DOI: 10.5061/dryad.547d7wm81
title: Molecular phylogenetics of the palm tribe Lepidocaryeae (Calamoideae: Arecaceae) and description of a new species of Mauritiella

description: 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.
description: This repository contains the supplementary material associated
 with the paper <strong>"Molecular Phylogenetics of the Palm
 Tribe Lepidocaryeae (Calamoideae: Arecaceae) and Description of a New
 Species of Mauritiella".</strong> 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
 <em>Mauritiella disticha</em> samples.
 Appendix 7: Dendogram of <em>Mauritiella
 disticha</em> 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
 <em>Mauritiella</em> samples. Supplementary
 figure 5: Fruit and scale size comparison between <em>Mauritiella
 disticha</em> and <em>M. armata</em>.
 Supplementary figure 6: Species distribution of all species
 within Lepidocaryeae inferred from GBIF data.
description: SRR and BioProject information for all samples is available in
 Appendix 1.