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Publications & Data

Our manuscripts and associated data.

Peer-reviewed ( **Denotes equal authorship. Entries in order of final publication)


  1. TR Schultz, J Sosa-Calvo, MP Kweskin, MW Lloyd, B Dentinger, PW Kooij3, EC Vellinga, SA Rehner, A Rodrigues, QV Montoya, H Fernández-Marín, A Ješovnik, T Niskanen, K Liimatainen, CA Leal-Dutra, SE Solomon, NM Gerardo, CR Currie, M Bacci Jr., HL Vasconcelos, C Rabeling, BC Faircloth, VP Doyle (2024). The coevolution of fungus-ant agriculture. Science 386:105-109. doi: 10.1126/science.adn7179

  2. S Wutke, SM BLank, J Boevé, BC Faircloth, F Kock, CR Linnen, T Malm, G Niu, M Prous, NM Schiff, S Schmidt, A Taegar, L Vilhelmsen, N Wahlberg, M Wei, T Nyman (2024).Phylogenomics and biogeography of sawflies and woodwasps (Hymenoptera, Symphyta). Molecular Phylogenetics and Evolution 199:108144. doi: 10.1016/j.ympev.2024.108144

  3. J Stiller, S Feng, A Chowdury, I Rivas-Gonzaléz, D Duchêne, Q Fang, Y Deng, A Kozlov, A Stamatakis, S Claramunt, JMT Nguyen, SYW Ho, BC Faircloth, J Haag, P Houde, J Cracraft, M Balaban, U Mai, G Chen, R Gao, C Zhou, Y Xie, Z Huang, Z Cao, Z Yan, HA Ogilvie, L Nakhleh, B Lindow, B Morel, J Fjeldså, P Hosner, RR da Fonseca, B Peterson, JA Tobias, T Székely, JD Kennedy, AH Reeve, A Liker, M Stervander, A Antunes, DT Tietze, M Bertelsen, F Lei, C Rahbek, GR Graves, MH Schierup, T Warnow, EL Braun, MTP Gilbert, ED Jarvis, S Mirarab, G Zhang (2024). Complexity of avian evolution revealed by family-level genomes. Nature 629:851-860. doi: 10.1038/s41586-024-07323-1

  4. RC Harrington, M Kolmann, JJ Day, BC Faircloth, M Friedman, TJ Near (2024). Dispersal sweepstakes: Biotic interchange propelled air breathing fishes across the globe. Journal of Biogeography 51:797-813. doi: 10.1111/jbi.14781

  5. EC Corbett, RT Brumfield, BC Faircloth (2024). The mechanistic, genetic and evolutionary causes of bird eye colour variation. Ibis 160:560-589. doi: 10.1111/ibi.13276

  6. JF Salter, RT Brumfield, BC Faircloth (2024). An island "endemic" born out of hybridization between introduced lineages. Molecular Ecology 33:e16990. doi: 10.1111/mec.16990

  7. AE Moncrieff, BC Faircloth, RR Remsen, AE Hiller, C Felix, AP Capparella, A Aleixo, T Valqui, RT Brumfield. (2024). Implications of headwater contact zones for the riverine barrier hypothesis: A case study of the Blue-capped Manakin (Lepidothrix coronata). Evolution 78:53-68. doi: 10.1093/evolut/qpad187

  8. JR Glass, RC Harrington, PF Cowman, BC Faircloth, TJ Near. (2023). Widespread sympatry in a species-rich clade of marine fishes (Carangoidea). Proceedings of the Royal Society B 290:20230657. doi: 10.1098/rspb.2023.0657

  9. EW Getz, VC Lanclos, CY Kojima, C Cheng, MW Henson, ME Schön, TJG Ettema, BC Faircloth, JC Thrash (2023). The AEGEAN-169 clade of bacterioplankton is synonymous with SAR11 subclade V (HIMB59) and metabolically distinct. mSystems 8:e00179-23. doi: 10.1128/msystems.00179-23

  10. EC Elizondo, BC Faircloth, RT Brumfield, SB Shakya, VA Ellis, CJ Schmidt, AI Kovach, WG Shriver (2023). A high quality de novo genome assembly for Clapper Rail (Rallus crepitans). G3: Genes | Genomes | Genetics 13:jkad097. doi: 10.1093/g3journal/jkad097

  11. WB Ludt, EC Corbett, J Kattawar III, P Chakrabarty, BC Faircloth (2023). A reference genome for Bluegill (Centrarchidae: Lepomis macrochirus). G3: Genes | Genomes | Genetics 13:jkad019. doi: 10.1093/g3journal/jkad019

  12. VC Lanclos, AN Rasmussen, CY Kojima, C Cheng, MW Henson, BC Faircloth, CA Francis, C Thrash (2023). Ecophysiology and genomics of the brackish water adapted SAR11 subclade IIIa. ISME Journal 17:620-629. doi: 10.1038/s41396-023-01376-2

  13. JMC Ribeiro, NJ Bayona-Vásquez, K Budachetri, D Kumar, JC Frederick, F Tahir, BC Faircloth, TC Glenn, S Karim (2023). A draft of the genome of the Gulf Coast tick, Amblyomma maculatum. Ticks and Tick-borne Diseases 14:102090. doi: 10.1016/j.ttbdis.2022.102090

