{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,10]],"date-time":"2026-10-10T15:18:19Z","timestamp":1791645499043,"version":"4.3.4"},"reference-count":130,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2021,6,12]],"date-time":"2021-06-12T00:00:00Z","timestamp":1623456000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100009754","name":"Museum of Vertebrate Zoology","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009754","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010948","name":"Department of Integrative Biology at the University of California at Berkeley","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010948","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006363","name":"National Geographic Society","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006363","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DEB-1258185"],"award-info":[{"award-number":["DEB-1258185"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DEB-1652988"],"award-info":[{"award-number":["DEB-1652988"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DEB-1457845"],"award-info":[{"award-number":["DEB-1457845"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,12,16]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The Lesser Sunda Archipelago offers exceptional potential as a model system for studying the dynamics of dispersal-driven diversification. The geographic proximity of the islands suggests the possibility for successful dispersal, but this is countered by the permanence of the marine barriers and extreme intervening currents that are expected to hinder gene flow. Phylogenetic and species delimitation analyses of flying lizards (genus Draco) using single mitochondrial genes, complete mitochondrial genomes, and exome-capture data sets identified 9\u201311 deeply divergent lineages including single-island endemics, lineages that span multiple islands, and parapatrically distributed nonsister lineages on the larger islands. Population clustering and PCA confirmed these genetic boundaries with isolation-by-distance playing a role in some islands or island sets. While gdi estimates place most candidate species comparisons in the ambiguous zone, migration estimates suggest 9 or 10 species exist with nuclear introgression detected across some intra-island contact zones. Initial entry of Draco into the archipelago occurred at 5.5\u20137.5 Ma, with most inter-island colonization events having occurred between 1\u20133 Ma. Biogeographical model testing favors scenarios integrating geographic distance and historical island connectivity, including an initial stepping-stone dispersal process from the Greater Sunda Shelf through the Sunda Arc as far eastward as Lembata Island. However, rather than reaching the adjacent island of Pantar by dispersing over the 15-km wide Alor Strait, Draco ultimately reached Pantar (and much of the rest of the archipelago) by way of a circuitous route involving at least five overwater dispersal events. These findings suggest that historical geological and oceanographic conditions heavily influenced dispersal pathways and gene flow, which in turn drove species formation and shaped species boundaries. [Biogeography; genomics, Indonesia; lizards; phylogeography; reptiles]<\/jats:p>","DOI":"10.1093\/sysbio\/syab043","type":"journal-article","created":{"date-parts":[[2021,6,7]],"date-time":"2021-06-07T19:43:24Z","timestamp":1623095004000},"page":"221-241","source":"Crossref","is-referenced-by-count":21,"title":["Phylogenomic Analysis Reveals Dispersal-Driven Speciation and Divergence with Gene Flow in Lesser Sunda Flying Lizards (Genus <i>Draco<\/i>)"],"prefix":"10.1093","volume":"71","author":[{"given":"Sean B","family":"Reilly","sequence":"first","affiliation":[{"name":"Museum of Vertebrate Zoology and Department of Integrative Biology, University of California , Berkeley, CA 94720, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander L","family":"Stubbs","sequence":"additional","affiliation":[{"name":"Museum of Vertebrate Zoology and Department of Integrative Biology, University of California , Berkeley, CA 94720, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Evy","family":"Arida","sequence":"additional","affiliation":[{"name":"Museum Zoologicum Bogoriense, Indonesian Institute of Sciences , Cibinong, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin R","family":"Karin","sequence":"additional","affiliation":[{"name":"Museum of Vertebrate Zoology and Department of Integrative Biology, University of California , Berkeley, CA 94720, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Umilaela","family":"Arifin","sequence":"additional","affiliation":[{"name":"School of Life Sciences and Technology, Institut Teknologi Bandung , Jalan Ganesha 10, Tamansari, Bandung 40132, Indonesia"},{"name":"Centrum f\u00fcr Naturkunde, Zoologisches Museum Hamburg, Universit\u00e4t Hamburg , Edmund-Siemers-Allee 1, 20146 Hamburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hinrich","family":"Kaiser","sequence":"additional","affiliation":[{"name":"Department of Vertebrate Zoology, Zoologisches Forschungsmuseum Alexander Koenig , Adenauerallee 160, 53113 Bonn, Germany"},{"name":"Department of Biology, Victor Valley College , Victorville, CA 92395, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ke","family":"Bi","sequence":"additional","affiliation":[{"name":"Museum