not spread through a population because individuals with that allele cannot reproduce

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

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

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

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

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

temporal isolation

subtle changes in breeding season can cause reproductive isolation

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

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

adaptive radiation

rapid diversification of a large number of descendant species from a single ancestor species that now inhabit a variety of environments