Unraveling the Phylogenomic Relationships of the Most Diverse African Palm Genus <i>Raphia</i> (Calamoideae, Arecaceae)
Palms are conspicuous floristic elements across the tropics. In continental Africa, even though there are less than 70 documented species, they are omnipresent across the tropical landscape. The genus <i>Raphia</i> has 20 accepted species in Africa and one species endemic to the Neotropi...
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-04-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/9/4/549 |
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| author | Andrew J. Helmstetter Suzanne Mogue Kamga Kevin Bethune Thea Lautenschläger Alexander Zizka Christine D. Bacon Jan J. Wieringa Fred Stauffer Alexandre Antonelli Bonaventure Sonké Thomas L. P. Couvreur |
| author_facet | Andrew J. Helmstetter Suzanne Mogue Kamga Kevin Bethune Thea Lautenschläger Alexander Zizka Christine D. Bacon Jan J. Wieringa Fred Stauffer Alexandre Antonelli Bonaventure Sonké Thomas L. P. Couvreur |
| author_sort | Andrew J. Helmstetter |
| collection | DOAJ |
| description | Palms are conspicuous floristic elements across the tropics. In continental Africa, even though there are less than 70 documented species, they are omnipresent across the tropical landscape. The genus <i>Raphia</i> has 20 accepted species in Africa and one species endemic to the Neotropics. It is the most economically important genus of African palms with most of its species producing food and construction material. <i>Raphia</i> is divided into five sections based on inflorescence morphology. Nevertheless, the taxonomy of <i>Raphia</i> is problematic with no intra-generic phylogenetic study available. We present a phylogenetic study of the genus using a targeted exon capture approach sequencing of 56 individuals representing 18 out of the 21 species. Our results recovered five well supported clades within the genus. Three sections correspond to those based on inflorescence morphology. <i>R. regalis</i> is strongly supported as sister to all other <i>Raphia</i> species and is placed into a newly described section: Erectae. Overall, morphological based identifications agreed well with our phylogenetic analyses, with 12 species recovered as monophyletic based on our sampling. Species delimitation analyses recovered 17 or 23 species depending on the confidence level used. Species delimitation is especially problematic in the Raphiate and Temulentae sections. In addition, our clustering analysis using SNP data suggested that individual clusters matched geographic distribution. The Neotropical species <i>R. taedigera</i> is supported as a distinct species, rejecting the hypothesis of a recent introduction into South America. Our analyses support the hypothesis that the <i>Raphia</i> individuals from Madagascar are potentially a distinct species different from the widely distributed <i>R. farinifera</i>. In conclusion, our results support the infra generic classification of <i>Raphia</i> based on inflorescence morphology, which is shown to be phylogenetically useful. Classification and species delimitation within sections remains problematic even with our phylogenomic approach. Certain widely distributed species could potentially contain cryptic species. More in-depth studies should be undertaken using morphometrics, increased sampling, and more variable markers. Our study provides a robust phylogenomic framework that enables further investigation on the biogeographic history, morphological evolution, and other eco-evolutionary aspects of this charismatic, socially, and economically important palm genus. |
| first_indexed | 2024-03-10T20:17:18Z |
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| id | doaj.art-5cf5c8364159434eaf07c24c1ac1f20e |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-10T20:17:18Z |
| publishDate | 2020-04-01 |
| publisher | MDPI AG |
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| series | Plants |
| spelling | doaj.art-5cf5c8364159434eaf07c24c1ac1f20e2023-11-19T22:28:50ZengMDPI AGPlants2223-77472020-04-019454910.3390/plants9040549Unraveling the Phylogenomic Relationships of the Most Diverse African Palm Genus <i>Raphia</i> (Calamoideae, Arecaceae)Andrew J. Helmstetter0Suzanne Mogue Kamga1Kevin Bethune2Thea Lautenschläger3Alexander Zizka4Christine D. Bacon5Jan J. Wieringa6Fred Stauffer7Alexandre Antonelli8Bonaventure Sonké9Thomas L. P. Couvreur10IRD, DIADE, University Montpellier, 34394 Montpellier, FranceLaboratoire de Botanique systématique et d’Ecologie, Department of Biological Sciences, University of Yaoundé I, Higher Teacher Training College, Yaoundé B.P. 047, CameroonIRD, DIADE, University Montpellier, 34394 Montpellier, FranceInstitute of Botany, Department of Biology, Faculty of Science, Technische Universität Dresden, 01062 Dresden, GermanyGerman Center for Integrative