Abstract Detail

Phylogenomics

Mitchell, Nora [1], Lewis, Paul [2], Lemmon, Emily [3], Lemmon, Alan R. [4], Holsinger, Kent [5].

Seeing the Protea for the (gene) trees: anchored phylogenomics resolves relationships in a rapid radiation.

Estimating phylogenetic relationships in recent evolutionary radiations is challenging, especially if short branches associated with recent divergence are combined with reticulation associated with hybridization. Short branches may lead to poor phylogenetic resolution because there are few changes to reflect shared history, or they may lead to incorrect resolution when gene trees conflict with species trees as a result of incomplete lineage sorting. We combined targeted sequencing with coalescent analyses to produce a robust estimate of phylogenetic relationships in the genus Protea (Proteaceae), a recent iconic radiation in South Africa, and we explore the extent to which poor phylogenetic resolution arises from a lack of shared changes, incomplete lineage sorting, and hybridization. We sampled multiple individuals within 59 species of Protea and six outgroup species for a total of 183 individuals, and we obtained sequences for 498 nuclear loci using “anchored phylogenomics”. We compare several approaches for building species trees, and we explore gene-tree species-tree discrepancies to determine potential causes of poor phylogenetic resolution. Phylogenetic estimates from available species tree approaches are similar to one another and recover previously well-supported clades within Protea, in addition to providing well-supported phylogenetic hypotheses for many intra-generic relationships that were poorly resolved in earlier studies. Species trees constructed with coalescent-based methods are more similar to one another than they are to a tree constructed from concatenated sequences, and individual gene trees are markedly different both from one another and from species trees. Species tree methods using hundreds of nuclear loci provided strong support for many previously unresolved relationships in the rapid radiation at the tips of the angiosperm tree in the genus Protea. In cases where support for particular relationships remains low, the cause appears to be a lack of shared changes rather than strongly supported disagreement among gene trees arising from ILS or hybridization.

1 - University Of Connecticut, Ecology & Evolutionary Biology, 75 North Eagleville Rd, U-3043, Storrs, CT, 06269, USA
2 - University Of Connecticut, Department Of Ecology & Evolutionary Biology, 75 N. Eagleville Road, Unit 43, Storrs, CT, 06269-3043, USA
3 - Florida State University, Department of Biology, 319 Stadium Drive, P.O. Box 3064295, Tallahassee, FL, 32306, USA
4 - Florida State University, Department of Scientific Computing, Dirac Science Library, Tallahassee, FL, 32306, USA
5 - University Of Connecticut, Department Of Ecology & Evolutionary Biology, 75 N. Eagleville Road, U-3043, STORRS, CT, 06269-3043, USA

Keywords:
anchored phylogenomics
Coalescence
phylogenetics
Proteaceae
radiation.

Presentation Type: Oral Paper
Session: 1, Phylogenomics I
Location: 101/Savannah International Trade and Convention Center
Date: Monday, August 1st, 2016
Time: 8:45 AM
Number: 1004
Abstract ID:161
Candidate for Awards:Margaret Menzel Award