publications

Smith BT, Thom G, Joseph L. 2024. Revised evolutionary and taxonomic synthesis for parrots (Order: Psittaciformes) guided by phylogenomic analysis. Bulletin of the American Museum of Natural History, 2024(468), 1-87.

Thom G, Moreira LR, Batista R, Gehara M, Aleixo A, Smith BT. 2024. Genomic architecture predicts tree topology, population structuring, and demographic history in Amazonian birds. Genome Biology and Evolution, evae002.

Oswald JA, Smith BT, Allen JM, Guralnick RP, Steadman DW, LeFebvre MJ. 2023. Changes in parrot diversity after human arrival to the Caribbean. Proceedings of the National Academy of Sciences, 120(41), e2301128120.

Wood A, Szpiech Z, Lovette IJ, Smith BT, Toews D. 2023. Genomes of the extinct Bachman's Warbler shows high divergence and no evidence of admixture with other extant Vermivora Warblers. Current Biology, 33 (13), 2823-2829.

Moreira LR, Smith BT. 2023. Convergent genomic signatures of local adaptation across a continental-scale environmental gradient. Science Advances, 9(20), eadd0560.

Klicka J, Epperly K, Smith BT, Spellman GM, Chaves JA, Escalante P, Witt CC, Canales-del-Castillo R, Zink RM 2023. Lineage diversity in a widely distributed New World passerine bird, the House Wren. Ornithology, p.ukad018 https://doi.org/10.1093/ornithology/ukad018

Smith BT, Merwin J, Provost KL, Thom G, Brumfield RT, Ferreira M, Mauck III WM, Moyle RG, Wright T. Joseph L. 2023. Phylogenomic analysis of the parrots of the world distinguishes artifactual from biological sources of gene tree discordance. Systematic Biology, 72(1), 228-241.

Reeve AH, Gower G, Pujolar JM, Smith BT, Petersen B, Olsson U, Haryoko T, Koane B, Maiah G, Blom MP, Ericson PG, Irestedt M, Racimo F, Jønsson KA. 2023. Population genomics of the island thrush elucidates one of earth’s great archipelagic radiations. Evolution Letters. 7(1), 24-36.

Moreira LR, Klicka J, Smith BT. 2022. Demography and linked selection interact to shape the genomic landscape of codistributed woodpeckers during the Ice Age. Molecular Ecology, 32(7), 1739-1759.

Provost K, Shue SY, Forcellati M, Smith BT. 2022. The genomic landscapes of desert birds form over multiple time scales. Molecular Biology and Evolution, 39(10), msac200.

Burbrink FT, Crother BI, Murray CM, Smith BT, Ruane S, Myers EA, Pyron RA, 2022. Empirical and philosophical problems with the subspecies rank. Ecology and Evolution, 12(7), p.e9069.

Musher LJ, Giakoumis M, Albert J, Del-Rio G, Rego M, Thom G, Aleixo A, Ribas CC, Brumfield, RT, Smith BT, Cracraft J, 2022. River network rearrangements promote speciation in lowland Amazonian birds. Science Advances, 8(14), p.eabn1099.

Thom G, Gehara M, Smith BT, Miyaki CY, do Amaral FR. 2021. Microevolutionary dynamics show tropical valleys are deeper for montane birds of the Atlantic Forest. Nature Communications, 12(1), 1-10.

Olah G, Smith BT, Joseph L, Banks SC, Heinsohn R. 2021. Advancing genetic methods in the study of parrot biology and conservation. Diversity, 521.

Raxworthy CJ, Smith BT. 2021. Mining museums for historical DNA: advances and challenges in museomics. Trends in Ecology & Evolution. https://doi.org/10.1016/j.tree.2021.07.009.

Provost KL, Myers EA, Smith BT. 2021. Community phylogeographic patterns reveal how a barrier filters and structures taxa in North American warm deserts. Journal of Biogeography, 48, 1267-1283

Smith BT, Gehara M, Harvey MG. 2021. The demography of extinction in eastern North American birds. Proc R Soc. B, 28820201945. 

