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Publications

Our manuscripts.

Peer-reviewed ( ** denotes equal authorship )


  1. JA Esselstyn, CH Oliveros, MT Swanson, BC Faircloth (In Press). Investigating difficult nodes in the placental mammal tree with expanded taxon sampling and thousands of ultraconserved elements. Genome Biol Evol. doi: 10.1093/gbe/evx168

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

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

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

  5. 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

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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

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

  19. 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

  20. 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

  21. 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

  22. 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

  23. 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

  24. 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

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

  26. 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

  27. 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

  28. 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

  29. 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

  30. 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

  31. 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

  32. 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

  33. 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

  34. 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

  35. 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

  36. 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

  37. 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

  38. 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

  39. 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

  40. 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

  41. 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

  42. 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

  43. 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

  44. 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

  45. 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

  46. 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

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

  48. 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

  49. 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

  50. 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

  51. 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

  52. 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

  53. 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

  54. 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

  55. 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

  56. 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.

  57. 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

  58. 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

  59. 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

  60. 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

  61. 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

  62. 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

  63. 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

  64. 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

  65. 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

  66. 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

  67. 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

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

  69. 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. 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