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Abstract Detail


Robert Eaton, Deren Alexander [1], Park, Brian [2], Spriggs, Elizabeth L. [3], Donoghue, Michael [4].

Shape and scale in RAD-seq phylogenomics: Approaches for inferring trees for hundreds of taxa and millions of SNPs.

Restriction-site associated DNA sequencing (RAD-seq) methods can be used to efficiently sample sequence data for many individuals and species for phylogenetics. However, as the size of these data sets grows, both in terms of the number of species (e.g., hundreds) and the number of sites (e.g., millions) they become computationally unfeasible to analyze with many standard phylogenetic methods. As an example, we have assembled a RAD-seq data set for the angiosperm clade Viburnum in which our largest supermatrix is composed of 180 taxa and >35 million base pairs, and includes >3 million parsimony informative SNPs. We compare multiple approaches including concatenation, quartet-based species/super-tree construction, and concordance factor analysis, all of which yield similar results, but with a few pointed differences. Due to the size and structure of RAD-seq data sets we propose that quartet-based methods are particularly promising, and we describe new software and approaches for optimizing this type of analysis for RAD-seq data.

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1 - Yale University, Committee On Evolutionary Biology, 21 Sachem St., New Haven, CT, 06511, USA
2 - Yale University, Ecology and Evolutionary Biology, Environmental Science Center 366, New Haven, CT, 06511, United States
3 - 498 Whitney Ave Apt 1D, New Haven, CT, 06511, USA
4 - Yale University, Department Of Ecology And Evolutionary Biology, 21 Sachem Street, PO BOX 208105, New Haven, CT, 06511, USA


Presentation Type: Oral Paper
Session: 16, Phylogenomics II
Location: 202/Savannah International Trade and Convention Center
Date: Tuesday, August 2nd, 2016
Time: 9:00 AM
Number: 16005
Abstract ID:564
Candidate for Awards:Margaret Menzel Award

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