Publications

Lab publications are listed below, by year. The linked titles will take you to the paper on the publisher’s webpage. If you don’t have a subscription and would like to request a reprint, click on the relevant pdf link below. My Google Scholar profile is here.

2022

Handika, H, JA Esselstyn. 2022. SEGUL: An ultrafast, memory-efficient alignment manipulation and summary tool for phylogenomics. Authorea Preprints

Hernández-Canchola, G, L León-Paniagua, JA Esselstyn. 2022. Mitochondrial DNA and other lines of evidence clarify species diversity in the Peromyscus truei species group (Cricetidae: Neotominae). Mammalia

2021

Colunga-Salas, P, G Hernández-Canchola, E Grostieta, I Becker. 2021. Bats as hosts of important unicellular endoparasites. Pp. 331-348 in Lim, BK et al. (eds) 50 Years of Bat Research. Springer, Cham.

Esselstyn, JA, AS Achmadi, H Handika, MT Swanson, TC Giarla, KC Rowe. 2021. Fourteen new, endemic species of shrew (genus Crocidura) from Sulawesi reveal a spectacular island radiation. Bulletin of the American Museum of Natural History. 454: 1-108.

Handika, H, AS Achmadi, JA Esselstyn, KC Rowe. 2021. Molecular and morphological systematics of the Bunomys division (Rodentia: Muridae), an endemic radiation on Sulawesi. Zoologica Scripta. 50: 141-154. PDF

Hernández-Canchola, G, LD Verde Arregoitia, P Colunga-Salas, YA Gomez-Jimenez, L León-Paniagua. 2021. A global review of phylogeographic studies on bats. Pp. 289-309 in Lim, BK et al. (eds) 50 Years of Bat Research. Springer, Cham.

Hernández-Canchola, G, L. León-Paniagua, JA Esselstyn. 2021. Mitochondrial DNA indicates paraphyletic relationships of disjunct populations in the Neotoma mexicana species group. Therya. doi: 10.12933/therya-21-1082. PDF

Nations, JA, GG Mount, SM Morere, AS Achmadi, KC Rowe, JA Esselstyn. 2021. Locomotory mode transitions alter phenotypic evolution and lineage diversification in an ecologically rich clade of mammals. Evolution. 75:376–393. doi: 10.1111/evo.14156. PDF

Nations, JA, A Mursyid, RD Busta, SP Adrian, H Handika, Apandi, AS Achmadi, JA Esselstyn. 2021. The first report of albinism in a Sundaland endemic rodent. Mammalia. 85:168-172. doi: 10.1515/mammalia-2020-0047. PDF

Roycroft, E, A Achmadi, CM Callahan, JA Esselstyn, JM Good, A Moussalli, KC Rowe. 2021. Molecular evolution of ecological specialisation: genomic insights from the diversification of murine rodents. Genome Biology and Evolution. doi: 10.1093/gbe/evab103.

Upham, NS, JA Esselstyn, W Jetz. 2021. Molecules and fossils tell distinct yet complementary stories of mammal diversification. Current Biology. doi: 10.1016/j.cub.2021.07.012. PDF

2020

Babb-Biernacki, SJ, JA Esselstyn, VP Doyle. 2020. Rethinking host range in Pneumocystis. PLoS Pathogens. 16(9): e1008824.

Colunga-Salas, P, G Hernández-Canchola. 2020. Bats and humans during the SARS-CoV-2 outbreak: The case of bat-coronaviruses from Mexico. Transboundary and Emerging Diseases. doi: 10.1111/tbed.13751. PDF

Colunga-Salas, P, G Hernández-Canchola, S Sánchez-Montes, Y N Lozano-Sardandeta, I Becker. 2020. Genetic diversity of Borrelia burgdorferi sensu stricto: Novel strains from Mexican wild rodents. Transboundary and Emerging Diseases. doi: 10.1111/tbed.13780. PDF

Martinez, Q, J Clavel, JA Esselstyn, AS Achmadi, C Grohe, N Pirot, P-H Fabre. 2020. Convergent evolution of olfactory and thermoregulatory capacities in small amphibious mammals. Proceedings of the National Academy of Sciences, USA. 117:8958-8965. doi: 10.1073/pnas.1917836117. PDF

