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Items: 1 to 50 of 69

1.

Adapterama II: universal amplicon sequencing on Illumina platforms (TaggiMatrix).

Glenn TC, Pierson TW, Bayona-Vásquez NJ, Kieran TJ, Hoffberg SL, Thomas Iv JC, Lefever DE, Finger JW, Gao B, Bian X, Louha S, Kolli RT, Bentley KE, Rushmore J, Wong K, Shaw TI, Rothrock MJ Jr, McKee AM, Guo TL, Mauricio R, Molina M, Cummings BS, Lash LH, Lu K, Gilbert GS, Hubbell SP, Faircloth BC.

PeerJ. 2019 Oct 11;7:e7786. doi: 10.7717/peerj.7786. eCollection 2019.

2.

Adapterama I: universal stubs and primers for 384 unique dual-indexed or 147,456 combinatorially-indexed Illumina libraries (iTru & iNext).

Glenn TC, Nilsen RA, Kieran TJ, Sanders JG, Bayona-Vásquez NJ, Finger JW, Pierson TW, Bentley KE, Hoffberg SL, Louha S, Garcia-De Leon FJ, Del Rio Portilla MA, Reed KD, Anderson JL, Meece JK, Aggrey SE, Rekaya R, Alabady M, Belanger M, Winker K, Faircloth BC.

PeerJ. 2019 Oct 11;7:e7755. doi: 10.7717/peerj.7755. eCollection 2019.

3.

Adapterama III: Quadruple-indexed, double/triple-enzyme RADseq libraries (2RAD/3RAD).

Bayona-Vásquez NJ, Glenn TC, Kieran TJ, Pierson TW, Hoffberg SL, Scott PA, Bentley KE, Finger JW, Louha S, Troendle N, Diaz-Jaimes P, Mauricio R, Faircloth BC.

PeerJ. 2019 Oct 11;7:e7724. doi: 10.7717/peerj.7724. eCollection 2019.

4.

A Highly Contiguous Reference Genome for Northern Bobwhite (Colinus virginianus).

Salter JF, Johnson O, Stafford NJ, Herrin WF, Schilling D, Cedotal C, Brumfield RT, Faircloth BC.

G3 (Bethesda). 2019 Oct 14. pii: g3.400609.2019. doi: 10.1534/g3.119.400609. [Epub ahead of print]

5.

Phylogenomic species delimitation in microendemic frogs of the Brazilian Atlantic Forest.

Pie MR, Bornschein MR, Ribeiro LF, Faircloth BC, McCormack JE.

Mol Phylogenet Evol. 2019 Sep 17;141:106627. doi: 10.1016/j.ympev.2019.106627. [Epub ahead of print]

PMID:
31539606
6.

A phylogenomic framework for pelagiarian fishes (Acanthomorpha: Percomorpha) highlights mosaic radiation in the open ocean.

Friedman M, Feilich KL, Beckett HT, Alfaro ME, Faircloth BC, Černý D, Miya M, Near TJ, Harrington RC.

Proc Biol Sci. 2019 Sep 11;286(1910):20191502. doi: 10.1098/rspb.2019.1502. Epub 2019 Sep 11.

PMID:
31506051
7.

Comparison of ultraconserved elements (UCEs) to microsatellite markers for the study of avian hybrid zones: a test in Aphelocoma jays.

Vinciguerra NT, Tsai WLE, Faircloth BC, McCormack JE.

BMC Res Notes. 2019 Jul 24;12(1):456. doi: 10.1186/s13104-019-4481-z.

8.

Earth history and the passerine superradiation.

Oliveros CH, Field DJ, Ksepka DT, Barker FK, Aleixo A, Andersen MJ, Alström P, Benz BW, Braun EL, Braun 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.

Proc Natl Acad Sci U S A. 2019 Apr 16;116(16):7916-7925. doi: 10.1073/pnas.1813206116. Epub 2019 Apr 1.

9.

Resolving Deep Nodes in an Ancient Radiation of Neotropical Fishes in the Presence of Conflicting Signals from Incomplete Lineage Sorting.

