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

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.

Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1)

“…Another approach could be to produce a phylogeny with large amounts of data representing multiple independent nuclear loci generated with next-generation sequencing methods. Nicholls et al (2015) showed how such an approach substantially improved phylogenetic resolution and support in the tropical tree genus Inga , for which ITS and plastid phylogenies are largely unresolved. Whatever the origin of Calamagrostis / Deyeuxia , the lack of resolution (short branch lengths) in the phylogenetic trees suggests diversification of species of Calamagrostis / Deyeuxia occurred very rapidly.…”

Macroevolutionary patterns in overexpression of tyrosine: An anti‐herbivore defence in a speciose tropical tree genus, Inga (Fabaceae)

“…Previous phylogenetic work on Inga , using 6,000+ base pairs from seven chloroplast DNA loci and one nuclear locus (nuclear ribosomal internal transcribed spacers), generated through Sanger sequencing, resulted in a poorly resolved phylogeny with multiple polytomies (Dexter et al, ; Kursar et al, ; Richardson et al, ). We therefore employed transcriptome data from three Inga species to design a bait‐capture set that targeted 264 nuclear loci for enrichment from whole‐genome libraries for subsequent sequencing (Nicholls et al, ). A preliminary unpublished maximum‐likelihood analysis of these hybrid‐capture data (over 300,000 base pairs) showed excellent resolution of the Inga phylogeny, with high support for nearly all nodes at all depths within the phylogeny.…”

Molecular ecology studies of species radiations: current research gaps, opportunities and challenges

“…Approaches for sequence capture have been in place for several years now, and currently used methods (either in solution or on arrays) greatly outperform conventional PCR amplicon sequencing in terms of throughput, efficiency and practicability (Mamanova et al 2010;Meyer & Kircher 2010). Thus, sequence capture is rapidly becoming the method of choice for evolutionary genetic studies from the micro-to the macroscale (Lemmon et al 2012;Nadeau et al 2012;Rohland & Reich 2012;Nicholls et al 2015). We expect that targeted resequencing will greatly help students and researchers of species radiations to overcome the challenge of sequencing many individuals, populations and species for fairly large numbers of functionally interesting genome regions.…”

“…Sequence capture has been applied successfully to multispecies settings including radiations (Lemmon et al 2012;Nadeau et al 2012;Nicholls et al 2015), and clever indexing/multiplexing strategies enable standard secondgeneration (e.g. Illumina) sequencing of thousands of samples (Rohland & Reich 2012).…”

“…On the other hand, microevolutionary approaches based on the analytical tools of population genetics have proven to be highly useful for understanding the actual mechanisms acting during population divergence and speciation 'in real time', as exemplified by rapid recent progress in the field of speciation genomics (Smadja & Butlin 2011;The Marie Curie SPECIATION network 2012;Feder et al 2012;Nosil 2012;Seehausen et al 2014). Only recently, connecting these two conceptual worlds within one single convincing study or research programme has come truly within reach for many groups of taxa, thanks mainly to the availability of high-throughput genomic technologies and analytical tools for analysing these novel types of data across the relevant taxonomic, spatial, temporal and hierarchical/organismal scales (The Heliconius Genome Consortium 2012; Brawand et al 2014;Cornetti et al 2015;Lamichhaney et al 2015;Nicholls et al 2015;Charlesworth & Charlesworth 2016;Novikova et al 2016).…”