Biodiversity Research (iDiv) Halle-Leipzig-Jena, 04103 Leipzig, GermanyDepartment of Biological and Environmental Sciences and Gothenburg Global Biodiversity Centre, University of Gothenburg, 405 30 Gothenburg, SwedenNaturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The NetherlandsDepartment of Botany and Plant Biology, Conservatory and Botanical Garden of the City of Geneva, University of Geneva, 1205 Geneva, SwitzerlandDepartment of Biological and Environmental Sciences and Gothenburg Global Biodiversity Centre, University of Gothenburg, 405 30 Gothenburg, SwedenLaboratoire de Botanique systématique et d’Ecologie, Department of Biological Sciences, University of Yaoundé I, Higher Teacher Training College, Yaoundé B.P. 047, CameroonIRD, DIADE, University Montpellier, 34394 Montpellier, FrancePalms are conspicuous floristic elements across the tropics. In continental Africa, even though there are less than 70 documented species, they are omnipresent across the tropical landscape. The genus <i>Raphia</i> has 20 accepted species in Africa and one species endemic to the Neotropics. It is the most economically important genus of African palms with most of its species producing food and construction material. <i>Raphia</i> is divided into five sections based on inflorescence morphology. Nevertheless, the taxonomy of <i>Raphia</i> is problematic with no intra-generic phylogenetic study available. We present a phylogenetic study of the genus using a targeted exon capture approach sequencing of 56 individuals representing 18 out of the 21 species. Our results recovered five well supported clades within the genus. Three sections correspond to those based on inflorescence morphology. <i>R. regalis</i> is strongly supported as sister to all other <i>Raphia</i> species and is placed into a newly described section: Erectae. Overall, morphological based identifications agreed well with our phylogenetic analyses, with 12 species recovered as monophyletic based on our sampling. Species delimitation analyses recovered 17 or 23 species depending on the confidence level used. Species delimitation is especially problematic in the Raphiate and Temulentae sections. In addition, our clustering analysis using SNP data suggested that individual clusters matched geographic distribution. The Neotropical species <i>R. taedigera</i> is supported as a distinct species, rejecting the hypothesis of a recent introduction into South America. Our analyses support the hypothesis that the <i>Raphia</i> individuals from Madagascar are potentially a distinct species different from the widely distributed <i>R. farinifera</i>. In conclusion, our results support the infra generic classification of <i>Raphia</i> based on inflorescence morphology, which is shown to be phylogenetically useful. Classification and species delimitation within sections remains problematic even with our phylogenomic approach. Certain widely distributed species could potentially contain cryptic species. More in-depth studies should be undertaken using morphometrics, increased sampling, and more variable markers. Our study provides a robust phylogenomic framework that enables further investigation on the biogeographic history, morphological evolution, and other eco-evolutionary aspects of this charismatic, socially, and economically important palm genus.https://www.mdpi.com/2223-7747/9/4/549AfricaexonsMadagascarrain forestsphylogenomics<i>Raphia</i> |
| spellingShingle | Andrew J. Helmstetter Suzanne Mogue Kamga Kevin Bethune Thea Lautenschläger Alexander Zizka Christine D. Bacon Jan J. Wieringa Fred Stauffer Alexandre Antonelli Bonaventure Sonké Thomas L. P. Couvreur Unraveling the Phylogenomic Relationships of the Most Diverse African Palm Genus <i>Raphia</i> (Calamoideae, Arecaceae) Plants Africa exons Madagascar rain forests phylogenomics <i>Raphia</i> |
| title | Unraveling the Phylogenomic Relationships of the Most Diverse African Palm Genus <i>Raphia</i> (Calamoideae, Arecaceae) |
| title_full | Unraveling the Phylogenomic Relationships of the Most Diverse African Palm Genus <i>Raphia</i> (Calamoideae, Arecaceae) |
| title_fullStr | Unraveling the Phylogenomic Relationships of the Most Diverse African Palm Genus <i>Raphia</i> (Calamoideae, Arecaceae) |
| title_full_unstemmed | Unraveling the Phylogenomic Relationships of the Most Diverse African Palm Genus <i>Raphia</i> (Calamoideae, Arecaceae) |
| title_short | Unraveling the Phylogenomic Relationships of the Most Diverse African Palm Genus <i>Raphia</i> (Calamoideae, Arecaceae) |
| title_sort | unraveling the phylogenomic relationships of the most diverse african palm genus i raphia i calamoideae arecaceae |
| topic | Africa exons Madagascar rain forests phylogenomics <i>Raphia</i> |
| url | https://www.mdpi.com/2223-7747/9/4/549 |
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