Molecular evolution of genes in avian genomes

Nam K, Mugal C, Nabholz B, Schielzeth H, Wolf JBW, Backström N, Künstner A, Balakrishnan CN, Heger A, Ponting CP, Clayton DF, et al. (2010)
Genome Biology 11(6): R68.

Download
Es wurde kein Volltext hochgeladen. Nur Publikationsnachweis!
Zeitschriftenaufsatz | Veröffentlicht | Englisch
Autor
; ; ; ; ; ; ; ; ; ; ;
Alle
Abstract / Bemerkung
Background: Obtaining a draft genome sequence of the zebra finch (Taeniopygia guttata), the second bird genome to be sequenced, provides the necessary resource for whole-genome comparative analysis of gene sequence evolution in a non-mammalian vertebrate lineage. To analyze basic molecular evolutionary processes during avian evolution, and to contrast these with the situation in mammals, we aligned the protein-coding sequences of 8,384 1:1 orthologs of chicken, zebra finch, a lizard and three mammalian species. Results: We found clear differences in the substitution rate at fourfold degenerate sites, being lowest in the ancestral bird lineage, intermediate in the chicken lineage and highest in the zebra finch lineage, possibly reflecting differences in generation time. We identified positively selected and/or rapidly evolving genes in avian lineages and found an overrepresentation of several functional classes, including anion transporter activity, calcium ion binding, cell adhesion and microtubule cytoskeleton. Conclusions: Focusing specifically on genes of neurological interest and genes differentially expressed in the unique vocal control nuclei of the songbird brain, we find a number of positively selected genes, including synaptic receptors. We found no evidence that selection for beneficial alleles is more efficient in regions of high recombination; in fact, there was a weak yet significant negative correlation between ω and recombination rate, which is in the direction predicted by the Hill-Robertson effect if slightly deleterious mutations contribute to protein evolution. These findings set the stage for studies of functional genetics of avian genes.
Erscheinungsjahr
Zeitschriftentitel
Genome Biology
Band
11
Zeitschriftennummer
6
Seite
R68
ISSN
PUB-ID

Zitieren

Nam K, Mugal C, Nabholz B, et al. Molecular evolution of genes in avian genomes. Genome Biology. 2010;11(6):R68.
Nam, K., Mugal, C., Nabholz, B., Schielzeth, H., Wolf, J. B. W., Backström, N., Künstner, A., et al. (2010). Molecular evolution of genes in avian genomes. Genome Biology, 11(6), R68. doi:10.1186/gb-2010-11-6-r68
Nam, K., Mugal, C., Nabholz, B., Schielzeth, H., Wolf, J. B. W., Backström, N., Künstner, A., Balakrishnan, C. N., Heger, A., Ponting, C. P., et al. (2010). Molecular evolution of genes in avian genomes. Genome Biology 11, R68.
Nam, K., et al., 2010. Molecular evolution of genes in avian genomes. Genome Biology, 11(6), p R68.
K. Nam, et al., “Molecular evolution of genes in avian genomes”, Genome Biology, vol. 11, 2010, pp. R68.
Nam, K., Mugal, C., Nabholz, B., Schielzeth, H., Wolf, J.B.W., Backström, N., Künstner, A., Balakrishnan, C.N., Heger, A., Ponting, C.P., Clayton, D.F., Ellegren, H.: Molecular evolution of genes in avian genomes. Genome Biology. 11, R68 (2010).
Nam, Kiwoong, Mugal, Carina, Nabholz, Benoit, Schielzeth, Holger, Wolf, Jochen BW, Backström, Niclas, Künstner, Axel, Balakrishnan, Christopher N, Heger, Andreas, Ponting, Chris P, Clayton, David F, and Ellegren, Hans. “Molecular evolution of genes in avian genomes”. Genome Biology 11.6 (2010): R68.

46 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Whole-genome resequencing reveals signatures of selection and timing of duck domestication.