Harvey MG, Bravo GA, Claramunt S, Cuervo AM, Derryberry GE, Battilana J, Seeholzer GF, McKay JS, O’Meara BC, Faircloth BC, Edwards SV, Pérez-Emán J, Moyle RG, Sheldon FH, Alexio A, Smith BT, Chesser RT, Silveira LF, Cracraft J, Brumfield RT, Derryberry EP. 2020. The evolution of a tropical biodiversity hotspot. Science, 370(6522), 1343-1348.

Moreira LR, Hernandez‐Baños BE, Smith BT. 2020. Spatial predictors of genomic and phenotypic variation differ in a lowland Middle American bird (Icterus gularis). Molecular Ecology, 29 (16), 3084-3101.

Joseph L, Merwin J, Smith BT. 2020. Improved systematics of lorikeets reflects their evolutionary history and frames conservation priorities. Emu–Austral Ornithology, 120 (3), 201-215. pdf

Smith BT, Mauck III WM, Benz B, Andersen MJ. 2020. Uneven missing data skew phylogenomic relationships within the lories and lorikeets. Genome Biology and Evolution, 12 (7), 1131–1147.

Thom G, Smith BT, Gehara M, Montesanti J, Lima-Ribeiro MS, Piacentini VQ, Miyaki CY, do Amaral FR. 2020. Climatic dynamics and topography control genetic variation in Atlantic Forest montane birds. Molecular Phylogenetics and Evolution, 106812.

Merwin JT, Seeholzer GF, Smith BT. 2020. Macroevolutionary bursts and constraints generate a rainbow in a clade of tropical birds. BMC Evolutionary Biology, 30, 32.

McCullough JM, Moyle RG, Smith BT, Andersen MJ. 2019. A Laurasian origin for a pantropical bird radiation is supported by genomic and fossil data (Aves: Coraciiformes). Proceedings of the Royal Society B, 286(1910), 20190122.

Kimball RT, Oliveros CH, Wang N, White ND, Barker FK, Field DJ, Ksepka DT, Chesser RT, Moyle RG, Braun MJ, Brumfield RT, Faircloth BC, Smith BT, Braun EL. A phylogenomic supertree of birds. Diversity, 2019, 11, 109. *cover image

Oliveros CH, Field DJ, Ksepka, DT, Barker FK, Aleixo A, Andersen MJ, Bravo GA, Brumfield RT, Chesser RT, Claramunt S, Cracraft J, Cuervo AM, Derryberry EP, Glenn TC, Harvey MG, Hosner PA, Joseph L, Kimball RT, Mack AL, Miskelly CM, Peterson AT, Robbins MB, Sheldon FH, Silveira LF, Smith BT, White ND, Moyle RG, Faircloth BC. 2019. Earth history and the passerine superradiation. Proceedings of the National Academy of Sciences, 116(16), 7916-7925.

Provost KL, Mauck WM, Smith BT. 2018. Genomic divergence in allopatric Northern Cardinals of the North American warm deserts is associated with behavioral differentiation. Ecology and Evolution, 8, 12456–12478.

Smith BT, Bryson Jr RW, Mauck III WM, Chaves J, Robbins MB, Aleixo A, Klicka J. 2018. Species delimitation and biogeography of the gnatcatchers and gnatwrens (Aves: Polioptilidae). Molecular Phylogenetics and Evolution, 126, 45-57.

Andersen MJ, McCullough JM, Mauck WM III, Smith BT, Moyle RG. 2018. A phylogeny of kingfishers reveals an Indomalayan origin and elevated rates of diversification on oceanic islands. Journal of Biogeography, 45, 269–281.

Provost KL, Joseph L, Smith BT. 2018. Resolving a phylogenetic hypothesis for parrots: implications from systematics to conservation. Emu–Austral Ornithology, 118, 7-21. pdf

Andersen MJ, Fatdal L, Mauck WM II, Smith BT. 2017. An ornithological survey of Vanuatu on the islands of Éfaté, Malakula, Gaua, and Vanua Lava. Check List, 13, 755–782.

