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Advances in Bayesian Inference for S...

Lee, Hui-Jie.

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Advances in Bayesian Inference for Species Divergence Times.

Record Type:	Electronic resources : Monograph/item
Title/Author:	Advances in Bayesian Inference for Species Divergence Times./
Author:	Lee, Hui-Jie.
Description:	145 p.
Notes:	Source: Dissertation Abstracts International, Volume: 76-04(E), Section: B.
Contained By:	Dissertation Abstracts International76-04B(E).
Subject:	Evolution & development. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3647647
ISBN:	9781321413977

Advances in Bayesian Inference for Species Divergence Times.
Lee, Hui-Jie.

Advances in Bayesian Inference for Species Divergence Times. - 145 p.

Source: Dissertation Abstracts International, Volume: 76-04(E), Section: B.

Thesis (Ph.D.)--North Carolina State University, 2014.

This item must not be sold to any third party vendors.

The amount of sequence divergence depends on the product of the rate of molecular evolution and the time since common ancestry. When only sequence data are available, these rates and times are confounded. Conventionally, rates and times are disentangled by supplementing interspecific sequence information with additional time information (e.g., information from fossils or from "ancient" DNA). Alternative approaches of separating evolutionary rates and divergence times are explored by supplementing interspecific sequence data with information about rates in this dissertation.

ISBN: 9781321413977Subjects--Topical Terms:

3172418
Evolution & development.

Advances in Bayesian Inference for Species Divergence Times.
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020 $a 9781321413977
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035 $a AAI3647647
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100 1 $a Lee, Hui-Jie. $3 3175590
245 1 0 $a Advances in Bayesian Inference for Species Divergence Times.
300 $a 145 p.
500 $a Source: Dissertation Abstracts International, Volume: 76-04(E), Section: B.
500 $a Adviser: Jeffrey Thorne.
502 $a Thesis (Ph.D.)--North Carolina State University, 2014.
506 $a This item must not be sold to any third party vendors.
520 $a The amount of sequence divergence depends on the product of the rate of molecular evolution and the time since common ancestry. When only sequence data are available, these rates and times are confounded. Conventionally, rates and times are disentangled by supplementing interspecific sequence information with additional time information (e.g., information from fossils or from "ancient" DNA). Alternative approaches of separating evolutionary rates and divergence times are explored by supplementing interspecific sequence data with information about rates in this dissertation.
520 $a The possibility of employing mutation data to assist with the inference of divergence times is investigated in Chapter 2. The basic idea is that the rate of selectively neutral molecular evolution equals the mutation rate and, with the advent of high-throughput sequencing, it is becoming increasingly practical to characterize mutation rates and patterns from parento. spring data and/or from mutation accumulation lines. The BEAST (Bayesian Evolutionary Analysis Sampling Trees) software package has been modified so that divergence times can be estimated from interspecific sequence data together with information on mutation that is collected by high-throughout sequencing. The approach can be applied when evolutionary rates are treated as being constant through time and also when the evolutionary rates themselves evolve. This research direction will have particular value when studying parts of the tree of life that have poor fossil records and also when studying how mutation rates evolve. Analytical and asymptotic properties of the mutation model are discussed in Chapter 3, and some of the modeling extensions are described in Chapter 5.
520 $a Because point mutations can arise from a variety of molecular mechanisms, the change in substitution rate over time can differ among substitution types. The molecular clock assumption is relaxed to different degrees for different substitution types in Chapter 4. To quantify the rate variation among substitution types and to improve divergence time estimation, substitution histories of homologous sequences according to their posterior distribution are sampled. These histories allow "substitution lengths" for each combination of branch and substitution type on a phylogenetic tree to be inferred. The degree to which substitution types vary in their tendency to change rates can then be examined. In addition, this information can be used to infer divergence times. A nice feature of the approach is that context-dependent substitution (e.g., CpG hotspots) can be accommodated. In accord with previous findings, there is comparatively little rate variation over time for CpG transitions. Separately considering these relatively clocklike substitutions yields improved divergence time estimates.
590 $a School code: 0155.
650 4 $a Evolution & development. $3 3172418
650 4 $a Statistics. $3 517247
690 $a 0412
690 $a 0463
710 2 $a North Carolina State University. $3 1018772
773 0 $t Dissertation Abstracts International $g 76-04B(E).
790 $a 0155
791 $a Ph.D.
792 $a 2014
793 $a English
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3647647