of Vertebrate Zoology and Department of Integrative Biology, University of California , Berkeley, CA 94720, USA"},{"name":"Computational Genomics Resource Laboratory, California Institute for Quantitative Biosciences, University of California , Berkeley, CA 94720, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Djoko T","family":"Iskandar","sequence":"additional","affiliation":[{"name":"Indonesian Academy of Sciences , Jalan Medan Merdeka Selatan No. 11, Jakarta 10110, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jimmy A","family":"McGuire","sequence":"additional","affiliation":[{"name":"Museum of Vertebrate Zoology and Department of Integrative Biology, University of California , Berkeley, CA 94720, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,6,12]]},"reference":[{"key":"2022061600104991700_B1","first-page":"335","article-title":"Population biology of the \u201cflying\u201d lizard, Draco volans, on Negros Island, Philippines","volume":"20","author":"Alcala","year":"1967","journal-title":"Nat. Appl. Sci. Bull."},{"key":"2022061600104991700_B2","doi-asserted-by":"crossref","first-page":"922","DOI":"10.1111\/brv.12683","article-title":"Wallace\u2019s line, Wallacea, and associated divides and areas: history of a tortuous tangle of ideas and labels","volume":"96","author":"Ali","year":"2021","journal-title":"Biol. Rev."},{"key":"2022061600104991700_B3","doi-asserted-by":"crossref","first-page":"2762","DOI":"10.1093\/molbev\/msx197","article-title":"Large variation in the ratio of mitochondrial to nuclear mutation rate across animals: implications for genetic diversity and the use of mitochondrial DNA as a molecular marker","volume":"34","author":"Allio","year":"2017","journal-title":"Mol. Biol. Evol."},{"key":"2022061600104991700_B4","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1144\/SP355.12","article-title":"Tectonic post-collision processes in Timor","volume":"355","author":"Audley-Charles","year":"2011","journal-title":"Geol. Soc. Spec. Publ."},{"key":"2022061600104991700_B5","first-page":"39","article-title":"The herpetofauna of Komodo, with notes on adjacent areas","volume":"25","author":"Auffenberg","year":"1980","journal-title":"Bull. Fla. Mus. Nat. Hist."},{"key":"2022061600104991700_B6","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1186\/1471-2164-13-403","article-title":"Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales","volume":"13","author":"Bi","year":"2012","journal-title":"BMC Genomics"},{"key":"2022061600104991700_B7","doi-asserted-by":"crossref","first-page":"6018","DOI":"10.1111\/mec.12516","article-title":"Unlocking the vault: next-generation museum population genomics","volume":"22","author":"Bi","year":"2013","journal-title":"Mol. Ecol."},{"key":"2022061600104991700_B8","doi-asserted-by":"crossref","first-page":"20160181","DOI":"10.1098\/rspb.2016.0181","article-title":"Convergence across a continent: adaptive diversification in a recent radiation of Australian lizards","volume":"283","author":"Blom","year":"2016","journal-title":"Proc. R. Soc. B."},{"key":"2022061600104991700_B9","doi-asserted-by":"crossref","first-page":"20182575","DOI":"10.1098\/rspb.2018.2575","article-title":"Habitat preference modulates trans-oceanic dispersal in a terrestrial vertebrate","volume":"286","author":"Blom","year":"2019","journal-title":"Proc. R. Soc. B."},{"key":"2022061600104991700_B10","first-page":"311","article-title":"Investigations of recent and fossil coral reefs in eastern Indonesia (Snellius-II Expedition): a preliminary report","volume":"6","author":"Borel-Best","year":"1985","journal-title":"Proc. Fifth Int. Coral Reef Cong."},{"key":"2022061600104991700_B11","doi-asserted-by":"crossref","first-page":"830","DOI":"10.1111\/brv.12256","article-title":"Oceanic island biogeography through the lens of the general dynamic model: assessment and prospect","volume":"92","author":"Borregaard","year":"2017","journal-title":"Biol. Rev."},{"issue":"4","key":"2022061600104991700_B12","doi-asserted-by":"crossref","first-page":"e1003537","DOI":"10.1371\/journal.pcbi.1003537","article-title":"BEAST 2: a software platform for Bayesian evolutionary analysis","volume":"10","author":"Bouckaert","year":"2014","journal-title":"PLOS Comput. Biol."},{"key":"2022061600104991700_B13","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1093\/sysbio\/syq045","article-title":"Accommodating heterogenous rates of evolution in molecular divergence dating methods: an example using intercontinental dispersal of Plestiodon (Eumeces) lizards","volume":"60","author":"Brandley","year":"2011","journal-title":"Syst. Biol."},{"key":"2022061600104991700_B14","doi-asserted-by":"crossref","first-page":"1540","DOI":"10.1111\/j.1365-2699.2009.02098.x","article-title":"Wallacea and its nectarivorous birds: nestedness and modules","volume":"36","author":"Carstensen","year":"2009","journal-title":"J. Biogeogr."},{"key":"2022061600104991700_B15","doi-asserted-by":"crossref","first-page":"739","DOI":"10.1111\/j.1365-2699.2011.02628.x","article-title":"Biogeographical modules and island roles: a comparison of Wallacea and the West Indies","volume":"39","author":"Carstensen","year":"2012","journal-title":"J. Biogeogr."},{"key":"2022061600104991700_B16","doi-asserted-by":"crossref","first-page":"3970","DOI":"10.1111\/mec.15603","article-title":"Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex","volume":"29","author":"Chan","year":"2020","journal-title":"Mol. Ecol."