DOI: 10.5061/dryad.rr4xgxd73
title: The evolutionary history of sedges (Cyperaceae) in Madagascar

description: Aim: Madagascar is renowned for its unparalleled biodiversity and
 endemism. With many ecosystems under threat, research is urgently needed
 on its unique plant diversity. This applies both to Madagascar’s forests
 and treeless vegetation types. Sedges (Cyperaceae) are among the top ten
 species-richest angiosperm families in Madagascar (310 native species, 38%
 endemic), of which two thirds occur in open habitats. We aimed to infer
 the evolutionary history of sedges in Madagascar, by estimating the
 number, age and origins of endemic lineages, and how they diversified on
 the island. We tested contrasting hypotheses of (i) few colonisations but
 important in situ radiations against (ii) a high number
 of anagenetic colonisations. Location: Madagascar and the
 surrounding Indian Ocean islands, integrated within a global dataset.
 Taxon: Sedge family Cyperaceae. Methods: We estimated
 time-calibrated molecular phylogenies encompassing a large proportion of
 Madagascar’s known sedge flora (incl. 55% of native species), integrating
 sequence data for 1382 accessions representing almost 25% of the c. 5600
 sedge species worldwide, combined with ancestral area reconstruction,
 diversification analyses and Bayesian stochastic mapping.
 Results: Cyperaceae lineages arrived in Madagascar from c. 40 mya
 with many arriving more recently. About 20 endemic lineages of Cyperaceae
 occur on the island, of which only six encompass more than five species.
 All except one of the endemic lineages that diversified in Madagascar use
 the C3 photosynthetic pathway. The main biogeographical links of
 Madagascar’s sedge flora are to Southern and Tropical Africa. Main
 conclusions: The biogeographical history of Cyperaceae in
 Madagascar is a chronicle of relatively recent multiple in and out
 processes of long-distance dispersal colonisations constrained by
 distance. Also, the Madagascar region is not only a “sink” for immigrant
 taxa, in situ diversification and dispersal to other
 regions also occurred. Some of the most diverse endemic lineages show
 clear adaptation to local environments.
description: <b>Taxon sampling</b> Our total taxon sampling encompasses 1382 accessions, including four species of <i>Juncus</i> (Juncaceae) as outgroup (Table S2). We aimed to sample (1) nearly all Cyperaceae genera, (2) species from the global distribution range of each genus, and (3) as many species as possible native to Madagascar and/or the Madagascar region (Madagascar plus islands from the Western Indian Ocean, i.e. Comoros, Mascarenes and Seychelles). The ingroup sampling includes 185 species (represented by 190 accessions) native to the Madagascar region. Of these, 171 species are native to Madagascar (176 accessions), 42 species (43 accessions) are endemic to Madagascar, and a further 14 species are endemic to the Western Indian Ocean Islands but not native to Madagascar. Our sampling includes 55% of sedge species native to Madagascar. <b>DNA sequence data and phylogenetic analyses</b> A large dataset of two nuclear ribosomal (ETS, ITS) and seven chloroplast markers (<i>matK</i>, <i>ndhF</i>, <i>rbcL</i>, <i>rpl32-trnL</i>, <i>rps16</i>, <i>trnH-psbA</i>, <i>trnL-F</i>) was used to estimate a time-calibrated phylogeny. The dataset included (ETS: 848 accessions, ITS: 1008, <i>matK</i>: 1586, <i>ndhF</i>: 404, <i>rbcL</i>: 737, <i>rpl32-trnL</i>: 171, rps16: 405, <i>trnH-psbA</i>: 156, <i>trnL-F</i>: 181). Gene regions were each aligned independently using Muscle v3.8.31 (Edgar, 2004) and then manually assessed to ensure alignment accuracy. The resulting concatenated supermatrix was analysed using maximum likelihood under the GTRCAT model in RAxML v.8.2.12 (Stamatakis, 2014) as implemented on the CIPRES Scientific Gateway (Miller, Pfeiffer & Schwartz, 2010), following similar Cyperaceae-wide analyses (Spalink et al., 2018; Márquez-Corro, Martín-Bravo, Spalink, Luceño & Escudero, 2019).
description: ETS_Cyperaceae_Madagascar_Final.fasta
 ITS_Cyperaceae_Madagascar_Final.fasta
 matK_Cyperaceae_Madagascar_Final.fasta
 ndhF_Cyperaceae_Madagascar_Final.fasta
 rbcL_Cyperaceae_Madagascar_Final.fasta
 rpl32-trnL_Cyperaceae_Madagascar_Final.fasta
 rps16_Cyperaceae_Madagascar_Final.fasta
 trnH-psbA_Cyperaceae_Madagascar_Final.fasta