DOI: 10.5061/dryad.qv9s4mwg2
title: Supplementary information for Paleoceanographic changes in the late Pliocene promoted rapid diversification in pelagic seabirds

description: Aim: Paleoceanographic changes can act as drivers of diversification and
 speciation, even in highly mobile marine organisms. Shearwaters are a
 group of globally distributed and highly mobile pelagic seabirds. Despite
 a recent well resolved phylogeny, shearwaters have controversial species
 limits, and show periods of both slow and rapid diversification. Here, we
 explore the role of paleoceanographic changes on the diversification and
 speciation in these highly mobile pelagic seabirds. We investigate
 shearwater biogeography and the evolution of a key phenotypic trait, body
 size, and we assess the validity of the current taxonomy of the group.
 Location: Worldwide. Taxa: Shearwaters (Order Procellariiformes, Family
 Procellariidae, Genera Ardenna, Calonectris and Puffinus). Methods: We
 generated genomic data (double-digest restriction site-associated DNA) for
 almost all extant shearwater species to infer a time-calibrated species
 tree. We estimated ancestral ranges and evaluated the roles of founder
 events, vicariance and surface ocean currents in driving shearwater
 diversification. We performed phylogenetic generalized least squares to
 identify potential predictors of variability in body size along the
 phylogeny. To assess the validity of the current taxonomy of the group, we
 analysed genomic patterns of recent shared ancestry and differentiation
 among shearwater taxa. Results: We identified a period of high dispersal
 and rapid speciation during the Late Pliocene - early Pleistocene. Species
 dispersal appears to be favoured by surface ocean currents, and
 biogeographic reconstructions support founder events as the main mode of
 speciation in these highly mobile pelagic seabirds. Body mass shows
 significant associations with life strategies and local conditions. The
 current taxonomy shows some incongruences with the patterns of genomic
 divergence. Main Conclusions: A reduction of neritic areas during the
 Pliocene seems to have driven global extinctions of shearwater species,
 followed by a subsequent burst of speciation and dispersal probably
 promoted by Plio-Pleistocene climatic shifts. Our findings extend our
 understanding on the drivers of speciation and dispersal of highly mobile
 pelagic seabirds and shed new light on the important role of
 paleoceanographic events.
description: Blood and tissue samples were collected in the field or from
 museum loans for 26 species of Shearwaters and were sequenced
 for PE-ddRAD-Seq.
description: This repository contains: 1) VCF files used
 for SNAPP analyses (2 files: all SNPs and only transitions;
 Shearwaters_minmac2_snps_filtered.vcf.gz,
 Shearwaters_minmac2_transitions_filtered.vcf.gz) 2) XML
 files used for SNAPP analyses (6 files; snapp_fixtop_root_minmac2.xml,
 snapp_nofixtop_root_minmac2.xml, snapp_fixtop_calibs_root_minmac2.xml,
 snapp_fixtop_root15_minmac2.xml, snapp_fixtop_allSNPs_root_minmac2.xml,
 snapp_fixtop_root_minmac3.xml) 3) Maximum Clade
 Credibility SNAPP trees (6 files; snapp_fixtop_root_minmac2.tree,
 snapp_nofixtop_root_minmac2.tree, snapp_fixtop_calibs_root_minmac2.tree,
 snapp_fixtop_root15_minmac2.tree, snapp_fixtop_allSNPs_root_minmac2.tree,
 snapp_fixtop_root_minmac3.tree) 4) PHYLIP format file
 for COEVOL analysis (Shearwaters_coevol.phy.gz) 5)
 Finestructure input file
 (Shearwaters_finestructure_minmac2.haps_chunks.out)