2019

Esselstyn, JA, AS Achmadi, H Handika, TC Giarla, KC Rowe. 2019. A new climbing shrew from Sulawesi highlights the tangled taxonomy of an endemic radiation. Journal of Mammalogy. 100:1713-1725. doi: 10.1093/jmammal/gyz077. PDF

Nations, JA, LR Heaney, TC Demos, AS Achmadi, KC Rowe, JA Esselstyn. 2019. A simple skeletal measurement effectively predicts climbing behaviour in a diverse clade of small mammals. Biological Journal of the Linnean Society. 128:323-336. doi: 10.1093/biolinnean/blz085. PDF

Rickart, EA, DS Balete, RM Timm, PA Alviola, JA Esselstyn, LR Heaney. 2019. Two new species of shrew-rats (Rhynchomys: Muridae: Rodentia) from Luzon Island, Philippines. Journal of Mammalogy. 100:1112-1129. doi: 10.1093/jmammal/gyz066. PDF

Rowe, KC, AS Achmadi, P-H Fabre, JJ Schenk, SJ Steppan, JA Esselstyn. 2019. Oceanic islands of Wallacea as a source for dispersal and diversification of murine rodents. Journal of Biogeography. doi: 10.1111/jbi.13720. PDF

Roycroft, EJ, JA Nations, KC Rowe. 2019. Environment predicts repeated body size shifts in a recent radiation of Australian mammals. Evolution. doi: 10.1111/evo.13859. PDF

Swanson, MT, CH Oliveros, JA Esselstyn. 2019. A phylogenomic rodent tree reveals the repeated evolution of masseter architectures. Proceedings of the Royal Society B, Biological Sciences. 286. doi: 10.1098/rspb.2019.0672. PDF

Upham, NS, JA Esselstyn, W Jetz. 2019. Ecological causes of uneven diversification and richness in the mammal tree of life. bioRxiv. 504803.

Upham, NS, JA Esselstyn, W Jetz. 2019. Inferring the mammal tree: Species level sets of phylogenies for questions in ecology, evolution, and conservation. PLoS Biology. 17(12): e3000494.

2018

Eldridge, RA, AS Achmadi, TC Giarla, KC Rowe, JA Esselstyn. 2018. Geographic isolation and elevational gradients promote diversification in an endemic shrew on Sulawesi. Molecular Phylogenetics and Evolution. 118:306-317. PDF

Giarla, TC, SP Maher, AS Achmadi, MK Moore, MT Swanson, KC Rowe, JA Esselstyn. 2018. Isolation by marine barriers and climate explain areas of endemism in an island rodent. Journal of Biogeography. 45:2053-2066. PDF

Hutterer, R, DS Balete, TC Giarla, LR Heaney, JA Esselstyn. 2018. A new genus and species of shrew (Mammalia: Soricidae) from Palawan Island, Philippines. Journal of Mammalogy. 99:518-536. PDF

Martinez, Q, R Lebrun, AS Achmadi, JA Esselstyn, AR Evans, LR Heaney, RP Miguez, KC Rowe, P-H Fabre. 2018. Convergent evolution of an extreme dietary specialisation, the olfactory system of worm-eating rodents. Scientific Reports. 8:17806.

2017

Esselstyn, JA, CH Oliveros, MT Swanson, BC Faircloth. 2017. Investigating difficult nodes in the placental mammal tree with expanded taxon sampling and thousands of ultraconserved elements. Genome Biology and Evolution. 9:2308–2321.