  14. A Ghezelayagh, RC Harrington, ED Burress, MA Campbell, J Buckner, P Chakrabarty, JR Glass, WT McCraney, PJ Unmack, CE Thacker, ME Alfaro, ST Friedman, WB Ludt, M Friedman, SA Price, A Dornburg, BC Faircloth, PE Wainwright, TJ Near (2022). Prolonged morphological expansion of the spiny-rayed fishes following the end-Cretaceous. Nature Ecology and Evolution 6:1211-1220. doi: 10.1038/s41559-022-01801-3

  15. JF Salter, PA Hosner, WL Tsai, JE McCormack, EL Braun, RT Kimball, RT Brumfield, BC Faircloth (2022). Historical specimens and the limits of subspecies phylogenomics in the New World quails (Odontophoridae). Molecular Phylogenetics and Evolution 175:107559. doi: 10.1016/j.ympev.2022.107559

  16. AE Moncrieff, BC Faircloth, RT Brumfield (2022). Systematics of Lepidothrix manakins (Aves: Passeriformes: Pipridae) using RADcap markers. Molecular Phylogenetics and Evolution 173:107525. doi: 10.1016/j.ympev.2022.107525

  17. N Buainain, M Ferreira, JE Avendaño, CD Cadena, BC Faircloth, RT Brumfield, J Cracraft, CC Ribas (2022). Biogeography of a neotropical songbird radiation reveals similar diversification dynamics between montane and lowland clades. Journal of Biogeography 49:1260-1273. doi: 10.1111/jbi.14379

  18. BF Melo, BL Sidlauskas, TJ Near, FF Roxo, A Ghezelayagh, LE Ochoa, MLJ Stiassny, J Arroyave, J Chang, BC Faircloth, DJ MacGuigan, RC Harrington, RC Benine, MD Burns, K Hoekzema, NC Sanches, JA Maldonado-Ocampo, RMC Castro, F Foresti, ME Alfaro, C Oliveira (2022). Accelerated diversification explains the exceptional species richness of tropical characoid fishes. Systematic Biology 71:78-92. doi: 10.1093/sysbio/syab040

  19. G Del-Rio, MA Rego, BM Whitney, F Schunck, L Silveira, BC Faircloth, RT Brumfield (2022). Displaced clines in an avian hybrid zone (Thamnophilidae: Rhegmatorhina) within an Amazonian interfluve. Evolution 76:455-475. doi: 10.1111/evo.14377

  20. AE Hiller, RT Brumfield, BC Faircloth (2021). A reference genome for the nectar-robbing Black-throated Flowerpiercer (Diglossa brunneiventris). G3: Genes | Genomes | Genetics 11:jkab271. doi: 10.1093/g3journal/jkab271

  21. JC Buckner, RC Sanders, BC Faircloth, P Chakrabarty (2021). The critical importance of vouchers in genomics. eLife 10:e68264. doi: 10.7554/eLife.68264

  22. N Buainain, MFA Maximiano, M Ferreira, A Aleixo, BC Faircloth, RT Brumfield, J Cracraft, CC Ribas (2021). Multiple species and deep genomic divergences despite little phenotypic differentiation in an ancient Neotropical songbird, Tunchiornis ochraceiceps (Sclater, 1860) (Aves: Vireonidae). Molecular Phylogenetics and Evolution 162:107206. doi: 10.1016/j.ympev.2021.107206

  23. JT Burley, JR Kellner, SP Hubbell, BC Faircloth (2021). Genome assemblies for two neotropical trees: Jacaranda copaia and Handroanthus guayacan (Family: Bignoniaceae). G3: Genes | Genomes | Genetics 11:jkab010. doi: 10.1093/g3journal/jkab010

  24. Stiller, RR da Fonseca, ME Alfaro, BC Faircloth, NG Wilson, GW Rouse (2021). Using UCEs to track the influence of sea level change on leafy seadragon populations. Molecular Ecology. doi: 10.1111/mec.15744

  25. MG Harvey, GA Bravo, S Claramunt, AM Cuervo, GE Derryberry, J Battilana, GF Seeholzer, JS McKay, BC O'Meara, BC Faircloth, SV Edwards, J Pérez-Emán, RG Moyle, FH Sheldon, A Aleixo, BT Smith, RT Chesser, LF Silveira, J Cracraft, RT Brumfield, EP Derryberry (2020). The evolution of a tropical biodiversity hotspot. Science 370:1343-1348. doi: 10.1126/science.aaz6970

  26. S Feng, J Stiller, Y Deng, J Armstrong, Q Fang, AH Reeve, D Xie, G Chen, C Guo, BC Faircloth, [116 others], G Del-Rio, [13 others], B Paten, G Zhang (2020). Dense sampling of bird diversity increases power of comparative genomics. Nature 587:252-257. doi: 10.1038/s41586-020-2873-9

  27. JF McLaughlin, BC Faircloth, TC Glenn, K Winker (2020). Divergence, gene flow, and the speciation continuum in nine lineages of trans-Beringian birds. Molecular Ecology. doi: 10.1111/mec.15574

  28. AM Quattrini, E. Rodríguez, BC Faircloth, PF Cowman, MR Brugler, GA Farfan, ME Hellberg, MV Kitahara, CL Morrison, DA Paz-García, JD Reimer, CS McFadden (2020). Paleoclimate ocean conditions shaped the evolution of corals and their skeletal composition through deep time. Nature Ecology and Evolution 4:1531-1538. doi: 10.1038/s41559-020-01291-1

