Bio 221 Midterm 2

Population

Group of interacting and potentially interbreeding individuals of a particular species

Population Genetics

Study of allele distributions within and among populations and how they change over time

No population subdivision

Individuals can interact with one another very easily

Intermediate population subdivision

Little pockets of individuals that can move between subdivisions but not continuously ex. snowshoe hares on campus

Extreme population subdivision

Populations that are completely isolated from each other ex. bears in different national parks

H-W violations

Lead to evolution: mutation, natural selection, migration, drift

Random Allelic Change

Due to drift and mutation

Genetic Drift

Random changes in the frequencies of 2 or more alleles/haplotypes/genotypes, force that can do allelic change that is not due to selection, often considered sampling error, ex. elephant stepping on ladybugs so only yellow survives

Haplotype

Multiple genetic loci that pass on together

Drift Impact

Dependent on population size, allelic frequencies change genotypic frequencies

Larger the population the more genetic stability

Smaller population have the biggest fluctuations, more variation in allelic frequency and fixation is less likely

Drosophila lab experiment

8 males and 8 females are randomly mated, found over 19 generations the brown eyed allele is lost and other allele is fixed after 30 generations

Biggest problems with genetic drift

• problem with conservation, favours fixation with is not stable at 2 extremes

• At the point of species being endangered, fixation probability increases

• Loss of genetic diversity

Bottleneck

Type of drift, when’s population undergoes a rapid constriction in population size and then expands, allelic frequency in surviving groups may not reflect frequency in original population, rare alleles more likely to be lost, ex. Northern elephant seal was hunted to near extinction then the population expansion showed less genetic diversity

Founder Effect

Occurs when an offshoot of a bigger population establishes a new population, new population alleles dependant on the alleles the founders carry, more common alleles will be represented but some randomness, ex. Many people on a ship experience migraines and are related

Inbreeding

Mating with close relatives, violates random mating and H-W

Selfing

Extreme form of inbreeding, reduces heterozygous proportion

Sib-mating

Sibling mating, follow alleles through generations, after one generation 50% change of an allele being passed down to both son/daughter, if the 2 siblings mate, 25% chance that the offspring will have alleles from grandfather (will be less diverse), can lead to Autozygosity

Autozygosity

Homozygosity with 2 copies of the same allele due to common decent ex. Bad trait can be passed down when inbreeding

Allozygosity

Allleles an individual carries are not due to common decent

Inbreeding Coefficient

F (equal to proportion of individuals that are autozygous), calculate the degree that an individual is inbre(1-F) are allozygous, F=0 if no inbreeding

problem with inbreeding

Does not change allelic frequency but increases homozygousity, Increased homozygosity allows recessive, deleterious alleles to persist and reduce viability, Their effect only obvious when homozygous, Homozygous individuals purged from population, Only heterozygous individuals remain (and those homozygous for non-lethal alleles), ex. Drosophila pseudoobscura revealed that when chromosomes were forced to be identical (and hence all genes homozygous in offspring), a huge number were deleterious

Inbreeding depression

increases homozygosity, and brings, recessive (and sometimes deleterious) alleles to surface, declines in survival and fecundity are due to human inbreeding

Sedentary Population

Low gene flow, and will genetically differentiate over time due to drift ex. Bighorn sheep

Landscape Genetics

Knowledge of geography allows researchers to explore how genotypes vary across landscapes, further the barrier the greater the genetic difference, ex. Different genotypes in monarch butterflies in Canada and Mexico

Population fingerprints

Geographical distance can determine which population an individual originated from

Gene Flow

Differences between populations can be countered by immigration of new individuals and alleles, landscape genetics (including man made roads) can reveal effects of reduced gene flow, increased gene flow means more increased variation and less drift

Complex phenotypes

usually influenced by many genes (are polygenic), Often show a normal distribution, Example: Increasing the number of genes that influence body size can create a much more continuous (and potentially normal) distribution in size

Quantitative Genectics

Study of continuous phenotypic traits and underlying evolutionary mechanisms

Variance

Statistic measurement of the dispersion of a trait about the mean, In some cases, the environment is a stronger influence on variation than is genotype, Some genetic variance can be due to additive effects of alleles some to dominant effects, and some to interactions among alleles at different loci

Vp

Total phenotype variance, If the environment has no effect, then it equals the proportion of phenotypic variance attributable to Vg and not Ve

