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Exploring biodiversification.

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  1. Grismer J, Scott P, Toffelmier E, Hinds B, Klabacka R, Stewart G, White V, Oaks J, Shaffer HB. 2022. Genomic data reveal local endemism in Southern California Rubber Boas (Serpentes: Boidae, \emphCharina) and the critical need for enhanced conservation actions. Molecular Phylogenetics and Evolution 174:107542. DOI: 10.1016/j.ympev.2022.107542. Link.
  2. Oaks JR, Wood, Jr. PL, Siler CD, Brown RM. 2022. Generalizing Bayesian phylogenetics to infer shared evolutionary events. Proceedings of the National Academy of Sciences 119:e2121036119. DOI: 10.1073/pnas.2121036119. Link.
  3. Klabacka RL, Parry HA, Yap KN, Cook RA, Herron VA, Horne LM, Wolak ME, Maldonado JA, Kavazis AN, Fujita MK, Oaks JR, Schwartz TS. 2022. Reduced mitochondrial respiration in hybrid asexual lizards. The American Naturalist 199:719–728. DOI: 10.1086/719014. Link.
  4. The results of four recent joint expeditions to the Gobi Desert: Lacertids and agamids. 2021. Russian Journal of Herpetology 28:15–32. DOI: 10.30906/1026-2296-2021-28-1-15-32. Link.
  5. Wan T, Oaks JR, Jiang X-L, Huang H, Knowles LL. 2021. Differences in Quaternary co-divergence reveals community-wide diversification in the mountains of southwest China varied among species. Proceedings of the Royal Society B: Biological Sciences 288:20202567. DOI: 10.1098/rspb.2020.2567. Link.
  6. Grismer LL, Rujirawan A, Termprayoon K, Ampai N, Yodthong S, Wood, Jr. PL, Oaks JR, Aowphol A. 2020. A new species of \emphCyrtodactylus Gray (Squamata; Gekkonidae) from the Thai Highlands with a discussion on the evolution of habitat preference. Zootaxa 4852:401–427. DOI: 10.11646/zootaxa.4852.4.1. Link.
  7. Klabacka RL, Wood, Jr. PL, McGuire JA, Oaks JR, Grismer LL, Grismer JL, Aowphol A, Sites, Jr. JW. 2020. Rivers of Indochina as potential drivers of lineage diversification in the spotted flying lizard (\emphDraco maculatus) species complex. Molecular Phylogenetics and Evolution 150:106861. DOI: 10.1016/j.ympev.2020.106861. Link.
  8. Weinell JL, Barley AJ, Siler CD, Orlov NL, Ananjeva NB, Oaks JR, Burbrink FT, Brown RM. 2020. Phylogenetic relationships and biogeographic range evolution in Cat-eyed Snakes \emphBoiga (Serpentes: Colubridae). Zoological Journal of the Linnean Society. DOI: 10.1093/zoolinnean/zlaa090. Link.
  9. David KT, Oaks JR, Halanych KM. 2020. Patterns of Gene Evolution Following Duplications and Speciations in Vertebrates. PeerJ 8:e8813. DOI: 10.7717/peerj.8813. Link.
  10. O’Connell KA, Oaks JR, Hamidy A, Shaney KJ, Kurniawan N, Smith EN, Fujita MK. 2020. Impacts of the Toba eruption and montane forest expansion on diversification in Sumatran parachuting frogs (\emphRhacophorus). Molecular Ecology 29:2994–3009. DOI: 10.1111/mec.15541. Link.
  11. Grismer LL, Chan KO, Oaks JR, Thy N, Sokun L, Murdoch ML, Stuart BL, Grismer JL. 2020. A new insular species of the \emphCyrtodactylus intermedius (Squamata: Gekkonidae) group from Cambodia with a discussion of habitat preference and ecomorphology. Zootaxa 4830:75–102. DOI: 10.11646/zootaxa.4830.1.3. Link.
  12. Grismer LL, Wood, Jr. PL, Grismer MS, Quah ESH, Thura MK, Oaks JR, Lin A, Lim DY. 2020. Integrative taxonomic and geographic variation analyses in \emphCyrtodactylus aequalis (Squamata: Gekkonidae) from southern Myanmar (Burma): one species, two different stories. Israel Journal of Ecology \& Evolution. DOI: 10.1163/22244662-20191082. Link.
  13. Leaché AD, Oaks JR, Ofori-Boateng C, Fujita MK. 2020. Comparative phylogeography of West African amphibians and reptiles. Evolution 74:716–724. DOI: 10.1111/evo.13941. Link.
