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Using target sequence capture to improve the phylogenetic resolution of a rapid radiation in New Zealand Veronica.

Accepted version
Peer-reviewed

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Type

Article

Change log

Authors

Igea, Javier 
Meudt, Heidi M 
Albach, Dirk C 
Lee, William G 

Abstract

PREMISE: Recent, rapid radiations present a challenge for phylogenetic reconstruction. Fast successive speciation events typically lead to low sequence divergence and poorly resolved relationships with standard phylogenetic markers. Target sequence capture of many independent nuclear loci has the potential to improve phylogenetic resolution for rapid radiations. METHODS: Here we applied target sequence capture with 353 protein-coding genes (Angiosperms353 bait kit) to Veronica sect. Hebe (common name hebe) to determine its utility for improving the phylogenetic resolution of rapid radiations. Veronica section Hebe originated 5-10 million years ago in New Zealand, forming a monophyletic radiation of ca 130 extant species. RESULTS: We obtained approximately 150 kbp of 353 protein-coding exons and an additional 200 kbp of flanking noncoding sequences for each of 77 hebe and two outgroup species. When comparing coding, noncoding, and combined data sets, we found that the latter provided the best overall phylogenetic resolution. While some deep nodes in the radiation remained unresolved, our phylogeny provided broad and often improved support for subclades identified by both morphology and standard markers in previous studies. Gene-tree discordance was nonetheless widespread, indicating that additional methods are needed to disentangle fully the history of the radiation. CONCLUSIONS: Phylogenomic target capture data sets both increase phylogenetic signal and deliver new insights into the complex evolutionary history of rapid radiations as compared with traditional markers. Improving methods to resolve remaining discordance among loci from target sequence capture is now important to facilitate the further study of rapid radiations.

Description

Keywords

Plantaginaceae, discordance, noncoding sequences, phylogenomics, polyploidy, Biological Evolution, Cell Nucleus, New Zealand, Phylogeny, Veronica

Journal Title

Am J Bot

Conference Name

Journal ISSN

0002-9122
1537-2197

Volume Title

108

Publisher

Wiley

Rights

All rights reserved
Sponsorship
Society of Systematic Biology Graduate Research Award Linnean Society of London Systematics Research Fund Gates Cambridge Trust