Vg

Variation of genetic causes, can be broken down to Vi, Va, Vd

Vd

Dominance variance, due to dominance effects of alleles, ex. allelic series

Vi

Interactive variance, when expression of one locus is dependent on genotype of another locus, does not play a huge role in quantitative variation, hard to figure out because of independent assortment

Va

Additive variation, when multiple loci attribute to the phenotype in an additive manner, most important for evolution

Ve

Variation due to genetic causes

Sample Variance

Individual measurement against the mean

Heritability

measure the proportion of phenotypic variances that is just attributable to vg, (genetic sources)

H2 (squared)

Broad sense heritability, For all variation of a trait, too broad, only represents genetic variation as a single value

h2 (squared)

Narrow sense heritability, proportion of total phenotypic variance attributable to the additive effects of alleles, greater value means greater heritability, if offspring resembled the parent the population will evolve predictably in response to selection, Captures only the variation that is due to additive genetics

h2 calculation

Difficult to calculate, one way is to breed individuals together and measure the trait in parents and offspring, measurementsofthree phenotypic traits in offspring are regressed against the values of those traits expressed by their parents

Stabilizing selection

If selection favours average or against extremes, mean doesn’t shift and stabilize, variance decreases and distribution narrows

Disruptive selection

If selection works against average, mean stays the same, variance increases or doesn’t change and may produce 2 distinct peaks, ex. fruit fly bristles, researchers only allowed flies with exceptionally high or low numbers of bristles to reproduce, resulting in bimodel distribution

Directional selection

If selection favours a phenotype at one end of the distribution, favours one’ extreme over the other, population can change such that mean shifts in the favoured direction ex. 100 years of corn breeding, Each year select strains that produce the most or least oil and breed

Evolutionary Response to Selection

How quickly a population responds to selective pressure depends both on h2 and on the amount of variation available in the population

A high h2 but no variation, or a lot of variation but no heritability, will not result in evolutionary change no matter how strong the selective force

No heritability means no change between generations, if no variation no change is possible

S

difference between the mean value of a given trait in successfully reproducing individuals and the mean of all members of that population, including those who don’t reproduce, represents selection differential, the strength of selection pressure, small value if variability is less related to fitness, ex. body size, individuals who deviate from the mean have high reproductive success

R

Population response to selection, population can experience selection for non habitable traits and it will not drive evolution,

Breeders equation

R = h2 x S, used for intermediate levels of heritability

Molecular Data

Helps to trace back traits even without morphological data, but morphological data is more informative of speciation even

Genetic Data Homolog

Is a homologous sequence that is derived from an ancestral sequence, ex. substitution of G —> T (BRCAI gene, breast cancer)

Polymorphism

Multiple forms of a genetic sequence

Coalescence

Merging of a homologous copies of a sequence in a common ancestor, doesn’t mean that the population consisted originally of a single individual organism with that ancestral copy of the sequence, each trait has their own ancestor

Orthologs

Homologous sequences separated by speciation events, occur in different species

Paralogs

Homologous sequences separated by duplication events in same organization, occur within a species

Gene tree

History of a DNA sequence, does not always correspond exactly with that of the species or populations that house the DNA, “Gene trees do not always equal species evolution” because mutations can occur without speciation events and without phenotype differences and many genes do not change in speciation events, sequence change accrues very slowly

Sorting

can have different versions of the sequence to have a pattern different from that of actual speciation

Incomplete Sorting

occurs when a genetic polymorphism persists through several speciation events, the pattern in the retention of alleles may yield a different tree than the true phylogeny of a species, ex. human ancestry with gorillas and chimps (correct species tree has us more closely related to chimps than gorillas, But due to incomplete sorting, some portions of our genomes are more closely related to gorillas than chimps, or equally so)

Molecular phylogenetics Pros and Cons

Uses entire genomes

Pros: identifying molecular character states is easy (with A, C, T or G), allows for uses of 1000s and millions of characters

Cons: restricted to extant taxa, harder to differentiate homoplasy vs homology (independent mutations can result in same change)

Maximum Parsimony

Statistical method of Molecular phylogenetics, draw most parsimonious tree, greater reliability obtained by giving more emphasis to characteristics less likely subjected to homoplasy, requires computer computation

Bootstrapping

Randomly selecting a subset of characters and redo trees by adding a characteristic each run for maximum parsimony trees

Neighbour Joining

Calculates distance between taxa, doesn’t rely on knowing ancestral/derived states of characters, calculates tree starting with most closely related taxa (shortest distance), requires lots of data and computer but less reliable

