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.

Taxon sampling

Our total taxon sampling encompasses 1382 accessions, including four species of Juncus (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.

DNA sequence data and phylogenetic analyses

A large dataset of two nuclear ribosomal (ETS, ITS) and seven chloroplast markers (matK, ndhF, rbcL, rpl32-trnL, rps16, trnH-psbA, trnL-F) was used to estimate a time-calibrated phylogeny. The dataset included (ETS: 848 accessions, ITS: 1008, matK: 1586, ndhF: 404, rbcL: 737, rpl32-trnL: 171, rps16: 405, trnH-psbA: 156, trnL-F: 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).

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