  14. Grismer LL, Wood, Jr. PL, Quah ESH, Thura MK, Oaks JR, Lin A. 2020. Four new Burmese species of \emphHemiphyllodactylus Bleeker (Squamata: Gekkonidae) from distantly related parapatric clades from the Shan Plateau and Salween Basin. Zootaxa 4758:45–82. DOI: 10.11646/zootaxa.4758.1.2. Link.
  15. Grismer LL, Wood, Jr. PL, Quah ESH, Grismer MS, Thura MK, Oaks JR, Lin A. 2020. Two new species of \emphCyrtodactylus Gray, 1827 (Squamata: Gekkonidae) from a karstic archipelago in the Salween Basin of southern Myanmar (Burma). Zootaxa 4718:151–183. DOI: 10.11646/zootaxa.4718.2.1. Link.
  16. Wright AM, Schwartz RS, Oaks JR, Newman CE, Flanagan SP. 2020. The why, when, and how of computing in biology classrooms. F1000Research 8:1854. DOI: 10.12688/f1000research.20873.2. Link.
  17. Oaks JR, L’Bahy N, Cobb KA. 2020. Insights from a general, full-likelihood Bayesian approach to inferring shared evolutionary events from genomic data: Inferring shared demographic events is challenging. Evolution 74:2184–2206. DOI: 10.1111/evo.14052. Link.
  18. Wood, Jr. PL, Grismer LL, Muin MA, Anuar S, Oaks JR, Sites, Jr. JW. 2020. A new potentially endangered limestone-associated Bent-toed Gecko of the \textitCyrtodactylus pulchellus (Squamata: Gekkonidae) complex from northern Peninsular Malaysia. Zootaxa 4751:437–460. DOI: 10.11646/zootaxa.4751.3.2. Link.
  19. Oaks JR, Cobb KA, Minin VN, Leaché AD. 2019. Marginal likelihoods in phylogenetics: a review of methods and applications. Systematic Biology 68:681–697. DOI: 10.1093/sysbio/syz003. Link.
  20. Quah ESH, Grismer LL, Wood, Jr. PL, Thura MK, Oaks JR, Lin A. 2019. Discovery of the westernmost population of the genus \emphAnsonia Stoliczka (Anura, Bufonidae) with the description of a new species from the Shan Plateau of eastern Myanmar. Zootaxa 4656:545–571. DOI: 10.11646/zootaxa.4656.3.11. Link.
  21. Grismer LL, Wood, Jr. PL, Quah ESH, Thura MK, Oaks JR, Lin A. 2019. A new species of Bent-toed Gecko (Squamata, Gekkonidae, \emphCyrtodactylus) from the Shan Plateau in eastern Myanmar (Burma). Zootaxa 4624:301–321. DOI: 10.11646/zootaxa.4624.3.1. Link.
  22. Oaks JR, Siler CD, Brown RM. 2019. The comparative biogeography of Philippine geckos challenges predictions from a paradigm of climate-driven vicariant diversification across an island archipelago. Evolution 73:1151–1167. DOI: 10.1111/evo.13754. Link.
  23. Zohdy S, Schwartz TS, Oaks JR. 2019. The Coevolution Effect as a Driver of Spillover. Trends in Parasitology. DOI: 10.1016/ Link.
  24. Oaks JR. 2019. Full Bayesian comparative phylogeography from genomic data. Systematic Biology 68:371–395. DOI: 10.1093/sysbio/syy063. Link.
  25. Folt B, Bauder J, Spear S, Stevenson D, Hoffman M, Oaks JR, Wood, Jr. PL, Jenkins C, Steen DA, Guyer C. 2019. Taxonomic and conservation implications of population genetic admixture, mito-nuclear discordance, and male-biased dispersal of a large endangered snake, \emphDrymarchon couperi. PLOS ONE 14:1–21. DOI: 10.1371/journal.pone.0214439. Link.
  26. Leaché AD, Oaks JR. 2017. The utility of single nucleotide polymorphism (SNP) data in phylogenetics. Annual Review of Ecology, Evolution, and Systematics 48:69–84. DOI: 10.1146/annurev-ecolsys-110316-022645. Link.
  27. Lira-Noriega A, Toro-Núñez O, Oaks JR, Mort ME. 2015. The roles of history and ecology in chloroplast phylogeographic patterns of the bird-dispersed plant parasite \textitPhoradendron californicum Nutt. (Viscaceae) in the Sonoran Desert. American Journal of Botany 102:149–164. DOI: 10.3732/ajb.1400277. Link.
