Phylogenomics, Species Discovery and Integrative Taxonomy in Dalbergia (Fabaceae) Precious Woods from Madagascar

Crameri, Simon

doi:10.3929/ethz-b-000487274

Cited by 4 publications

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“…Work towards a refined taxonomy of Dalbergia species from Madagascar is currently in progress, and has so far led to the description of two new species from northern Madagascar and an emended description for a third species (Wilding et al 2021b), the proposition of required nomenclatural changes and the reinstatement of a previous synonym to species rank (Wilding et al 2021a), and several additional manuscripts in preparation. These taxonomic changes are supported by phylogenomic and population genomic analyses based on more than 600 accessions of Malagasy Dalbergia (Crameri 2020).…”

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confidence: 89%

“…1944), including 11 species that were posthumously described as new (Viguier 1952). Recent collection efforts, integrative analyses, and additional taxonomic work have revealed numerous problems in the application of Bosser and Rabevohitra's species-level taxonomy (Crameri 2020), despite the fact that it is relatively recent. Work towards a refined taxonomy of Dalbergia species from Madagascar is currently in progress, and has so far led to the description of two new species from northern Madagascar and an emended description for a third species (Wilding et al 2021b), the proposition of required nomenclatural changes and the reinstatement of a previous synonym to species rank (Wilding et al 2021a), and several additional manuscripts in preparation.…”

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“…Integrated analyses of genetic, morphometric, and eco-geographic data also confirmed further taxonomic problems, including three polyphyletic species (D. madagascariensis Vatke, D. maritima R.Vig., and D. neoperrieri Bosser & R.Rabev. ), several cases in which apparently widely distributed species are separable into two or more morphologically and eco-geographically distinct entities, at least two cases of synonymy involving species recognized by Bosser and Rabevohitra (1996, 2005, and several potentially new species, specimens of which have questionably been included in known species or collected only recently (Crameri 2020;Madagascar Catalogue 2021). Taken together, these findings suggest that the diversity of Malagasy Dalbergia has been vastly underestimated, and that in reality it is comparable to or more likely exceeds the current number of recognized species in the much larger tropical zones of continental Africa, the Americas, and Southeast Asia, each of which has ca.…”

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“…06 on p. 116 in Crameri 2020). A fourth described rosewood species, D. normandii Bosser & R.Rabev., forms an early-branching group in the Maritima clade (Crameri 2020) and is morphologically clearly distinct from all other Malagasy species by its long, glabrous leaves, few and large leaflets with an acuminate apex, and large flowers (Bosser and Rabevohitra 2002).…”

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Taxonomic Studies on Malagasy Dalbergia (Fabaceae). III. Two New Species from Southeastern Madagascar and an Emended Description of the Rosewood Species Dalbergia maritima

et al. 2022

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Abstract— The Malagasy rosewood species Dalbergia maritima has a long history of unsustainable exploitation for its beautiful, burgundy-colored heartwood. As currently circumscribed, D. maritima has a wide geographic distribution in eastern Madagascar and exhibits significant morphological, ecological, and genetic variation, suggesting it may comprise more than a single entity. Multivariate analyses of leaf, flower, and inflorescence characters as well as eco-geographic features reveal several morphologically well delimited entities with distinct habitat preferences and/or geographic ranges, which are consistent with results from recent phylogenomic and population genomic studies of Malagasy Dalbergia. Based on these findings, we describe and illustrate two new species from southeastern Madagascar comprising material previously assigned to D. maritima, viz. D. pseudomaritima, characterized by paniculate inflorescences and small, broadly elliptic to orbicular, glabrous leaflets, and D. razakamalalae, distinguished by racemose inflorescences with large flowers, and narrowly ovate to narrowly elliptic, glabrous leaflets. Dalbergia maritima is consequently re-circumscribed to include only populations from east-central Madagascar, within which we recognize two subspecies, D. maritima subsp. maritima, with glabrous leaves, inflorescence axes, and gynoecia, occurring in littoral forest habitats, and D. maritima subsp. pubescens, with indument on these structures, and growing in evergreen humid forest farther inland. Photos are provided for each taxon, along with line drawings for the two new species. Provisional IUCN Red List assessments indicate that all three species are Endangered, D. maritima and D. razakamalalae mainly because of selective logging for trade in their high-quality heartwood, and D. pseudomaritima primarily because of habitat degradation due to land clearing and fire for subsistence agriculture, which has important implications for their conservation and sustainable management.

