@article{Zeng2015neutral,
title={Neutral Models of Microbiome Evolution},
author={Zeng, Qinglong and Sukumaran, Jeet and Wu, Steven and Rodrigo, Allen},
journal={PLOS Comput Biol},
volume={11},
number={7},
pages={e1004365},
year={2015},
publisher={Public Library of Science}
}

@article{Oaks2014,
author = {Oaks, Jamie R and Linkem, Charles W and Sukumaran, Jeet},
title = {{Implications of uniformly distributed, empirically informed priors for phylogeographical model selection: a reply to Hickerson et al.}},
journal = {Evolution; international journal of organic evolution},
year = {2014},
volume = {68},
number = {12},
pages = {3607--3617},
month = dec
}

@article{Oaks2013,
abstract = {Approximate Bayesian computation (ABC) is rapidly gaining popularity in population genetics. One example, msBayes, infers the distribution of divergence times among pairs of taxa, allowing phylogeographers to test hypotheses about historical causes of diversification in co-distributed groups of organisms. Using msBayes, we infer the distribution of divergence times among 22 pairs of populations of vertebrates distributed across the Philippine Archipelago. Our objective was to test whether sea-level oscillations during the Pleistocene caused diversification across the islands. To guide interpretation of our results, we perform a suite of simulation-based power analyses. Our empirical results strongly support a recent simultaneous divergence event for all 22 taxon pairs, consistent with the prediction of the Pleistocene-driven diversification hypothesis. However, our empirical estimates are sensitive to changes in prior distributions, and our simulations reveal low power of the method to detect random variation in divergence times and bias toward supporting clustered divergences. Our results demonstrate that analyses exploring power and prior sensitivity should accompany ABC model selection inferences. The problems we identify are potentially mitigable with uniform priors over divergence models (rather than classes of models) and more flexible prior distributions on demographic and divergence-time parameters.},
author = {Oaks, Jamie R. and Sukumaran, Jeet and Esselstyn, Jacob A. and Linkem, Charles W. and Siler, Cameron D. and Holder, Mark T. and Brown, Rafe M.},
journal = {Evolution},
keywords = {Approximate Bayesian computation,Biogeography,Diversification,Model choice,MsBayes,Philippines,Pleistocene,Simultaneous divergence},
number = {4},
pages = {991--1010},
pmid = {23550751},
title = {{Evidence for climate-driven diversification? A caution for interpreting abc inferences of simultaneous historical events}},
volume = {67},
year = {2013}
}

@article{Vos2012,
abstract = {In scientific research, integration and synthesis require a common understanding of where data come from, how much they can be trusted, and what they may be used for. To make such an understanding computer-accessible requires standards for exchanging richly annotated data. The challenges of conveying reusable data are particularly acute in regard to evolutionary comparative analysis, which comprises an ever-expanding list of data types, methods, research aims, and subdisciplines. To facilitate interoperability in evolutionary comparative analysis, we present NeXML, an XML standard (inspired by the current standard, NEXUS) that supports exchange of richly annotated comparative data. NeXML defines syntax for operational taxonomic units, character-state matrices, and phylogenetic trees and networks. Documents can be validated unambiguously. Importantly, any data element can be annotated, to an arbitrary degree of richness, using a system that is both flexible and rigorous. We describe how the use of NeXML by the TreeBASE and Phenoscape projects satisfies user needs that cannot be satisfied with other available file formats. By relying on XML Schema Definition, the design of NeXML facilitates the development and deployment of software for processing, transforming, and querying documents. The adoption of NeXML for practical use is facilitated by the availability of (1) an online manual with code samples and a reference to all defined elements and attributes, (2) programming toolkits in most of the languages used commonly in evolutionary informatics, and (3) input-output support in several widely used software applications. An active, open, community-based development process enables future revision and expansion of NeXML.},
author = {Vos, Rutger A. and Balhoff, James P. and Caravas, Jason A. and Holder, Mark T. and Lapp, Hilmar and Maddison, Wayne P. and Midford, Peter E. and Priyam, Anurag and Sukumaran, Jeet and Xia, Xuhua and Stoltzfus, Arlin},
issn = {10635157},
journal = {Systematic Biology},
keywords = {Data standards,evolutionary informatics,interoperability,phyloinformatics,semantic web,syntax format},
number = {4},
pages = {675--689},
pmid = {22357728},
title = {{NeXML: Rich, extensible, and verifiable representation of comparative data and metadata}},
volume = {61},
year = {2012}
}

