Genomic resources for the Neotropical tree genus Cedrela (Meliaceae) and its relatives

Finch, Kristen N.; Jones, F. Andrew; Cronn, Richard

doi:10.1186/s12864-018-5382-6

Cited by 18 publications

(26 citation statements)

References 83 publications

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“…Other recent studies have also demonstrated the efficacy of taxon-specific probe sets in resolving species-level relationships from herbarium DNA (Finch et al, 2019;Soto Gomez et al, 2019;White et al, 2019). Whereas Kadlec et al (2017) argued that high sequence variability across angiosperm orders precluded the usefulness of universal probes in resolving species-level relationships, Chau et al (2018) found that general purpose probes can be as effective as taxon-specific ones.…”

Section: Efficacy Of Universal Probesmentioning

confidence: 99%

Reconstructing the Complex Evolutionary History of the Papuasian Schefflera Radiation Through Herbariomics

et al. 2020

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With its large proportion of endemic taxa, complex geological past, and location at the confluence of the highly diverse Malesian and Australian floristic regions, Papuasia-the floristic region comprising the Bismarck Archipelago, New Guinea, and the Solomon Islands-represents an ideal natural experiment in plant biogeography. However, scattered knowledge of its flora and limited representation in herbaria have hindered our understanding of the drivers of its diversity. Focusing on the woody angiosperm genus Schefflera (Araliaceae), we ask whether its morphologically defined infrageneric groupings are monophyletic, when these lineages diverged, and where (within Papuasia or elsewhere) they diversified. To address these questions, we use a high-throughput sequencing approach (Hyb-Seq) which combines target capture (with an angiosperm-wide bait kit targeting 353 single-copy nuclear loci) and genome shotgun sequencing (which allows retrieval of regions in high-copy number, e.g., organellar DNA) of historical herbarium collections. To reconstruct the evolutionary history of the genus we reconstruct molecular phylogenies with Bayesian inference, maximum likelihood, and pseudo-coalescent approaches, and co-estimate divergence times and ancestral areas in a Bayesian framework. We find strong support for most infrageneric morphological groupings, as currently circumscribed, and we show the efficacy of the Angiosperms-353 probe kit in resolving both deep and shallow phylogenetic relationships. We infer a sequence of colonization to explain the present-day distribution of Schefflera in Papuasia: from the Sunda Shelf, Schefflera arrived to the Woodlark plate (presentday eastern New Guinea) in the late Oligocene (when most of New Guinea was submerged) and, subsequently (throughout the Miocene), it migrated westwards (to the Maoke and Bird's Head Plates and thereon) and further diversified, in agreement with previous reconstructions.

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Section: Efficacy Of Universal Probesmentioning

confidence: 99%

Reconstructing the Complex Evolutionary History of the Papuasian Schefflera Radiation Through Herbariomics

et al. 2020

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“…S1) from Peru and surrounding countries. Hybridization capture probes were designed based on gene models of a C. odorata individual originating in Mexico as described in Finch et al (2019). Sequencing yield and depth were assessed using methods previously described (Finch 2018;Finch et al 2019) and included in the Supporting Information for this article (Appendix 1; Table S2) (Finch 2019a, b).…”

Section: Design Panel Sequencingmentioning

confidence: 99%

Predicting the geographic origin of Spanish Cedar (Cedrela odorata L.) based on DNA variation

et al. 2020

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The legality of wood products often depends on their origin, creating a need for forensic tools that verify claims of provenance for wood products. The neotropical tree species Cedrela odorata (Spanish cedar) is economically valuable for its wood and faces threats of overexploitation. We developed a 140 SNP assay for geographic localization of C. odorata specimens. Target capture and short-read sequencing of 46 C. odorata specimens allowed us to identify 140 spatially informative SNPs that differentiate C. odorata specimens by latitude, temperature, and precipitation. We assessed the broad applicability of these SNPs on 356 specimens from eight Cedrela species, three tissue types, and a range of DNA mass inputs. Origin prediction error was evaluated with discrete and continuous spatial assignment methods focusing on C. odorata specimens. Discrete classification with random forests readily differentiated specimens originating in Central America versus South America (5.8% error), while uncertainty increased as specimens were divided into smaller regions. Continuous spatial prediction with SPASIBA showed a median prediction error of 188.7 km. Our results demonstrate that array SNPs and resulting genotypes accurately validate C. odorata geographic origin at the continental scale and show promise for country-level verification, but that finer-scale assignment likely requires denser spatial sampling. Our study underscores the important role of herbaria for developing genomic resources, and joins a growing list of studies that highlight the role of genomic tools for conservation of threatened species.

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“…The increasing availability of genomic and transcriptomic data across the tree of life and the accessibility of pipelines to identify potential orthologs with low or single copy number ( Chamala et al., 2015 ; Faircloth, 2016 ) help support the design of clade-specific bait sets ( e.g. Vatanparast et al., 2018 ; Finch et al., 2019 ; Soto Gomez et al., 2019 ). Larridon et al.…”

Section: Introductionmentioning

confidence: 99%

Unraveling the Spiraling Radiation: A Phylogenomic Analysis of Neotropical Costus L

et al. 2020

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The family of pantropical spiral gingers (Costaceae Nakai; c. 125 spp.) can be used as a model to enhance our understanding of the mechanisms underlying Neotropical diversity. Costaceae has higher taxonomic diversity in South and Central America (c. 72 Neotropical species, c. 30 African, c. 23 Southeast Asian), particularly due to a radiation of Neotropical species of the genus Costus L. (c. 57 spp.). However, a well-supported phylogeny of the Neotropical spiral gingers including thorough sampling of proposed species encompassing their full morphologic and geographic variation is lacking, partly due to poor resolution recovered in previous analyses using a small sampling of loci. Here we use a phylogenomic approach to estimate the phylogeny of a sample of Neotropical Costus species using a targeted enrichment approach. Baits were designed to capture conserved elements' variable at the species level using available genomic sequences of Costus species and relatives. We obtained 832 loci (generating 791,954 aligned base pairs and 31,142 parsimony informative sites) for samples that encompassed the geographical and/or morphological diversity of some recognized species. Higher support values that improve the results of previous studies were obtained when including all the available loci, even those producing unresolved gene trees and having a low proportion of variable sites. Concatenation and coalescent-based species trees methods converge in almost the same topology suggesting a robust estimation of the relationships, even under the high levels of gene tree conflict presented here. The bait set design here presented made inferring a robust phylogeny to test taxonomic hypotheses possible and will improve our understanding of the origins of the charismatic diversity of the Neotropical spiral gingers.

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Genomic resources for the Neotropical tree genus Cedrela (Meliaceae) and its relatives

Cited by 18 publications

References 83 publications

Reconstructing the Complex Evolutionary History of the Papuasian Schefflera Radiation Through Herbariomics

Reconstructing the Complex Evolutionary History of the Papuasian Schefflera Radiation Through Herbariomics

Predicting the geographic origin of Spanish Cedar (Cedrela odorata L.) based on DNA variation

Unraveling the Spiraling Radiation: A Phylogenomic Analysis of Neotropical Costus L

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