Abstract Detail

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

Jantzen, Johanna [1], Freitas Oliveira, Ana Luiza [2], Guimaraes, Paulo [3], Soltis, Douglas [4], Soltis, Pamela [5].

Polyploidy complicates resolution of evolutionary relationships in Tibouchina s.s. (Melastomataceae).

Phylogenomic approaches using target enrichment represent vast improvements over phylogenetic analyses based on only a few nuclear or plastid loci. However, polyploidy can present challenges when attempting to use many putatively single-copy nuclear loci obtained via target capture to resolve phylogenies. This issue can be especially problematic when the extent of polyploidy is unknown in the study system, as is the case in Tibouchina s.s. (Melastomataceae). While polyploid series have been documented in closely related taxa, the extent of polyploidy in Tibouchina s.s. is unknown. Target enrichment and sequencing in this clade, targeting 384 putatively single-copy loci for 144 individuals from 35 species, recovered a high proportion of loci with paralogs. Ploidy assessment using both flow cytometry and a sequence-based approach (nQuire) identified several species as polyploid. However, ploidy estimates differed between these two approaches, potentially highlighting some limitations of sequence-based estimates. When used for phylogeny reconstruction, target enrichment loci presented several difficulties. Individual loci failed to resolve relationships among most species due to a lack of informative characters, resulting in challenges with extracting individual orthologs from paralog trees. Where loci were informative, high levels of inter- and intragenic conflict were observed, and the topology of the phylogeny differed slightly when including or excluding the putatively polyploid taxa. The lack of resolution in the phylogeny and the observed conflict are likely the result of both biological and methodological factors, meaning that challenges remain in applying target enrichment methods successfully to resolve relationships within polyploid systems.

1 - University Of Florida, Biology, Dickinson Hall, 1659 Museum Road, Gainesville, FL, 32611, United States
2 - UNESP Rio Claro, Institute of Biosciences, Rio Claro, SP, Brazil
3 - Instituto de Pesquisas Jardim Botanico do Rio de Janeiro, Rio de Janeiro, Brazil
4 - University Of Florida, Florida Museum Of Natural History, Dickinson Hall, Gainesville, FL, 32611, United States
5 - University Of Florida, Florida Museum Of Natural History, Po Box 117800, Gainesville, FL, 32611, United States

Keywords:
polyploidy
Target Enrichment
phylogenomics
Melastomataceae.

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: 10:30 AM
Number: COL04003
Abstract ID:282
Candidate for Awards:George R. Cooley Award