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Items: 1 to 50 of 78

1.

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]

2.

Diversification history in the Dendrocincla fuliginosa complex (Aves: Dendrocolaptidae): Insights from broad geographic sampling.

Schultz ED, Pérez-Emán J, Aleixo A, Miyaki CY, Brumfield RT, Cracraft J, Ribas CC.

Mol Phylogenet Evol. 2019 Nov;140:106581. doi: 10.1016/j.ympev.2019.106581. Epub 2019 Aug 17.

PMID:
31430551
3.

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.

4.

Fifty shades of brown: Macroevolution of plumage brightness in the Furnariida, a large clade of drab Neotropical passerines.

Marcondes RS, Brumfield RT.

Evolution. 2019 Apr;73(4):704-719. doi: 10.1111/evo.13707. Epub 2019 Mar 14.

PMID:
30816993
5.

Evolutionary dynamics of hybridization and introgression following the recent colonization of Glossy Ibis (Aves: Plegadis falcinellus) into the New World.

Oswald JA, Harvey MG, Remsen RC, Foxworth DU, Dittmann DL, Cardiff SW, Brumfield RT.

Mol Ecol. 2019 Apr;28(7):1675-1691. doi: 10.1111/mec.15008. Epub 2019 Apr 10.

PMID:
30614583
6.

The dual role of Amazonian rivers in the generation and maintenance of avian diversity.

Naka LN, Brumfield RT.

Sci Adv. 2018 Aug 1;4(8):eaar8575. doi: 10.1126/sciadv.aar8575. eCollection 2018 Aug.

7.

Ecological drivers of song evolution in birds: Disentangling the effects of habitat and morphology.

Derryberry EP, Seddon N, Derryberry GE, Claramunt S, Seeholzer GF, Brumfield RT, Tobias JA.

Ecol Evol. 2018 Jan 13;8(3):1890-1905. doi: 10.1002/ece3.3760. eCollection 2018 Feb.

9.

Habitat Association Predicts Genetic Diversity and Population Divergence in Amazonian Birds.

Harvey MG, Aleixo A, Ribas CC, Brumfield RT.

Am Nat. 2017 Nov;190(5):631-648. doi: 10.1086/693856. Epub 2017 Sep 11.

PMID:
29053360
10.

Correction: A latitudinal phylogeographic diversity gradient in birds.

Smith BT, Seeholzer GF, Harvey MG, Cuervo AM, Brumfield RT.

PLoS Biol. 2017 Jul 14;15(7):e1002610. doi: 10.1371/journal.pbio.1002610. eCollection 2017 Jul.

11.

Positive association between population genetic differentiation and speciation rates in New World birds.

Harvey MG, Seeholzer GF, Smith BT, Rabosky DL, Cuervo AM, Brumfield RT.

Proc Natl Acad Sci U S A. 2017 Jun 13;114(24):6328-6333. doi: 10.1073/pnas.1617397114. Epub 2017 May 30.

12.

A latitudinal phylogeographic diversity gradient in birds.

Smith BT, Seeholzer GF, Harvey MG, Cuervo AM, Brumfield RT.

PLoS Biol. 2017 Apr 13;15(4):e2001073. doi: 10.1371/journal.pbio.2001073. eCollection 2017 Apr. Erratum in: PLoS Biol. 2017 Jul 14;15(7):e1002610.

13.

Niche evolution and diversification in a Neotropical radiation of birds (Aves: Furnariidae).

Seeholzer GF, Claramunt S, Brumfield RT.

Evolution. 2017 Mar;71(3):702-715. doi: 10.1111/evo.13177. Epub 2017 Feb 8.

PMID:
28071791
14.

Behavioural response to song and genetic divergence in two subspecies of white-crowned sparrows (Zonotrichia leucophrys).

Lipshutz SE, Overcast IA, Hickerson MJ, Brumfield RT, Derryberry EP.

Mol Ecol. 2017 Jun;26(11):3011-3027. doi: 10.1111/mec.14002. Epub 2017 Jan 27.

PMID:
28036146
15.

Systematics and biogeography of the Automolus infuscatus complex (Aves; Furnariidae): Cryptic diversity reveals western Amazonia as the origin of a transcontinental radiation.

Schultz ED, Burney CW, Brumfield RT, Polo EM, Cracraft J, Ribas CC.

Mol Phylogenet Evol. 2017 Feb;107:503-515. doi: 10.1016/j.ympev.2016.12.023. Epub 2016 Dec 22.

16.

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
17.

The Mouse-colored Tyrannulet (Phaeomyias murina) is a species complex that includes the Cocos Flycatcher (Nesotriccus ridgwayi), an island form that underwent a population bottleneck.

Zucker MR, Harvey MG, Oswald JA, Cuervo A, Derryberry E, Brumfield RT.

Mol Phylogenet Evol. 2016 Aug;101:294-302. doi: 10.1016/j.ympev.2016.04.031. Epub 2016 Apr 25.

PMID:
27126184
18.

Comparative Gut Microbiota of 59 Neotropical Bird Species.

Hird SM, Sánchez C, Carstens BC, Brumfield RT.

