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1/2N
number of y chromosomes in gene pool
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2N
number of genes in gene pool
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3/2N
number of x chromasomes in gene pool
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3N
time to coalesce for x chromosomal sex-linked alleles
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4N
time to coalesce for autosomal alleles
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ALIVE Study
silent versus replacement substitutions aka synonymous versus nonsynonymous in SI in V3 region producing a transitional branch
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Allelic Diversity
comparing allelic frequencies within and between demes
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Ancestral Reconstruction
- infer an ancestral protein that no longer exists based on maximum likelihood and Baysian methods
- can be constructed from amino acids and tested for functionality
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Bottleneck Effect
a large population had one or more generations of small size in the past
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Conservative Selection
DN/DS<1
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Directional Selection
DN/DS>1
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Evolution by Shifting Balance
- interactions between natural selection, genetic drift, and gene flow in a metapopulation, which causes it to explore selective peaks
- drift: shifts average excess of alleles for fitness in a deme
- selection:directs a deme toward a different peak
- gene flow: migrants from deme that reaches highest peak add alleles to neighboring demes to increase metapopulation
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Fisher’s Fundamental Theorem of Natural Selection
- rate of increase in fitness of a population at any time equals its additive genetic variance in fitness at that time in a single locus model
- natural selection is and destroys heritable variance in fitness
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Fitness (W)
- viability, mating success, fecundity
- fertility
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Forces of Evolution
- mutation: causes variance within a population and between populations
- genetic drift: variation between populations increases but is decreased within a population
- gene flow: variation within a population is increase but is decreased between populations
- natural selection:
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Founder Event
- bottleneck coincides with a new geographic settlement
- drastically alters allele frequencies
- change non-additive to additive genetic variance
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Functional Density
proportion of amino acid sites that perform specific functions
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gene flow
movement of genes between demes
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General Functions
charge, isoelectric point, solubility
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Geographic Range Expansion
younger haplotypes can have geographic distributions outside of ranges of ancestral haplotypes
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HIV-1
- evolves a million time faster that nuclear genomes
- retrovirus that first attacks macrophages and later T cells
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Ideal Population
constant size, random mating, poisson fecundity, non-overlapping generations, even sex ratios, no selection
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Inbreeding Effective Size
accumulation of identity by descent
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Isolation by Distance
- Sewall Wright-most geneflow is between neighboring demes
- gametic differences among populations are proportional to geographic distance
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Lemba Sailors
- married Bantu women
- supported by y chromosomal haplotype tree
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m
fraction of a deme that migrates to another one before mating
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Macrophage
white blood cell that attacks virus
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Metapopulation
- large population subdivided geographically into many local demes
- most matings occur within a local population but sometimes individuals mate outside their local deme
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Monomorphic Condition
no broad-sense heritability
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N
time to coalesce for y chromosomal sex-linked alleles
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Ne Effective Population Number
size of ideal population whose rate of random genetic drift equals that of the real population
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Neutral Alleles
- non-Darwinian evolution
- rate of neutral evolution=(rate of mutation)(rate of loss of alleles)
- rate of loss=(100/(% habitat remaining))(# of fragments)
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Polymorphic Condition
broad-sense heritability exists
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Pseudogene
gene that lost function and therefore evolves rapidly because mutations are neutral alleles
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Reduces overall genetic variation
creates linkage disequilibrium
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Salinas, Dominican Republic
founder event turns little girls into boys
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Selective Equilibrium
- no additive variance in fitness
- selection moves a population toward it
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Synonymous
mutation site that does not alter amino acid aka neutral allele
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UEP
time needed for 1% amino acid sequence divergence between homologous proteins
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V3
region in envelope protein gene in HIV-1
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Variance Effective Size
change of allele frequency
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