February, 2002 Genetics 453 Evolutionary Genetics...
Transcript of February, 2002 Genetics 453 Evolutionary Genetics...
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February, 2002Genetics 453
Evolutionary Genetics
Coalescents
Joe Felsenstein
Department of Genome SciencesUniversity of Washington, Seattle
email: [email protected]
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Cann, R. L., M. Stoneking, and A. C. Wilson. 1987. Mitochondrial DNAand human evolution. Nature 325:a 31-36.
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Time
A random−mating population
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Time
A random−mating population
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Time
A random−mating population
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Time
A random−mating population
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Time
A random−mating population
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Time
A random−mating population
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Time
A random−mating population
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Time
A random−mating population
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Time
A random−mating population
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Time
A random−mating population
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Time
A random−mating population
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Time
A random−mating population
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Time
Genealogy of gene copies, after reordering the copies
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Time
Genealogy of a small sample of genes from the population
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Time
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each gene comes from a random copyin the previous generation
a chance of 1 out of 2N that anotherone comes from the same copy
hence it takes about 2N generations fortwo lineages to coalesce�
under the Wright−Fisher model
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u9u
8u
7u6u
5
u4
u3
u2
Coalescent trees of gene copies within species (Kingman, 1982)Random collision of lineages as go back in time (sans recombination)
Collision is faster the smaller the effective population size
Average time for �
k copies to coalesce to k−1 = k(k−1)
4N�
e
Average time for �
n 1 − 1n ( generations (copies to coalesce = 4N
�
e
Average time for two copies to coalesce = �
generationse2N
In a diploid population of effective population size eN
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Two levels of variability
can reduce variability by looking at(i) more gene copies, or(ii) more loci
(2) Randomness of coalescence of lineages
can reduce variance of
branch by examining more sitesnumber of mutations per site per
affected by the u
(1) Randomness of mutation
Necoalescence times allow estimation of
Neaffected by effective population size
mutation rate
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Coalescent with population size changing through time
During a population bottleneckthere is expected to be aburst of coalescence
Down near the root of the treeeffects of population sizebecome difficult to see
size of population
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Time
population #1 population #2
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Recomb.
A recombining coalescent
Different markers have slightly different coalescent trees
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Africa
Europe Asia
"Out of Africa" hypothesis
(vertical scale is not time or evolutionary change)
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Svante Paabo
Krings, M., H. Geisert, R. W. Schmitz, H. Krainitzki, and S. Paabo.1999. DNA sequence of the mitochondrial hypervariable region II from theneandertal type specimen. Proceedings of the Natonal Academy of SciencesUSA 96: 5581-5585.
Ovchinnikov, I. V., A. Gotherstrom, G. P. Romanova, V. M. Kharitonov, K.Liden, and W. Goodwin. 2000. Molecular analysis of Neanderthal DNA fromthe northern Caucasus. Nature 404: 490-493.
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Tree of gene copies, compared with the phylogeny of the speciesfor the case in which effective population size is small
compared to the number of generations between speciations
The tree of gene copies has topology consistent with the phylogeny
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Tree of gene copies, compared with the phylogeny of the species
compared to the number of generations between speciationsfor the case in which effective population size is large
The tree of gene copies has topology inconsistent with the phylogeny
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Jody Hey Rich Kliman and friend
Kliman, R. M., and J. Hey. 1993. DNA sequence variation at the periodlocus within and among species of the Drosophila melanogaster complex.Genetics 133: 375-87
Hey, J. and R. M. Kliman. 1993. Population genetics and phylogenetics ofDNA sequence variation at multiple loci within the Drosophila melanogasterspecies complex. Molecular Biology Evolution 10: 804-822.
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East Africa
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This freeware-friendly presentation prepared with
• Linux (operating system)
• PDFLaTeX (mathematical typesetting and PDF preparation)
• Idraw (drawing program to modify plots and draw figures)
• Adobe Acrobat Reader (to display the PDF in full-screen mode)
(except that we had to use Microsoft Windows to project this as the Xserver I have in Linux is not too great)