  29. BC Faircloth, F Alda, K Hoekzma, MD Burns, C Oliveira, JS Albert, BF Melo, LE Ochoa, FF Roxo, P Chakrabarty, BL Sidlauskas, ME Alfaro (2020). A target enrichment bait set for studying relationships among ostariophysan fishes. Copeia 108:47-60. doi: 10.1643/CG-18-139

  30. JF Salter, CH Oliveros, PA Hosner, JD Manthey, MB Robbins, RG Moyle, RT Brumfield, BC Faircloth (2020). Extensive paraphyly in the typical owl family (Strigidae). The Auk 137:1-15. doi: 10.1093/auk/ukz070

  31. JF Salter, O Johnson, NJ Stafford, III, WF Herrin, Jr, D Schilling, C Cedotal, RT Brumfield, BC Faircloth (2019). A highly contiguous reference genome for Northern Bobwhite (Colinus virginianus). G3: Genes | Genomes | Genetics 9:3929-3932. doi: 10.1534/g3.119.400609

  32. MR Pie, MR Bornschein, LF Ribiero, BC Faircloth, JE McCormack (2019). Phylogenomic species delimitation in microendemic frogs of the Brazilian Atlantic Forest. Molecular Phylogenetics and Evolution 141:10662. doi: 10.1016/j.ympev.2019.106627

  33. NJ Bayona-Vasquez, TC Glenn, TJ Kieran, TW Pierson, SL Hoffberg, PA Scott, KE Bentley, JW Finger Jr., PR Watson, S Louha, N Troendle, P Diaz-Jaimes, R Mauricio, BC Faircloth (2019). Adapterama III: Quadruple-indexed, double/triple-enzyme RADseq libraries (2RAD/3RAD). PeerJ 7:e7724. doi: 10.7717/peerj.7724

  34. TC Glenn, TW Pierson, NJ Bayona-Vásquez, TJ Kieran, SL Hoffberg, JC Thomas IV, DE Lefever, JW Finger Jr., B Gao, X Bian, S Louha, RT Kolli, K Bentley, J Rushmore, K Wong, TI Shaw, MJ Rothrock Jr., AM McKee, TL Guo, R Mauricio, M Molina, BS Cummings, LH Lash, K Lu, GS Gilbert, SP Hubbell, BC Faircloth (2019). Adapterama II: Universal amplicon sequencing on Illumina platforms (TaggiMatrix). PeerJ 7:e7786. doi: 10.7717/peerj.7786

  35. TC Glenn, RA Nilsen, TJ Kieran, JW Finger Jr., TW Pierson, KE Bentley, SL Hoffberg, S Louha, FJ García-De León, MA Del Rio Portilla, KD Reed, JL Anderson, JK Meece, SE Aggrey, R Rekaya, M Alabady, M Belanger, K Winker, BC Faircloth (2019). Adapterama I: Universal stubs and primers for 384 unique dual-indexed or 147,456 combinatorially-indexed Illumina libraries (iTru & iNext). PeerJ 7:e7755. doi: 10.7717/peerj.7755

  36. M Friedman, R Harrington, HT Beckett, K Feilich, TJ Near, ME Alfaro, BC Faircloth, D Černý, M Miya (2019). Ancient adaptive radiation in the open ocean: Rapid divergence in Pelagiaria (Acanthomorpha: Percomorpha) near the Cretaceous-Paleogene boundary. Proceedings of the Royal Society B 286:20191502. doi: 10.1098/rspb.2019.1502

  37. NT Vinciguerra, WLE Tsai, BC Faircloth, JE McCormack (2019). Comparison of ultraconserved elements (UCEs) to microsatellite markers for the study of avian hybrid zones: a test in Aphelocoma jays. BMC Research Notes 12:456. doi: 10.1186/s13104-019-4481-z

  38. RT Kimball, CH Oliveros, N Wang, ND White, FK Barker, DJ Field, DT Ksepka, RT Chesser, RG Moyle, MJ Braun, RT Brumfield, BC Faircloth, BT Smith, EL Braun (2019). A phylogenomic supertree of birds. Diversity 11:109. doi: 10.3390/d11070109

  39. CH Oliveros, DJ Field, DT Ksepka, FK Barker, A Aleixo, MJ Andersen, P Alström, BW Benz, EL Braun, MJ Braun, GA Bravo, RT Brumfield, RT Chesser, S Claramunt, J Cracraft, AM Cuervo, EP Derryberry, TC Glenn, MG Harvey, PA Hosner, L Joseph, R Kimball, AL Mack, CM Miskelly, AT Peterson, MB Robbins, FH Sheldon, LF Silveira, BT Smith, ND White, RG Moyle, BC Faircloth (2019). Earth history and the passerine superradiation. Proceedings of the National Academy of Sciences U S A 116:7916-7925. doi: 10.1073/pnas.1813206116

  40. K Winker, TC Glenn, J Withrow, SG Sealy, BC Faircloth (2019). Speciation despite gene flow in two owls (Aegolius ssp.): Evidence from 2,517 loci with ultraconserved elements (UCEs). Auk. doi: 10.1093/auk/ukz012