Alda F, Tagliacollo VA, Bernt MJ, Waltz BT, Ludt WB, Faircloth BC, Alfaro ME, Albert JS, Chakrabarty P.

Syst Biol. 2019 Jul 1;68(4):573-593. doi: 10.1093/sysbio/syy085.

PMID:
30521024
10.

Genome-wide signals of drift and local adaptation during rapid lineage divergence in a songbird.

Friis G, Fandos G, Zellmer AJ, McCormack JE, Faircloth BC, Milá B.

Mol Ecol. 2018 Dec;27(24):5137-5153. doi: 10.1111/mec.14946. Epub 2018 Dec 21.

PMID:
30451354
11.

Insight from an ultraconserved element bait set designed for hemipteran phylogenetics integrated with genomic resources.

Kieran TJ, Gordon ERL, Forthman M, Hoey-Chamberlain R, Kimball RT, Faircloth BC, Weirauch C, Glenn TC.

Mol Phylogenet Evol. 2019 Jan;130:297-303. doi: 10.1016/j.ympev.2018.10.026. Epub 2018 Oct 22.

PMID:
30359745
12.

What are the roles of taxon sampling and model fit in tests of cyto-nuclear discordance using avian mitogenomic data?

Tamashiro RA, White ND, Braun MJ, Faircloth BC, Braun EL, Kimball RT.

Mol Phylogenet Evol. 2019 Jan;130:132-142. doi: 10.1016/j.ympev.2018.10.008. Epub 2018 Oct 12.

PMID:
30321694
13.

Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event.

Winker K, Glenn TC, Faircloth BC.

PeerJ. 2018 Oct 5;6:e5735. doi: 10.7717/peerj.5735. eCollection 2018.

14.

Correction: Ultraconserved elements (UCEs) resolve the phylogeny of Australasian smurf-weevils.

Van Dam MH, Lam AW, Sagata K, Gewa B, Laufa R, Balke M, Faircloth BC, Riedel A.

PLoS One. 2018 Sep 27;13(9):e0205049. doi: 10.1371/journal.pone.0205049. eCollection 2018.

15.

Allele Phasing Greatly Improves the Phylogenetic Utility of Ultraconserved Elements.

Andermann T, Fernandes AM, Olsson U, Töpel M, Pfeil B, Oxelman B, Aleixo A, Faircloth BC, Antonelli A.

Syst Biol. 2019 Jan 1;68(1):32-46. doi: 10.1093/sysbio/syy039.

16.

Cultivation and genomics of the first freshwater SAR11 (LD12) isolate.

Henson MW, Lanclos VC, Faircloth BC, Thrash JC.

ISME J. 2018 Jun;12(7):1846-1860. doi: 10.1038/s41396-018-0092-2. Epub 2018 Mar 29.

17.

Explosive diversification of marine fishes at the Cretaceous-Palaeogene boundary.

Alfaro ME, Faircloth BC, Harrington RC, Sorenson L, Friedman M, Thacker CE, Oliveros CH, Černý D, Near TJ.

Nat Ecol Evol. 2018 Apr;2(4):688-696. doi: 10.1038/s41559-018-0494-6. Epub 2018 Mar 12.

PMID:
29531346
18.

Ultraconserved elements (UCEs) resolve the phylogeny of Australasian smurf-weevils.

Van Dam MH, Lam AW, Sagata K, Gewa B, Laufa R, Balke M, Faircloth BC, Riedel A.

PLoS One. 2017 Nov 22;12(11):e0188044. doi: 10.1371/journal.pone.0188044. eCollection 2017. Erratum in: PLoS One. 2018 Sep 27;13(9):e0205049.

19.

Universal target-enrichment baits for anthozoan (Cnidaria) phylogenomics: New approaches to long-standing problems.

Quattrini AM, Faircloth BC, Dueñas LF, Bridge TCL, Brugler MR, Calixto-Botía IF, DeLeo DM, Forêt S, Herrera S, Lee SMY, Miller DJ, Prada C, Rádis-Baptista G, Ramírez-Portilla C, Sánchez JA, Rodríguez E, McFadden CS.

