/publications/index.xml /publications/index.xml

Publications

  1. Wong TKF, Li T, Ranjard L, Wu S, Sukumaran J, Rodrigo AG (2021) An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes. PLOS Computational Biology.
  2. Miralles A, Ducasse J, Brouillet S, Flouri T, Fujisawa T, Kapli P, Knowles LL, Kumari S, Stamatakis A, Sukumaran J, Lutteropp S, Vences M, Puillandre N (2021) SPART: A versatile and standardized data exchange format for species partition information. Molecular Ecology Resources. doi:https://doi.org/10.1111/1755-0998.13470.
  3. Sukumaran J, Holder M, Knowles LL (2021) Incorporating the speciation process into species delimitation. PLOS Computational Biology 17(5):e1008924. doi: https://doi.org/10.1371/journal.pcbi.1008924.
  4. Li J, Huang J-P, Sukumaran J, Knowles LL (2018) Microevolutionary processes impact macroevolutionary patterns. BMC evolutionary biology 18(1):123. doi:10.1186/s12862-018-1236-8.
  5. Sukumaran J, Knowles LL (2018) Trait-dependent biogeography:(Re) integrating biology into probabilistic historical biogeographical models. Trends in Ecology & Evolution. doi:10.1016/j.tree.2018.03.010.
  6. Knowles LL, Huang H, Sukumaran J, Smith SA (2018) A matter of phylogenetic scale: Distinguishing incomplete lineage sorting from lateral gene transfer as the cause of gene tree discord in recent versus deep diversification histories. American Journal of Botany 105(3):376–384. doi:10.1002/ajb2.1064.
  7. Zeng Q, Wu S, Sukumaran J, Rodrigo A (2017) Models of microbiome evolution incorporating host and microbial selection. Microbiome 5(1):127. doi:10.1186/s40168-017-0343-x.
  8. Huang H, Sukumaran J, Smith SA, Knowles L (2017) Cause of gene tree discord? Distinguishing incomplete lineage sorting and lateral gene transfer in phylogenetics. PeerJ PrePrints:5:e3489v1. doi:10.7287/peerj.preprints.3489v1.
  9. Sukumaran J, Knowles LL (2017) Multispecies coalescent delimits structure, not species. Proceedings of the National Academy of Sciences 114(7):1607–1612. doi:10.1073/pnas.1607921114.
  10. Sukumaran J, Economo EP, Knowles LL (2016) Machine-learning biogeographic processes from biotic patterns: A new trait-dependent dispersal and diversification model with model-choice by simulation-trained discriminant analysis. Systematic Biology 65(3):525–545. Available at: http://sysbio.oxfordjournals.org/content/65/3/525.
  11. Zeng Q, Sukumaran J, Wu S, Rodrigo A (2015) Neutral models of microbiome evolution. PLOS Computational Biology 11(7):e1004365. Available at: http://www.ncbi.nlm.nih.gov/pubmed/26200800.
  12. 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(12):3607–3617. Available at: http://www.ncbi.nlm.nih.gov/pubmed/25213163.
  13. Das I, Yaakob N, Sukumaran J, Leong TM (2014) Conservation status of the amphibians of Malaysia and Singapore. Conservation Biology of Amphibians of Asia (Status of Conservation and Decline of Amphibians: Eastern Hemisphere), eds Heatwole H, Das I (Natural History Publications (Borneo), Kota Kinabalu), pp 281–299. Available at: http://www.nhpborneo.com/book/amphibians-asia/#.Vfg1_mRVhBc.
  14. 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(4):991–1010. Available at: http://www.ncbi.nlm.nih.gov/pubmed/23550751.
  15. Stoltzfus A, Lapp H, Matasci N, Deus H, Sidlauskas B, Zmasek CM, Vaidya G, Pontelli E, Cranston K, Vos R, Webb CO, Harmon LJ, Pirrung M, O’Meara B, Pennell MW, Mirarab S, Rosenberg MS, Balhoff JP, Bik HM, Heath TA, Midford PE, Brown JW, McTavish EJ, Sukumaran J, Westneat M, Alfaro ME, Steele A, Jordan G (2013) Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. BMC Bioinformatics 14(1):158. Available at: http://www.ncbi.nlm.nih.gov/pubmed/23668630.
  16. Vos RA, Balhoff JP, Caravas JA, Holder MT, Lapp H, Maddison WP, Midford PE, Priyam A, Sukumaran J, Xia X, Stoltzfus A (2012) NeXML: Rich, extensible, and verifiable representation of comparative data and metadata. Systematic Biology 61(4):675–689. Available at: http://www.ncbi.nlm.nih.gov/pubmed/22357728.
  17. Jiménez-Valverde A, Barve N, Lira-Noriega A, Maher SP, Nakazawa Y, Papes M, Soberón J, Sukumaran J, Peterson AT (2011) Dominant climate influences on North American bird distributions. Global Ecology and Biogeography 20(1):114–118. Available at: http://onlinelibrary.wiley.com/doi/10.1111/j.1466-8238.2010.00574.x/abstract.