Zhang Z, Jia Y, Almeida P, Mank JE, van Tuinen M, Wang Q, Jiang Z, Chen Y, Zhan K, Hou S, Zhou Z, Li H, Yang F, He Y, Ning Z, Yang N, Qu L., Gigascience 7(4), 2018
PMID: 29635409
Evolution of genomic variation in the burrowing owl in response to recent colonization of urban areas.
Mueller JC, Kuhl H, Boerno S, Tella JL, Carrete M, Kempenaers B., Proc Biol Sci 285(1878), 2018
PMID: 29769357
A global analysis of selection at the avian MHC.
Minias P, Pikus E, Whittingham LA, Dunn PO., Evolution 72(6), 2018
PMID: 29665025
Insulinlike Growth Factor 1 Gene Variation in Vertebrates.
Rotwein P., Endocrinology 159(6), 2018
PMID: 29697760
The first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies.
Liu Y, Liu S, Yeh CF, Zhang N, Chen G, Que P, Dong L, Li SH., Sci Rep 8(1), 2018
PMID: 30356056
Growth factor gene IGF1 is associated with bill size in the black-bellied seedcracker Pyrenestes ostrinus.
vonHoldt BM, Kartzinel RY, Huber CD, Le Underwood V, Zhen Y, Ruegg K, Lohmueller KE, Smith TB., Nat Commun 9(1), 2018
PMID: 30451848
Isolation with asymmetric gene flow during the nonsynchronous divergence of dry forest birds.
Oswald JA, Overcast I, Mauck WM, Andersen MJ, Smith BT., Mol Ecol 26(5), 2017
PMID: 28100029
Self-domestication in Homo sapiens: Insights from comparative genomics.
Theofanopoulou C, Gastaldon S, O'Rourke T, Samuels BD, Martins PT, Delogu F, Alamri S, Boeckx C., PLoS One 12(10), 2017
PMID: 29045412
Natural selection shaped the rise and fall of passenger pigeon genomic diversity.
Murray GGR, Soares AER, Novak BJ, Schaefer NK, Cahill JA, Baker AJ, Demboski JR, Doll A, Da Fonseca RR, Fulton TL, Gilbert MTP, Heintzman PD, Letts B, McIntosh G, O'Connell BL, Peck M, Pipes ML, Rice ES, Santos KM, Sohrweide AG, Vohr SH, Corbett-Detig RB, Green RE, Shapiro B., Science 358(6365), 2017
PMID: 29146814
Detecting signatures of positive selection associated with musical aptitude in the human genome.
Liu X, Kanduri C, Oikkonen J, Karma K, Raijas P, Ukkola-Vuoti L, Teo YY, Järvelä I., Sci Rep 6(), 2016
PMID: 26879527
Positive selection rather than relaxation of functional constraint drives the evolution of vision during chicken domestication.
Wang MS, Zhang RW, Su LY, Li Y, Peng MS, Liu HQ, Zeng L, Irwin DM, Du JL, Yao YG, Wu DD, Zhang YP., Cell Res 26(5), 2016
PMID: 27033669
Gene Regulatory Evolution During Speciation in a Songbird.
Davidson JH, Balakrishnan CN., G3 (Bethesda) 6(5), 2016
PMID: 26976438
Direct estimate of the rate of germline mutation in a bird.
Smeds L, Qvarnström A, Ellegren H., Genome Res 26(9), 2016
PMID: 27412854
Gene turnover in the avian globin gene families and evolutionary changes in hemoglobin isoform expression.
Opazo JC, Hoffmann FG, Natarajan C, Witt CC, Berenbrink M, Storz JF., Mol Biol Evol 32(4), 2015
PMID: 25502940
Whole-genome sequence of the Tibetan frog Nanorana parkeri and the comparative evolution of tetrapod genomes.