Demos, TC, AS Achmadi, H Handika, KC Rowe, JA Esselstyn. 2017. A new species of shrew (Soricomorpha: Crocidura) from Java, Indonesia: possible character displacement despite intraspecific gene flow. Journal of Mammalogy. 98:183–193. PDF

2016

Cook, JA, SE Greiman, SJ Agosta, RP Anderson, BS Arbogast, RJ Baker, W Boeker, RD Bradley, DR Brooks, R Cole, JR Demboski, AP Dobson, JL Dunnum, RP Eckerlin, J Esselstyn, KE Galbreath, J Hawdon, HE Hoekstra, SJ Kutz, JE Light, LE Olson, BD Patterson, JL Patton, AJ Phillips, E Rickart, DS Rogers, ME Siddall, VV Tkach, EP Hoberg. 2016. Transformational principles for NEON sampling of mammalian parasites and pathogens: A response to Springer and colleagues. BioScience. 66:917–919. PDF

Demos, TC, AS Achmadi, TC Giarla, H Handika, Maharadatunkamsi, KC Rowe, JA Esselstyn. 2016. Local endemism and within-island diversification of shrews illustrate the importance of speciation in building Sundaland mammal diversity. Molecular Ecology. 25:5158–5173. PDF

Esselstyn, JA. 2016. Speciation in shrews (Crocidura) in the Philippine Archipelago. Pp. 64–65 in Heaney, LR, DS Balete, EA Rickart, The Mammals of Luzon Island: Biogeography and Natural History of a Philippine Fauna. Johns Hopkins University Press, Baltimore.

Rowe, KC, AS Achmadi, JA Esselstyn. 2016. Repeated evolution of carnivory among Indo-Australian rodents. Evolution. 70:653–665. PDF

Rowe, KC, AS Achmadi, JA Esselstyn. 2016. A new genus and species of omnivorous rodent (Muridae: Murinae) from Sulawesi, nested within a clade of endemic carnivores. Journal of Mammalogy. 97:978–991. PDF

2015

Esselstyn, JA, AS Achmadi, H Handika, KC Rowe. 2015. A hog-nosed shrew rat (Rodentia: Muridae) from Sulawesi Island, Indonesia. Journal of Mammalogy. 96:895–907. PDF

Giarla, TC, JA Esselstyn. 2015. The challenges of resolving a rapid, recent radiation: Empirical and simulated phylogenomics of Philippine shrews. Systematic Biology. 64:727–740. PDF

Justiniano, R, JJ Schenk, DS Balete, EA Rickart, JA Esselstyn, LR Heaney, SJ Steppan. 2015. Testing diversification models of endemic Philippine forest mice (Apomys) with nuclear phylogenies across elevational gradients reveals repeated colonization of isolated mountain ranges. Journal of Biogeography. 42:51–64. PDF

Stanley, WT, R Hutterer, TC Giarla, JA Esselstyn. 2015. Phylogeny, phylogeography and geographic variation in the Crocidura monax (Soricidae) species complex from the montane islands of Tanzania, with descriptions of three new species. Zoological Journal of the Linnean Society. 174:185–215. PDF

2014

Achmadi, AS, KC Rowe, JA Esselstyn. 2014. New records of two rarely encountered, endemic rats (Rodentia: Muridae: Murinae) from Gunung Gandangdewata, West Sulawesi province. Treubia. 41:51-60. PDF

Amar, A, JA Esselstyn. 2014. Positive association between rat abundance and breeding success of the critically endangered Mariana crow Corvus kubaryi. Bird Conservation International. 24:192-200. PDF

Brown, RM, JA Weghorst, KV Olson, MRM Duya, AJ Barley, MV Duya, M Shekelle, I Neri-Arboleda, JA Esselstyn, NJ Dominy, PS Ong, GL Moritz, A Luczon, MLL Diesmos, AC Diesmos, CD Siler. 2014. Conservation genetics of the Philippine tarsier: Cryptic genetic variation restructures conservation priorities for an island archipelago primate. PLoS ONE. DOI: 101371/journal.pone.0104340.