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Taxonomic Studies on Malagasy Dalbergia (Fabaceae). III. Two New Species from Southeastern Madagascar and an Emended Description of the Rosewood Species Dalbergia maritima

et al. 2022

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“…There is a shortage of collections and experts focusing on this taxonomically challenging genus, and current treatments heavily rely on leaves and flowers and/or fruits for identification (Bosser & Rabevohitra, 2002;de Carvalho, 1997;Lachenaud, 2016), which are rarely encountered together in the field. As a result, the taxonomy of the genus is in need of extensive revision (Wilding et al, 2021a), which could be supported by phylogenomic analyses targeting the nuclear genome (Crameri, 2020).…”

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A target capture approach for phylogenomic analyses at multiple evolutionary timescales in rosewoods (Dalbergiaspp.) and the legume family (Fabaceae)

Crameri

Fior

Zoller

et al. 2021

Preprint

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Understanding the genetic changes associated with the evolution of biological diversity is of fundamental interest to molecular ecologists. The assessment of genetic variation at hundreds or thousands of unlinked genetic loci forms a sound basis to address questions ranging from micro- to macro-evolutionary timescales, and is now possible thanks to advances in sequencing technology. Major difficulties are associated with i) the lack of genomic resources for many taxa, especially from tropical biodiversity hotspots, ii) scaling the numbers of individuals analyzed and loci sequenced, and iii) building tools for reproducible bioinformatic analyses of such datasets. To address these challenges, we developed a set of target capture probes for phylogenomic studies of the highly diverse, pantropically distributed and economically significant rosewoods (Dalbergia spp.), explored the performance of an overlapping probe set for target capture across the legume family (Fabaceae), and built a general-purpose bioinformatics pipeline. Phylogenomic analyses of Dalbergia species from Madagascar yielded highly resolved and well supported hypotheses of evolutionary relationships. Population genomic analyses identified differences between closely related species and revealed the existence of a potentially new species, suggesting that the diversity of Malagasy Dalbergia species has been underestimated. Analyses at the family level corroborated previous findings by the recovery of monophyletic subfamilies and many well-known clades, as well as high levels of gene tree discordance, especially near the root of the family. The new genomic and bioinformatics resources will hopefully advance systematics and ecological genetics research in legumes, and promote conservation of the highly diverse and endangered Dalbergia rosewoods.

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A target capture approach for phylogenomic analyses at multiple evolutionary timescales in rosewoods (Dalbergia spp.) and the legume family (Fabaceae)

Crameri

Fior

Zoller

et al. 2022

Molecular Ecology Resources

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Understanding the genetic changes associated with the evolution of biological diversity is of fundamental interest to molecular ecologists. The assessment of genetic variation at hundreds or thousands of unlinked genetic loci forms a sound basis to address questions ranging from micro‐ to macroevolutionary timescales, and is now possible thanks to advances in sequencing technology. Major difficulties are associated with (i) the lack of genomic resources for many taxa, especially from tropical biodiversity hotspots; (ii) scaling the numbers of individuals analysed and loci sequenced; and (iii) building tools for reproducible bioinformatic analyses of such data sets. To address these challenges, we developed target capture probes for genomic studies of the highly diverse, pantropically distributed and economically significant rosewoods (Dalbergia spp.), explored the performance of an overlapping probe set for target capture across the legume family (Fabaceae), and built the general purpose bioinformatic pipeline CaptureAl. Phylogenomic analyses of Malagasy Dalbergia species yielded highly resolved and well supported hypotheses of evolutionary relationships. Population genomic analyses identified differences between closely related species and revealed the existence of a potentially new species, suggesting that the diversity of Malagasy Dalbergia species has been underestimated. Analyses at the family level corroborated previous findings by the recovery of monophyletic subfamilies and many well‐known clades, as well as high levels of gene tree discordance, especially near the root of the family. The new genomic and bioinformatic resources, including the Fabaceae1005 and Dalbergia2396 probe sets, will hopefully advance systematics and ecological genetics research in legumes, and promote conservation of the highly diverse and endangered Dalbergia rosewoods.

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Phylogenomics, Species Discovery and Integrative Taxonomy in Dalbergia (Fabaceae) Precious Woods from Madagascar

Cited by 4 publications

References 0 publications

Taxonomic Studies on Malagasy Dalbergia (Fabaceae). III. Two New Species from Southeastern Madagascar and an Emended Description of the Rosewood Species Dalbergia maritima

Taxonomic Studies on Malagasy Dalbergia (Fabaceae). III. Two New Species from Southeastern Madagascar and an Emended Description of the Rosewood Species Dalbergia maritima

A target capture approach for phylogenomic analyses at multiple evolutionary timescales in rosewoods (Dalbergiaspp.) and the legume family (Fabaceae)

A target capture approach for phylogenomic analyses at multiple evolutionary timescales in rosewoods (Dalbergia spp.) and the legume family (Fabaceae)

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