Front Microbiol. 2015 Dec 21;6:1403. doi: 10.3389/fmicb.2015.01403. eCollection 2015.

19.

Similarity thresholds used in DNA sequence assembly from short reads can reduce the comparability of population histories across species.

Harvey MG, Judy CD, Seeholzer GF, Maley JM, Graves GR, Brumfield RT.

PeerJ. 2015 Apr 21;3:e895. doi: 10.7717/peerj.895. eCollection 2015.

20.

Geographic variation and phylogenetic relationships of Myiopagis olallai (Aves: Passeriformes; Tyrannidae), with the description of two new taxa from the Northern Andes.

Cuervo AM, Stiles FG, Lentino M, Brumfield RT, Derryberry EP.

Zootaxa. 2014 Oct 14;3873(1):1-24. doi: 10.11646/zootaxa.3873.1.1.

PMID:
25544202
21.

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.

22.

Genomic variation in a widespread Neotropical bird (Xenops minutus) reveals divergence, population expansion, and gene flow.

Harvey MG, Brumfield RT.

Mol Phylogenet Evol. 2015 Feb;83:305-16. doi: 10.1016/j.ympev.2014.10.023. Epub 2014 Nov 13.

PMID:
25450096
23.

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
24.

Adaptation to ephemeral habitat may overcome natural barriers and severe habitat fragmentation in a fire-dependent species, the Bachman's Sparrow (Peucaea aestivalis).

Cerame B, Cox JA, Brumfield RT, Tucker JW, Taylor SS.

PLoS One. 2014 Sep 2;9(9):e105782. doi: 10.1371/journal.pone.0105782. eCollection 2014.

25.

Adaptive processes drive ecomorphological convergent evolution in antwrens (Thamnophilidae).

Bravo GA, Remsen JV Jr, Brumfield RT.

Evolution. 2014 Oct;68(10):2757-74. doi: 10.1111/evo.12506. Epub 2014 Sep 17.

PMID:
25135629
26.

Inundicola Bravo, Isler, and Brumfield 2013 is a junior synonym of Akletos Dunajewski 1948 (Aves: Passeriformes: Thamnophilidae).

Isler ML, Bravo GA, Brumfield RT.

Zootaxa. 2014 Mar 17;3779:399-400. doi: 10.11646/zootaxa.3779.3.10. No abstract available.

PMID:
24871736
27.

Sampling locality is more detectable than taxonomy or ecology in the gut microbiota of the brood-parasitic Brown-headed Cowbird (Molothrus ater).

Hird SM, Carstens BC, Cardiff SW, Dittmann DL, Brumfield RT.

PeerJ. 2014 Mar 20;2:e321. doi: 10.7717/peerj.321. eCollection 2014.

28.

HZAR: hybrid zone analysis using an R software package.

Derryberry EP, Derryberry GE, Maley JM, Brumfield RT.

Mol Ecol Resour. 2014 May;14(3):652-63. doi: 10.1111/1755-0998.12209. Epub 2013 Dec 27.

PMID:
24373504
29.

Species coexistence and the dynamics of phenotypic evolution in adaptive radiation.

Tobias JA, Cornwallis CK, Derryberry EP, Claramunt S, Brumfield RT, Seddon N.

Nature. 2014 Feb 20;506(7488):359-63. doi: 10.1038/nature12874. Epub 2013 Dec 22.

PMID:
24362572
30.

Target capture and massively parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales.

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

Syst Biol. 2014 Jan 1;63(1):83-95. doi: 10.1093/sysbio/syt061. Epub 2013 Sep 10.

PMID:
24021724
31.

The genomic consequences of adaptive divergence and reproductive isolation between species of manakins.

Parchman TL, Gompert Z, Braun MJ, Brumfield RT, McDonald DB, Uy JA, Zhang G, Jarvis ED, Schlinger BA, Buerkle CA.

Mol Ecol. 2013 Jun;22(12):3304-17. doi: 10.1111/mec.12201. Epub 2013 Feb 26.

PMID:
23441849
32.

A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing.

McCormack JE, Harvey MG, Faircloth BC, Crawford NG, Glenn TC, Brumfield RT.

PLoS One. 2013;8(1):e54848. doi: 10.1371/journal.pone.0054848. Epub 2013 Jan 29.

34.

Correlated evolution of beak morphology and song in the neotropical woodcreeper radiation.

Derryberry EP, Seddon N, Claramunt S, Tobias JA, Baker A, Aleixo A, Brumfield RT.

Evolution. 2012 Sep;66(9):2784-97. doi: 10.1111/j.1558-5646.2012.01642.x. Epub 2012 May 21.

PMID:
22946803
35.

DNA sequence data reveal a subfamily-level divergence within Thamnophilidae (Aves: Passeriformes).

Bravo GA, Remsen JV Jr, Whitney BM, Brumfield RT.

Mol Phylogenet Evol. 2012 Oct;65(1):287-93. doi: 10.1016/j.ympev.2012.06.016. Epub 2012 Jul 1.

PMID:
22760026
36.

More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs.