@article{Jimenez-Valverde2011,
abstract = {Aim Geographic distributions of species are constrained by several factors acting at different scales, with climate assumed to be a major determinant at broad extents. Recent studies, however, have challenged this statement and indicated that climate may not dominate among the factors governing geographic distributions of species. Here, we argue that these results are misleading due to the lack of consideration of the geographic area that has been accessible to the species.Location North America.Methods We generated null distributions for 75 North American endemic and 19 non-endemic bird species. For each species, climatic envelopes of observed and null distributions were modelled using neural networks and generalized linear models, and seven climatic predictors. Values of the area under the receiver-operating characteristic curve (AUC) based on models of observed distributions were compared with corresponding AUC values for the null distributions.Results More than 82\% of the endemic species showed AUC higher for the observed than for the null distributions, while 63\% of the non-endemic species showed such a pattern.Main conclusions We demonstrate a dominant climatic signal in shaping North American bird distributions. Our results attest to the importance of climate in determining species distributions and support the use of climate-envelope models for estimating potential distributional areas at the appropriate spatial scales. -� 2010 Blackwell Publishing Ltd},
author = {Jim\'{e}nez-Valverde, Alberto and Barve, Narayani and Lira-Noriega, Andr\'{e}s and Maher, Sean P. and Nakazawa, Yoshinori and Papeş, Monica and Sober\'{o}n, Jorge and Sukumaran, Jeet and Peterson, A. Townsend},
issn = {1466822X},
journal = {Global Ecology and Biogeography},
keywords = {Biogeography,Birds,Climate-envelope models,North America,Null models,Spatial extent,Species distributions},
number = {1},
pages = {114--118},
title = {{Dominant climate influences on North American bird distributions}},
volume = {20},
year = {2011}
}

@article{Sukumaran2011,
author = {Jeet Sukumaran and Mark T. Holder},
title = {Ginkgo: spatially-explicit simulator of complex phylogeographic histories},
journal={Molecular Ecology Resources},
volume={11},
number={2},
pages={364--369},
year={2011},
publisher={Wiley Online Library}
}

@article{Brown2010,
abstract = {Southeast Asia's widespread species offer unique opportunities to explore the effects of geographical barriers to dispersal on patterns of vertebrate lineage diversification. We analyzed mitochondrial gene sequences (16S rDNA) from a geographically widespread sample of 266 Southeast Asian tree frogs, including 244 individuals of Polypedates leucomystax and its close relatives. Our expectation was that lineages on island archipelagos would exhibit more substantial geographic structure, corresponding to the geological history of terrestrial connectivity in this region, compared to the Asian mainland. Contrary to predictions, we found evidence of numerous highly divergent lineages from a limited area on the Asian mainland, but fewer lineages with shallower divergences throughout oceanic islands of the Philippines and Indonesia. Surprisingly and in numerous instances, lineages in the archipelagos span distinct biogeographical provinces. Phylogeographic analyses identified four major haplotype clades; summary statistics, mismatch distributions, and Bayesian coalescent inference of demography provide support for recent range expansion, population growth, and/or admixture in the Philippine and some Sulawesi populations. We speculate that the current range of P. leucomystax in Southeast Asia is much larger now than in the recent past. Conversion of forested areas to monoculture agriculture and transportation of agricultural products between islands may have facilitated unprecedented population and range expansion in P. leucomystax throughout thousands of islands in the Philippine and Indonesian archipelagos. ?? 2010 Elsevier Inc.},
author = {Brown, Rafe M. and Linkem, Charles W. and Siler, Cameron D. and Sukumaran, Jeet and Esselstyn, Jacob A. and Diesmos, Arvin C. and Iskandar, Djoko T. and Bickford, David and Evans, Ben J. and McGuire, Jimmy A. and Grismer, Lee and Supriatna, Jatna and Andayani, Noviar},
issn = {10557903},
journal = {Molecular Phylogenetics and Evolution},
keywords = {Asia,Cryptic species,Genetic diversity,Human-mediated dispersal,Panmixia,Range expansion,Widespread species},
number = {2},
pages = {598--619},
pmid = {20601009},
title = {{Phylogeography and historical demography of Polypedates leucomystax in the islands of Indonesia and the Philippines: Evidence for recent human-mediated range expansion?}},
volume = {57},
year = {2010}
}