  41. S Grove, NP Saarman, GS Gilbert, BC Faircloth, KA Haubensak, IM Parker (2019). Ectomycorrhizas and tree seedling establishment are strongly influenced by forest edge proximity but not soil inoculum. Ecological Applications 29:e01867. doi: 10.1002/eap.1867

  42. F Alda, V Tagliacollo, M Bernt, B Waltz, W Ludt, BC Faircloth, ME Alfaro, J Albert, P Chakrabarty (2019). Resolving deep nodes in an ancient radiation of neotropical fishes in the presence of conflicting signals from incomplete lineage sorting. Systematic Biology. doi: 10.1093/sysbio/syy085

  43. TJ Kieran, ERL Gordon, M Forthman, R Hoey-Chamberlain, RT Kimball, BC Faircloth, C Weirauch, TC Glenn (2019). Insight from an ultraconserved element bait set designed for hemipteran phylogenetics integrated with genomic resources. Molecular Phylogenetics and Evolution 130:297-303. doi: 10.1016/j.ympev.2018.10.026

  44. R Tamashiro, ND White, ME Braun, BC Faircloth, EL Braun, R Kimball (2019). What are the roles of taxon sampling and model fit in tests of cyto-nuclear discordance using avian mitogenomic data? Molecular Phylogenetics and Evolution 130:132-142. doi: 10.1016/j.ympev.2018.10.008

  45. T Hofmann, A Fernandes, U Olsson U, M Töpel, B Pfeil, B Oxelman, A Aleixo, BC Faircloth, A Antonelli (2019). Allele phasing greatly improves the phylogenetic utility of ultraconserved elements. Systematic Biology 68:32–46. doi: 10.1093/sysbio/syy039

  46. G Friss, G Fandos, A Zellmer, JE McCormack, BC Faircloth, B Milá (2018). Genome-wide signals of drift and local adaptation during rapid lineage divergence in a songbird. Molecular Ecology 27:5137-5153. doi: 10.1111/mec.14946

  47. K Winker, TC Glenn, BC Faircloth (2018). Ultraconserved elements (UCEs) illuminate the pop- ulation genomics of a recent, high-latitude avian speciation event. PeerJ 6:e5735. doi: 10.7717/peerj.5735

  48. MR Pie, BC Faircloth, LF Ribiero, MR Bornschein, JE McCormack (2018). Phylogenomics of montane frogs of the Brazilian Atlantic Forest supports a scenario of isolation in sky islands fol- lowed by relative climatic stability. Biological Journal of the Linnaen Society 125:72-82. doi:10.1093/biolinnean/bly093

  49. MW Henson, VC Lanclos, BC Faircloth, JC Thrash (2018).Cultivation and genomics of the first freshwater SAR11 (LD12) isolate. ISME Journal 12:1846–1860. doi: 10.1038/s41396-018-0092-2

  50. ME Alfaro, BC Faircloth, RC Harrington, L Sorenson, M Friedman, CE Thacker, and TJ Near (2018). Explosive diversification of marine fishes at the Cretaceous-Paleogene boundary. Nature Ecol Evol. doi: 10.1038/s41559-018-0494-6

  51. AM Quattrini, BC Faircloth, LF Dueñas, TCL Bridge, M Brugler, IF Calixto-Botía, DM DeLeo, S Forêt, S Herrera, S Lee, DJ Miller, C Prada, G Rádis-Baptista, C Ramírez-Portilla, JA Sánchez, E Rodríguez, and CS McFadden (In Press). Universal target-enrichment baits for anthozoan (Cnidaria) phylogenomics: New approaches to long-standing problems. Mol Ecol Res. doi: 10.1111/1755-0998.12736

  52. RN Platt, BC Faircloth, KAM Sullivan, T Kieran, TC Glenn, MW Vandewege, TE Lee, R Baker, RD Stevens, DA Ray (2018). Conflicting evolutionary histories of the mitochondrial and nuclear genomes in New World Myotis. Syst Biol 67:236–249. doi: 10.1093/sysbio/syx070

  53. MH Van Dam, AW Lam, K Sagata, B Gewa, R Laufa, M Blake, BC Faircloth, A Riedel (2017). Ultraconserved elements (UCEs) resolve the phylogeny of Australasian smurf-weevils.. PLoS One 12: e0188044. doi: 10.1371/journal.pone.0188044

  54. JA Esselstyn, 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 Biol Evol 9:2308–2321. doi: 10.1093/gbe/evx168

  55. M Pie, P Ströher, R Belmonte-Lopes, M Bornschein, L Ribiero, BC Faircloth, JE McCormack (2017). Phylogenetic relationships of diurnal, phytotelm-breeding Melanophryniscus (Anura: Bufonidae) based on mitogenomic data. Gene 628:194-199. doi: 10.1016/j.gene.2017.07.048

  56. S Castrezana, BC Faircloth, W Bridges, PA Gowaty (2017). Polyandry enhances offspring viability with survival costs to mothers only when exposed exclusively to virgin males in Drosophila melanogaster. Ecol Evol 7:7515–7526. doi: 10.1002/ece3.3152

  57. BC Faircloth (2017). Identifying conserved genomic elements and designing universal probe sets to enrich them. Methods Ecol Evol 8:1103-1112. doi: 10.1111/2041-210X.12754

