DOI: 10.5061/dryad.6q3t1
title: Data from: Phylogeography and diversification history of the day-gecko genus Phelsuma in the Seychelles islands

description: BACKGROUND: Lying in a shallow continental shelf cyclically affected by
 oscillating sea levels since the Miocene, the Seychelles islands are
 particularly interesting for evolutionary studies. Recent molecular
 studies are generating an emerging picture of the origin of its biota, yet
 very little is known regarding their phylogeographic structure or on the
 factors promoting diversification within the archipelago. Here we aimed to
 obtain a detailed depiction of the genetic structure and evolution of one
 of the most widespread vertebrate groups in the archipelago: the
 day-geckos of the genus Phelsuma. In parallel, we aimed to infer
 divergence times between species and subspecies, testing a long-standing
 hypothesis that argues for different time since sympatry between species
 as the cause of their different morphological differentiation across the
 archipelago. RESULTS: Molecular data corroborated the existence of two
 main lineages, corresponding to the two currently recognized species.
 Divergences between species likely date back to the Mio- Pliocene, while
 more recent, Pleistocenic, divergences are suggested within each species.
 Populations from outer islands share mtDNA haplotypes with inner island
 populations, suggesting very recent dispersals (or introductions). We
 found no evidence of current gene flow between species, but results
 pointed to the possibility of gene flow between (now allopatric)
 subspecies. Time estimates suggest a synchronous divergence within each
 species (between island groups). CONCLUSIONS: The geographic patterns of
 genetic variation agree with previous taxonomic subdivisions within each
 species and the origin of outer islands populations is clearly tracked.
 The similar intraspecific divergence time estimates obtained suggest that
 the differential body-size differentiation between species within each
 group of islands may be driven by factors other than character
 displacement proportional to time since sympatry, as previously suggested.
 These factors could include different habitats/resources available within
 each island group, niche differentiation and/or character displacement. We
 also bring again into consideration the hypothesis of body size being
 influenced by the distribution of native vegetation and social systems
 within this group, although it remains to be tested. Our results highlight
 not only the necessity of clarifying the role of ecology and interspecific
 interactions in this group’s morphological diversification and community
 assemblage, but also the importance of co-evolutionary mechanisms and
 their importance for appropriate conservation of island biodiversity.
 Further, we provide a detailed description of the phylogeographic
 structure of these taxa across these islands, which still remain poorly
 characterized in this respect.
description: 1_phelsuma_citb_hapsHaplotype data used for phylogenetic inference from mtDNA (tree from Figure 2)2_phelsuma_variability_estimates_networksfasta-formated data from cytb and nuclear genes (infered phases) used for genetic variability estimates, neutrality tests and haplotype networks. Divided by groups as in Table 1. Non resolved phases (&lt;80PP) are coded as N. "Outer" islands and "migrants" (see ms) are indicated and were not used for variability estimates and neutrality tests. Check file for internal comments.3_IMa2_inputfile_betweenspeciesinput file for Ima2 inference between species4_IMa2_inputfile_Pastriata5_IMa2_inputfile_Psundbergiinput file for Ima2 inference within P. sundbergi6_SBeast_SpeciesTreeDataset_allgenesnexus files used for species-tree inference (subset of individuals of each lineage of each species)