@incollection {HolderSB2010,
title = {Recent Developments in {B}ayesian Phylogenetics},
booktitle = {Bayesian Modeling in Bioinformatics},
year = {2010},
pages = {in press},
publisher = {Chapman \& Hall/CRC},
organization = {Chapman \& Hall/CRC},
author = {Mark T. Holder and Jeet Sukumaran and Rafe M. Brown},
editor = {Dipak K. Dey and Samiran Ghosh and Bani K. Mallick}
}

@article{Sukumaran2010,
author = {Jeet Sukumaran and Mark T. Holder},
title = {{DendroPy}: a {Python} library for phylogenetic computing},
journal = {Bioinformatics},
year = {2010},
pages = "1569-1571",
volume= "26"
}

@article{Matsui2010561,
title = "{Phylogenetic relationships of \textit{Ansonia} from Southeast Asia inferred from mitochondrial DNA sequences: Systematic and biogeographic implications (Anura: Bufonidae)}",
journal = "Molecular Phylogenetics and Evolution",
volume = "54",
number = "2",
pages = "561 - 570",
year = "2010",
author = "Masafumi Matsui and Atsushi Tominaga and Wanzhao Liu and Wichase Khonsue and Lee L. Grismer and Arvin C. Diesmos and Indraneil Das and Ahmad Sudin and Paul Yambun and Hoisen Yong and Jeet Sukumaran and Rafe M. Brown",
}

@article{Wiens2009,
author = {John Wiens and Jeet Sukumaran and Alex Pyron and Rafe Brown},
title = {{Evolutionary and biogeographic origins of high tropical diversity in Old World frogs (Ranidae)}},
journal = {Evolution},
year = {2009},
volume = 63,
pages = {1217--1231}
}

@article{Sukumaran2009,
author = {Jeet Sukumaran and Charles W. Linkem},
title = {Choice of topology estimators in {B}ayesian phylogenetic analysis},
journal = {Molecular Biology and Evolution},
year = {2009},
volume = {26},
number = {1},
pages = {1--3},
}

@article{Holder2008,
author = {Mark T. Holder and Jeet Sukumaran and Paul Lewis},
title = {A Justification for reporting the majority-rule consensus tree in {B}ayesian phylogenetics},
journal = {Systematic Biology},
year = {2008},
volume = {57},
number = {5},
pages = {814--8221},
}

@article{Das2007,
author = {Indraneil Das and Norsham Yaakob and Jeet Sukumaran},
title = {{A new species of \textit{Microhyla} (Anura: Microhylidae) from the Malay Peninsula}},
journal = {Hamadryad},
year = {2007},
volume = {31},
number = {2},
pages = {304--314},
}

@article{Sukumaran2006a,
author = {Jeet Sukumaran and Indraneil Das and Alexander Haas},
title = {A synopsis of bioacoustic studies of {A}nuran amphibians of {B}orneo},
journal = {Herpetological Review},
year = {2006},
volume = {37},
number = {3},
pages = {288--293},
}

@article{Sukumaran2006b,
author = {Jeet Sukumaran and Norshaam Yaakob and Dennis Yong},
title = {{The herpetofauna of the Southeast Pahang peat-swamp forests}},
journal = {Hamadryad},
year = {2006},
volume = {30},
number = {1\&2},
pages = {75--91},
}

@article{Brown2006,
author = {Rafe M. Brown and S. Richards and Jeet Sukumaran and J. Fougopoulos},
title = {A new morphologically cryptic species of forest frog (genus \textit{{P}latymantis}) from {New Britain Island, Bismarck Archipelago}},
journal = {Zootaxa},
year = {2006},
volume = {1334},
pages = {45--68},
}

@article{Yaakob2006,
author = {Norsham Yaakob and Jeet Sukumaran},
title = {An inventory of the amphibians of {Pasoh Forest Reserve, Negeri Sembilan, Peninsular Malaysia}},
journal = {Hamadryad},
year = {2006},
volume = {30},
number = {1\&2},
pages = {102--107},
}

@article{Grismer2005,
author = {Lee Grismer and Jeet Sukumaran and Jesse Grismer and Tim Youmans and Perry Wood and Renee Johnson},
title = {Report on the herpetofauna from the {Temengor Forest Reserve, Perak, West Malaysia}},
journal = {Hamadryad},
year = {2005},
volume = {29},
number = {1},
pages = {15--35},
}

@article{Sukumaran2002,
author = {Jeet Sukumaran},
title = {{The amphibian fauna of a forested area in Temengor, Northern Peninsular Malaysia}},
journal = {Hamadryad},
year = {2002},
volume = {27},
number = {1},
pages = {1--10},
}