Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae).

James A Nicholls,Lynsey Bunnefeld,Kyle G Dexter,R Toby Pennington,Graham N Stone,Colin E Hughes,Jack Hearn,Catherine A Kidner,Erik J M Koenen

doi:10.3389/fpls.2015.00710

James A Nicholls, Lynsey Bunnefeld + Show 7 more

Open Access

https://doi.org/10.3389/fpls.2015.00710

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Abstract

Evolutionary radiations are prominent and pervasive across many plant lineages in diverse geographical and ecological settings; in neotropical rainforests there is growing evidence suggesting that a significant fraction of species richness is the result of recent radiations. Understanding the evolutionary trajectories and mechanisms underlying these radiations demands much greater phylogenetic resolution than is currently available for these groups. The neotropical tree genus Inga (Leguminosae) is a good example, with ~300 extant species and a crown age of 2–10 MY, yet over 6 kb of plastid and nuclear DNA sequence data gives only poor phylogenetic resolution among species. Here we explore the use of larger-scale nuclear gene data obtained though targeted enrichment to increase phylogenetic resolution within Inga. Transcriptome data from three Inga species were used to select 264 nuclear loci for targeted enrichment and sequencing. Following quality control to remove probable paralogs from these sequence data, the final dataset comprised 259,313 bases from 194 loci for 24 accessions representing 22 Inga species and an outgroup (Zygia). Bayesian phylogenies reconstructed using either all loci concatenated or a gene-tree/species-tree approach yielded highly resolved phylogenies. We used coalescent approaches to show that the same targeted enrichment data also have significant power to discriminate among alternative within-species population histories within the widespread species I. umbellifera. In either application, targeted enrichment simplifies the informatics challenge of identifying orthologous loci associated with de novo genome sequencing. We conclude that targeted enrichment provides the large volumes of phylogenetically-informative sequence data required to resolve relationships within recent plant species radiations, both at the species level and for within-species phylogeographic studies.

Highlights

Evolutionary radiations are ubiquitous and prevalent across disparate plant lineages in diverse geographical and ecological settings (Linder, 2008; Bouchenak-Khelladi et al, 2015; Donoghue and Sanderson, 2015; Hughes and Atchison, 2015; Hughes et al, 2015), yet the trajectories of rapid species diversifications through time and space and the mechanisms and evolutionary processes underlying them remain poorly understood
We examine the utility of the resulting datasets in (i) resolving phylogenetic relationships among 22 Inga species, and compare the resulting phylogenetic hypothesis with those obtained from plastid and nuclear loci routinely used for phylogenetics; and (ii) resolving relationships among four geographically diverse populations of a single Inga species, and provide power analyses that explore the numbers of loci required to discriminate between alternative population histories over two contrasting timescales
We have demonstrated the utility of targeted enrichment of nuclear gene sequences for resolving phylogenies of recent plant radiations

Summary

Introduction

Evolutionary radiations are ubiquitous and prevalent across disparate plant lineages in diverse geographical and ecological settings (Linder, 2008; Bouchenak-Khelladi et al, 2015; Donoghue and Sanderson, 2015; Hughes and Atchison, 2015; Hughes et al, 2015), yet the trajectories of rapid species diversifications through time and space and the mechanisms and evolutionary processes underlying them remain poorly understood. We know rather little about the evolutionary diversification of species-rich clades in the hyperdiverse neotropical rain forests Many of these are recent, with extant species dating from the late Miocene (Richardson et al, 2001; Erkens et al, 2007; Särkinen et al, 2007; Koenen et al, 2015), and there are many competing hypotheses, but no consensus, about what has driven rapid species diversification of rain forest clades (Hughes et al, 2013). Lack of resolution remains the hallmark of current phylogenies for the majority of recent plant radiations

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