Mol Ecol Resour. 2018 Mar;18(2):281-295. doi: 10.1111/1755-0998.12736. Epub 2017 Dec 6.

PMID:
29131534
20.

Conflicting Evolutionary Histories of the Mitochondrial and Nuclear Genomes in New World Myotis Bats.

Platt RN 2nd, Faircloth BC, Sullivan KAM, Kieran TJ, Glenn TC, Vandewege MW, Lee TE Jr, Baker RJ, Stevens RD, Ray DA.

Syst Biol. 2018 Mar 1;67(2):236-249. doi: 10.1093/sysbio/syx070.

21.

Polyandry enhances offspring viability with survival costs to mothers only when mating exclusively with virgin males in Drosophila melanogaster.

Castrezana S, Faircloth BC, Bridges WC, Gowaty PA.

Ecol Evol. 2017 Aug 14;7(18):7515-7526. doi: 10.1002/ece3.3152. eCollection 2017 Sep.

22.

Investigating Difficult Nodes in the Placental Mammal Tree with Expanded Taxon Sampling and Thousands of Ultraconserved Elements.

Esselstyn JA, Oliveros CH, Swanson MT, Faircloth BC.

Genome Biol Evol. 2017 Sep 1;9(9):2308-2321. doi: 10.1093/gbe/evx168.

23.

Phylogenetic relationships of diurnal, phytotelm-breeding Melanophryniscus (Anura: Bufonidae) based on mitogenomic data.

Pie MR, Ströher PR, Belmonte-Lopes R, Bornschein MR, Ribeiro LF, Faircloth BC, McCormack JE.

Gene. 2017 Sep 10;628:194-199. doi: 10.1016/j.gene.2017.07.048. Epub 2017 Jul 15.

24.

Phylogenomic analysis of Lake Malawi cichlid fishes: Further evidence that the three-stage model of diversification does not fit.

Hulsey CD, Zheng J, Faircloth BC, Meyer A, Alfaro ME.

Mol Phylogenet Evol. 2017 Sep;114:40-48. doi: 10.1016/j.ympev.2017.05.027. Epub 2017 Jun 1.

PMID:
28579077
25.

Phylogenomic analysis of a rapid radiation of misfit fishes (Syngnathiformes) using ultraconserved elements.

Longo SJ, Faircloth BC, Meyer A, Westneat MW, Alfaro ME, Wainwright PC.

Mol Phylogenet Evol. 2017 Aug;113:33-48. doi: 10.1016/j.ympev.2017.05.002. Epub 2017 May 6.

PMID:
28487262
26.

Dry habitats were crucibles of domestication in the evolution of agriculture in ants.

Branstetter MG, Ješovnik A, Sosa-Calvo J, Lloyd MW, Faircloth BC, Brady SG, Schultz TR.

Proc Biol Sci. 2017 Apr 12;284(1852). pii: 20170095. doi: 10.1098/rspb.2017.0095.

27.

Phylogenomic Insights into the Evolution of Stinging Wasps and the Origins of Ants and Bees.

Branstetter MG, Danforth BN, Pitts JP, Faircloth BC, Ward PS, Buffington ML, Gates MW, Kula RR, Brady SG.

Curr Biol. 2017 Apr 3;27(7):1019-1025. doi: 10.1016/j.cub.2017.03.027.

28.

Phylogenomic Systematics of Ostariophysan Fishes: Ultraconserved Elements Support the Surprising Non-Monophyly of Characiformes.

Chakrabarty P, Faircloth BC, Alda F, Ludt WB, Mcmahan CD, Near TJ, Dornburg A, Albert JS, Arroyave J, Stiassny MLJ, Sorenson L, Alfaro ME.

Syst Biol. 2017 Nov 1;66(6):881-895. doi: 10.1093/sysbio/syx038.

PMID:
28334176
29.

Use of sonic tomography to detect and quantify wood decay in living trees.