Harvey MG, Seeholzer GF, Smith BT, Rabosky DL, Cuervo AM, Brumfield RT. 2017. Positive association between population genetic differentiation and speciation rates in New World birds. Proceedings of the National Academy of Sciences, 114(24), 6328-6333.

Chua VL, Smith BT, Burner RC, Rahman MA, Lakim M, Prawiradilaga DM, Moyle RG, Sheldon FH. 2017. Evolutionary and ecological forces influencing population diversification in Bornean montane passerines. Molecular Phylogenetics and Evolution, 113, 139-149.

Smith BT, Seeholzer GF, Harvey MG, Cuervo AM, Brumfield RT. 2017. A latitudinal phylogeographic diversity gradient in birds. PLoS Biology 15, e2001073. *cover image

Oswald JA, Overcast I, Mauck WM, Andersen MJ, Smith BT. 2017. Isolation with asymmetric gene flow during the nonsynchronous divergence of dry forest birds. Molecular Ecology, 26, 1386–1400.

Burbrink F, Chan Y, Myers E, Ruane S, Smith BT, Hickerson M. 2016. Asynchronous demographic responses to Pleistocene climate change in Eastern Nearctic vertebrates. Ecology Letters, 19, 1457-1467.

Harvey MG, Smith BT, Glenn T, Faircloth BC, Brumfield RT. 2016. Sequence capture versus restriction site associated DNA sequencing for shallow systematics. Systematic Biology, 65, 910-924.

Bacon CD, Silvestro D, Jaramillo C, Smith BT, Chakrabarty P, Antonelli A. 2015. Reply to Lessios and Marko et al.: Early and progressive migration across the Isthmus of Panama is robust to missing data and biases. Proceedings of the National Academy of Sciences, 112, E5767-E5768.

Seeholzer GF, Justiniano MA, Harvey MG, Smith BT. 2015. Ornithological inventory along an elevational gradient in the río Cotacajes Valley, dptos. La Paz and Cochabamba, Bolivia. Cotinga, 37, 87-100.

Bacon CD, Silvestro D, Jaramillo C, Smith BT, Chakrabarty P, Antonelli A. 2015. Biological evidence supports an early and complex emergence of the Isthmus of Panama. Proceedings of the National Academy of Sciences, 112, 6110-6115.

Smith BT, McCormack JE, Cuervo AM, Hickerson MJ, Aleixo A, Cadena CD, Pérez-Emán J, Burney CW, Xie X, Harvey MG, Faircloth BC, Glenn TC, Derryberry EP, Prejean J, Fields S, Brumfield RT. 2014. The drivers of tropical speciation. Nature, 515, 406-409.

Bryson Jr R, Smith BT, Nieto-Montes A, Garcia U, Riddle B. 2014. Conflicting gene histories confound phylogeographical inference in a widespread group of Nearctic treefrogs. Zoological Journal of the Linnean Society, 172, 103-116.

van Els P, Spellman GM, Smith BT, Klicka J. 2014. Extensive gene flow characterizes the phylogeography of a widespread North American migrant bird: Black-headed grosbeak (Pheucticus melanocephalus). Molecular Phylogenetics and Evolution, 78, 148-159.

Houston DD, Shiozawa DK, Smith BT, Riddle BR. 2014. Investigating the effects of Pleistocene events on genetic divergence within Richardsonius balteatus, a widely distributed western North American minnow. BMC Evolutionary Biology, 14, 111.

Harvey MG, Lane DF, Hite J, Terrill RS, Figueroa-Ramírez S, Smith BT, Klicka J, Campos W. 2014. Notes on bird species in bamboo in Northern Madre de Dios, Peru, including the first Peruvian record of Acre Tody-Tyrant (Hemitriccus cohnhafti). Occ. Pap. LSU Mus. Nat. Sci., 81, 1-31.

