Phyletica bio photo

Phyletica

Exploring biodiversification.

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Publications

  1. Oaks JR., L’Bahy N., Cobb KA. 2019. Insights from a general, full-likelihood Bayesian approach to inferring shared evolutionary events from genomic data: Inferring shared demographic events is challenging. bioRxiv (In review at Molecular Ecology). DOI: 10.1101/679878. Link.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. Zohdy S., Schwartz TS., Oaks JR. 2019. The Coevolution Effect as a Driver of Spillover. Trends in Parasitology. DOI: 10.1016/j.pt.2019.03.010. Link.
  7. Oaks JR. 2019. Full Bayesian comparative phylogeography from genomic data. Systematic Biology 68:371–395. DOI: 10.1093/sysbio/syy063. Link.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. 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.