Abstract Detail

Phylogenomics

Heyduk, Karolina [1], Trapnell, Dorset [1], Leebens-Mack, Jim [1].

Estimating relationships among Sabal species through analysis of gene capture data.

With the increasing availability of high-throughput sequencing, phylogenetic analyses are no longer limited by the use of a few loci. Various biological processes, like deep coalescence and hybridization, can make any two gene trees incongruent, highlighting the need for comprehensive genome-wide phylogenetic analyses. Here, we focus on the phylogenetics of Sabal (Arecaceae), a palm species native to the southeastern US, Caribbean, and Central America. RNA probes were developed and used to enrich DNA samples for putatively low copy nuclear genes and the plastomes of all Sabal species and two outgroup species. Sequence data was generated on an Illumina MiSeq sequencer and target sequences were assembled using custom workflows. Gene trees for 169 nuclear genes were used to estimate species trees in STAR, MP-EST, and BUCKy. The chloroplast genomes showed generally low resolution with regards to species relationships, further emphasizing the need for multi-locus phylogenetics. Estimated species relationships largely reflect biogeographic distributions and to a lesser extent previous morphology-based hypotheses, but interesting exceptions were inferred with high statistical support. Beyond the biological implications, this research validates a high-throughput methodology for generating a large number of genes for coalescence-based phylogenetic analyses.

Broader Impacts:

1 - University of Georgia, Department of Plant Biology, 2502 Miller Plant Sciences Building, Athens, GA, 30602, USA

Keywords:
Phylogenomics
Arecaceae
Deep coalescence.

Presentation Type: Oral Paper:Papers for Topics
Session: 36
Location: Magnolia/Riverside Hilton
Date: Tuesday, July 30th, 2013
Time: 3:30 PM
Number: 36008
Abstract ID:617
Candidate for Awards:Margaret Menzel Award