genetic loci have their

own genealogy

change from G to T represents a

genetic synapomorphy

gene tree

refers to the branched genealogical lineage of homologous alleles that traces their evolution back to an ancestral allele

alleles from different populations or species are used to

construct phylogenies

alleles can be sampled from

different populations or species, revealing their phylogenies over much greater spans of time

gene tree for BRCA1 gene in mammals descending from a

common ancestor approximately 160 millions years ago

coalescent theory

a model of how alleles sampled from a population may have originated from a common ancestor (no recombination, natural selection, nor gene flow or population structure, so each variant is equally like to be passed from one generation to the next) model look backwards in time, merging alleles into.a single ancestral copy according to random process in coalescence events

in coalescent theory model, the expected time between successice coalescnce increases almost

exponentially back in time (with wide variance) and variance comes from random allele passing from one generation to the next and random mutations in the alleles

coalescence time varies for

different genes

tracking phylogenies back in time leads to

nodes in gene trees that represent coalescence, or common ancestry

hypothetical gene tree for BRCA1 shows

the historical relationships among 20 alleles samples from a single population

because diploid individuals have two copies for each gene, ___

studies typically focus on sampled alleles which figures depicts a sample coalescent allele in a constant population

ortholog

is one or more homologous genes separated by a speciation event (e.g. BRCA1 in humans is an ortholog of PIGBRCA1 in swine)

introgression

describes the movement of alleles from one species (due to hybridization) or population to another

sampling the same gene in one individual of each species, we can ____

trace back their genealogies until they coalescence in an ancestral allele

incomplete lineage sorting

occurs when a genetic polymorphism (2+ variant forms of a DNA sequence) persist through multiple speciation events

when fixation of alternative alleles eventually occurs in the descendent species, ___

the pattern of retention of alleles may yield a gene tree that differs from the true phylogeny

correct trees are genrated by

evaluating entire genomes

kronenberg

lined up segments and estimated the divergence of the human segment with that of other species

each nuclotide is a

potentially informative character

homoplasy is common (only 4 possible character states) so ___

the probability that separate lineages independently arrive at the same character state can be high

genes differ in

rate of evolution

slowly evolving genes are useful for

distantly related species (purifying selection)

rapidly evolving genes are useful for

closely related lineages

homoplasy can present a

misleading picture of the parsimonious tree

exon regions

evolve very slowly when they are under strong purifying selection

purifying selection

removes deleterious from a population

introns (non coding region within genes) and intergene regions (region between genes) are

often effectively neutral with respect to selection

introns and intergene regions have

more variable sequences, providing more info to use in building a tree. However, they have more homoplasy due to random convergence of base pairs.

maximum parsimony

simplest explanation favored

bootstrapping

repeated resampling of a subset of the data

assigns measures of accuracy to sample estimates

distance matrix (neighbor joining)

clusters taxa base on genetic distance

maximum likelihood

finds most likely tree given specific model of molecular evolution

bayesian methods

looks at probability that a tree is correct given a specific model of moleculat evolution

distance-matrix method

procedure for constructing phylogen etic trees by clustering taxa based on the proximity between protein or DNA sequences

neighbor joining

distance-matix method that identifies the tree topology with the shortest possible branch lengths

multiregional model (of human origins)

homo sapiens evolved gradually across the entire old world over the last 1 millions years from an older species of hominin

out of africa model (of human origins)

homo sapiens evolved in africa alone; other hominin fossils from the past million years represent extinct brances

examines using microsatellites,

a noncoding stretch of DNA containing a string of short repeated segments

phylogenetic data supports

out of africa model (because humans have been in africa much longer than other parts of the world, africans today are muc more genetically diverse than other humans)

the evolutionary tree of HIV-1 (using maximum-likelihood) shows

the virus jumped hosts multiple times

the evolution of living organisms is the consequence of two processes

-evolution depends on the gentic variability generated by mutation, which continuously arise within population

