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Items: 41

1.

Selection, Linkage, and Population Structure Interact To Shape Genetic Variation Among Threespine Stickleback Genomes.

Nelson TC, Crandall JG, Ituarte CM, Catchen JM, Cresko WA.

Genetics. 2019 Jun 18. pii: genetics.302261.2019. doi: 10.1534/genetics.119.302261. [Epub ahead of print]

2.

Antarctic blackfin icefish genome reveals adaptations to extreme environments.

Kim BM, Amores A, Kang S, Ahn DH, Kim JH, Kim IC, Lee JH, Lee SG, Lee H, Lee J, Kim HW, Desvignes T, Batzel P, Sydes J, Titus T, Wilson CA, Catchen JM, Warren WC, Schartl M, Detrich HW 3rd, Postlethwait JH, Park H.

Nat Ecol Evol. 2019 Mar;3(3):469-478. doi: 10.1038/s41559-019-0812-7. Epub 2019 Feb 25.

PMID:
30804520
3.

Hybridization and postzygotic isolation promote reinforcement of male mating preferences in a diverse group of fishes with traditional sex roles.

Moran RL, Zhou M, Catchen JM, Fuller RC.

Ecol Evol. 2018 Aug 24;8(18):9282-9294. doi: 10.1002/ece3.4434. eCollection 2018 Sep.

4.

Repeated Selection of Alternatively Adapted Haplotypes Creates Sweeping Genomic Remodeling in Stickleback.

Bassham S, Catchen J, Lescak E, von Hippel FA, Cresko WA.

Genetics. 2018 Jul;209(3):921-939. doi: 10.1534/genetics.117.300610. Epub 2018 May 24.

5.

Genomic diversity is similar between Atlantic Forest restorations and natural remnants for the native tree Casearia sylvestris Sw.

Gomes Viana JP, Bohrer Monteiro Siqueira MV, Araujo FL, Grando C, Sanae Sujii P, Silvestre EA, Novello M, Pinheiro JB, Cavallari MM, Brancalion PHS, Rodrigues RR, Pereira de Souza A, Catchen J, Zucchi MI.

PLoS One. 2018 Mar 7;13(3):e0192165. doi: 10.1371/journal.pone.0192165. eCollection 2018.

6.

When structure leads to sex: Untangling signals in population genetic data sets.

Catchen J.

Mol Ecol. 2017 Dec;26(24):6763-6766. doi: 10.1111/mec.14422.

PMID:
29282805
7.

Deriving genotypes from RAD-seq short-read data using Stacks.

Rochette NC, Catchen JM.

Nat Protoc. 2017 Dec;12(12):2640-2659. doi: 10.1038/nprot.2017.123. Epub 2017 Nov 30.

PMID:
29189774
8.

The Novel Evolution of the Sperm Whale Genome.

Warren WC, Kuderna L, Alexander A, Catchen J, Pérez-Silva JG, López-Otín C, Quesada V, Minx P, Tomlinson C, Montague MJ, Farias FHG, Walter RB, Marques-Bonet T, Glenn T, Kieran TJ, Wise SS, Wise JP Jr, Waterhouse RM, Wise JP Sr.

Genome Biol Evol. 2017 Dec 1;9(12):3260-3264. doi: 10.1093/gbe/evx187. Erratum in: Genome Biol Evol. 2018 Apr 1;10(4):1063.

9.

Male and female contributions to behavioral isolation in darters as a function of genetic distance and color distance.

Moran RL, Zhou M, Catchen JM, Fuller RC.

Evolution. 2017 Oct;71(10):2428-2444. doi: 10.1111/evo.13321. Epub 2017 Sep 14.

10.

Winter storms drive rapid phenotypic, regulatory, and genomic shifts in the green anole lizard.

Campbell-Staton SC, Cheviron ZA, Rochette N, Catchen J, Losos JB, Edwards SV.

Science. 2017 Aug 4;357(6350):495-498. doi: 10.1126/science.aam5512. Epub 2017 Aug 3.