},{"key":"2022061600104991700_B17","volume-title":"Speciation","author":"Coyne","year":"2004"},{"key":"2022061600104991700_B18","volume-title":"Zoogeography: the geographical distribution of animals","author":"Darlington","year":"1957"},{"key":"2022061600104991700_B19","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1038\/nmeth.2109","article-title":"jModelTest 2: more models, new heuristics and parallel computing","volume":"9","author":"Darriba","year":"2012","journal-title":"Nat. Methods"},{"key":"2022061600104991700_B20","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1016\/j.tree.2009.01.009","article-title":"Gene tree discordance, phylogenetic inference and the multispecies coalescent","volume":"24","author":"Degnan","year":"2009","journal-title":"Trends Ecol. Evol."},{"key":"2022061600104991700_B21","doi-asserted-by":"crossref","first-page":"405","DOI":"10.2144\/000113370","article-title":"DIVEIN: a web server to analyze phylogenies, sequence divergence, diversity, and informative sites","volume":"48","author":"Deng","year":"2010","journal-title":"Biotechniques"},{"key":"2022061600104991700_B22","doi-asserted-by":"crossref","first-page":"2239","DOI":"10.1093\/molbev\/msr048","article-title":"Testing for ancient admixture between closely related populations","volume":"28","author":"Durand","year":"2011","journal-title":"Mol. Biol. Evol."},{"key":"2022061600104991700_B23","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1007\/s12686-011-9548-7","article-title":"STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method","volume":"4","author":"Earl","year":"2012","journal-title":"Conserv. Genet. Resour."},{"key":"2022061600104991700_B24","doi-asserted-by":"crossref","first-page":"689","DOI":"10.1093\/sysbio\/syt032","article-title":"Inferring phylogeny and introgression using RADseq data: an example from flowering plants (Pedicularis: Orobanchaceae)","volume":"62","author":"Eaton","year":"2013","journal-title":"Syst. Biol."},{"key":"2022061600104991700_B25","doi-asserted-by":"crossref","first-page":"2587","DOI":"10.1111\/evo.12758","article-title":"Historical introgression among the American live oaks and the comparative nature of tests for introgression","volume":"69","author":"Eaton","year":"2015","journal-title":"Evolution"},{"key":"2022061600104991700_B26","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2022061600104991700_B27","doi-asserted-by":"crossref","first-page":"2611","DOI":"10.1111\/j.1365-294X.2005.02553.x","article-title":"Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study","volume":"14","author":"Evanno","year":"2005","journal-title":"Mol. Ecol."},{"key":"2022061600104991700_B28","doi-asserted-by":"crossref","first-page":"2585","DOI":"10.1093\/molbev\/msy147","article-title":"Species tree inference with BPP using genomic sequences and the multispecies coalescent","volume":"35","author":"Flouri","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"2022061600104991700_B29","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1016\/S1367-9120(97)90107-3","article-title":"Neogene basin history and paleomagnetism of a rifted and inverted forearc region, on-and offshore Sumba, Eastern Indonesia","volume":"15","author":"Fortuin","year":"1997","journal-title":"J. Asian Earth Sci."},{"key":"2022061600104991700_B30","doi-asserted-by":"crossref","first-page":"e1004016","DOI":"10.1371\/journal.pgen.1004016","article-title":"Genome sequencing highlights the dynamic early history of dogs","volume":"10","author":"Freedman","year":"2014","journal-title":"PLoS Genet."},{"key":"2022061600104991700_B31","doi-asserted-by":"crossref","first-page":"480","DOI":"10.1016\/j.tree.2012.04.012","article-title":"Coalescent-based species delimitation in an integrative taxonomy","volume":"27","author":"Fujita","year":"2012","journal-title":"Trends Ecol. Evol."},{"key":"2022061600104991700_B32","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1111\/jbi.13503","article-title":"Extending phylogeography to account for lineage fusion","volume":"46","author":"Garrick","year":"2019","journal-title":"J. Biogeogr."},{"key":"2022061600104991700_B33","doi-asserted-by":"crossref","first-page":"12217","DOI":"10.1029\/95JC03860","article-title":"The effect of the Indonesian throughflow on ocean circulation and heat exchange with the atmosphere: a review","volume":"101","author":"Godfrey","year":"1996","journal-title":"J. Geophys. Res. Oceans"},{"key":"2022061600104991700_B34","volume-title":"Ecology of insular Southeast Asia: the Indonesian archipelago","author":"Goltenboth","year":"2006"},{"key":"2022061600104991700_B35","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1038\/379146a0","article-title":"Pathways of water between the Pacific and Indian oceans in the Indonesian seas","volume":"379","author":"Gordon","year":"1996","journal-title":"Nature"},{"key":"2022061600104991700_B36","doi-asserted-by":"crossref","first-page":"2821","DOI":"10.1098\/rstb.2008.0051","article-title":"Fission and fusion of Darwin\u2019s finches populations","volume":"363","author":"Grant","year":"2008","journal-title":"Philos. Trans. R. Soc. B"},{"key":"2022061600104991700_B37","doi-asserted-by":"crossref","first-page":"710","DOI":"10.1126\/science.1188021","article-title":"A draft sequence of the Neandertal genome","volume":"328","author":"Green","year":"2010","journal-title":"Science"},{"key":"2022061600104991700_B38","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1186\/s12862-016-0611-6","article-title":"The Eurasian invasion: phylogenomic data reveal multiple Southeast Asian origins for Indian Dragon Lizards","volume":"16","author":"Grismer","year":"2016","journal-title":"BMC Evol. Bio."