Chapter 8: The History in Our Genes

genetic hitchhiking

allele increases in frequency because it is physically linked to a positively selected allele at a nearby locus.

selective sweep

strong selection can sweep a favorable allele to fixation within a population so fast that there is little opportunity for recombination. alleles in large stretches of DNA flanking the favorable allele will also reach high frequency.

purifying selection

=negative selection removes deleterious alleles form a population. common form of stabilizing selection

nonsynonymous subsitution

alters the amino acid sequence of a protein. can affect phenotype and more subject to selection.

maximum likelihood

approach used to estimate parameter values for a statistical model. maximum likelihood and the similar Bayesian method are used in phylogeny reconstruction to find the tree topologies that are most likely, given a precise model for molecular evolution and a particular data set.

gene tree

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

neutral evolution

can serve as null model

synapomorphy

derived form of a trait that is shared by a group of related species (that is, one that evolved in the immediate common ancestor of the group and was inherited by all its descendants)

neutral theory of molecular evolution

describes the pattern of nucleotide sequence evolution under the forces of mutation and random genetic drift in the absence of selection. predicts that neutral mutations will yield nucleotide substitutions in a population at a rate equivalent to the rate of mutation, regardless of popn. size as long as mutation rates remain fairly constant thru time, neutral variation should accumulate at a steady rate, generating a molecular signature that can be used to date events in the distant past. positive selection and purifying selection both leave distinctive signatures in nucleotide or aa sequences that can be detected using statistical tests.

Fst outlier method

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

neighbor joining

distance method for reconstructing phylogenies. neighbor joining identifies the tree topology with the shortest possible branch lengths give the data.

statistical models

help scientists sift through volumes of molecular evidence to determine the best hypothesis or hypotheses that explain the data.

phylogenetic trees

hypotheses about the relationships among species or groups of individuals

both ___ and ___ result in gene trees that differ from the true phylogeny of the species

incomplete linage sorting and introgression

statistical methods to resolve data and develop phylogenetic hyptohesiese

maximum parsimony, bootstrapping, distance matrixes, maximum likelihood, Bayesian approaches

molecular clock

method used to determine time based on base pairr substitutions. use the rates of molecular change to deduce the divergence time between linages in a phylogeny for example. they work best when they can be "calibrated" with other markers of time, i.e. fossils. scientists use this to estimate the origin of diseases and major clades.

Introgression

movement of alleles from one species or population to another

nucleotide sequences evolve neutrally in absence of selection as a result of ____ and ___

mutation and random genetic drift human genome shows patterns of neutral evolution

microsatellite

noncoding DNA containing a string of short (1-6 base pair) repeated segments. Number of repetitive segments can be highly polymorphic, and for this reason they are valuable genetic characters for comparing populations and assigning relatedness among individuals (DNA fingerprinting)

introgression

occasionally, gene copies from one species will be introduced into the genome of a second species

incomplete lineage sorting

occurs when a genetic polymorphism persists through several 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 of the species. because alternative alleles sometimes persist side by side for a long time, they may be passed down to daughter species in a fashion that does not reflect the actual branching history of the species (incomplete lineage sorting)

distance-matrix method

procedure for constructing phylogenetic trees by clustering taxa based on proximity between their DNA or protein sequences. these methods place closely related sequences under the same internal branch and they estimate branch lengths from the observed distances between sequences.

coalescence

process in which the genealogy of any pair of homologous alleles merges in a common ancestor. smaller population=faster rate than bigger population

bootstrapping

statistical method that allows for assigning measures of accuracy to sample estimates; scientists use it for estimating the strength of evidence that .a particular node in a phylogeny exists.

Genomics

study of the structure and function of genomes, including mapping genes and DNA sequencing. this discipline unites molecular and cell biology, classical genetics, and computational science.

synonymous substitution

substitution that does not alter the amino acid sequence of a protein. less prone to selection and often free from selection completely

Bayesian methods

tests that are similar to maximum likelihood; they use statistical models to determine the probability of data given an evolutionary model and a phylogenetic tree.

phylogeny of a single segment of DNA may be different from the phylogeny of the species that carry it it

thus use several genes when examining phylogenetic relationships

it is possible to trace the genealogies of genes back thru time, reconstructing when mutations generated new alleles and how these alleles subsequently spread.

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neutral mutations accumulate in a clocklike fashion in genomes

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scientists use coalescence to trace the alleles of a gene shared by all individuals of a population back to a single common ancestor.

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