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Bayesian Markov chain Monte Carlo ph...

Hwang, Dick G.

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Bayesian Markov chain Monte Carlo phylogenetic analysis of mammalian evolution reveals varying substitution patterns along the sequence and across lineages.

Record Type:	Electronic resources : Monograph/item
Title/Author:	Bayesian Markov chain Monte Carlo phylogenetic analysis of mammalian evolution reveals varying substitution patterns along the sequence and across lineages./
Author:	Hwang, Dick G.
Description:	151 p.
Notes:	Source: Dissertation Abstracts International, Volume: 66-07, Section: B, page: 3526.
Contained By:	Dissertation Abstracts International66-07B.
Subject:	Biology, Genetics. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3183370
ISBN:	9780542246203

Bayesian Markov chain Monte Carlo phylogenetic analysis of mammalian evolution reveals varying substitution patterns along the sequence and across lineages.
Hwang, Dick G.

Bayesian Markov chain Monte Carlo phylogenetic analysis of mammalian evolution reveals varying substitution patterns along the sequence and across lineages. - 151 p.

Source: Dissertation Abstracts International, Volume: 66-07, Section: B, page: 3526.

Thesis (Ph.D.)--University of Washington, 2005.

We describe a model of DNA evolution that allows substitution rates at a site to depend on the two flanking nucleotides, the branch of the phylogenetic tree, and the position within the sequence. We develop a Bayesian Markov chain Monte Carlo approach to statistical inference, and apply it to characterize phylogenetic variation in context-dependent substitution patterns in a 1.7-megabase genomic region in a broad sampling of mammalian species. In contrast to other substitution types, CpG transition substitutions have accumulated in a relatively clock-like fashion. More broadly, our results support the notion that context-dependent DNA replication errors, cytosine deamination, and biased gene conversion are major sources of naturally occurring mutations, whose relative contributions have varied in mammalian evolution as a result of changes in generation times, effective population sizes, and recombination rates. We then extend our evolutionary model and inference approach to allow lineage-dependent selection in coding regions and to accommodate variation in substitution rate along the sequence and across the phylogeny. We analyze orthologous mammalian sequences from four distinct genomic regions and find variation in substitution pattern both between regions and locally within a region. Both the pattern and overall rate of substitution varies with G + C content, which may reflect biased gene conversion. We did not uncover consistent evidence of lineage-specific variation in the efficiency of natural selection.

ISBN: 9780542246203Subjects--Topical Terms:

1017730
Biology, Genetics.

Bayesian Markov chain Monte Carlo phylogenetic analysis of mammalian evolution reveals varying substitution patterns along the sequence and across lineages.
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035 $a (UnM)AAI3183370
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100 1 $a Hwang, Dick G. $3 1911838
245 1 0 $a Bayesian Markov chain Monte Carlo phylogenetic analysis of mammalian evolution reveals varying substitution patterns along the sequence and across lineages.
300 $a 151 p.
500 $a Source: Dissertation Abstracts International, Volume: 66-07, Section: B, page: 3526.
500 $a Chair: Phil Green.
502 $a Thesis (Ph.D.)--University of Washington, 2005.
520 $a We describe a model of DNA evolution that allows substitution rates at a site to depend on the two flanking nucleotides, the branch of the phylogenetic tree, and the position within the sequence. We develop a Bayesian Markov chain Monte Carlo approach to statistical inference, and apply it to characterize phylogenetic variation in context-dependent substitution patterns in a 1.7-megabase genomic region in a broad sampling of mammalian species. In contrast to other substitution types, CpG transition substitutions have accumulated in a relatively clock-like fashion. More broadly, our results support the notion that context-dependent DNA replication errors, cytosine deamination, and biased gene conversion are major sources of naturally occurring mutations, whose relative contributions have varied in mammalian evolution as a result of changes in generation times, effective population sizes, and recombination rates. We then extend our evolutionary model and inference approach to allow lineage-dependent selection in coding regions and to accommodate variation in substitution rate along the sequence and across the phylogeny. We analyze orthologous mammalian sequences from four distinct genomic regions and find variation in substitution pattern both between regions and locally within a region. Both the pattern and overall rate of substitution varies with G + C content, which may reflect biased gene conversion. We did not uncover consistent evidence of lineage-specific variation in the efficiency of natural selection.
590 $a School code: 0250.
650 4 $a Biology, Genetics. $3 1017730
650 4 $a Statistics. $3 517247
690 $a 0369
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710 2 0 $a University of Washington. $3 545923
773 0 $t Dissertation Abstracts International $g 66-07B.
790 1 0 $a Green, Phil, $e advisor
790 $a 0250
791 $a Ph.D.
792 $a 2005
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3183370