},{"key":"2022061600104991700_B39","doi-asserted-by":"crossref","first-page":"1031","DOI":"10.1038\/ng.937","article-title":"Bayesian inference of ancient human demography from individual genome sequences","volume":"43","author":"Gronau","year":"2011","journal-title":"Nat. Genet."},{"key":"2022061600104991700_B40","doi-asserted-by":"crossref","first-page":"875","DOI":"10.1080\/08120090701392739","article-title":"Carbonate pelagites in the post-Gondwana succession (Cretaceous \u2013 Neogene) of East Timor","volume":"54","author":"Haig","year":"2007","journal-title":"Aust. J. Earth Sci."},{"key":"2022061600104991700_B41","doi-asserted-by":"crossref","first-page":"148","DOI":"10.3767\/000651909X475941","article-title":"Southeast Asia\u2019s changing paleogeography","volume":"54","author":"Hall","year":"2009","journal-title":"Blumea"},{"key":"2022061600104991700_B42","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1144\/SP355.5","article-title":"Australia-SE Asia collision: plate tectonics and crustal flow","volume":"355","author":"Hall","year":"2011","journal-title":"Geol. Soc. Spec. Publ."},{"key":"2022061600104991700_B43","doi-asserted-by":"crossref","first-page":"215e223","DOI":"10.1007\/BF00303634","article-title":"Quaternary uplifted coral reef terraces on Alor Island, East Indonesia","volume":"13","author":"Hantoro","year":"1994","journal-title":"Coral Reefs"},{"key":"2022061600104991700_B44","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1007\/978-3-540-88558-0_7","article-title":"The nature of the Banda arc-continent collision in the Timor region","volume-title":"Arc continent collision","author":"Harris","year":"2011"},{"key":"2022061600104991700_B45","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1007\/BF00142213","article-title":"A synopsis of climatic and vegetational change in Southeast Asia","volume":"19","author":"Heaney","year":"1991","journal-title":"Clim. Change"},{"key":"2022061600104991700_B46","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1670\/18-123","article-title":"Species delimitation in herpetology","volume":"53","author":"Hillis","year":"2019","journal-title":"J. Herpetol."},{"key":"2022061600104991700_B47","first-page":"329","article-title":"Biogeography of the Indonesian archipelago: mitochondrial DNA variation in the fruit bat, Eonycteris spelaea","volume":"65","author":"Hisheh","year":"1998","journal-title":"Biol. J. Linn. Soc."},{"key":"2022061600104991700_B48","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1093\/molbev\/msx281","article-title":"UFBoot2: Improving the ultrafast bootstrap approximation","volume":"35","author":"Hoang","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"2022061600104991700_B49","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1046\/j.1365-2699.1997.00150.x","article-title":"Biogeography of Indonesian snakes","volume":"24","author":"How","year":"1997","journal-title":"J. Biogeogr."},{"key":"2022061600104991700_B50","first-page":"294","article-title":"On the classification and distribution of the Alectoromorphae and Heteromorphae","volume":"1868","author":"Huxley","year":"1868","journal-title":"Proc. Zool. Soc. Lond."},{"key":"2022061600104991700_B51","first-page":"799","article-title":"Species delimitation with gene flow","volume":"66","author":"Jackson","year":"2017","journal-title":"Syst. Biol."},{"key":"2022061600104991700_B52","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1093\/sysbio\/syaa052","article-title":"Defining species when there is gene flow","volume":"70","author":"Jiao","year":"2021","journal-title":"Syst. Biol."},{"key":"2022061600104991700_B53","doi-asserted-by":"crossref","first-page":"1403","DOI":"10.1093\/bioinformatics\/btn129","article-title":"adegenet: a R package for the multivariate analysis of genetic markers","volume":"24","author":"Jombart","year":"2008","journal-title":"Bioinformatics"},{"key":"2022061600104991700_B54","doi-asserted-by":"crossref","first-page":"2206","DOI":"10.1021\/acs.jproteome.9b00077","article-title":"Venom composition in a phenotypically variable pit viper (Trimeresurus insularis) across the Lesser Sunda Archipelago","volume":"18","author":"Jones","year":"2019","journal-title":"J. Proteome Res."},{"key":"2022061600104991700_B55","doi-asserted-by":"crossref","first-page":"1669","DOI":"10.1093\/bioinformatics\/btq243","article-title":"The Newick utilities: high-throughput phylogenetic tree processing in the Unix shell","volume":"26","author":"Junier","year":"2010","journal-title":"Bioinformatics"},{"key":"2022061600104991700_B56","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: Fast model selection for accurate phylogenetic estimates","volume":"14","author":"Kalyaanamoorthy","year":"2017","journal-title":"Nat. Methods"},{"key":"2022061600104991700_B57","doi-asserted-by":"crossref","first-page":"106599","DOI":"10.1016\/j.quascirev.2020.106599","article-title":"Forty-thousand years of specialized maritime subsistence near a changing shoreline on Alor Island (Indonesia)","volume":"249","author":"Kealy","year":"2020","journal-title":"Quat. Sci. Rev."