TY - JOUR
T1 - Species Delimitation, Phylogenomics, and Biogeography of Sulawesi Flying Lizards
T2 - A Diversification History Complicated by Ancient Hybridization, Cryptic Species, and Arrested Speciation
AU - McGuire, Jimmy A.
AU - Huang, Xiaoting
AU - Reilly, Sean B.
AU - Iskandar, Djoko T.
AU - Wang-Claypool, Cynthia Y.
AU - Werning, Sarah
AU - Chong, Rebecca A.
AU - Lawalata, Shobi Z.S.
AU - Stubbs, Alexander L.
AU - Frederick, Jeffrey H.
AU - Brown, Rafe M.
AU - Evans, Ben J.
AU - Arifin, Umilaela
AU - Riyanto, Awal
AU - Hamidy, Amir
AU - Arida, Evy
AU - Koo, Michelle S.
AU - Supriatna, Jatna
AU - Andayani, Noviar
AU - Hall, Robert
N1 - Funding Information:
This work was supported by the Museum of Vertebrate Zoology, the Department of Integrative Biology at the University of California at Berkeley, and the National Science Foundation (DEB-1258185, DEB-1652988, DEB-1457845, DEB-0640967, DEB-0328700 awarded to J.A.M. and DEB 0640737 issued to RMB). This study utilized the Vincent J. Coates Genomic Sequencing Laboratory at U.C. Berkeley, supported by NIH S10 Instrumentation Grants S10RR029668 and S10RR027303.
Publisher Copyright:
© 2023 The Author(s).
PY - 2023/7
Y1 - 2023/7
N2 - The biota of Sulawesi is noted for its high degree of endemism and for its substantial levels of in situ biological diversification. While the island's long period of isolation and dynamic tectonic history have been implicated as drivers of the regional diversification, this has rarely been tested in the context of an explicit geological framework. Here, we provide a tectonically informed biogeographical framework that we use to explore the diversification history of Sulawesi flying lizards (the Draco lineatus Group), a radiation that is endemic to Sulawesi and its surrounding islands. We employ a framework for inferring cryptic speciation that involves phylogeographic and genetic clustering analyses as a means of identifying potential species followed by population demographic assessment of divergence-timing and rates of bi-directional migration as means of confirming lineage independence (and thus species status). Using this approach, phylogenetic and population genetic analyses of mitochondrial sequence data obtained for 613 samples, a 50-SNP data set for 370 samples, and a 1249-locus exon-capture data set for 106 samples indicate that the current taxonomy substantially understates the true number of Sulawesi Draco species, that both cryptic and arrested speciations have taken place, and that ancient hybridization confounds phylogenetic analyses that do not explicitly account for reticulation. The Draco lineatus Group appears to comprise 15 species - 9 on Sulawesi proper and 6 on peripheral islands. The common ancestor of this group colonized Sulawesi ~11 Ma when proto-Sulawesi was likely composed of two ancestral islands, and began to radiate ~6 Ma as new islands formed and were colonized via overwater dispersal. The enlargement and amalgamation of many of these proto-islands into modern Sulawesi, especially during the past 3 Ma, set in motion dynamic species interactions as once-isolated lineages came into secondary contact, some of which resulted in lineage merger, and others surviving to the present. [Genomics; Indonesia; introgression; mitochondria; phylogenetics; phylogeography; population genetics; reptiles.
AB - The biota of Sulawesi is noted for its high degree of endemism and for its substantial levels of in situ biological diversification. While the island's long period of isolation and dynamic tectonic history have been implicated as drivers of the regional diversification, this has rarely been tested in the context of an explicit geological framework. Here, we provide a tectonically informed biogeographical framework that we use to explore the diversification history of Sulawesi flying lizards (the Draco lineatus Group), a radiation that is endemic to Sulawesi and its surrounding islands. We employ a framework for inferring cryptic speciation that involves phylogeographic and genetic clustering analyses as a means of identifying potential species followed by population demographic assessment of divergence-timing and rates of bi-directional migration as means of confirming lineage independence (and thus species status). Using this approach, phylogenetic and population genetic analyses of mitochondrial sequence data obtained for 613 samples, a 50-SNP data set for 370 samples, and a 1249-locus exon-capture data set for 106 samples indicate that the current taxonomy substantially understates the true number of Sulawesi Draco species, that both cryptic and arrested speciations have taken place, and that ancient hybridization confounds phylogenetic analyses that do not explicitly account for reticulation. The Draco lineatus Group appears to comprise 15 species - 9 on Sulawesi proper and 6 on peripheral islands. The common ancestor of this group colonized Sulawesi ~11 Ma when proto-Sulawesi was likely composed of two ancestral islands, and began to radiate ~6 Ma as new islands formed and were colonized via overwater dispersal. The enlargement and amalgamation of many of these proto-islands into modern Sulawesi, especially during the past 3 Ma, set in motion dynamic species interactions as once-isolated lineages came into secondary contact, some of which resulted in lineage merger, and others surviving to the present. [Genomics; Indonesia; introgression; mitochondria; phylogenetics; phylogeography; population genetics; reptiles.
UR - http://www.scopus.com/inward/record.url?scp=85164530287&partnerID=8YFLogxK
U2 - 10.1093/sysbio/syad020
DO - 10.1093/sysbio/syad020
M3 - Article
C2 - 37074804
AN - SCOPUS:85164530287
SN - 1063-5157
VL - 72
SP - 885
EP - 911
JO - Systematic Biology
JF - Systematic Biology
IS - 4
ER -