Sun YB, Xiong ZJ, Xiang XY, Liu SP, Zhou WW, Tu XL, Zhong L, Wang L, Wu DD, Zhang BL, Zhu CL, Yang MM, Chen HM, Li F, Zhou L, Feng SH, Huang C, Zhang GJ, Irwin D, Hillis DM, Murphy RW, Yang HM, Che J, Wang J, Zhang YP., Proc Natl Acad Sci U S A 112(11), 2015
PMID: 25733869
Genomic Analyses Reveal Potential Independent Adaptation to High Altitude in Tibetan Chickens.
Wang MS, Li Y, Peng MS, Zhong L, Wang ZJ, Li QY, Tu XL, Dong Y, Zhu CL, Wang L, Yang MM, Wu SF, Miao YW, Liu JP, Irwin DM, Wang W, Wu DD, Zhang YP., Mol Biol Evol 32(7), 2015
PMID: 25788450
Transcriptomic analyses of regenerating adult feathers in chicken.
Ng CS, Chen CK, Fan WL, Wu P, Wu SM, Chen JJ, Lai YT, Mao CT, Lu MY, Chen DR, Lin ZS, Yang KJ, Sha YA, Tu TC, Chen CF, Chuong CM, Li WH., BMC Genomics 16(), 2015
PMID: 26445093
A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing.
Prum RO, Berv JS, Dornburg A, Field DJ, Townsend JP, Lemmon EM, Lemmon AR., Nature 526(7574), 2015
PMID: 26444237
Population genomics of eusocial insects: the costs of a vertebrate-like effective population size.
Romiguier J, Lourenco J, Gayral P, Faivre N, Weinert LA, Ravel S, Ballenghien M, Cahais V, Bernard A, Loire E, Keller L, Galtier N., J Evol Biol 27(3), 2014
PMID: 26227898
Molecular cloning, expression and characterization of Pekin duck interferon-λ.
Yao Q, Fischer KP, Arnesen K, Tyrrell DL, Gutfreund KS., Gene 548(1), 2014
PMID: 24992029
A role for migration-linked genes and genomic islands in divergence of a songbird.
Ruegg K, Anderson EC, Boone J, Pouls J, Smith TB., Mol Ecol 23(19), 2014
PMID: 24954641
Highly variable recombinational landscape modulates efficacy of natural selection in birds.
Gossmann TI, Santure AW, Sheldon BC, Slate J, Zeng K., Genome Biol Evol 6(8), 2014
PMID: 25062920
The draft genome of the large yellow croaker reveals well-developed innate immunity.
Wu C, Zhang D, Kan M, Lv Z, Zhu A, Su Y, Zhou D, Zhang J, Zhang Z, Xu M, Jiang L, Guo B, Wang T, Chi C, Mao Y, Zhou J, Yu X, Wang H, Weng X, Jin JG, Ye J, He L, Liu Y., Nat Commun 5(), 2014
PMID: 25407894
Genomic diversity and evolution of the head crest in the rock pigeon.
Shapiro MD, Kronenberg Z, Li C, Domyan ET, Pan H, Campbell M, Tan H, Huff CD, Hu H, Vickrey AI, Nielsen SC, Stringham SA, Hu H, Willerslev E, Gilbert MT, Yandell M, Zhang G, Wang J, Wang J., Science 339(6123), 2013
PMID: 23371554
Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence.
Rands CM, Darling A, Fujita M, Kong L, Webster MT, Clabaut C, Emes RD, Heger A, Meader S, Hawkins MB, Eisen MB, Teiling C, Affourtit J, Boese B, Grant PR, Grant BR, Eisen JA, Abzhanov A, Ponting CP., BMC Genomics 14(), 2013
PMID: 23402223
The duck genome and transcriptome provide insight into an avian influenza virus reservoir species.
Huang Y, Li Y, Burt DW, Chen H, Zhang Y, Qian W, Kim H, Gan S, Zhao Y, Li J, Yi K, Feng H, Zhu P, Li B, Liu Q, Fairley S, Magor KE, Du Z, Hu X, Goodman L, Tafer H, Vignal A, Lee T, Kim KW, Sheng Z, An Y, Searle S, Herrero J, Groenen MAM, Crooijmans RPMA, Faraut T, Cai Q, Webster RG, Aldridge JR, Warren WC, Bartschat S, Kehr S, Marz M, Stadler PF, Smith J, Kraus RHS, Zhao Y, Ren L, Fei J, Morisson M, Kaiser P, Griffin DK, Rao M, Pitel F, Wang J, Wang J, Li N., Nat Genet 45(7), 2013
PMID: 23749191
Recombination drives vertebrate genome contraction.