},{"key":"2022061600104991700_B58","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1029\/149GM16","article-title":"Neogene history of the Indonesian throughflow","volume-title":"Continent-ocean interactions within East Asian marginal seas","author":"Kuhnt","year":"2004"},{"key":"2022061600104991700_B59","doi-asserted-by":"crossref","first-page":"818","DOI":"10.1111\/1755-0998.12972","article-title":"Inferring introgression using RADseq and DFOIL: power and pitfalls revealed in a case study of spiny lizards (Sceloporus)","volume":"19","author":"Lambert","year":"2019","journal-title":"Mol. Ecol. Resour."},{"key":"2022061600104991700_B60","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1093\/sysbio\/syy051","article-title":"The spectre of too many species","volume":"68","author":"Leach\u00e9","year":"2019","journal-title":"Syst. Biol."},{"key":"2022061600104991700_B61","doi-asserted-by":"crossref","first-page":"302","DOI":"10.1186\/1471-2148-10-302","article-title":"A maximum pseudo-likelihood approach for estimating species trees under the coalescent model","volume":"10","author":"Liu","year":"2010","journal-title":"BMC Evol. Biol."},{"key":"2022061600104991700_B62","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1146\/annurev-ecolsys-102710-145001","article-title":"Biogeography of the Indo-Australian archipelago","volume":"42","author":"Lohman","year":"2011","journal-title":"Annu. Rev. Ecol. Evol. Syst."},{"key":"2022061600104991700_B63","doi-asserted-by":"crossref","DOI":"10.5962\/bhl.title.31155","volume-title":"A geographical history of mammals","author":"Lydekker","year":"1896"},{"key":"2022061600104991700_B64","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1093\/oxfordjournals.molbev.a025706","article-title":"Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome","volume":"14","author":"Macey","year":"1997","journal-title":"Mol. Biol. Evol."},{"key":"2022061600104991700_B65","doi-asserted-by":"crossref","first-page":"1817","DOI":"10.1101\/gr.159426.113","article-title":"Genome-wide evidence for speciation with gene flow in Heliconius butterflies","volume":"23","author":"Martin","year":"2013","journal-title":"Genome Res."},{"key":"2022061600104991700_B66","author":"Matzke","year":"2013","journal-title":"BioGeoBEARS: BioGeography with Bayesian (and likelihood) evolutionary analysis in R Scripts"},{"key":"2022061600104991700_B67","doi-asserted-by":"crossref","first-page":"951","DOI":"10.1093\/sysbio\/syu056","article-title":"Model selection in historical biogeography reveals that founder-event speciation is a crucial process in island clades","volume":"63","author":"Matzke","year":"2014","journal-title":"Syst. Biol."},{"key":"2022061600104991700_B68","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1086\/394684","article-title":"Wallace\u2019s line in the light of recent zoogeographic studies","volume":"19","author":"Mayr","year":"1944","journal-title":"Q. Rev. Biol."},{"key":"2022061600104991700_B69","doi-asserted-by":"crossref","first-page":"81","DOI":"10.2307\/1467046","article-title":"A taxonomic revision of the flying lizards (Iguania: Agamidae: Draco) of the Philippine Islands, with a description of a new species","volume":"14","author":"McGuire","year":"2000","journal-title":"Herp. Monogr."},{"key":"2022061600104991700_B70","first-page":"203","article-title":"Phylogenetic systematics of Southeast Asian flying lizards (Iguania: Agamidae: Draco) as inferred from mitochondrial DNA sequence data","volume":"72","author":"McGuire","year":"2001","journal-title":"Biol. J. Linn. Soc."},{"key":"2022061600104991700_B71","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1655\/07-012.1","article-title":"The flying lizards of the Draco lineatus group (Squamata: Iguania: Agamidae): a taxonomic revision with descriptions of two new species","volume":"21","author":"McGuire","year":"2007","journal-title":"Herp. Monogr."},{"key":"2022061600104991700_B72","doi-asserted-by":"crossref","first-page":"983","DOI":"10.1093\/icb\/icr090","article-title":"The biology of gliding in flying lizards (Genus Draco) and their fossil and extant analogs","volume":"51","author":"McGuire","year":"2011","journal-title":"Integr. Comp. Biol."},{"key":"2022061600104991700_B73","first-page":"213","article-title":"Variable rates of Late Quaternary surface uplift along the Banda Arc\u2013Australian plate collision zone, eastern Indonesia","volume-title":"Coastal tectonics. Special Publication","author":"Merritts","year":"1998"},{"key":"2022061600104991700_B74","first-page":"115","article-title":"Die amphibien und reptilien der inseln Bali, Lombok, Sumbawa und Flores","volume":"42","author":"Mertens","year":"1930","journal-title":"Abh. Senckenberg. Naturf. Ges."},{"key":"2022061600104991700_B75","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1111\/j.1095-8312.2010.01473.x","article-title":"Biogeology of Wallacea: geotectonic models, areas of endemism, and natural biogeographical units","volume":"101","author":"Michaux","year":"2010","journal-title":"Biol. J. Linn. Soc."},{"key":"2022061600104991700_B76","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era","volume":"37","author":"Minh","year":"2020","journal-title":"Mol. Biol. Evol."