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Abstract Detail



Phylogenomics

Blischak, Paul [1], Wolfe, Andrea [2], Kubatko, Laura [3].

Inferring large phylogenies under the coalescent model using SNPs from next-generation sequence data.

Coalescent methods for the inference of species trees from multilocus data have become common tools for phylogeneticists. Typical implementations of the multispecies coalescent involve either estimating a species tree from gene trees (STEM, STEAC, STAR, STELLS) or inferring a species tree directly from sequence data using MCMC (BEST, *BEAST). More recently, methods to estimate species trees from biallelic markers such as SNPs or AFLPs have also been developed (SNAPP). While these programs can often work well for moderately sized data sets, they do not scale easily to data generated by high throughput sequencing technologies. Furthermore, assessments of these methods with simulated and empirical next-generation sequence data have mostly been used to infer species trees for small numbers of taxa (~4-10). Here we explore the utility of a new species tree inference method that uses SNP site patterns to estimate a species tree topology. Though the model is designed for SNP data, it can also estimate a species tree from multilocus data. The basic idea behind the model is to use site patterns of repeatedly sampled, random quartets to infer the species tree. Unlike previous studies of coalescent methods, we also aim to explore the extent to which an approach such as quartet sampling will work for the inference of large (100+ taxa) species trees. Using simulations, we generate sequence data under the coalescent model on a birth-death tree under multiple experimental settings (increasing number of taxa, increasing number of loci, different values of Ne). We also evaluate the method using empirical examples pulled from the literature.


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1 - Ohio State Univeristy, Evolution, Ecology and Organismal Biology, 318 W. 12th Ave., Columbus, OH, 43210, USA
2 - Ohio State University, Department Of Ecology, Evolution, And Organismal Biology, 318 W. 12th Avenue, COLUMBUS, OH, 43210-1293, USA
3 - Ohio State Univeristy, Evolution, Ecology and Organismal Biology; Statistics, 318 W. 12th Avenue, Columbus, OH, 43210, USA

Keywords:
Coalescent
species tree
quartet sampling
next-generation sequencing
simulation.

Presentation Type: Oral Paper:Papers for Topics
Session: 43
Location: Evergreen/Grove
Date: Wednesday, July 30th, 2014
Time: 1:30 PM
Number: 43001
Abstract ID:569
Candidate for Awards:Margaret Menzel Award


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