Nam K, Ellegren H., PLoS Genet 8(5), 2012
PMID: 22570634
The singing genome.
Ellegren H., Heredity (Edinb) 106(4), 2011
PMID: 20823906
Evolutionary constraint in flanking regions of avian genes.
Künstner A, Nabholz B, Ellegren H., Mol Biol Evol 28(9), 2011
PMID: 21393603
Next generation sequencing and analysis of a conserved transcriptome of New Zealand's kiwi.
Subramanian S, Huynen L, Millar CD, Lambert DM., BMC Evol Biol 10(), 2010
PMID: 21156082

123 References

Daten bereitgestellt von Europe PubMed Central.

Genetic basis of fitness differences in natural populations.
Ellegren H, Sheldon BC., Nature 452(7184), 2008
PMID: 18337813
The calmodulin pathway and evolution of elongated beak morphology in Darwin's finches.
Abzhanov A, Kuo WP, Hartmann C, Grant BR, Grant PR, Tabin CJ., Nature 442(7102), 2006
PMID: 16885984
Bmp4 and morphological variation of beaks in Darwin's finches.
Abzhanov A, Protas M, Grant BR, Grant PR, Tabin CJ., Science 305(5689), 2004
PMID: 15353802
Conserved genetic basis of a quantitative plumage trait involved in mate choice.
Mundy NI, Badcock NS, Hart T, Scribner K, Janssen K, Nadeau NJ., Science 303(5665), 2004
PMID: 15031505
Animal Genome Size Database
AUTHOR UNKNOWN, 0
The repetitive landscape of the chicken genome.
Wicker T, Robertson JS, Schulze SR, Feltus FA, Magrini V, Morrison JA, Mardis ER, Wilson RK, Peterson DG, Paterson AH, Ivarie R., Genome Res. 15(1), 2004
PMID: 15256510
The evolution of the avian genome as revealed by comparative molecular cytogenetics.
Griffin DK, Robertson LB, Tempest HG, Skinner BM., Cytogenet. Genome Res. 117(1-4), 2007
PMID: 17675846
Faced with inequality: chicken do not have a general dosage compensation of sex-linked genes.
Ellegren H, Hultin-Rosenberg L, Brunstrom B, Dencker L, Kultima K, Scholz B., BMC Biol. 5(), 2007
PMID: 17883843
Dosage compensation is less effective in birds than in mammals.
Itoh Y, Melamed E, Yang X, Kampf K, Wang S, Yehya N, Van Nas A, Replogle K, Band MR, Clayton DF, Schadt EE, Lusis AJ, Arnold AP., J. Biol. 6(1), 2007
PMID: 17352797
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.
International Chicken Genome Sequencing Consortium., Nature 432(7018), 2004
PMID: 15592404
Strong regional biases in nucleotide substitution in the chicken genome.
Webster MT, Axelsson E, Ellegren H., Mol. Biol. Evol. 23(6), 2006
PMID: 16551647
Exponential decay of GC content detected by strand-symmetric substitution rates influences the evolution of isochore structure.
Karro JE, Peifer M, Hardison RC, Kollmann M, von Grunberg HH., Mol. Biol. Evol. 25(2), 2007
PMID: 18042807
Natural selection in avian protein-coding genes expressed in brain.
Axelsson E, Hultin-Rosenberg L, Brandstrom M, Zwahlen M, Clayton DF, Ellegren H., Mol. Ecol. 17(12), 2008
PMID: 18482257
The genome of a songbird.
Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Kunstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP, Jarvis ED, Mello CV, Minx P, Lovell P, Velho TA, Ferris M, Balakrishnan CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J, Southey B, Gunaratne P, Watson M, Nam K, Backstrom N, Smeds L, Nabholz B, Itoh Y, Whitney O, Pfenning AR, Howard J, Volker M, Skinner BM, Griffin DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente XS, Olender T, Lancet D, Smit AF, Hubley R, Konkel MK, Walker JA, Batzer MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J, Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H, Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang SP, Li X, Graves T, Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER, Wilson RK., Nature 464(7289), 2010
PMID: 20360741
Natural selection on protein-coding genes in the human genome.
Bustamante CD, Fledel-Alon A, Williamson S, Nielsen R, Hubisz MT, Glanowski S, Tanenbaum DM, White TJ, Sninsky JJ, Hernandez RD, Civello D, Adams MD, Cargill M, Clark AG., Nature 437(7062), 2005
PMID: 16237444
A scan for positively selected genes in the genomes of humans and chimpanzees.
Nielsen R, Bustamante C, Clark AG, Glanowski S, Sackton TB, Hubisz MJ, Fledel-Alon A, Tanenbaum DM, Civello D, White TJ, J Sninsky J, Adams MD, Cargill M., PLoS Biol. 3(6), 2005
PMID: 15869325
Neurons generated in the adult brain are recruited into functional circuits.
Paton JA, Nottebohm FN., Science 225(4666), 1984
PMID: 6474166
Proposal to Sequence the Genome of the Zebra Finch (Taeniopygia guttata)
AUTHOR UNKNOWN, 0
Birdsong and human speech: common themes and mechanisms.
Doupe AJ, Kuhl PK., Annu. Rev. Neurosci. 22(), 1999
PMID: 10202549
Learned birdsong and the neurobiology of human language.
Jarvis ED., Ann. N. Y. Acad. Sci. 1016(), 2004
PMID: 15313804
Calibration of avian molecular clocks.
van Tuinen M, Hedges SB., Mol. Biol. Evol. 18(2), 2001
PMID: 11158379
Integrating genomes, brain and behavior in the study of songbirds.
Clayton DF, Balakrishnan CN, London SE., Curr. Biol. 19(18), 2009
PMID: 19788884
Accelerated evolution of nervous system genes in the origin of Homo sapiens.
Dorus S, Vallender EJ, Evans PD, Anderson JR, Gilbert SL, Mahowald M, Wyckoff GJ, Malcom CM, Lahn BT., Cell 119(7), 2004
PMID: 15620360
Birdsong "transcriptomics": neurochemical specializations of the oscine song system.
Lovell PV, Clayton DF, Replogle KL, Mello CV., PLoS ONE 3(10), 2008
PMID: 18941504
A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate.
Groenen MA, Wahlberg P, Foglio M, Cheng HH, Megens HJ, Crooijmans RP, Besnier F, Lathrop M, Muir WM, Wong GK, Gut I, Andersson L., Genome Res. 19(3), 2008
PMID: 19088305
The recombination landscape of the zebra finch Taeniopygia guttata genome.
Backstrom N, Forstmeier W, Schielzeth H, Mellenius H, Nam K, Bolund E, Webster MT, Ost T, Schneider M, Kempenaers B, Ellegren H., Genome Res. 20(4), 2010
PMID: 20357052
The effect of linkage on limits to artificial selection.
Hill WG, Robertson A., Genet. Res. 8(3), 1966
PMID: 5980116
Linkage limits the power of natural selection in Drosophila.
Betancourt AJ, Presgraves DC., Proc. Natl. Acad. Sci. U.S.A. 99(21), 2002
PMID: 12370444
No effect of recombination on the efficacy of natural selection in primates.
Bullaughey K, Przeworski M, Coop G., Genome Res. 18(4), 2008
PMID: 18199888
Reduced purifying selection prevails over positive selection in human copy number variant evolution.