  58. P Chakrabarty, BC Faircloth, CD McMahan, WB Ludt, WL Fink, TJ Near, A Dornberg, JS Albert, J Arroyave, MLJ Stiassny, L Sorenson, ME Alfaro (2017). Comparative systematics of Ostariophysan fishes with a focus on the perplexing characins (Ostariophysi: Characiformes) using ultraconserved elements, traditional genes, and morphologya. Syst Biol 66:881-895. doi: 10.1093/sysbio/syx038

  59. CD Hulsey, J Zheng, BC Faircloth, A Meyer, ME Alfaro (2017). Lake Malawi cichlid phylogenomics rejects a strict three-stage model of diversification. Mol Phylogenet Evol 114:40-48. doi: 10.1016/j.ympev.2017.05.027

  60. MG Branstetter, JT Longino, PS Ward, BC Faircloth (2017). Enriching the ant tree of life: enhanced UCE bait set for genome-scale phylogenetics of ants and other Hymenoptera. Methods Ecol Evol 8:768-776. doi: 10.1111/2041-210X.12742

  61. J Starrett, S Derkarabetian, M Hedin, RW Bryson Jr., JE McCormack, BC Faircloth (2017). High phylogenetic utility of an ultraconserved element probe set designed for Arachnida. Mol Ecol Res 17:812-823. doi: 10.1111/1755-0998.12621

  62. SJ Longo, BC Faircloth, A Meyer, ME Westneat, ME Alfaro, PC Wainright (2017). Phylogenomic analysis of a rapid radiation of misfit fishes (Syngnathiformes) using ultraconserved elements. Mol Phylogenet Evol 113:33-48. doi: 10.1016/j.ympev.2017.05.002

  63. MG Branstetter, A Ješovnik, J Sosa-Calvo, MW LLoyd, BC Faircloth, SG Brady, TR Schultz (2017). Dry habitats were crucibles of domestication in the evolution of agriculture in ants. Proc R Soc Lond B Biol Sci 284:20170095. doi: 10.1098/rspb.2017.0095

  64. MG Branstetter, BN Danforth, JP Pitts, BC Faircloth, PS Ward, ML Buffington, MW Gates, RR Kula, SG Brady (2017). Phylogenomic analysis of ants, bees and stinging wasps: improved taxon sampling enhances understanding of hymenopteran evolution. Curr Biol 27:1019-1025. doi: 10.1016/j.cub.2017.03.027

  65. MR Pie, PR Ströher, MR Bornschein, LF Ribiero, BC Faircloth, JE McCormack (2017). The mitochondrial genome of Brachycephalus brunneus (Anura: Brachycephalidae), with comments on the phylogenetic position of Brachycephalidae. Biochem Syst Ecol. doi: 10.1016/j.bse.2016.12.009

  66. GS Gilbert, JO Ballesteros, CA Barrios-Rodriguez, EF Bonadies, ML Cedeño Sánchez, NJ Fossatti-Caballero, MM Trejos-Rodríguez, JM Pérez-Suñiga, KS Holub-Young, KAW Henn, JB Thompson, CG Garciá-López4, AC Romo, DC Johnston, PP Barrick, FA Jordan , S Hershcovich , Natalie Russo, Juan David Sánchez , JP Fábrega, R Lumpkin, HA McWilliams, KN Chester, AC Burgos, EB Wong, JH Diab, SA Renteria, JT Harrower, DA Hooton, TC Glenn, BC Faircloth, SP Hubbell (2016). Use of acoustic tomography to detect and quantify wood decay in living trees. Applications in Plant Sciences 4:1600060. doi: 10.3732/apps.1600060

  67. RC Harrington, BC Faircloth, RI Eytan, WL Smith, TJ Near, ME Alfaro, M Friedman (2016). Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye. BMC Evol Biol 7:12709. doi: 10.1186/s12862-016-0786-x

  68. RG Moyle, CH Oliveros, MJ Andersen, PA Hosner, BW Benz, JD Manthey, SL Travers, RM Brown, BC Faircloth (2016). Tectonic collision and uplift of Wallacea triggered the global songbird radiation. Nat Commun 7:12709. doi: 10.1038/ncomms12709

  69. E Zarza, BC Faircloth, W Tsai, R Bryson Jr., J Klicka, JE McCormack (2016). Hidden histories of gene flow in highland birds revealed with genomic markers. Mol Ecol 25:5144-5157. doi: 10.1111/mec.13813

  70. TC Glenn, BC Faircloth (2016). Capturing Darwin's dream. Mol Ecol Res 16:1051–1058. doi: 10.1111/1755-0998.12574

  71. S Hoffberg, TJ Kieran, JM Catchen, A Devault, BC Faircloth, R Mauricio, TC Glenn (2016). RADcap: Sequence capture of dual-digest radseq libraries with identifiable duplicates. Mol Ecol Res 16:1264-1278. doi: 10.1111/1755-0998.12566

  72. MG Harvey, BT Smith, TC Glenn, BC Faircloth, and RT Brumfield (2016). Sequence capture versus restriction site associated DNA sequencing for shallow systematics. Syst Biol 65:910-924. doi: 10.1093/sysbio/syw036

  73. RW Bryson Jr., BC Faircloth, WLE Tsai, JE McCormack, J Klicka (2016). Target enrichment of thousands of ultraconserved elements sheds new light on early relationships within New World sparrows (Aves: Passerellidae). Auk 133:451-458. doi: 10.1642/AUK-16-26.1

