Abstract Detail

Phylogenomics

Crowl, Andrew [1], Tiley, George [1], Manos, Paul [1], Sessa, Emily [2], Solis-Lemus, Claudia [3], Yoder, Anne [1], Burleigh, Gordon [4].

Phasing Polyploid Alleles from Target Enrichment Data.

Accurately reconstructing the evolutionary histories of polyploids remains a central challenge for understanding plant evolution. Although phylogenetic networks can provide insights into relationships among polyploid lineages, inferring such networks may be hampered by the complexities of homology determination in polyploid taxa. We present a novel pipeline (PATÉ: Phasing Alleles from Target Enrichment data) that leverages recent advances in phasing algorithms to reliably phase alleles from polyploids. This pipeline is especially appropriate for target enrichment (or HybSeq) data, where depth of coverage is typically high enough to phase entire loci. We use simulations to demonstrate that phasing alleles from allopolyploid individuals can improve inference of phylogenetic networks under the multispecies coalescent. Phased allelic data also improve divergence time estimates for networks, which can be important for interpreting allopolyploid speciation hypotheses and proposing speciation mechanisms.
The phasing pipeline is available at: https://github.com/gtiley/Phasing

Related Links:
Phasing pipeline

1 - Duke University, Department of Biology, Durham, NC, 27708, USA
2 - University Of Florida, Biology, Box 118525, Gainesville, FL, 32611, United States
3 - University of Wisconsin-Madison, Department of Plant Pathology , Madison, WI, 53715, USA
4 - University Of Florida, Department Of Biology, P.O. Box 118526, Gainesville, FL, 32611, United States

Keywords:
Alleles
Hyb-Seq
Target enrichment
Phasing
Polyploids
bioinformatics
hybridization
Phylogenetic Networks.

Presentation Type: Poster
Session: P3, Phylogenomics Posters
Location: Virtual/Virtual
Date: Wednesday, July 21st, 2021
Time: 5:00 PM(EDT)
Number: P3PL024
Abstract ID:1032
Candidate for Awards:None