Maximum Likelihood

Based on prior knowledge of how mutations tend to occur in particular regions of DNA, Researchers first select a maximum likelihood model relevant to the sequences they have (ex. A —> C mutation is more likely than A —> T), algorithm calculates the probability of observing the data set given the tree and the model and the tree is assigned a maximum likelihood value, Requires significant computing power

Bayesian Method

researchers specify a particular statistical model of mutations in sequences, uses inverse probability, based on what has already happened, involves starting with a particular tree shape, seeing what probability it has, tweaking the tree shape, checking the probability, etc. etc. until one maximises the probability of a tree or set of trees, need significant computing power, inversion of Maximum Likelihood

Tetrapod test

Fossils strongly indicate that tetrapods evolved from lobe-finned fish ancestors, Only two extant lobe-finned fish groups: coelacanth and lungfishes, used 251 gene molecular phylogeny to test morphological phylogeny

“Out of Africa” Hypothesis

population-level molecular phylogenetic analysis of relationships among modern humans supports the out-of-Africa hypothesis for the origin of non-African populations, greatest genetic variation amongst native Americans

HIV origin

Molecular phylogenetic analysis indicates that HIV is polyphyletic at two levels

• HIV-1 comes from chimpanzee simian immunodeficiency virus (SIV), and HIV-2 comes from an SIV originally in sooty mangabey

• HIV-1 jumped into humans twice, once directly from chimpanzees, and once from gorillas (which themselves had got SIV from chimps)

Likely entered humans through bushmeat trade o

Motoo Kimura

argued much of the variation observed in genomes was drift rather natural selection, predicted: the rate at which mutations accumulate is constant and predictable, mutation should accumulate more rapidly in areas of genome that don’t influence phenotype (synonymous mutations accumulate more rapidly than non-synonymous)

Neutral Theory

Null hypothesis for natural selection, neutral mutations should accumulate at a roughly regular rate over time, early piece of evidence supporting this was a 1970 study that compared the differences in the cytochrome c gene between pairs of mammalian species, positive relationship between time of divergence and number of number of mutations accumulated

Molecular Clock

Neutral mutations occur at a constant rate, correlated to differences among taxa, can be used to estimate time of divergence among taxa, allow for tree reconstruction with dimension of time and calibration of hypothesized time profile, need to have a calibrated anchor to know when the event started eg. Darwin’s finches probably didn’t diverge before islands form

Molecular Clock cons

Inaccurate when determining relationships between long ago diverged taxa because there can be reversals, or a series of mutations that lead back to the original base pair. Closely related species (=recently diverged) pairs show higher slope of differentiation, As divergence time between pairs increases, slope plateaus, Because sequences differences are saturated, i.e., any new mutation overwrites an old one

Saturation

Recent divergence in molecular clock, linearity, 10-20mya slope plateaus

Universal Molecular clock hypothesis

prediction that rates of sequence evolution should be constant across phyletic lineages, not well supported because some of the factors important in neutral theory (especially generation time) not always known or factored in, ex. Martin & Palumbi (1993) showed that sequence divergence rates were negatively correlated with body size (~generation time) and that metabolic rate also affected divergence rates

Molecular Clock Example

When generation times are very fast, molecular clocks can be used to date even recent events, Mutation rates for HIV are fast and can be readily observed as it moves from individual to individual, In addition, preserved blood samples from a hospital in Kinshasa (DRC) provided a ‘palaeontological’ calibration point for HIV-1, If generation time is fast for the organism of interest (virus, bacteria) can use molecular clocks to determine origins, Using these blood samples, alongside molecular clocks, researchers have been able to estimate that the jump of HIV from chimps to humans occurred sometime between 1883 and 1925, This period corresponded with European colonialization in the Congo (“Scramble for Africa”), leading to an increased bushmeat trade.

How to detect molecular evidence of selection that happened millions of years ago

Mathematically: assume any differences among species in homologous sequences is due to natural selection done by comparing rate of synonymous with non-synonymous at potential site, ex. if assumptions of natural theory are rejected, differences probably due to natural selection

Only drift

non-synonymous equals synonymous

Strong directional selection

change in non-synonymous would be greater than synonymous

Stabilizing selection

number of synonymous would be greater than non-synonymous

Genome Evolution

size of a species’ genome itself can evolve through selection and drift, bacteria with the smallest known genomes are almost all intracellular endosymbionts (Most likely have abandoned genes for functions that their host cell does for them), eukaryotes have a bloated, big genome