-it also relies on changes in the frequency of alleles within populations over time

fate of those mutations that affect the fitness of their carrier is partly determined by

natural selection

mutations may have

different effect on fitness

synonymous (silent) mutation

does not alter the amino acid sequence of the protein (changing one of the nucleotides btut not altering sequence)

nonsynonymous mutation

alters the amino acid sequence of the protein (can affect phenotype and thus are more likely to be subject to selection)

positive or directional selection

higher fitness tend to increase in frequency over time until they reach fixation, thus replacing the ancestral allele in the population

negative or purifying selection

new mutations that decrease the carriers fitness tend to disappear from populations through a process

mutation is advantageous only in

heterozygotes but not in homozygotes

balancing selection

alleles tend to be maintained at an intermediate frequency in populations by way of the process

genetic drift

allelic frequencies may change simply as a consequence of this random process of gamete sampling

diff between genetic drift and natural selection is that

changes in allele frequency cause by genetic drift are random rather than directional (genetic drift leads to the fixation of some allele and the loss of others)

neutral theory of molecular evolution

motoo mimura states that most evolution at the molecular level is neutral (due to drift). neutral mutations become fixed in lineages at a regular, clocklike rate (molecular clocks)

neutral evolution

-underlying basis of selection tests

-provide info about molecular processes that are involved in genome functioning

-can ultimately contribute to phenotypic evolution and to species adaptation

distantly related paris of species have a

large number of diff substitutions in the cytochrome c gene

diff types of DNA segments evolve at

different rates

pseudogenes

have a far faster rate of nucleotide substitution than do nonsynonymous (replacement) sites in protein coding genes

sorobey

used early samples of HIV1 from the DCR to calibrate estimates of the rate of molecular evolution of HIV1 (growth of major settlements in central africa coincides with the emergence of HIV1)

alleles can spread quickly through population when subjected to

strong natural selection

selective sweep

adaptive alleles spreads through a population more quickly than recombination acts to separate it from neighboring alleles

genetic hitchhicking

strongly selected alleles are frequently found in a population surrounded by the same set of alleles at neighboring locations

strong natural selection leaves

a signature in neighboring alleles

loci adjacent to the selected allele will be

less variable than expected

lactose intolerance is an example of

genetic hitchhiking

F(ST)

method detects loci with allele frequencies that are more different than expected between populations. these outlier loci are likely to be near to regions of the genome experiencing strong selection

synonymous substitution

do not change protein (should evolce at a neutral rate)

nonsynonymous substitution

change protein

faster evolution than synonymous sites

indicates positive selection

slower evolution than synonymous sites

indicates purifying selection

the number of synonymous substitutions per nonsynonymous site in the pseudogene is

dN

the number of synonymous substitutions per synonymous site is

dS

one sign of positive selection is

the accumulation of an unusually high level of substitutions that can change the structure of proteins

under neutral evolution, we expect that

dN = dS

positive selection produces a gene in which there are more nonsynonymous mutations than would be expected, so

dN > dS

genetic drift results in alleles with synonymous mutations becoming more frequent, so

dS > dN

Genome size

varies tremendously

Bacterial genome size is

dependant mainly on number of genes

eukaryotic genomes vary more in

size due to noncoding DNA

bacterial symbionts often exeprience a

reduction in genome size

different alleles for genes coexists in populations, each with a

lineage that traces their history back through time

gene trees are used to reconstruct the historical relationships among

alleles in populations and species

it is possible to trace gene tree genealogies back in time to

discover when mutations produced new alleles

invomplete lineage sorting and introgression both result in gene trees that

differ from true phylogenies

scientists can test predictions of phylogenetic hypotheses developed with

one line of evidence by using other independent lines of evidence to draw conclusions

neutral mutations accumulate with

clocklike regularity in genomes

molecular clocks can be used to

estimate the origin of diseases and major clades

the neutral theory of molecular evolution describes

patterns of nucleotide substitution predicted under drift alone

neutral theory predicts the

neutral mutations will yield nucleotide substitutions at a rate equivalent to the rate of mutations

neutral variation should

accucmulate in a clocklike fashion

both positive and purifying selections leave

distinctive genetic signatures that can be detected

bacteria usually have small genomes made up if mostly genes, but eukaryotes have

genomes that vary greatly in size

as more genomes are sequenced,

our understanding of genome evolution is changing