},{"key":"2022061600104991700_B77","first-page":"109","article-title":"Uber den Charakter der Thierwelt auf den Inseln des indischen Archipels","volume":"12","author":"Muller","year":"1846","journal-title":"Arch. Naturg."},{"key":"2022061600104991700_B78","doi-asserted-by":"crossref","first-page":"109","DOI":"10.9795\/bullgsj.53.109","article-title":"Tectonic, volcanic and stratiagraphic geology of the Bajawa geothermal field, central Flores, Indonesia","volume":"53","author":"Muraoka","year":"2002","journal-title":"Bull. Geol. Surv. Japan"},{"key":"2022061600104991700_B79","first-page":"1","article-title":"Geology and geothermal systems in the Bajawa volcanic rift zone, Flores, Eastern Indonesia","volume":"2005","author":"Muraoka","year":"2005","journal-title":"Proc. World Geoth. Cong."},{"key":"2022061600104991700_B80","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1007\/s12686-019-01087-x","article-title":"Comp-D: a program for comprehensive computation of D-statistics and population summaries of reticulated evolution","volume":"12","author":"Mussmann","year":"2020","journal-title":"Conserv. Genet. Resour."},{"key":"2022061600104991700_B81","first-page":"1","article-title":"Taxonomy of the genus Draco L","volume":"199","author":"Musters,","year":"1983","journal-title":"(Agamidae, Lacertilia, Reptilia). Zool. Verh."},{"key":"2022061600104991700_B82","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1130\/G33420.1","article-title":"Rapid Pliocene uplift of Timor","volume":"41","author":"Nguyen","year":"2013","journal-title":"Geology"},{"key":"2022061600104991700_B83","doi-asserted-by":"crossref","first-page":"2101","DOI":"10.1093\/molbev\/msx126","article-title":"StarBEAST2 brings faster species tree inference and accurate estimates of substitution rates","volume":"34","author":"Ogilvie","year":"2017","journal-title":"Mol. Biol. Evol."},{"key":"2022061600104991700_B84","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1016\/j.epsl.2013.02.040","article-title":"Linear volcanic segments in the central Sunda Arc, Indonesia, identified using Hough Transform analysis: Implications for arc lithosphere control upon volcano distribution","volume":"369","author":"Pacey","year":"2013","journal-title":"Earth Planet. Sci. Lett."},{"key":"2022061600104991700_B85","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1093\/sysbio\/syv023","article-title":"Detection and polarization of introgression in a five-taxon phylogeny","volume":"64","author":"Pease","year":"2015","journal-title":"Syst. Biol."},{"key":"2022061600104991700_B86","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1016\/0025-3227(93)90062-Z","article-title":"A one million-year-long sequence of marine terraces on Sumba Island, Indonesia","volume":"109","author":"Pirazzoli","year":"1993","journal-title":"Mar. Geol."},{"key":"2022061600104991700_B87","doi-asserted-by":"crossref","first-page":"945","DOI":"10.1093\/genetics\/155.2.945","article-title":"Inference of population structure using multilocus genotype data","volume":"155","author":"Pritchard","year":"2000","journal-title":"Genetics"},{"key":"2022061600104991700_B88","doi-asserted-by":"crossref","first-page":"1864","DOI":"10.1111\/j.1365-294X.2011.05239.x","article-title":"ABGD, automatic barcode gap discovery for primary species delimitation","volume":"21","author":"Puillandre","year":"2012","journal-title":"Mol. Ecol."},{"key":"2022061600104991700_B89","first-page":"1","article-title":"Tectonic and compositional variation in Flores Island, Indonesia: implication for volcanic structure and geothermal occurrences","volume":"2019","author":"Purwandono","year":"2019","journal-title":"Eur. Geoth. Congress"},{"key":"2022061600104991700_B90","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1093\/sysbio\/syy032","article-title":"Posterior summarization in Bayesian phylogenetics using Tracer 1.7","volume":"67","author":"Rambaut","year":"2018","journal-title":"Syst. Biol."},{"key":"2022061600104991700_B91","doi-asserted-by":"crossref","first-page":"1645","DOI":"10.1093\/genetics\/164.4.1645","article-title":"Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci","volume":"164","author":"Rannala","year":"2003","journal-title":"Genetics"},{"key":"2022061600104991700_B92","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1093\/sysbio\/syw119","article-title":"Efficient Bayesian species tree inference under the multispecies coalescent","volume":"66","author":"Rannala","year":"2017","journal-title":"Syst. Biol."},{"key":"2022061600104991700_B93","volume-title":"Historical biogeography of reptiles and amphibians from the Lesser Sunda Islands of Indonesia","author":"Reilly","year":"2016"},{"key":"2022061600104991700_B94","doi-asserted-by":"crossref","first-page":"5029","DOI":"10.1111\/gcb.13877","article-title":"Toxic toad invasion of Wallacea: A biodiversity hotspot characterized by extraordinary endemism","volume":"23","author":"Reilly","year":"2017","journal-title":"Glob. Chang. Biol."},{"key":"2022061600104991700_B95","doi-asserted-by":"crossref","first-page":"757","DOI":"10.1111\/jbi.13526","article-title":"Leap-frog dispersal and mitochondrial introgression: Phylogenomics and biogeography of Limnonectes fanged frogs in the Lesser Sundas Archipelago of Wallacea","volume":"46","author":"Reilly","year":"2019","journal-title":"J. Biogeogr."