Bacteria DNA replication is faster because smaller genome and pseudogenes

measure variation of quantitative traits in natural populations

Morphological changes usually occur over time spans longer than a human lifetime, and except for human induced artificial selection, it was hypothesized that we would not be able to observe such patterns

Survivorship Comparison

compare survival of individuals that differ in trait of interest, measure size of trait (z) before and after selective pressure

j

Variance after selection, if + diversifying selection is occurring and variance increases, if - stabilizing selection is occurring, if 0 no change

If selection is stabilizing or diversifying, then change in range of phenotypic values within a generation can indicate selection on variance

i

[(mean after selection)-(mean before selection)]/square root(variance in that trait), intensity of selection, if values all positive suggests directional selection

Selection Gradient

This is done by measuring the slope, represented by beta, of the the relationship between phenotypic value of a trait and the fitness associated with that phenotype as estimated in a regression

The steeper the slope, the stronger is the relationship between changing the value of a trait and changing fitness

Beta is positive = larger values of fitness

Beta is negative = negative selection, fitness decreases, selection against phenotypic variation

Darwin’s Finches

project on the Medium Ground Finch by Peter and Rosemary Grant (Geospiza fortis), tracked reproductive success and created genealogies for the finches, found beak size and depth was heritable, bigger beaked birds ate caltrop seeds and smaller beaked birds ate spurge seeds. After drought spurge seeds died

Peter and Rosemary Grant Found Using Darwin’s Finches

• natural selection can vary in intensity over time

• Direction of selective pressure can change overtime and time is measurable

• Evolution in morphology can happen quickly in nature

Ecological Character Displacement

Evolution is driven by competition for resources in which a trait in one or both species evolved to reduce overlap in resource use

ex. Large-beaked G. fortis were in competition for large seeds with G. magnirostris, which was much better at cracking them and was a superior competitor for large seeds, fortis beak decreased to survive

Directional Selection Example

Hoeksta Lab’s work on oldfield mice in the Gulf coast of the US, Hoekstra’s light and dark oldfield mice match the backgrounds they are usually found on in the Gulf Coast area of the U.S. To test the idea that this matching is the result of selective pressure from visual predators, researchers made plasticene models that did or did not match soil colour in different areas, found mismatched model mice got more damaged by predators

Crypsis

Camouflage, ex. Hoekstra’s light and dark oldfield mice, molecular analysis suggested 2 independent origins of light color in mice

Disruptive Selection Example

Gall fly female lays eggs in stems of goldenrod plants, Larva causes plant to form a swelling (= gall) and then feeds on tissues inside the gall

Birds eat large galls because it’s easier to see, wasps oviposit better in small gals because it’s easier to puncture, results in stabilizing selection

Disruptive Selection

different selective pressures can push a trait in opposite directions simultaneously

Lack of Predation Pressure Example

Three-spined stickleback fish (Gasterosteus aculeatus) are originally marine, but in many coastal areas around the world have independently invaded fresh water, marine fish have armour (low-eda allele) but freshwater have less because of less predators in freshwater

Molecular Fingerprints of Past Selection Example

Lactose Intolerance, lactase enzyme production turns off in adulthood but about 30% of the adult human population retains the ability to produce lactase into adulthood (this is called lactase persistence), due to a number of different mutations in LCT, domestication of cattle arose independently in Europeans and Africa, loci near LCT gene are inherited together

Selective Sweep

Strong selection on a favourable allele to fixation and becomes the only allele with no chance for recombination

Hitchhiking

Loci on either side of selected allele increase in frequency without selection

Molecular Fingerprints

molecular fingerprint of a previous selective sweep can be visible in a modern genome

Humans as Selective Agents

artificial selection in which humans deliberately selected for variants that we found more useful or more interesting

Inbreeding in ‘purebred’ lines of plants and animals can result in accidental selection of deleterious recessive alleles

Plant Artificial Selection Example

All cruciferous vegetables are the same species, selected plants based on the traits we desire the most – big kernal’s of corn, or big fruity tomatoes

This selection has been strong enough over decades, centuries, and millenia to the point where our domesticated lineages bear little resemblance to their wild ancestors

Animal Artificial Selection Example

Hunting and fishing by humans also selection for certain traits, Many species that are hunted by humans reach maturity sooner now, so they can reproduce before being shot

Animals lose trophies like tusks because hunters hunt for trophies

Because we favor large fish, there is a decline in the physical body size of fish in regions with high fishing pressure from humans

Complex Adaptations

consisting of modifications to more than one part of the genome that have to work in concert to produce the final phenotypic product