Publications & Data
Our manuscripts and associated data.
Our manuscripts and associated data.
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. doi: 10.1038/s41586-024-07323-1
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. doi: 10.1111/jbi.14781
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
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
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
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
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
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
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
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
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
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
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
AE Moncrieff, BC Faircloth, RT Brumfield (2022). Systematics of
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
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
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
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
JC Buckner, RC Sanders, BC Faircloth, P Chakrabarty (2021). The critical importance of vouchers in genomics. eLife 10:e68264. doi: 10.7554/eLife.68264
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
TC Glenn, BC Faircloth (2016). Capturing Darwin's dream. Mol Ecol Res 16:1051–1058. doi: 10.1111/1755-0998.12574
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
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
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
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
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
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
BC Faircloth (2016). PHYLUCE is a software package for the analysis of conserved genomic loci. Bioinformatics 32:786-788. doi: 10.1093/bioinformatics/btv646
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
JE McCormack, BC Faircloth (2013) Next-generation phylogenetics takes root. Mol Ecol 22:19-21. doi:10.1111/mec.12050
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
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
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
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
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
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
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
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
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.
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
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
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
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
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
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
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
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
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
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
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
BC Faircloth, WE Palmer, JP Carroll (2005) Post-hatching brood amalgamation in Northern Bobwhites. J Field Ornithol 76:175-182.
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
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
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