Crawford NG, Faircloth BC, McCormack JE, Brumfield RT, Winker K, Glenn TC.

Biol Lett. 2012 Oct 23;8(5):783-6. doi: 10.1098/rsbl.2012.0331. Epub 2012 May 16.

37.

Ecological opportunity and diversification in a continental radiation of birds: climbing adaptations and cladogenesis in the Furnariidae.

Claramunt S, Derryberry EP, Brumfield RT, Remsen JV Jr.

Am Nat. 2012 May;179(5):649-66. doi: 10.1086/664998. Epub 2012 Mar 29.

PMID:
22504546
38.

Non-monophyly and deep genetic differentiation across low-elevation barriers in a Neotropical montane bird (Basileuterus tristriatus; Aves: Parulidae).

Gutiérrez-Pinto N, Cuervo AM, Miranda J, Pérez-Emán JL, Brumfield RT, Cadena CD.

Mol Phylogenet Evol. 2012 Jul;64(1):156-65. doi: 10.1016/j.ympev.2012.03.011. Epub 2012 Mar 29.

PMID:
22484358
39.

The role of physical barriers in the location of avian suture zones in the Guiana Shield, northern Amazonia.

Naka LN, Bechtoldt CL, Henriques LM, Brumfield RT.

Am Nat. 2012 Apr;179(4):E115-32. doi: 10.1086/664627. Epub 2012 Mar 1.

PMID:
22437185
40.

Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales.

Faircloth BC, McCormack JE, Crawford NG, Harvey MG, Brumfield RT, Glenn TC.

Syst Biol. 2012 Oct;61(5):717-26. doi: 10.1093/sysbio/sys004. Epub 2012 Jan 9.

PMID:
22232343
41.

Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis.

McCormack JE, Faircloth BC, Crawford NG, Gowaty PA, Brumfield RT, Glenn TC.

Genome Res. 2012 Apr;22(4):746-54. doi: 10.1101/gr.125864.111. Epub 2011 Dec 29.

42.

Applications of next-generation sequencing to phylogeography and phylogenetics.

McCormack JE, Hird SM, Zellmer AJ, Carstens BC, Brumfield RT.

Mol Phylogenet Evol. 2013 Feb;66(2):526-38. doi: 10.1016/j.ympev.2011.12.007. Epub 2011 Dec 14. Review.

PMID:
22197804
43.

High dispersal ability inhibits speciation in a continental radiation of passerine birds.

Claramunt S, Derryberry EP, Remsen JV Jr, Brumfield RT.

Proc Biol Sci. 2012 Apr 22;279(1733):1567-74. doi: 10.1098/rspb.2011.1922. Epub 2011 Nov 16.

44.

Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences.

McCormack JE, Maley JM, Hird SM, Derryberry EP, Graves GR, Brumfield RT.

Mol Phylogenet Evol. 2012 Jan;62(1):397-406. doi: 10.1016/j.ympev.2011.10.012. Epub 2011 Oct 31. Erratum in: Mol Phylogenet Evol. 2013 Jan;66(1):440.

PMID:
22063264
45.

Lineage diversification and morphological evolution in a large-scale continental radiation: the neotropical ovenbirds and woodcreepers (aves: Furnariidae).

Derryberry EP, Claramunt S, Derryberry G, Chesser RT, Cracraft J, Aleixo A, Pérez-Emán J, Remsen JV Jr, Brumfield RT.

Evolution. 2011 Oct;65(10):2973-86. doi: 10.1111/j.1558-5646.2011.01374.x. Epub 2011 Jul 4.

PMID:
21967436
46.

Genomic insights into adaptation to high-altitude environments.

Cheviron ZA, Brumfield RT.

Heredity (Edinb). 2012 Apr;108(4):354-61. doi: 10.1038/hdy.2011.85. Epub 2011 Sep 21. Review.

47.

PRGmatic: an efficient pipeline for collating genome-enriched second-generation sequencing data using a 'provisional-reference genome'.

Hird SM, Brumfield RT, Carstens BC.

Mol Ecol Resour. 2011 Jul;11(4):743-8. doi: 10.1111/j.1755-0998.2011.03005.x. Epub 2011 Mar 24.

PMID:
21676202
48.

Speciation genetics of biological invasions with hybridization.

Brumfield RT.

Mol Ecol. 2010 Dec;19(23):5079-83. doi: 10.1111/j.1365-294X.2010.04896.x.

PMID:
21091659
49.

A phylogenetic approach to disentangling the role of competition and habitat filtering in community assembly of Neotropical forest birds.

Gómez JP, Bravo GA, Brumfield RT, Tello JG, Cadena CD.

J Anim Ecol. 2010 Nov;79(6):1181-92. doi: 10.1111/j.1365-2656.2010.01725.x.

PMID:
20642767
50.

Song divergence by sensory drive in Amazonian birds.

Tobias JA, Aben J, Brumfield RT, Derryberry EP, Halfwerk W, Slabbekoorn H, Seddon N.

Evolution. 2010 Oct;64(10):2820-39. doi: 10.1111/j.1558-5646.2010.01067.x. Epub 2010 Aug 19.

PMID:
20561048

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