ArticleFrontiers in plant science2015
Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae).
Article in Frontiers in plant science, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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49 citing papers in PubMed, 144 citations in OpenAlex.
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- Improved phylogenetic resolution within the Neotropical rainforest genusFrontiers in plant science · 2026Article
- Rampant Reticulation in a Rapid Radiation of Tropical Trees-Insights from Inga (Fabaceae).Systematic biology · 2025Article
- Continuous colonization of the Atlantic coastal rain forests of South America from Amazônia.Proceedings. Biological sciences · 2025Article
- Phylogenomic analysis reveals five independently evolved African forage grass clades in the genus Urochloa.Annals of botany · 2024Article
- Repeated upslope biome shifts in Saxifraga during late-Cenozoic climate cooling.Nature communications · 2024Article
- Advances in Legume Systematics 14. Classification of Caesalpinioideae. Part 2: Higher-level classification.PhytoKeys · 2024Article
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- A target capture approach for phylogenomic analyses at multiple evolutionary timescales in rosewoods (Dalbergia spp.) and the legume family (Fabaceae).Molecular ecology resources · 2022Article
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- Highly Resolved Papilionoid Legume Phylogeny Based on Plastid Phylogenomics.Frontiers in plant science · 2022Article
- Phylogenomic assessment prompts recognition of the Serianthes clade and confirms the monophyly ofPhytoKeys · 2022Article
- Phylogenomic analysis of 997 nuclear genes reveals the need for extensive generic re-delimitation in Caesalpinioideae (Leguminosae).PhytoKeys · 2022Article
- New segregates from the Neotropical genusPhytoKeys · 2022Article
- Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae).Frontiers in plant science · 2022Article
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- Analysis of Paralogs in Target Enrichment Data Pinpoints Multiple Ancient Polyploidy Events in Alchemilla s.l. (Rosaceae).Systematic biology · 2021Article
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
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.
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