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

Nicholls JA, Pennington RT, Koenen EJ, Hughes CE, Hearn J, Bunnefeld L, Dexter KG, Stone GN, Kidner CA - Front Plant Sci (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Ashworth Labs, Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh Edinburgh, UK ; Royal Botanic Garden Edinburgh Edinburgh, UK.

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.

No MeSH data available.


Majority-rule consensus trees of 22 Inga species based on 183 nuclear loci obtained through targeted enrichment of genomic libraries and next-generation sequencing (A,B), or eight plastid genes and one nuclear gene (ITS) obtained through Sanger sequencing (C,D). (A) Analysis of concatenated next-generation data applying a single substitution model with no molecular clock; (B) majority-rule consensus cladogram of 22 Inga species based on a species tree analysis implemented in ASTRAL. Numbers next to nodes indicate bootstrap support; (C) analysis of concatenated Sanger data with gene-specific substitution models and no molecular clock; (D) species tree analysis of two loci (all plastid data and ITS) with locus-specific substitution models and relaxed clocks. Numbers next to nodes indicate posterior probability support.
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Figure 2: Majority-rule consensus trees of 22 Inga species based on 183 nuclear loci obtained through targeted enrichment of genomic libraries and next-generation sequencing (A,B), or eight plastid genes and one nuclear gene (ITS) obtained through Sanger sequencing (C,D). (A) Analysis of concatenated next-generation data applying a single substitution model with no molecular clock; (B) majority-rule consensus cladogram of 22 Inga species based on a species tree analysis implemented in ASTRAL. Numbers next to nodes indicate bootstrap support; (C) analysis of concatenated Sanger data with gene-specific substitution models and no molecular clock; (D) species tree analysis of two loci (all plastid data and ITS) with locus-specific substitution models and relaxed clocks. Numbers next to nodes indicate posterior probability support.

Mentions: The concatenated analyses produced identical and fully resolved tree topologies in relaxed clock and no-clock models, with posterior probabilities of one for all but two nodes in the no-clock MrBayes analysis (Figure 2A) and all but one node in the relaxed clock BEAST analysis (Supplementary Figure 7). Both types of species tree analyses also produced near-identical tree topologies that were almost fully resolved, albeit with lower support at some nodes (ASTRAL analysis in Figure 2B; *BEAST analysis in Supplementary Figure 8). The species tree approach showed minor but well-supported topological differences within some of the major lineages relative to the concatenation approach. Inga auristellea is sister to I. cylindrica in the species tree analysis, but sister to I. nouragensis in the concatenated analysis. The species tree analysis also fails to resolve relationships among I. edulis, I. setosa, I. sapindoides, and I. thibaudiana. This degree of topological variation is to be expected between analyses with and without explicit incorporation of the gene tree discordance that is likely to be prevalent within the major lineages.


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

Nicholls JA, Pennington RT, Koenen EJ, Hughes CE, Hearn J, Bunnefeld L, Dexter KG, Stone GN, Kidner CA - Front Plant Sci (2015)

Majority-rule consensus trees of 22 Inga species based on 183 nuclear loci obtained through targeted enrichment of genomic libraries and next-generation sequencing (A,B), or eight plastid genes and one nuclear gene (ITS) obtained through Sanger sequencing (C,D). (A) Analysis of concatenated next-generation data applying a single substitution model with no molecular clock; (B) majority-rule consensus cladogram of 22 Inga species based on a species tree analysis implemented in ASTRAL. Numbers next to nodes indicate bootstrap support; (C) analysis of concatenated Sanger data with gene-specific substitution models and no molecular clock; (D) species tree analysis of two loci (all plastid data and ITS) with locus-specific substitution models and relaxed clocks. Numbers next to nodes indicate posterior probability support.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4584976&req=5

Figure 2: Majority-rule consensus trees of 22 Inga species based on 183 nuclear loci obtained through targeted enrichment of genomic libraries and next-generation sequencing (A,B), or eight plastid genes and one nuclear gene (ITS) obtained through Sanger sequencing (C,D). (A) Analysis of concatenated next-generation data applying a single substitution model with no molecular clock; (B) majority-rule consensus cladogram of 22 Inga species based on a species tree analysis implemented in ASTRAL. Numbers next to nodes indicate bootstrap support; (C) analysis of concatenated Sanger data with gene-specific substitution models and no molecular clock; (D) species tree analysis of two loci (all plastid data and ITS) with locus-specific substitution models and relaxed clocks. Numbers next to nodes indicate posterior probability support.
Mentions: The concatenated analyses produced identical and fully resolved tree topologies in relaxed clock and no-clock models, with posterior probabilities of one for all but two nodes in the no-clock MrBayes analysis (Figure 2A) and all but one node in the relaxed clock BEAST analysis (Supplementary Figure 7). Both types of species tree analyses also produced near-identical tree topologies that were almost fully resolved, albeit with lower support at some nodes (ASTRAL analysis in Figure 2B; *BEAST analysis in Supplementary Figure 8). The species tree approach showed minor but well-supported topological differences within some of the major lineages relative to the concatenation approach. Inga auristellea is sister to I. cylindrica in the species tree analysis, but sister to I. nouragensis in the concatenated analysis. The species tree analysis also fails to resolve relationships among I. edulis, I. setosa, I. sapindoides, and I. thibaudiana. This degree of topological variation is to be expected between analyses with and without explicit incorporation of the gene tree discordance that is likely to be prevalent within the major lineages.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Ashworth Labs, Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh Edinburgh, UK ; Royal Botanic Garden Edinburgh Edinburgh, UK.

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.

No MeSH data available.