The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back 40 Myr ago. Recent studies, however, suggest that much of Sulawesi’s fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted diversification, and that much of its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions with genetic and morphometric data sets derived from Sulawesi’s three largest mammals: the Babirusa, Anoa, and Sulawesi warty pig. Our results indicate that although these species most likely colonized the area that is now Sulawesi at different times (14 Myr ago to 2-3 Myr ago), they experienced an almost synchronous expansion from the central part of the island. Geological reconstructions indicate that this area was above sea level for most of the last 4 Myr, unlike most parts of the island. We conclude that emergence of land on Sulawesi (~1–2 Myr) may have allowed species to expand synchronously. Altogether, our results indicate that the establishment of the highly endemic faunal assemblage on Sulawesi was driven by geological events over the last few million years.

Anoa mtDNAFasta files containing Anoa mtDNA dataAnoa_cytb.fastaAnoa microsatelliteTSV files containing Anoa microsatellite dataAnoa_microsat.tsvBabirusa mtDNAFasta files containing Babirusa mtDNA dataBabirusa_dloop.fastaBabirusa microsatelliteTSV files containing Babirusa microsatellite dataBabirusa_microsat.tsvSWP mtDNAFasta files containing SWP mtDNA dataSus_dloop.fastaSWP microsatelliteTSV files containing SWP microsatellite dataSus_microsat.tsvCentroid size of lower second of Babirusa and SWPCentroid size for the lower M2BabSus-lowerM2-CS.NTSShape of lower second molar of Babirusa and SWPShape coordinates after superimposition for the lower M2BabSus-lowerM2-aligned.TPSSample list for second lower molar TPS and NTS filesBabSus-lowerM2-ind.csvShape of third second molar of Babirusa and SWPShape coordinates after superimposition for the lower M3BabSus-lowerM3-aligned.TPSCentroid size of lower third molar of Babirusa and SWPCentroid size for the lower M3BabSus-lowerM3-CS.NTSSample list for third lower molar TPS and NTS filesBabSus-lowerM3-CS-ind.csvTable S1Sample information for all three speciesTable_S1.xlsx