Abstract Detail

Exploring the utility and limits of target enrichment methods to study polyploidy and reticulate evolution

Tiley, George [1], Crowl, Andrew [2], Sessa, Emily [3], Burleigh, Gordon [4].

Phasing alleles improves phylogenetic network inference with allopolyploids.

Accurately reconstructing the evolutionary histories of allopolyploids is important for understanding plant speciation mechanisms, systematics, and trait evolution. Phylogenetic networks can resolve these complex relationships; however, polyploids still present practical challenges when assembling loci from target enrichment libraries. We have leveraged recent advances in phasing algorithms to develop a pipeline capable of phasing alleles from polyploid individuals. These applications are especially appropriate for target enrichment data, regardless of probe set, where depth of coverage is typically high enough to phase entire loci. Simulations suggest that phasing alleles from allopolyploid individuals can improve inference of phylogenetic networks under the multispecies coalescent, which can leverage information from multiple alleles per species. We demonstrate how phasing can improve network inference with an empirical target enrichment dataset of Dryopteris species.

1 - Duke University, Biology, 330 Bio Sci Bldg, Durham, NC, 27708, USA
2 - Duke University, Biology, 330 Bio Sci Bldg, Durham, NC, 27708, United States
3 - University Of Florida, Biology, Box 118525, 521A Bartram Hall, Gainesville, FL, 32611, United States
4 - University of Florida, Department of Biology, 876 Newell Drive, Gainesville, Florida, 32611, United States

Keywords:
phasing
polyploidy
Multispecies Coalescent
networks
Dryopteris
Target Enrichment.

Presentation Type: Colloquium Presentations
Session: COL04, Exploring the utility and limits of target enrichment methods to study polyploidy and reticulate evolution
Location: Virtual/Virtual
Date: Tuesday, July 28th, 2020
Time: 10:45 AM
Number: COL04004
Abstract ID:489
Candidate for Awards:None