PMID:
28774927
11.

Unbroken: RADseq remains a powerful tool for understanding the genetics of adaptation in natural populations.

Catchen JM, Hohenlohe PA, Bernatchez L, Funk WC, Andrews KR, Allendorf FW.

Mol Ecol Resour. 2017 May;17(3):362-365. doi: 10.1111/1755-0998.12669. Epub 2017 Apr 11.

PMID:
28319339
12.

The genome of the Gulf pipefish enables understanding of evolutionary innovations.

Small CM, Bassham S, Catchen J, Amores A, Fuiten AM, Brown RS, Jones AG, Cresko WA.

Genome Biol. 2016 Dec 20;17(1):258.

13.

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
14.

Corrigendum: The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons.

Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J, Berlin AM, Campbell MS, Barrell D, Martin KJ, Mulley JF, Ravi V, Lee AP, Nakamura T, Chalopin D, Fan S, Wcisel D, Cañestro C, Sydes J, Beaudry FE, Sun Y, Hertel J, Beam MJ, Fasold M, Ishiyama M, Johnson J, Kehr S, Lara M, Letaw JH, Litman GW, Litman RT, Mikami M, Ota T, Saha NR, Williams L, Stadler PF, Wang H, Taylor JS, Fontenot Q, Ferrara A, Searle SM, Aken B, Yandell M, Schneider I, Yoder JA, Volff JN, Meyer A, Amemiya CT, Venkatesh B, Holland PW, Guiguen Y, Bobe J, Shubin NH, Di Palma F, Alfo Ldi J, Lindblad-Toh K, Postlethwait JH.

Nat Genet. 2016 May 27;48(6):700. doi: 10.1038/ng0616-700c. No abstract available.

PMID:
27230688
15.

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons.

Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J, Berlin AM, Campbell MS, Barrell D, Martin KJ, Mulley JF, Ravi V, Lee AP, Nakamura T, Chalopin D, Fan S, Wcisel D, Cañestro C, Sydes J, Beaudry FE, Sun Y, Hertel J, Beam MJ, Fasold M, Ishiyama M, Johnson J, Kehr S, Lara M, Letaw JH, Litman GW, Litman RT, Mikami M, Ota T, Saha NR, Williams L, Stadler PF, Wang H, Taylor JS, Fontenot Q, Ferrara A, Searle SM, Aken B, Yandell M, Schneider I, Yoder JA, Volff JN, Meyer A, Amemiya CT, Venkatesh B, Holland PW, Guiguen Y, Bobe J, Shubin NH, Di Palma F, Alföldi J, Lindblad-Toh K, Postlethwait JH.

Nat Genet. 2016 Apr;48(4):427-37. doi: 10.1038/ng.3526. Epub 2016 Mar 7.

16.

Evolution of stickleback in 50 years on earthquake-uplifted islands.

Lescak EA, Bassham SL, Catchen J, Gelmond O, Sherbick ML, von Hippel FA, Cresko WA.

Proc Natl Acad Sci U S A. 2015 Dec 29;112(52):E7204-12. doi: 10.1073/pnas.1512020112. Epub 2015 Dec 14.

17.

A RAD-tag genetic map for the platyfish (Xiphophorus maculatus) reveals mechanisms of karyotype evolution among teleost fish.

Amores A, Catchen J, Nanda I, Warren W, Walter R, Schartl M, Postlethwait JH.

Genetics. 2014 Jun;197(2):625-41. doi: 10.1534/genetics.114.164293. Epub 2014 Apr 2.

18.

Retinoic acid metabolic genes, meiosis, and gonadal sex differentiation in zebrafish.

Rodríguez-Marí A, Cañestro C, BreMiller RA, Catchen JM, Yan YL, Postlethwait JH.

PLoS One. 2013 Sep 10;8(9):e73951. doi: 10.1371/journal.pone.0073951. eCollection 2013.

