DOI: 10.5061/dryad.zkh189398
title: Diversification of the orchid genus Tridactyle: origin of endemism on the oceanic islands of São Tomé & Príncipe in the Gulf of Guinea

description: Aim: Oceanic islands have played an important role in our understanding of
 the diversification of organisms, and phylogenetic estimates have been
 used in this context to investigate the origin of island diversity and its
 relationship to the continent. Using a typical orchid genus rich in island
 endemics and with widespread continental relatives, we aim to compare
 alternative hypotheses of diversification with a focus on island endemism.
 Location: Tropical Africa and the Gulf of Guinea Islands of São Tomé
 & Príncipe, Central Africa. Taxon: Tridactyle genus (Orchidaceae).
 Methods: We used genome skimming to sequence the whole chloroplast genome
 and nuclear ribosomal genes from 157 individuals of 34 Tridactyle species
 and 15 individuals of 12 other orchid genera (outgroups) to infer a
 time-calibrated phylogenetic tree of the genus Tridactyle. We also used
 multiple statistical methods to infer the geographic ranges of the
 ancestral nodes from the estimated phylogeny. Alternative hypotheses for
 the origins of endemism on the islands of São Tomé and Príncipe were
 investigated based on the biogeographic reconstruction of the genus.
 Results: The estimated phylogeny of Tridactyle and reconstruction of
 geographic ranges for the ancestral nodes suggested a general history of
 allopatric speciation for the genus, in particular via colonisation of the
 islands of the Gulf of Guinea that induced a long period of geographic
 isolation. The most parsimonious hypothesis to explain island endemism in
 Tridactyle involved 6 independent colonisations of the islands from the
 continent. Main conclusions: In contrast to other cases of oceanic island
 endemism that involved adaptive radiation on an island or within an
 archipelago, endemism in Tridactyle is better explained by multiple
 colonisation events from the continent to São Tomé and Príncipe, with
 subsequent divergences due to geographic isolation but only one potential
 instance of further diversification on the islands.
description: Genome skimming on 157 samples from 34 species of
 <i>Tridactyle </i>(out of 47), sampled across the African
 continent and São Tomé and Príncipe. Most of the samples were obtained
 from fieldwork and the shadehouse network from Central Africa (Stévart,
 2003), from São Tomé, Príncipe, Equatorial Guinea, Guinea Conakry,
 Cameroon, Gabon, Rwanda, Kenya, Tanzania and South Africa. Plants from
 Cameroon and Gabon were grown in shadehouses monitored by our teams in
 Yaoundé (for those collected in Cameroon) and in Libreville, Tchimbélé and
 Sibang (for those collected in Gabon). Herbarium specimens from the Kew
 Botanical Garden collection were sampled, as well as living plants from
 the Botanical Garden of Meise. <br> <br> We conducted separate
 phylogenetic analyses on two separate datasets: one containing all samples
 (157 <em>Tridactyle </em>and 16 outgroups)  and the other
 including a single sample per species (61 samples).<br> <br>
 Alignement of 173 sequences (157 <em>Tridactyle </em>(34 out
 of 47), 4 other <em>Vandeae</em>, 9
 other <em>Epidendroideae</em> and
 3 <em>Orchidoideae</em>). It allowed us to obtain a
 plastid alignment of 162,994 bp, partitionned with IQ-Tree (Chernomor et
 al., 2016; Nguyen et al., 2015) (i.e. 173sequencesChloroPart.nex),
 a ribosomal genome of 7212 bp (i.e. 173sequencesRibo.nex), and a combined
 dataset of both, partitionned with IQ-Tree (i.e.
 173partitionned.nex) Alignement of 61 sequences
 (49 <em>Tridactyle</em>, 3 other <em>Vandeae</em>,
 7 other <em>Epidendroideae</em> and
 2 <em>Orchidoideae</em>). It allowed us to obtain a
 plastid alignment of 162,994 bp, partitionned with
 IQ-Tree (i.e. 61SequencesChloroOK.nex), a ribosomal genome of 7212 bp
 (i.e. 61sequencesRiboOK.nex), and a combined dataset of both, partitionned
 with IQ-Tree (i.e. 61Seq.nex) Chernomor, O.,
 von Haeseler, A., & Minh, B. Q. (2016). Terrace Aware Data
 Structure for Phylogenomic Inference from Supermatrices.
 <i>Systematic Biology</i>, <i>65</i>(6), 997‑1008.
 https://doi.org/10.1093/sysbio/syw037<br> Nguyen, L.-T., Schmidt, H.
 A., von Haeseler, A., & Minh, B. Q. (2015). IQ-TREE : A Fast and
 Effective Stochastic Algorithm for Estimating Maximum-Likelihood
 Phylogenies. <i>Molecular Biology and Evolution</i>,
 <i>32</i>(1), 268‑274.
 https://doi.org/10.1093/molbev/msu300