  28. Oaks JR, Linkem CW, Sukumaran J. 2014. Implications of uniformly distributed, empirically informed priors for phylogeographical model selection: A reply to Hickerson et al. Evolution 68:3607–3617. DOI: 10.1111/evo.12523. Link.
  29. Grismer JL, Bauer AM, Grismer LL, Thirakhupt K, Aowphol A, Oaks JR, Wood, Jr. PL, Chan KO, Thy N, Cota M, Jackman T. 2014. Multiple origins of parthenogenesis, and a species phylogeny for the Southeast Asian butterfly lizards, \emphLeiolepis. Biological Journal of the Linnean Society 113:1080–1093. DOI: 10.1111/bij.12367. Link.
  30. Oaks JR. 2014. An Improved Approximate-Bayesian Model-choice Method for Estimating Shared Evolutionary History. BMC Evolutionary Biology 14:150. DOI: 10.1186/1471-2148-14-150. Link.
  31. Siler CD, Oaks JR, Cobb K, Hidetoshi O, Brown RM. 2014. Critically endangered island endemic or peripheral population of a widespread species? Conservation genetics of Kikuchi’s gecko and the global challenge of protecting peripheral oceanic island endemic vertebrates. Diversity and Distributions 20:756–772. DOI: 10.1111/ddi.12169. Link.
  32. Welton LJ, Wood, Jr. PL, Oaks JR, Siler CD, Brown RM. 2014. Fossil-calibrated phylogeny and historical biogeography of Southeast Asian water monitors (\emphVaranus salvator Complex). Molecular Phylogenetics and Evolution 74:29–37. DOI: 10.1016/j.ympev.2014.01.016. Link.
  33. Oaks JR, Sukumaran J, Esselstyn JA, Linkem CW, Siler CD, Holder MT, Brown RM. 2013. Evidence for climate-driven diversification? A caution for interpreting ABC inferences of simultaneous historical events. Evolution 67:991–1010. DOI: 10.1111/j.1558-5646.2012.01840.x. Link.
  34. Brown RM, Siler CD, Oliveros CH, Esselstyn JA, Diesmos AC, Hosner PA, Linkem CW, Barley AJ, Oaks JR, Sanguila MB, Welton LJ, Moyle RG, Peterson AT, Alcala AC. 2013. Evolutionary processes of diversification in a model island archipelago. Annual Review of Ecology, Evolution, and Systematics 44:411–435. DOI: 10.1146/annurev-ecolsys-110411-160323. Link.
  35. Welton LJ, Siler CD, Oaks JR, Diesmos AC, Brown RM. 2013. Multilocus Phylogeny and Bayesian Estimates of Species Boundaries Reveal Hidden Evolutionary Relationships and Cryptic Diversity in Southeast Asian Monitor Lizards. Molecular Ecology 22:3495–3510. DOI: 10.1111/mec.12324. Link.
  36. Siler CD, Oaks JR, Welton LJ, Linkem CW, Swab J, Diesmos AC, Brown RM. 2012. Did geckos ride the Palawan raft to the Philippines? Journal of Biogeography 39:1217–1234. DOI: 10.1111/j.1365-2699.2011.02680.x. Link.
  37. Oaks JR. 2011. A time-calibrated species tree of Crocodylia reveals a recent radiation of the true crocodiles. Evolution 65:3285–3297. DOI: 10.1111/j.1558-5646.2011.01373.x. Link.
  38. Siler CD, Oaks JR, Esselstyn JA, Diesmos AC, Brown RM. 2010. Phylogeny and biogeography of Philippine bent-toed geckos (Gekkonidae: \emphCyrtodactylus) contradict a prevailing model of Pleistocene diversification. Molecular Phylogenetics and Evolution 55:699–710. DOI: 10.1016/j.ympev.2010.01.027. Link.
  39. Grismer LL, Neang T, Chav T, Wood, Jr. PL, Oaks JR, Holden J, Grismer JL, Szutz TR, Youmans TM. 2008. Additional amphibians and reptiles from the Phnom Samkos Wildlife Sanctuary in Northwestern Cardamom Mountains, Cambodia, with comments on their taxonomy and the discovery of four new species. Raffles Bulletin of Zoology 56:161–175. Link.
  40. Oaks JR, Daul JM, Adler GH. 2008. Life span of a tropical forest rodent, \emphProechimys semispinosus. Journal of Mammalogy 89:904–908. DOI: 10.1644/07-MAMM-A-045.1. Link.