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  4. Why to account for finite sites in population genetic studies and how to do this with Jaatha 2.0
 
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research article

Why to account for finite sites in population genetic studies and how to do this with Jaatha 2.0

Mathew, Lisha A.
•
Staab, Paul R.
•
Rose, Laura E.
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2013
Ecology And Evolution

With the advent of next-generation sequencing technologies, large data sets of several thousand loci from multiple conspecific individuals are available. Such data sets should make it possible to obtain accurate estimates of population genetic parameters, even for complex models of population history. In the analyses of large data sets, it is difficult to consider finite-sites mutation models (FSMs). Here, we use extensive simulations to demonstrate that the inclusion of FSMs is necessary to avoid severe biases in the estimation of the population mutation rate , population divergence times, and migration rates. We present a new version of Jaatha, an efficient composite-likelihood method for estimating demographic parameters from population genetic data and evaluate the usefulness of Jaatha in two biological examples. For the first application, we infer the speciation process of two wild tomato species, Solanum chilense and Solanum peruvianum. In our second application example, we demonstrate that Jaatha is readily applicable to NGS data by analyzing genome-wide data from two southern European populations of Arabidopsis thaliana. Jaatha is now freely available as an R package from the Comprehensive R Archive Network (CRAN).

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Type
research article
DOI
10.1002/ece3.722
Web of Science ID

WOS:000325486000002

Author(s)
Mathew, Lisha A.
•
Staab, Paul R.
•
Rose, Laura E.
•
Metzler, Dirk
Date Issued

2013

Publisher

Wiley-Blackwell

Published in
Ecology And Evolution
Volume

3

Issue

11

Start page

3647

End page

3662

Subjects

Demography estimation

•

infinite-sites model

•

model violation

•

mutation rate heterogeneity

•

next-generation sequencing

Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
IBI  
GHI  
Available on Infoscience
December 9, 2013
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/97760
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