19.

Replicate phylogenies and post-glacial range expansion of the pitcher-plant mosquito, Wyeomyia smithii, in North America.

Merz C, Catchen JM, Hanson-Smith V, Emerson KJ, Bradshaw WE, Holzapfel CM.

PLoS One. 2013 Sep 6;8(9):e72262. doi: 10.1371/journal.pone.0072262. eCollection 2013.

20.

Comparative oncogenomic analysis of copy number alterations in human and zebrafish tumors enables cancer driver discovery.

Zhang G, Hoersch S, Amsterdam A, Whittaker CA, Beert E, Catchen JM, Farrington S, Postlethwait JH, Legius E, Hopkins N, Lees JA.

PLoS Genet. 2013 Aug;9(8):e1003734. doi: 10.1371/journal.pgen.1003734. Epub 2013 Aug 29.

21.

The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing.

Catchen J, Bassham S, Wilson T, Currey M, O'Brien C, Yeates Q, Cresko WA.

Mol Ecol. 2013 Jun;22(11):2864-83. doi: 10.1111/mec.12330.

22.

Stacks: an analysis tool set for population genomics.

Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA.

Mol Ecol. 2013 Jun;22(11):3124-40. doi: 10.1111/mec.12354. Epub 2013 May 24.

23.

The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits.

Schartl M, Walter RB, Shen Y, Garcia T, Catchen J, Amores A, Braasch I, Chalopin D, Volff JN, Lesch KP, Bisazza A, Minx P, Hillier L, Wilson RK, Fuerstenberg S, Boore J, Searle S, Postlethwait JH, Warren WC.

Nat Genet. 2013 May;45(5):567-72. doi: 10.1038/ng.2604. Epub 2013 Mar 31.

24.

Footprints in time: comparative quantitative trait loci mapping of the pitcher-plant mosquito, Wyeomyia smithii.

Bradshaw WE, Emerson KJ, Catchen JM, Cresko WA, Holzapfel CM.

Proc Biol Sci. 2012 Nov 22;279(1747):4551-8. doi: 10.1098/rspb.2012.1917. Epub 2012 Sep 26.

25.

Population genomic analysis of model and nonmodel organisms using sequenced RAD tags.

Hohenlohe PA, Catchen J, Cresko WA.

Methods Mol Biol. 2012;888:235-60. doi: 10.1007/978-1-61779-870-2_14.

PMID:
22665285
26.

Stacks: building and genotyping Loci de novo from short-read sequences.

Catchen JM, Amores A, Hohenlohe P, Cresko W, Postlethwait JH.

G3 (Bethesda). 2011 Aug;1(3):171-82. doi: 10.1534/g3.111.000240. Epub 2011 Aug 1.

27.

Conserved synteny and the zebrafish genome.

Catchen JM, Braasch I, Postlethwait JH.

Methods Cell Biol. 2011;104:259-85. doi: 10.1016/B978-0-12-374814-0.00015-X.

PMID:
21924168
28.

Genome evolution and meiotic maps by massively parallel DNA sequencing: spotted gar, an outgroup for the teleost genome duplication.

Amores A, Catchen J, Ferrara A, Fontenot Q, Postlethwait JH.

Genetics. 2011 Aug;188(4):799-808. doi: 10.1534/genetics.111.127324.

29.

Genome-wide genetic marker discovery and genotyping using next-generation sequencing.

Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML.

Nat Rev Genet. 2011 Jun 17;12(7):499-510. doi: 10.1038/nrg3012. Review.

PMID:
21681211
30.

Effects of short read quality and quantity on a de novo vertebrate transcriptome assembly.

Garcia TI, Shen Y, Catchen J, Amores A, Schartl M, Postlethwait J, Walter RB.

Comp Biochem Physiol C Toxicol Pharmacol. 2012 Jan;155(1):95-101. doi: 10.1016/j.cbpc.2011.05.012. Epub 2011 Jun 1.

31.

