the analysis of genetic diversity helps us to
understand our evolutionary history
BRCA1 (breast cancer gene 1) and BRCA 2 (breast cancer gene 2) are genes that produce
proteins that help repair damaged DNA (genes are typically italized, while the proteins they produces are not)
BCRA1 and BRCA2 are sometimes called
tumor suppressor genes because when they have certin changes, called harmful variants, cancer can develop
phylogenies can be studied at the allele level
not all alleles are continuously transmitted to the next generation
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