  74. KA Meiklejohn, BC Faircloth, TC Glenn, RT Kimball, EL Braun (2016). Analysis of a rapid evolutionary radiation using ultraconserved elements (UCEs): Evidence for a bias in some multispecies coalescent methods. Syst Biol 65:612-627. doi: 10.1093/sysbio/syw014

  75. M McGee, BC Faircloth, SR Borstein, J Zheng, CD Hulsey, PC Wainwright, ME Alfaro (2016). Replicated divergence in cichlid radiations mirrors a major vertebrate innovation. Proc R Soc Lond B Biol Sci 283:20151413. doi: 10.1098/rspb.2015.1413

  76. PA Hosner, BC Faircloth, TC Glenn, EL Braun, RT Kimball (2016). Phylogenomic inference of landfowl (Aves: Galliformes): effects of missing data in concatenated and coalescent inference and evidence for a bias in gene tree reconciliation approaches. Mol Biol Evol 33:1110-1125. doi: 10.1093/molbev/msv347

  77. BC Faircloth (2016). PHYLUCE is a software package for the analysis of conserved genomic loci. Bioinformatics 32:786-788. doi: 10.1093/bioinformatics/btv646

  78. JE McCormack, WLE Tsai, BC Faircloth (2016). Sequence capture of ultraconserved elements from bird museum specimens. Mol Ecol Res 16:1189–1203. doi: 10.1111/1755-0998.12466

  79. SV Edwards, Z Xi, A Janke, BC Faircloth, JE McCormack, TC Glenn, B Zhon, S Wu, EM Lemmon, AR Lemmon, AD Leache, L Liu, CC Davis (2016). Implementing and testing the multispecies coalescent model: a valuable paradigm for phylogenomics. Mol Phylogenet Evol. 94(Pt A):447-62. doi: 10.1016/j.ympev.2015.10.027

  80. A Barberan, KL McGuire, JA Wolf, FA Jones, SJ Wright, BL Turner, A Essene, SP Hubbell, BC Faircloth, N Fierer (2015). Relating belowground microbial composition to the taxonomic, phylogenetic, and functional trait distributions of trees in a tropical forest. Ecol Lett 18:1397–1405. doi: 10.1111/ele.12536

  81. CL Pruett, L Wan, T Li, C Spern, SL Lance, TC Glenn, BC Faircloth, K Winker (2015). Development and characterization of microsatellite loci for common raven (Corvus corax) and cross species amplification in other Corvidae. BMC Res Notes 8:655 doi:10.1186/s13104-015-1643-5

  82. PS Gilbert, J Chang, C Pan, E Sobel, JS Sinsheimer, BC Faircloth, ME Alfaro (2015). Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers for the fish series Percomorpha. Mol Phylogenet Evol 92:140-146. doi:10.1016/j.ympev.2015.05.027

  83. NG Crawford, JF Parham, AB Sellas, BC Faircloth, TC Glenn, TJ Papenfuss, JB Henderson, MH Hansen, WB Simison (2015). A phylogenomic analysis of turtles. Mol Phylogenet Evol 83:250-257. pmid: 25450099. doi:10.1016/j.ympev.2014.10.021

  84. ED Jarvis, S Mirarab, A Aberer, B Li, P Houde, C Li, SYW Ho, BC Faircloth, B Nabholz, JT Howard, A Suh, CC Weber, RR da Fonseca, A Alfaro-Núñez, N Narula, L Liu, D Burt, H Ellegren, SV Edwards, A Stamatakis, DP Mindell, J Cracraft, EL Braun, T Warnow, W Jun, MTP Gilbert, G Zhang, and The Avian Phylogenomics Consortium. Phylogenomic Analyses Data of the Avian Phylogenomics Project. GigaScience 4:4. doi:10.1186/s13742-014-0038-1

  85. BC Faircloth, MG Branstetter, ND White, SG Brady (2015). Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera. Mol Ecol Res 15:489-501. doi:10.1111/1755-0998.12328

  86. ED Jarvis, S Mirarab, A Aberer, B Li, P Houde, C Li, SYW Ho, BC Faircloth, [94 others], T Warnow, W Jun, MTP Gilbert, G Zhang (2014). Whole genome analyses resolve the early branches in the tree of life of modern birds. Science 346:1320-1331. doi:10.1126/science.1253451

  87. RE Green, EL Braun, [49 others], BC Faircloth, FG Hoffman, TC Glenn, T Gabaldón, B Paten, DA Ray (2014). The genomes of three crocodilians provide insight into archosaur evolution. Science 346:1335. doi:10.1126/science.1254449

  88. BT Smith, JE McCormack, AM Cuervo, MJ Hickerson, A Aleixo, CD Cadena, J Pérez-Emén, A Flórez-Rodríguez, CW Burney, X Xie, MG Harvey, BC Faircloth, TC Glenn, EP Derryberry, J Prejean, A Fields, RT Brumfield (2014). The drivers of tropical speciation. Nature 515:406-409. doi:10.1038/nature13687

  89. AG Ramos, SO Nunziata, SL Lance, C Rodríguez, BC Faircloth, PA Gowaty, H Drummond (2014). Habitat structure and colony structure constrain extrapair paternity in a colonial bird. Anim Behav 95:121-127. doi:10.1016/j.anbehav.2014.07.003