Identification of transcriptome SNPs between Xiphophorus lines and species for assessing allele specific gene expression within F₁ interspecies hybrids.

Shen Y, Catchen J, Garcia T, Amores A, Beldorth I, Wagner J, Zhang Z, Postlethwait J, Warren W, Schartl M, Walter RB.

Comp Biochem Physiol C Toxicol Pharmacol. 2012 Jan;155(1):102-8. doi: 10.1016/j.cbpc.2011.03.012. Epub 2011 Apr 3.

32.

Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout.

Hohenlohe PA, Amish SJ, Catchen JM, Allendorf FW, Luikart G.

Mol Ecol Resour. 2011 Mar;11 Suppl 1:117-22. doi: 10.1111/j.1755-0998.2010.02967.x.

PMID:
21429168
33.

Resolving postglacial phylogeography using high-throughput sequencing.

Emerson KJ, Merz CR, Catchen JM, Hohenlohe PA, Cresko WA, Bradshaw WE, Holzapfel CM.

Proc Natl Acad Sci U S A. 2010 Sep 14;107(37):16196-200. doi: 10.1073/pnas.1006538107. Epub 2010 Aug 26.

34.

UDP xylose synthase 1 is required for morphogenesis and histogenesis of the craniofacial skeleton.

Eames BF, Singer A, Smith GA, Wood ZA, Yan YL, He X, Polizzi SJ, Catchen JM, Rodriguez-Mari A, Linbo T, Raible DW, Postlethwait JH.

Dev Biol. 2010 May 15;341(2):400-15. doi: 10.1016/j.ydbio.2010.02.035. Epub 2010 Mar 11.

35.

The gene history of zebrafish tlr4a and tlr4b is predictive of their divergent functions.

Sullivan C, Charette J, Catchen J, Lage CR, Giasson G, Postlethwait JH, Millard PJ, Kim CH.

J Immunol. 2009 Nov 1;183(9):5896-908. doi: 10.4049/jimmunol.0803285. Epub 2009 Oct 7.

36.

Evolution of developmental regulation in the vertebrate FgfD subfamily.

Jovelin R, Yan YL, He X, Catchen J, Amores A, Canestro C, Yokoi H, Postlethwait JH.

J Exp Zool B Mol Dev Evol. 2010 Jan 15;314(1):33-56. doi: 10.1002/jez.b.21307.

37.

Consequences of lineage-specific gene loss on functional evolution of surviving paralogs: ALDH1A and retinoic acid signaling in vertebrate genomes.

Cañestro C, Catchen JM, Rodríguez-Marí A, Yokoi H, Postlethwait JH.

PLoS Genet. 2009 May;5(5):e1000496. doi: 10.1371/journal.pgen.1000496. Epub 2009 May 29.

38.

Automated identification of conserved synteny after whole-genome duplication.

Catchen JM, Conery JS, Postlethwait JH.

Genome Res. 2009 Aug;19(8):1497-505. doi: 10.1101/gr.090480.108. Epub 2009 May 22.

39.

Expression profiling of zebrafish sox9 mutants reveals that Sox9 is required for retinal differentiation.

Yokoi H, Yan YL, Miller MR, BreMiller RA, Catchen JM, Johnson EA, Postlethwait JH.

Dev Biol. 2009 May 1;329(1):1-15. doi: 10.1016/j.ydbio.2009.01.002. Epub 2009 Jan 13.

40.

Evolution of a new function by degenerative mutation in cephalochordate steroid receptors.

Bridgham JT, Brown JE, Rodríguez-Marí A, Catchen JM, Thornton JW.

PLoS Genet. 2008 Sep 12;4(9):e1000191. doi: 10.1371/journal.pgen.1000191.

41.

Inferring ancestral gene order.

Catchen JM, Conery JS, Postlethwait JH.

Methods Mol Biol. 2008;452:365-83. doi: 10.1007/978-1-60327-159-2_17. Review.

PMID:
18566773

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