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Abstract Detail



Phylogenomics

Robert Eaton, Deren Alexander [1], Spriggs, Beth [1], Park, Brian [1], Donoghue, Michael [2].

Optimizing RADseq data for deep-scale phylogenomics: an example from Viburnum (Adoxaceae).

Restriction-site associated DNA sequencing methods (RADseq) were once thought to be limited in phylogenetic utility above the species level, but recent in silico and empirical studies have demonstrated otherwise. We sequenced high-coverage RADseq data for 95 individuals (65 species) of Viburnum with the aim of resolving phylogenetic relationships within both recent radiations and ancient branching events (crown age >50 Ma). Missing data are correlated with phylogenetic distance but, counter-intuitively, we found that this did not disproportionately affect phylogenetic informativeness deeper in the tree. Concatenation, species-tree, and a novel quartet-based supertree method all yielded concordant results, revealing new insights into Viburnum phylogeny at several levels. Within several closely related groups of species our RADseq data provide confident and sensible resolution of relationships, where a 10-gene (mostly cpDNA) dataset has proven to be ineffective. Although our RADseq data strongly supports almost all of the major clades that have recently been recognized within Viburnum, they conflict with previous results placing the Urceolata and Pseudotinus clades together, and in placing the Asian Punctata clade directly with the New World Lentago clade. In both of these cases, the RADseq tree simplifies hypotheses on character evolution. We discuss sampling strategies and phylogenetic inference methods for maximizing phylogenetic informativeness in RADseq phylogenomics.


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1 - Yale University, Ecology and Evolutionary Biology, 21 Sachem St., New Haven, CT, 06511, USA
2 - Yale University, Department Of Ecology And Evolutionary Biology, 21 Sachem Street, PO Box 208105, New Haven, CT, 06511, USA

Keywords:
RADseq
supertree
discordance
Phylogeny
missing data
informativeness.

Presentation Type: Oral Paper:Papers for Topics
Session: 73
Location: Salon 9/The Shaw Conference Centre
Date: Wednesday, July 29th, 2015
Time: 1:30 PM
Number: 73001
Abstract ID:966
Candidate for Awards:Margaret Menzel Award


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