Esselstyn, JA, AS Achmadi, Maharadatunkamsi. 2014. A new species of shrew (Soricomorpha: Crocidura) from West Java, Indonesia. Journal of Mammalogy. 95:216-224. PDF

Evans, BJ, K Zeng, JA Esselstyn, B Charleworth, D Melnick. 2014. Reduced representation genome sequencing suggests low diversity on the sex chromosomes of tonkean macaque monkeys. Molecular Biology and Evolution. 31:2425-2440. PDF

Heaney, LR, DS Balete, MJ Veluz, SJ Steppan, JA Esselstyn, AW Pfeiffer, EA Rickart. 2014. Two new species of Philippine forest mice (Apomys, Muridae, Rodentia) from Lubang and Luzon islands, with a redescription of Apomys sacobianus Johnson, 1962. Proceedings of the Biological Society of Washington. 126:395-413. PDF

Kang, HJ, WT Stanley, JA Esselstyn, SH Gu, R Yanagihara. 2014. Expanded host diversity and geographic distribution of hantaviruses in Sub-Saharan Africa. Journal of Virology 88:7663-7667. PDF

Musser, GG, AS Achmadi, JA Esselstyn, KC Rowe. 2014. Bunomys torajae, new species. In GG Musser. A systematic review of Sualwesi Bunomys (Muridae, Murinae) with the description of two new species. Bulletin of the American Museum of Natural History. 392:124-139.

Rowe, KC, AS Achmadi, JA Esselstyn. 2014. Convergent evolution of aquatic foraging in a new genus and species (Rodentia: Muridae) from Sulawesi Island, Indonesia. Zootaxa. 3815:541-564. PDF

2013

Achmadi, AS, JA Esselstyn, KC Rowe, I Maryanto, MT Abdulah. 2013. Phylogeny, diversity, and biogeography of Southeast Asian endemic spiny mice (Maxomys). Journal of Mammalogy. 94:1412-1423. PDF

Brown, RM, CD Siler, CH Oliveros, JA Esselstyn, AC Diesmos, PA Hosner, CW Linkem, AJ Barley, JR Oaks, MB Sanguila, LJ Welton, RG Moyle, AT Peterson, AC Alcala. 2013. Evolutionary processes of diversification in a model island archipelago. Annual Review of Ecology, Evolution, and Systematics. 44:1-24. PDF

Esselstyn, JA, Maharadatunkamsi, AS Achmadi, CD Siler, BJ Evans. 2013. Carving out turf in a biodiversity hotspot: Multiple previously unrecognized shrew species co-occur on Java Island, Indonesia. Molecular Ecology. 22:4972-4987. PDF

Oaks, JR, J Sukumaran, JA Esselstyn, CW Linkem, CD Siler, MT Holder, RM Brown. 2013. Evidence for climate-driven diversification? A caution for interpreting ABC inferences of simultaneous historical events. Evolution. 67:991-1010. PDF

Stanley, WT, LW Robbins, JM Malekani, SG Mbalitini, DA Migurima, JC Mukinzi, J Hulselmans, V Prévot, E Verheyen, R Hutterer, JB Doty, BP Moore, YJ Nakazawa, Z Braden, D Carroll, JC Kerbis Peterhans, JM Bates, JA Esselstyn. 2013. A new hero emerges: another exceptional mammalian spine and its potential adaptive significance. Biology Letters. DOI: 10.1098/rsbl.2013.0486. PDF

2012

Esselstyn JA, AS Achmadi, KC Rowe. 2012. Evolutionary novelty in a rat with no molars. Biology Letters. 8:990-993. PDF

Esselstyn JA, BJ Evans, JL Sedlock, FAA Khan, LR Heaney. 2012. Single-locus species delimitation: A test of the mixed Yule-coalescent model, with an empirical application to Philippine round-leaf bats. Proceedings of the Royal Society B: Biological Sciences. 279:3678-3686. PDF

2011

Esselstyn JA, SP Maher, RM Brown. 2011. Species interactions during diversification and community assembly in an island radiation of shrews. PLoS ONE. e21885.

Wiles, GJ, TJ O’Shea, DJ Worthington, JA Esselstyn, EW Valdez. 2011. Status and natural history of the last knwon population of Emballonura semicaudata rotensis. Acta Chiropterologica. 13:299-309. PDF

2010

Brown, RM, CW Linkem, CD Siler, J Sukumaran, JA Esselstyn, AC Diesmos, D Iskandar, D Bickford, BJ Evans, JA McGuire, J supriatna, N Andayani. 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. 57:598-619. PDF

Esselstyn, JA. 2010. At long last, an authoritative guide to the mammals of Indochina. Journal of Mammalian Evolution. 17:215-216.