  90. AG Ramos, SO Nunziata, SL Lance, C Rodríguez, BC Faircloth, PA Gowaty, H Drummond (2014). Interactive effects of male and female age on extra-pair paternity in a socially monogamous seabird. Behav Ecol Sociobiol 68:1603-1609. doi:10.1007/s00265-014-1769-9

  91. S Keping, Meiklejohn KA, BC Faircloth, Glenn TC, Braun EB, Kimball RT (2014). The evolution of peafowl and other taxa with ocelli (eyespots): A phylogenomic approach. Proc R Soc Lond B Biol Sci 281: 20140823. doi:10.1098/rspb.2014.0823

  92. FC Gowen, JM Maley, C Cicero, AT Peterson, BC Faircloth, TC Warr, JE McCormack (2014). Speciation in Western Scrub-Jays, Haldane's rule, and genetic clines in secondary contact. BMC Evolutionary Biology 14:135. doi:10.1186/1471-2148-14-135

  93. KA Meiklejohn, MJ Danielson, BC Faircloth, TC Glenn, EL Braun, RT Kimball (2014). Incongruence among different mitochondrial regions: A case study using complete mitogenomes. Mol Phylogenet Evol 78:314-323. doi:10.1016/j.ympev.2014.06.003

  94. BT Smith, MG Harvey, BC Faircloth, TC Glenn, RT Brumfield (2014) Target capture and massively parallel sequencing of ultraconserved elements (UCEs) for comparative studies at shallow evolutionary time scales. Syst Biol 63:83-95. doi:10.1093/sysbio/syt061

  95. CL Pruett, C Whelan, A Ricono, SL Lance, TC Glenn, BC Faircloth, K Winker (2014) Development and characterization of microsatellite loci for two species of Beringian birds, rock sandpiper (Calidris ptilocnemis) and Pacific wren (Troglodytes pacificus). Conserv Genet Res 6:175-177. doi:10.1007/s12686-013-0040-4

  96. TC Glenn, SL Lance, AM McKee, BL Webster, AM Emery, A Zerlotini, G Oliveira, D Rollinson, BC Faircloth (2013). Significant variance in genetic diversity among populations of Schistosoma haematobium detected using microsatellite DNA loci from a genome-wide database. Parasit Vectors 6:300.
    doi:10.1186/1756-3305-6-300

  97. BC Faircloth**, L Sorenson, F Santini, ME Alfaro** (2013) A Phylogenomic Perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements (UCEs). PLoS ONE 8(6): e65923. doi:10.1371/journal.pone.0065923

  98. JE McCormack, MG Harvey, BC Faircloth, NG Crawford, TC Glenn, RT Brumfield (2013) A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing. PLoS ONE 8(1): e54848. doi:10.1371/journal.pone.0054848

  99. JE McCormack, BC Faircloth (2013) Next-generation phylogenetics takes root. Mol Ecol 22:19-21. doi:10.1111/mec.12050

  100. BC Faircloth, TC Glenn (2012) Not all sequence tags are created equal: Designing and validating sequence identification tags robust to indels. PLoS ONE 7(8): e42543. doi:10.1371/journal.pone.0042543

  101. A Untergasser, I Cutcutache, T Koressaar, J Ye, BC Faircloth, M Remm, S Rozen (2012) Primer3 — New capabilities and interfaces. Nucleic Acids Res. 40:e115. doi:10.1093/nar/gks596

  102. NG Crawford, BC Faircloth, JE McCormack, RT Brumfield, K Winker, TC Glenn (2012) More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs. Biol Lett 8:783-786. doi:10.1098/rsbl.2012.0331

  103. JA St. John, EL Braun, SR Isberg, LG Miles, AY Chong, J Gongora, P Dalzell, C Moran, T Iguchi, B Bed’Hom, SC Burgess, AM Cooksey, TA Castoe, A Abzhanov, LD Densmore, M Venegas-Anya, MJ Greenwold, RH Sawyer, FG Hoffmann, NG Crawford, JC Drew, SV Edwards, MK Fujita, JM Howard, BC Faircloth, DE Janes, S Yar Khan, Si Kohno, APJ de Koning, SL Lance, FM McCarthy, JE McCormack, ME Merchant, DG Peterson, DD Pollock, N Pourmand, BJ Raney, KA Roessler, JR Sanford, CJ Schmidt, EW Triplett, TD Tuberville, ED Jarvis, LJ Guillette Jr, TC Glenn, RE Green, DA Ray (2012) Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biol 13:415-427. doi:10.1186/gb-2012-13-1-415

  104. BC Faircloth, JE McCormack, NG Crawford, MG Harvey, RT Brumfield, TC Glenn (2012) Ultraconserved elements anchor thousands of genetic markers for target enrichment spanning multiple evolutionary timescales. Syst Biol 61:717-726. doi:10.1093/sysbio/SYS004

  105. JE McCormack**, BC Faircloth**, NG Crawford, PA Gowaty, RT Brumfield, TC Glenn (2012) Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species tree analysis. Genome Res 26:746-754. doi:10.1101/gr.125864.111

