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Molecular phylogenetics of the palm tribe Lepidocaryeae (Calamoideae: Arecaceae) and description of a new species of Mauritiella

Citation

Torres Jimenez, Maria Fernanda (2021), Molecular phylogenetics of the palm tribe Lepidocaryeae (Calamoideae: Arecaceae) and description of a new species of Mauritiella, Dryad, Dataset, https://doi.org/10.5061/dryad.547d7wm81

Abstract

English: The palm tribe Lepidocaryeae (Arecaceae) comprises seven genera and 51 currently accepted species that are distributed in lowland tropical forests and savannas across Africa and the Americas. Subtribal relationships within Lepidocaryeae have been a persistent challenge, limiting our understanding of its systematics, morphology, and biogeography. Several aspects make the tribe an ideal system to study plant evolution and diversity: it is well-represented in the fossil record as a prolific pollen producer, its continental diversity contradicts common biodiversity patterns of lower species richness in Africa in comparison to South America, and it contains one of the most abundant Amazonian tree species, Mauritia flexuosa. Here, we investigated the systematics of the tribe by sampling 122 individuals representing 42 species (82% of the tribe), using target sequence capture. We recovered nearly 10,000 single nucleotide polymorphisms from nuclear and plastid DNA across 146 target sequences to separately infer a phylogenomic trees. Our results strongly support inter-generic and inter-specific relationships, where a majority of nodes were resolved with over 90% bootstrap support. We also identify strong phylogenetic support for the recognition of a new species from central and south Amazonia, Mauritiella disticha. The distichous phyllotaxy is diagnostic of the species within the genus. Rare and currently only known from the middle-lower Madeira River basin in the state of Amazonas, Brazil, M. disticha is restricted to open vegetation and forest edges growing in white sand habitats with saturated or well-drained soils. Our preliminary red list assessment suggests its threatened status to be vulnerable (VU). We use our phylogenomic inference to define and contextualize systematic relationships in the tribe, and present a formal species description.

 

Portuguese: As palmeiras Lepidocaryeae compreendem sete gêneros e 51 espécies aceitas actualmente, distribuídas em florestas tropicais de baixa altitude e savanas da África e América do Sul. As relações subtribais têm sido um problema taxonômico persistente no grupo, limitando sua compreensão sistemática, morfológica e biogeográfica. Vários fatores fazem da tribo Lepidocaryeae um sistema ideal para estudos de evolução e diversidade vegetal: a tribo é bem representada no registro fóssil como produtora prolífica de pólen, ela contradiz os padrões de biodiversidade comuns entre a África e a América do Sul e contém uma das espécies amazônicas mais abundantes, Mauritia flexuosa. Aqui, investigamos a sistemática da tribo amostrando 122 indivíduos representando 42 espécies (86% da tribo), usando o método de captura de sequência alvo (target sequence capture). Produzimos aproximadamente 10.000 polimorfismos de nucleotídeo único en 146 genes para inferir árvores filogenômicas. Nossos resultados suportam fortemente as relações intergenéricas e interespecíficas, nas quais a maioria dos nós foi resolvida com mais de 90% de suporte. Também identificamos um forte suporte filogenético para o reconhecimento de uma nova espécie da Amazônia central e sul, Mauritiella disticha. A espécie apresenta filotaxia dística, um caráter diagnóstico da espécie. Atualmente conhecida apenas para a bacia do médio-baixo rio Madeira, no estado do Amazonas, Brasil, M. disticha é restrita à vegetação aberta e bordas de forestas baixas em habitats de areia branca com solos saturados ou bem drenados. Nossa avaliação preliminar indica que esta espécie é vulnerável (VU) em relação ao nível de ameaça. Usamos nossa inferência filogenômica para definir e contextualizar as relações sistemáticas na tribo e apresentamos a descrição formal da nova espécie.

Methods

This repository contains the supplementary material associated with the paper "Molecular Phylogenetics of the Palm Tribe Lepidocaryeae (Calamoideae: Arecaceae) and Description of a New Species of Mauritiella".

Appendix 1: Metadata associated with the samples included in the analyzes.

Appendix 2: List of samples included in the analyzes and the mean read depth.

Appendix 3: Supplementary methods and supplementary figure legends.

Appendix 4: Nexus file with the species tree estimated from SNP data.

Appendix 5: Nexus file with the species tree estimated from IQTREE gene trees and summarized by ASTRAL III

Appendix 6: Geographic distance matrix between Mauritiella disticha samples.

Appendix 7: Dendogram of Mauritiella disticha samples based on geographic distances.

Supplementary figure 1: Species tree estimated from SNPs with UFboot support and voucher annotations.

Supplementary figure 2: Species tree estimated from IQTREE gene trees and summarized by ASTRAL III, with local posterior probabilities and voucher annotations.

Supplementary figure 3: Species tree from ASTRAL with Node ID annotations and support for all three possible topologies at each node across all nodes.

Supplementary figure 4: Weir and Cockerham Fst calculations for variable SNPs within Mauritiella samples.

Supplementary figure 5: Fruit and scale size comparison between Mauritiella disticha and M. armata.

Supplementary figure 6: Species distribution of all species within Lepidocaryeae inferred from GBIF data.

Usage Notes

SRR and BioProject information for all samples is available in Appendix 1.

Funding

Synthesis Centre for Biodiversity Sciences, Award: FZT 118

Agropolis Fondation, Award: ID 1403-026

Agence Nationale de la Recherche, Award: ANR-15- CE02-0002-01

Agence Nationale de la Recherche, Award: ANR-10-LABX001-01

Agropolis Fondation, Award: ANR-16-IDEX-0006

International Palm Society

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior

British Natural Environment Research Council, Award: NE/L002612/1

Brasenose College, Award: Clarendon Fund

Conselho Nacional de Desenvolvimento Científico e Tecnológico

Knut och Alice Wallenbergs Stiftelse

Royal Botanical Gardens, Kew

Biodiversity in a Changing Climate Strategic Research Area

Fundação Grupo O Boticário, Award: 0715_20061

Vetenskapsrådet, Award: 2017-04980

Synthesis Centre for Biodiversity Sciences, Award: FZT 118

International Palm Society

Brasenose College, Award: Clarendon Fund

Biodiversity in a Changing Climate Strategic Research Area

Fundação Grupo O Boticário, Award: 0715_20061