},{"key":"2022061600104991700_B96","doi-asserted-by":"crossref","first-page":"614","DOI":"10.1111\/zsc.12368","article-title":"Recent colonization and expansion through the Lesser Sundas by seven amphibian and reptile species","volume":"48","author":"Reilly","year":"2019","journal-title":"Zool. Scr."},{"key":"2022061600104991700_B97","first-page":"787","article-title":"New island records for anurans and squamates from the Lesser Sunda Archipelago","volume":"51","author":"Reilly","year":"2020","journal-title":"Herpetol. Rev."},{"key":"2022061600104991700_B98","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1163\/15685381-bja10048","article-title":"Genetic divergence of the Sunda ratsnake (Coelognathus subradiatus) across the Lesser Sunda Islands (Squamata: Colubridae)","volume":"42","author":"Reilly","year":"2021","journal-title":"Amphibia-Reptilia"},{"key":"2022061600104991700_B99","first-page":"225","article-title":"Structural and stratigraphic evolution of the Savu Basin, Indonesia","volume":"355","author":"Rigg","year":"2011","journal-title":"The SE Asian gateway: history and tectonics of the Australia\u2013Asia collision. Geol. Soc. Spec. Publ."},{"key":"2022061600104991700_B100","volume-title":"Modern applied statistics with S","author":"Ripley","year":"2002"},{"key":"2022061600104991700_B101","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1093\/sysbio\/sys029","article-title":"MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space","volume":"61","author":"Ronquist","year":"2012","journal-title":"Syst. Biol."},{"key":"2022061600104991700_B102","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/j.tecto.2009.04.009","article-title":"Surface uplift history of the incipient Banda arc-continent collision: geology and synorogenic foraminifera of Rote and Savu Islands, Indonesia","volume":"479","author":"Roosmawati","year":"2009","journal-title":"Tectonophysics"},{"key":"2022061600104991700_B103","doi-asserted-by":"crossref","first-page":"1654","DOI":"10.1093\/molbev\/msw079","article-title":"Fast coalescent-based computation of local branch support from quartet frequencies","volume":"33","author":"Sayyari","year":"2016","journal-title":"Mol. Biol. Evol."},{"key":"2022061600104991700_B104","doi-asserted-by":"crossref","first-page":"896","DOI":"10.1080\/10635150701772563","article-title":"Delimiting species in recent radiations","volume":"56","author":"Shaffer","year":"2007","journal-title":"Syst. Biol."},{"key":"2022061600104991700_B105","doi-asserted-by":"crossref","first-page":"7986","DOI":"10.1073\/pnas.1601078113","article-title":"Comparative phylogeography of ocean archipelagos: Hotspots for inferences of evolutionary process","volume":"113","author":"Shaw","year":"2016","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2022061600104991700_B106","first-page":"107","article-title":"Too many lines: the limits of the Oriental and Australian zoogeographic regions","volume":"121","author":"Simpson","year":"1977","journal-title":"Proc. Am. Philos. Soc."},{"key":"2022061600104991700_B107","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1126\/science.3576198","article-title":"Gene flow and the geographic structure of natural populations","volume":"236","author":"Slatkin","year":"1987","journal-title":"Science"},{"key":"2022061600104991700_B108","doi-asserted-by":"crossref","first-page":"216","DOI":"10.1111\/evo.13878","article-title":"Process-based species delimitation leads to identification of more biologically relevant species","volume":"74","author":"Smith","year":"2020","journal-title":"Evolution"},{"key":"2022061600104991700_B109","doi-asserted-by":"crossref","first-page":"843","DOI":"10.1093\/sysbio\/syw030","article-title":"Inconsistency of species tree methods under gene flow","volume":"65","author":"Sol\u00eds-Lemus","year":"2016","journal-title":"Syst. Biol."},{"key":"2022061600104991700_B110","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1038\/ngeo917","article-title":"Surface deformation and slab\u2013mantle interaction during Banda arc subduction rollback","volume":"3","author":"Spakman","year":"2010","journal-title":"Nat. Geosci."},{"key":"2022061600104991700_B111","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML Version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"key":"2022061600104991700_B112","first-page":"312","article-title":"Die vogel von Celebes","volume":"87","author":"Stresemann","year":"1939","journal-title":"Zoogeographie. J. Ornithol."},{"key":"2022061600104991700_B113","first-page":"19","article-title":"Geology and fossil sites of the Soa Basin, Flores, Indonesia","author":"","year":"2008","journal-title":"Geology, paleontology and archeology of the Pleistocene Soa Basin, Central Flores, Indonesia. Geological Survey Centre, Bandung, Indonesia"},{"key":"2022061600104991700_B114","doi-asserted-by":"crossref","first-page":"18793","DOI":"10.1038\/srep18793","article-title":"Macroevolution of hyperdiverse flightless beetles reflects the complex geological history of the Sunda Arc","volume":"6","author":"T\u00e4nzler","year":"2016","journal-title":"Sci. Rep."