Gilbert GS, Ballesteros JO, Barrios-Rodriguez CA, Bonadies EF, Cedeño-Sánchez ML, Fossatti-Caballero NJ, Trejos-Rodríguez MM, Pérez-Suñiga JM, Holub-Young KS, Henn LA, Thompson JB, García-López CG, Romo AC, Johnston DC, Barrick PP, Jordan FA, Hershcovich S, Russo N, Sánchez JD, Fábrega JP, Lumpkin R, McWilliams HA, Chester KN, Burgos AC, Wong EB, Diab JH, Renteria SA, Harrower JT, Hooton DA, Glenn TC, Faircloth BC, Hubbell SP.

Appl Plant Sci. 2016 Dec 16;4(12). pii: apps.1600060. doi: 10.3732/apps.1600060. eCollection 2016 Dec.

30.

Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye.

Harrington RC, Faircloth BC, Eytan RI, Smith WL, Near TJ, Alfaro ME, Friedman M.

BMC Evol Biol. 2016 Oct 21;16(1):224.

31.

High phylogenetic utility of an ultraconserved element probe set designed for Arachnida.

Starrett J, Derkarabetian S, Hedin M, Bryson RW Jr, McCormack JE, Faircloth BC.

Mol Ecol Resour. 2017 Jul;17(4):812-823. doi: 10.1111/1755-0998.12621. Epub 2016 Nov 19.

PMID:
27768256
32.

Tectonic collision and uplift of Wallacea triggered the global songbird radiation.

Moyle RG, Oliveros CH, Andersen MJ, Hosner PA, Benz BW, Manthey JD, Travers SL, Brown RM, Faircloth BC.

Nat Commun. 2016 Aug 30;7:12709. doi: 10.1038/ncomms12709.

33.

Hidden histories of gene flow in highland birds revealed with genomic markers.

Zarza E, Faircloth BC, Tsai WL, Bryson RW Jr, Klicka J, McCormack JE.

Mol Ecol. 2016 Oct;25(20):5144-5157. doi: 10.1111/mec.13813. Epub 2016 Sep 12.

PMID:
27543758
34.

Capturing Darwin's dream.

Glenn TC, Faircloth BC.

Mol Ecol Resour. 2016 Sep;16(5):1051-8. doi: 10.1111/1755-0998.12574.

35.

RADcap: sequence capture of dual-digest RADseq libraries with identifiable duplicates and reduced missing data.

Hoffberg SL, Kieran TJ, Catchen JM, Devault A, Faircloth BC, Mauricio R, Glenn TC.

Mol Ecol Resour. 2016 Sep;16(5):1264-78. doi: 10.1111/1755-0998.12566.

PMID:
27416967
36.

Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics.

Harvey MG, Smith BT, Glenn TC, Faircloth BC, Brumfield RT.

Syst Biol. 2016 Sep;65(5):910-24. doi: 10.1093/sysbio/syw036. Epub 2016 Jun 10. Review.

PMID:
27288477
37.

Analysis of a Rapid Evolutionary Radiation Using Ultraconserved Elements: Evidence for a Bias in Some Multispecies Coalescent Methods.

Meiklejohn KA, Faircloth BC, Glenn TC, Kimball RT, Braun EL.

Syst Biol. 2016 Jul;65(4):612-27. doi: 10.1093/sysbio/syw014. Epub 2016 Feb 10.

PMID:
26865273
38.

Replicated divergence in cichlid radiations mirrors a major vertebrate innovation.

McGee MD, Faircloth BC, Borstein SR, Zheng J, Darrin Hulsey C, Wainwright PC, Alfaro ME.

Proc Biol Sci. 2016 Jan 13;283(1822). pii: 20151413. doi: 10.1098/rspb.2015.1413.

39.

Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes).

Hosner PA, Faircloth BC, Glenn TC, Braun EL, Kimball RT.

Mol Biol Evol. 2016 Apr;33(4):1110-25. doi: 10.1093/molbev/msv347. Epub 2015 Dec 29.

PMID:
26715628
40.

PHYLUCE is a software package for the analysis of conserved genomic loci.

Faircloth BC.

Bioinformatics. 2016 Mar 1;32(5):786-8. doi: 10.1093/bioinformatics/btv646. Epub 2015 Nov 2.

PMID:
26530724
41.

Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics.