Esselstyn, JA, SM Goodman. 2010. New species of shrew (Soricidae: Crocidura) from Sibuyan Island, Philippines. Journal of Mammalogy. 91:1467-1472. PDF

Esselstyn JA, CH Oliveros. 2010. Colonization of the Philippines from Taiwan: a multi-locus test of the biogeographic and phylogenetic relationships of isolated populations of shrews. Journal of Biogeography. 37:1504-1514. PDF

Esselstyn JA, CH Oliveros, RG Moyle, AT Peterson, JA McGuire, RM Brown. 2010. Integrating phylogenetic and taxonomic evidence illuminates complex biogeographic patterns along Huxley’s modification of Wallace’s Line. Journal of Biogeography. 37:2054-2066. PDF

Heaney, LR, ML Dollar, DS Balete, JA Esselstyn, EA Rickart, JL Sedlock. 2010. Synopsis of Philippine mammals.

Patou, ML, A Wilting, P Gaubert, JA Esselstyn C Cruad, AP Jennings, J Fickel, G Veron. 2010. Evolutionary history of the Paradoxurus palm civets – a new model for Asian biogeography. Journal of Biogeography. 37:2077-2097. PDF

Siler, CD, JR Oaks, JA Esselstyn, AC Diesmos, RM Brown. 2010. Phylogeny and biogeography of Philippine bent-toed geckos (Gekkonidae: Cyrtodactylus) contradict a prevailing model of Pleistocene diversification. Molecular Phylogenetics and Evolution. 55:699-710. PDF

Stanley, WT, JA Esselstyn. 2010. Biogeography and diversity among montane populations of mouse shrew (Soricidae: Myosorex) in Tanzania. Biological Journal of the Linnean Society. 100:669-680. PDF

2009

Esselstyn, JA, RM Brown. 2009. The role of repeated sea-level fluctuations in the generation of shrew (Soricidae: Crocidura) diversity in the Philippine Archipelago. Molecular Phylogenetics and Evolution. 53:171-181. PDF

Esselstyn, JA, RM Timm, RM Brown. 2009. Do geological or climatic processes drive speciation in dynamic archipelagos? The tempo and mode of diversification in Southeast Asian shrews. Evolution. 63:2595-2610. PDF

2008

Amar, A, F Amidon, B Arroyo, JA Esselstyn, AP Marshall. 2008. Population trends of the forest bird community on the Pacific island of Rota, Mariana Islands. Condor. 110:421-427. PDF

Esselstyn, JA, HJD Garcia, MG Saulog, LR Heaney. 2008. A new species of Desmalopex (Pteropodidae) from the Philippines, with a phylogenetic analysis of the Pteropodini. Journal of Mammalogy. 89:815-825. PDF

2007 and earlier

Esselstyn, JA. 2007. A new species of stripe-faced fruit bat (Chiroptera: Pteropodidae: Styloctenium) from the Philippines. Journal of Mammalogy. 88:951-958. PDF

Esselstyn, JA. 2007. Should universal guidelines be applied to taxonomic research?. Biological Journal of the Linnean Society. 90:761-764. PDF

Esselstyn, JA, A Amar, D Janeke. 2006. Impact of post-typhoon hunting on Mariana fruit bats (Pteropus mariannus). Pacific Science. 60:531-539. PDF

Esselstyn, JA, P Widmann, LR Heaney. 2004. The mammals of Palawan Island, Philippines. Proceedings of the Biological Society of Washington. 117:271-302. PDF

Esselstyn, JA, GJ Wiles, A Amar. 2004. Habitat use of the Pacific sheath-tailed bat (Emballonura semicaudata) on Aguiguan, Mariana Islands. Acta Chiropterologica. 6:303-308. PDF

Esselstyn, JA, RC Wildman. 1997. Observations of Juga in the diet of larval Pacific giant salamanders (Dicamptodon tenebrosus). Northwestern Naturalist. 78:70-73. PDF