Amei A, Smith BT. 2014. Robust estimates of divergence times and selection with a Poisson Random Field model: a case study of comparative phylogeographic data. Genetics, 19, 225-233.

Gawin DF, Rahman MA, Ramji MFS, Smith BT, Lim HC, Moyle RG, Sheldon FH. 2014. Patterns of avian diversification in Borneo: The case of the endemic Mountain Black-eye (Chlorocharis emiliae). The Auk, 13, 86-99.

Bryson RW, Chaves J, Smith BT, Miller M, Winker K, Pérez-Emán J, Klicka J. 2014. Diversification across the New World within the “blue” cardinalids (Aves: Cardinalidae). Journal of Biogeography, 4, 587-599.

Smith BT, Harvey MG, Faircloth BC, Glenn TC, Brumfield RT. 2014. Target capture and massively parallel sequencing of ultraconserved elements (UCEs) for comparative studies at shallow evolutionary time scales. Systematic Biology, 63, 83-95. *cover image

Pulgarín-R PC, Smith BT, Bryson RW, Spellman GM, Klicka J. 2013. Multilocus phylogeny and biogeography of the New World Pheucticus grosbeaks (Aves: Cardinalidae). Molecular Phylogenetics and Evolution, 69, 1222–1227.

Whittaker A, Alexio A, Whitney BM, Smith BT, Klicka J. 2013. A distinctive new species of gnatcatcher in the Polioptila guianensis complex (Aves: Polioptilidae) from western Amazonian Brazil. In: Handbook of the Birds of the World. Special volume: new species and global index [J. del Hoyo, A. Elliott e D. Christie, eds.]. Lynx Edicions, Barcelona, Spain, pp. 301–305.

Smith BT, Klicka J. 2013. Examining the role of effective population size on mitochondrial and multilocus divergence time discordance in a songbird. PLoS ONE, 8, e55161.

Smith BT, Bryson RW, Chua V, Africa L, Klicka J. 2013. Speciational history of the North American Haemorhous finches (Aves: Fringillidae) inferred from multilocus data. Molecular Phylogenetics and Evolution, 66, 1055-1059.

Bryson RW, Riddle BR, Graham MR, Smith BT, Prendini L 2013. As old as the hills: montane scorpions in southwestern North America reveal ancient associations between biotic diversification and landscape history. PLoS ONE, 8, e52822.

Smith BT, Ribas CC, Whitney BW, Hernández-Baños BE, Klicka J. 2013. Identifying biases at different spatial and temporal scales of diversification: a case study using the Neotropical parrotlet genus Forpus. Molecular Ecology, 22, 483-494.

Smith BT, Bryson RW, Houston D, Klicka J. 2012. An asymmetry in niche conservatism contributes to the latitudinal species diversity gradient in New World vertebrates. Ecology Letters, 15, 1318-1325.

Ribas CC, Maldonado MC, Smith BT, Cabanne GS, D’Horta FM, Naka LN. 2012. Towards an integrated historical biogeography of the Neotropical lowland avifauna: combining diversification analysis and landscape evolution. Ornitología Neotropical, 23, 189-208.

Smith BT, Amei A, Klicka J. 2012. Evaluating the role of contracting and expanding rainforest in initiating cycles of speciation across the Isthmus of Panama. Proceedings of the Royal Society: Biological Sciences, 279, 3520-3526.

Smith BT, Escalante P, Hernández-Baños BE, Navarro-Sigüenza AG, Rowher S, Klicka J. 2011. The role of historical and contemporary processes on the phylogeography of the Northern Cardinal, Cardinalis cardinalis. BMC Evolutionary Biology, 11, 136.

Klicka J, Spellman GM, Winker KS, Chua V, Smith BT. 2011. Phylogeography and population-genetic analysis of a widespread, sedentary North American bird: The Hairy Woodpecker (Picoides villosus). The Auk, 128, 346-362. *cover image

Smith BT, Klicka J. 2010. Late Pliocene Panamanian uplift has profound affect on the exchange, diversification, and distribution of New World birds. Ecography, 33, 333-342.