Edwards SV, Xi Z, Janke A, Faircloth BC, McCormack JE, Glenn TC, Zhong B, Wu S, Lemmon EM, Lemmon AR, Leaché AD, Liu L, Davis CC.

Mol Phylogenet Evol. 2016 Jan;94(Pt A):447-62. doi: 10.1016/j.ympev.2015.10.027. Epub 2015 Oct 27. Review.

42.

Relating belowground microbial composition to the taxonomic, phylogenetic, and functional trait distributions of trees in a tropical forest.

Barberán A, McGuire KL, Wolf JA, Jones FA, Wright SJ, Turner BL, Essene A, Hubbell SP, Faircloth BC, Fierer N.

Ecol Lett. 2015 Dec;18(12):1397-405. doi: 10.1111/ele.12536. Epub 2015 Oct 16.

PMID:
26472095
43.

Sequence capture of ultraconserved elements from bird museum specimens.

McCormack JE, Tsai WL, Faircloth BC.

Mol Ecol Resour. 2016 Sep;16(5):1189-203. doi: 10.1111/1755-0998.12466. Epub 2015 Oct 24.

PMID:
26391430
44.

Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers in percomorph fishes.

Gilbert PS, Chang J, Pan C, Sobel EM, Sinsheimer JS, Faircloth BC, Alfaro ME.

Mol Phylogenet Evol. 2015 Nov;92:140-6. doi: 10.1016/j.ympev.2015.05.027. Epub 2015 Jun 12.

45.

Phylogenomic analyses data of the avian phylogenomics project.

Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Alfaro-Núñez A, Narula N, Liu L, Burt D, Ellegren H, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MT, Zhang G; Avian Phylogenomics Consortium.

Gigascience. 2015 Feb 12;4:4. doi: 10.1186/s13742-014-0038-1. eCollection 2015.

46.

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.

Green RE, Braun EL, Armstrong J, Earl D, Nguyen N, Hickey G, Vandewege MW, St John JA, Capella-Gutiérrez S, Castoe TA, Kern C, Fujita MK, Opazo JC, Jurka J, Kojima KK, Caballero J, Hubley RM, Smit AF, Platt RN, Lavoie CA, Ramakodi MP, Finger JW Jr, Suh A, Isberg SR, Miles L, Chong AY, Jaratlerdsiri W, Gongora J, Moran C, Iriarte A, McCormack J, Burgess SC, Edwards SV, Lyons E, Williams C, Breen M, Howard JT, Gresham CR, Peterson DG, Schmitz J, Pollock DD, Haussler D, Triplett EW, Zhang G, Irie N, Jarvis ED, Brochu CA, Schmidt CJ, McCarthy FM, Faircloth BC, Hoffmann FG, Glenn TC, Gabaldón T, Paten B, Ray DA.

Science. 2014 Dec 12;346(6215):1254449. doi: 10.1126/science.1254449. Epub 2014 Dec 11.

47.

Whole-genome analyses resolve early branches in the tree of life of modern birds.

Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MP, Prosdocimi F, Samaniego JA, Vargas Velazquez AM, Alfaro-Núñez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker FK, Jønsson KA, Johnson W, Koepfli KP, O'Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alström P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MT, Zhang G.

Science. 2014 Dec 12;346(6215):1320-31. doi: 10.1126/science.1253451.

48.

A phylogenomic analysis of turtles.

Crawford NG, Parham JF, Sellas AB, Faircloth BC, Glenn TC, Papenfuss TJ, Henderson JB, Hansen MH, Simison WB.

Mol Phylogenet Evol. 2015 Feb;83:250-7. doi: 10.1016/j.ympev.2014.10.021. Epub 2014 Nov 4.

PMID:
25450099
49.

The drivers of tropical speciation.

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.

Nature. 2014 Nov 20;515(7527):406-9. doi: 10.1038/nature13687. Epub 2014 Sep 10.

PMID:
25209666
50.

Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera.

Faircloth BC, Branstetter MG, White ND, Brady SG.

Mol Ecol Resour. 2015 May;15(3):489-501. doi: 10.1111/1755-0998.12328. Epub 2014 Sep 29.

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