},{"key":"2022061600104991700_B115","doi-asserted-by":"crossref","first-page":"1089","DOI":"10.1002\/2013TC003436","article-title":"Resolving spatial heterogeneities in exhumation and surface uplift in Timor-Leste: constraints on deformation processes in young orogens","volume":"33","author":"Tate","year":"2014","journal-title":"Tectonics"},{"key":"2022061600104991700_B116","doi-asserted-by":"crossref","first-page":"364","DOI":"10.1016\/j.gr.2017.06.008","article-title":"Reconciling regional continuity with local variability in structure, uplift and exhumation of the Timor orogen","volume":"49","author":"Tate","year":"2017","journal-title":"Gondwana Res."},{"key":"2022061600104991700_B117","doi-asserted-by":"crossref","first-page":"810","DOI":"10.1093\/biolinnean\/blaa008","article-title":"A glide over the Indo-Australian geological maze: repeated transgressions of Lydekker\u2019s and Wallace\u2019s Lines in archdukes, barons and dukes (Nymphalidae: Limenitidinae: Adoliadini)","volume":"129","author":"Toussaint","year":"2020","journal-title":"Biol. J. Linn. Soc."},{"key":"2022061600104991700_B118","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1046\/j.1365-2699.2001.00526.x","article-title":"Biogeography of Southeast Asia and the West Pacific","volume":"28","author":"Turner","year":"2001","journal-title":"J. Biogeogr."},{"key":"2022061600104991700_B119","doi-asserted-by":"crossref","first-page":"1514","DOI":"10.1111\/jbi.12727","article-title":"Evaluating the influence of connectivity and distance on biogeographical patterns in the south-western deserts of North America","volume":"43","author":"Van Dam","year":"2016","journal-title":"J. Biogeogr."},{"key":"2022061600104991700_B120","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1111\/j.1095-8312.2011.01647.x","article-title":"Wallace\u2019s Line and plant distributions: two or three phytogeographical areas and where to group Java?","volume":"103","author":"Van Welzen","year":"2011","journal-title":"Biol. J. Linn. Soc."},{"key":"2022061600104991700_B121","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1111\/j.1096-3642.1860.tb00090.x","article-title":"On the zoological geography of the Malay Archipelago","volume":"14","author":"Wallace","year":"1860","journal-title":"J. Proc. Linn. Soc. Lond. Zool."},{"key":"2022061600104991700_B122","first-page":"217","article-title":"On the physical geography of the Malay Archipelago","volume":"33","author":"Wallace","year":"1863","journal-title":"J. R. Geogr. Soc."},{"key":"2022061600104991700_B123","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1111\/j.0014-3820.2001.tb01294.x","article-title":"A comparative study of asymmetric migration events across a marine biogeographic boundary","volume":"55","author":"Wares","year":"2001","journal-title":"Evolution"},{"key":"2022061600104991700_B124","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1111\/ele.12398","article-title":"Islands as model systems in ecology and evolution: prospects fifty years after MacArthur-Wilson","volume":"18","author":"Warren","year":"2015","journal-title":"Ecol. Lett."},{"key":"2022061600104991700_B125","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1093\/sysbio\/syy015","article-title":"Inferring phylogenetic networks using PhyloNet","volume":"67","author":"Wen","year":"2018","journal-title":"Syst. Biol."},{"key":"2022061600104991700_B126","volume-title":"Island biogeography: ecology, evolution, and conservation","author":"Whittaker","year":"2007"},{"key":"2022061600104991700_B127","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1093\/genetics\/16.2.97","article-title":"Evolution in Mendelian populations","volume":"16","author":"Wright","year":"1931","journal-title":"Genetics"},{"key":"2022061600104991700_B128","doi-asserted-by":"crossref","first-page":"9264","DOI":"10.1073\/pnas.0913022107","article-title":"Bayesian species delimitation using multilocus sequence data","volume":"107","author":"Yang","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2022061600104991700_B129","doi-asserted-by":"crossref","first-page":"2869","DOI":"10.1093\/bioinformatics\/btt499","article-title":"A general species delimitation method with applications to phylogenetic placement","volume":"29","author":"Zhang","year":"2013","journal-title":"Bioinformatics"},{"key":"2022061600104991700_B130","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1186\/s12859-018-2129-y","article-title":"ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees","volume":"19","author":"Zhang","year":"2018","journal-title":"BMC Bioinform."}],"container-title":["Systematic Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/sysbio\/advance-article-pdf\/doi\/10.1093\/sysbio\/syab043\/39507282\/syab043.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/sysbio\/article-pdf\/71\/1\/221\/44082567\/syab043.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/sysbio\/article-pdf\/71\/1\/221\/44082567\/syab043.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,6,16]],"date-time":"2022-06-16T00:12:41Z","timestamp":1655338361000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/sysbio\/article\/71\/1\/221\/6297230"}},"subtitle":[],"editor":[{"given":"Lisa","family":"Barrow","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2021,6,12]]},"references-count":130,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2021,6,12]]},"published-print":{"date-parts":[[2021,12,16]]}},"URL":"https:\/\/doi.org\/10.1093\/sysbio\/syab043","relation":{},"ISSN":["1063-5157","1076-836X"],"issn-type":[{"value":"1063-5157","type":"print"},{"value":"1076-836X","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,1,1]]},"published":{"date-parts":[[2021,6,12]]}}}