  106. K Kusumi, RJ Kulathinal, A Abzhanov, S Boissinot, NG Crawford, BC Faircloth, TC Glenn, DE Janes, JB Losos, DB Menke, S Poe, TJ Sanger, C Schneider, J Stapley, J Wade, J Wilson-Rawls (2011) Developing a community-based genetic nomenclature for anole lizards. BMC Genomics 12:554-567. doi:10.1186/1471-2164-12-554

  107. BC Faircloth, A Title, K Tan, J Welty, JR Belthoff, PA Gowaty (2010) Eighteen microsatellite loci developed from western burrowing owls (Athene cunicularia hypugaea). Conserv Genet Res 2:167-171. doi:10.1007/s12686-010-9214-5

  108. TM Terhune, DC Sisson, WE Palmer, BC Faircloth, HL Stribling, JP Carroll (2010) Translocation to a fragmented landscape: survival, movement and site fidelity of Northern Bobwhites. Ecol Appl 20:1040-1052. doi:10.1890/09-1106.1.

  109. BC Faircloth, A Ramos, H Drummond, PA Gowaty (2009) Isolation and characterization of microsatellite loci from blue-footed boobies (Sula nebouxii). Conserv Genet Res 1:159-162. doi:10.1007/s12686-009-9038-3

  110. JS Skvarla, BC Faircloth, BM Shamblin, MJ Conroy (2009) Microsatellite loci from the black bear (Ursus americanus). Mol Ecol Resour 9:288-291. doi:10.1111/j.1755-0998.2008.02234.x

  111. KO Evans, LW Burger Jr., BC Faircloth, WE Palmer, JP Carroll (2009) Effects of tissue collection methods on morphometrics and survival of captive neonatal Northern Bobwhite. J Wildl Manage 73:1241-1244. doi:10.2193/2008-011

  112. BM Shamblin, BC Faircloth, MG Dodd, DA Bagley, LM Erhart, PH Dutton, A Frey, CJ Nairn (2009) Tetranucleotide markers from the loggerhead sea turtle (Caretta caretta) and their cross-amplification in other marine turtle species. Conserv Genet 10:577-580. doi:10.1007/s10592-008-9573-6

  113. BC Faircloth, TM Terhune, NA Schable, TC Glenn, WE Palmer, JP Carroll (2009) Ten microsatellite loci from Northern Bobwhite (Colinus virginianus). Conserv Genet 10:535-538. doi:10.1007/ s10592-008-9559-4

  114. BM Shamblin, BC Faircloth, SA Josserand, CD Nelson, CJ Nairn (2008) Microsatellite loci from the eastern hemlock (Tsuga canadensis). Mol Ecol Resour 8:1354-1356. doi:10.1111/j.1755-0998.2008.02274.x

  115. BC Faircloth. MSATCOMMANDER: detection of microsatellite repeat arrays and automated, locus-specific primer design (2008) Mol Ecol Resour 8:92-94. doi:10.1111/j.1471-8286.2007.01884.x

  116. BM Shamblin, BC Faircloth, M Dodd, A Wood-Jones, SB Castleberry, JP Carroll, CJ Nairn (2007) Tetranucleotide microsatellites from the loggerhead sea turtle (Caretta caretta). Mol Ecol Notes 7:784-787. doi:10.1111/j.1471-8286.2007.01701.x

  117. BC Faircloth. GMCONVERT: file conversion for GeneMapperTM output files (2006) Mol Ecol Notes 6:968-970. doi:10.1111/j.1471-8286.2006.01419.x

  118. BC Faircloth, GP Keller, CJ Nairn, WE Palmer, JP Carroll, PA Gowaty (2006) Microsatellite loci from Eastern Bluebirds (Sialia sialis). Mol Ecol Notes 6:646-649. doi:10.1111/j.1471-8286.2006.01408.x

  119. BC Faircloth, A Reid, T Valentine, SH Eo, TM Terhune, TC Glenn, WE Palmer, CJ Nairn, JP Carroll (2005) Tetranucleotide, trinucleotide, and dinucleotide microsatellite loci from the bobcat (Lynx rufus). Mol Ecol Notes 5:387-389. doi:10.1111/j.1471-8286.2005.00936.x

  120. BC Faircloth, WE Palmer, JP Carroll (2005) Post-hatching brood amalgamation in Northern Bobwhites. J Field Ornithol 76:175-182.

  121. NA Schable, BC Faircloth, WE Palmer, JP Carroll, LW Burger, LA Brennan, C Hagen, TC Glenn (2004) Tetranucleotide and dinucleotide loci from northern bobwhite (Colinus virginianus). Mol Ecol Notes 4:415-419. doi:10.1111/j.1471-8286.2004.00670.x

Book Chapters ( ** denotes equal authorship )


  1. McCormack JE, F Rodrígues-Gómez, WLE Tsai, BC Faircloth (2017). Transforming museum specimens into genomic resources. Pages 143-156 in The Extended Specimen: Emerginng Frontiers in Collections-based Ornithological Research (MS Webster, ed.). CRC Press, Boca Raton, FL. ISBN: 9780367657826

  2. Heyduk K, JD Stephens, BC Faircloth, TC Glenn (2016). Targeted DNA Region Re-sequencing. Pages 43-68 in Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing (Aransay AM and JLL Trueba, eds.). Springer International Publishing, Switzerland. doi: 10.1007/978-3-319-31350-4_3