  18. Sukumaran J, Holder MT (2011) Ginkgo: Spatially-explicit simulator of complex phylogeographic histories. Molecular Ecology Resources 11(2):364–369. Available at: http://www.ncbi.nlm.nih.gov/pubmed/21429145.
  19. Brown RM, Linkem CW, Siler CD, Sukumaran J, Esselstyn JA, Diesmos AC, Iskandar DT, Bickford D, Evans BJ, McGuire JA, Grismer L, Supriatna J, Andayani N (2010) Phylogeography and historical demography of Polypedates leucomystax in the islands of Indonesia and the Philippines: Evidence for recent human-mediated range expansion? Molecular Phylogenetics and Evolution 57(2):598–619. Available at: http://www.ncbi.nlm.nih.gov/pubmed/20601009.
  20. Holder MT, Sukumaran J, Brown RM (2010) Recent developments in Bayesian phylogenetics. Bayesian Modeling in Bioinformatics, eds Dey DK, Ghosh S, Mallick BK (Chapman & Hall/CRC; Chapman & Hall/CRC), pp 193–221. Available at: https://www.crcpress.com/Bayesian-Modeling-in-Bioinformatics/Dey-Ghosh-Mallick/9781420070170.
  21. Sukumaran J, Holder MT (2010) DendroPy: A Python library for phylogenetic computing. Bioinformatics 26:1569–1571. Available at: http://www.ncbi.nlm.nih.gov/pubmed/20421198.
  22. Matsui M, Tominaga A, Liu W, Khonsue W, Grismer LL, Diesmos AC, Das I, Sudin A, Yambun P, Yong H, Sukumaran J, Brown RM (2010) Phylogenetic relationships of Ansonia from Southeast Asia inferred from mitochondrial DNA sequences: Systematic and biogeographic implications (Anura: Bufonidae). Molecular Phylogenetics and Evolution 54(2):561–570. Available at: http://www.ncbi.nlm.nih.gov/pubmed/19679193.
  23. Wiens J, Sukumaran J, Pyron A, Brown R (2009) Evolutionary and biogeographic origins of high tropical diversity in Old World frogs (Ranidae). Evolution 63:1217–1231. Available at: http://www.ncbi.nlm.nih.gov/pubmed/19154386.
  24. Sukumaran J, Linkem CW (2009) Choice of topology estimators in Bayesian phylogenetic analysis. Molecular Biology and Evolution 26(1):1–3. Available at: http://www.ncbi.nlm.nih.gov/pubmed/18984901.
  25. Holder MT, Sukumaran J, Lewis P (2008) A justification for reporting the majority-rule consensus tree in Bayesian phylogenetics. Systematic Biology 57(5):814–8221. Available at: http://www.ncbi.nlm.nih.gov/pubmed/18853367.
  26. Das I, Yaakob N, Sukumaran J (2007) A new species of Microhyla (Anura: Microhylidae) from the Malay Peninsula. Hamadryad 31(2):304–314.
  27. Sukumaran J, Das I, Haas A (2006) A synopsis of bioacoustic studies of Anuran amphibians of Borneo. Herpetological Review 37(3):288–293.
  28. Sukumaran J, Yaakob N, Yong D (2006) The herpetofauna of the Southeast Pahang peat-swamp forests. Hamadryad 30(1&2):75–91.
  29. Brown RM, Richards S, Sukumaran J, Fougopoulos J (2006) A new morphologically cryptic species of forest frog (genus Platymantis) from New Britain Island, Bismarck Archipelago. Zootaxa 1334:45–68. Available at: https://bit.ly/2NYnseO.
  30. Yaakob N, Sukumaran J (2006) An inventory of the amphibians of Pasoh Forest Reserve, Negeri Sembilan, Peninsular Malaysia. Hamadryad 30(1&2):102–107.
  31. Grismer L, Sukumaran J, Grismer J, Youmans T, Wood P, Johnson R (2005) Report on the herpetofauna from the Temengor Forest Reserve, Perak, West Malaysia. Hamadryad 29(1):15–35.
  32. Shepherd C, Sukumaran J, Wich SA (2004) Open Season: an analysis of the pet trade in Medan, Sumatra 1997–2001 (TRAFFIC Southeast Asia; TRAFFIC Southeast Asia, Petaling Jaya) Available at: http://www.traffic.org/general-reports/traffic_pub_trade5.pdf.
  33. Azmi R, Sukumaran J (2002) Biodiversity assessments and conservation planning for sustainable production forestry in high-conservation value forests: a preliminary biodiversity assessment (WWF Malaysia; WWF Malaysia, Petaling Jaya) Available at: http://bit.ly/1KcZ9AE.
  34. Sukumaran J (2002) The amphibian fauna of a forested area in Temengor, Northern Peninsular Malaysia. Hamadryad 27(1):1–10.
  35. Sukumaran J (1999) Tiger parts in traditional Chinese medicine: a survey of traditional Chinese medicine shops in Peninsular Malaysia (WWF Malaysia; WWF Malaysia, Petaling Jaya).
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