Nguyen DQ, Webber C, Hehir-Kwa J, Pfundt R, Veltman J, Ponting CP., Genome Res. 18(11), 2008
PMID: 18687881
Is the synonymous substitution rate in mammals gene-specific?
Williams EJ, Hurst LD., Mol. Biol. Evol. 19(8), 2002
PMID: 12140253
Diversification of Neoaves: integration of molecular sequence data and fossils.
Ericson PG, Anderson CL, Britton T, Elzanowski A, Johansson US, Kallersjo M, Ohlson JI, Parsons TJ, Zuccon D, Mayr G., Biol. Lett. 2(4), 2006
PMID: 17148284
Paleontological evidence to date the tree of life.
Benton MJ, Donoghue PC., Mol. Biol. Evol. 24(1), 2006
PMID: 17047029
A phylogenomic study of birds reveals their evolutionary history.
Hackett SJ, Kimball RT, Reddy S, Bowie RC, Braun EL, Braun MJ, Chojnowski JL, Cox WA, Han KL, Harshman J, Huddleston CJ, Marks BD, Miglia KJ, Moore WS, Sheldon FH, Steadman DW, Witt CC, Yuri T., Science 320(5884), 2008
PMID: 18583609

AUTHOR UNKNOWN, 1990
Toward resolving deep neoaves phylogeny: data, signal enhancement, and priors.
Pratt RC, Gibb GC, Morgan-Richards M, Phillips MJ, Hendy MD, Penny D., Mol. Biol. Evol. 26(2), 2008
PMID: 18981298
An evaluation of the molecular clock hypothesis using mammalian DNA sequences.
Li WH, Tanimura M, Sharp PM., J. Mol. Evol. 25(4), 1987
PMID: 3118047
Calibration of avian molecular clocks.
van Tuinen M, Hedges SB., Mol. Biol. Evol. 18(2), 2001
PMID: 11158379
Early penguin fossils, plus mitochondrial genomes, calibrate avian evolution.
Slack KE, Jones CM, Ando T, Harrison GL, Fordyce RE, Arnason U, Penny D., Mol. Biol. Evol. 23(6), 2006
PMID: 16533822
The quality of the fossil record of Mesozoic birds.
Fountaine TM, Benton MJ, Dyke GJ, Nudds RL., Proc. Biol. Sci. 272(1560), 2005
PMID: 15705554
Weak preservation of local neutral substitution rates across mammalian genomes.
Imamura H, Karro JE, Chuang JH., BMC Evol. Biol. 9(), 2009
PMID: 19416516
Conservation of neutral substitution rate and substitutional asymmetries in mammalian genes.
Mugal CF, Wolf JB, von Grunberg HH, Ellegren H., Genome Biol Evol 2(), 2010
PMID: 20333222
Recombination and mammalian genome evolution.
Eyre-Walker A., Proc. Biol. Sci. 252(1335), 1993
PMID: 8394585
Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution.
Hardison RC, Roskin KM, Yang S, Diekhans M, Kent WJ, Weber R, Elnitski L, Li J, O'Connor M, Kolbe D, Schwartz S, Furey TS, Whelan S, Goldman N, Smit A, Miller W, Chiaromonte F, Haussler D., Genome Res. 13(1), 2003
PMID: 12529302
Recombination drives the evolution of GC-content in the human genome.
Meunier J, Duret L., Mol. Biol. Evol. 21(6), 2004
PMID: 14963104
Mutations in a human homologue of Drosophila crumbs cause retinitis pigmentosa (RP12).
den Hollander AI, ten Brink JB, de Kok YJ, van Soest S, van den Born LI, van Driel MA, van de Pol DJ, Payne AM, Bhattacharya SS, Kellner U, Hoyng CB, Westerveld A, Brunner HG, Bleeker-Wagemakers EM, Deutman AF, Heckenlively JR, Cremers FP, Bergen AA., Nat. Genet. 23(2), 1999
PMID: 10508521
Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios.
Clark AG, Glanowski S, Nielsen R, Thomas PD, Kejariwal A, Todd MA, Tanenbaum DM, Civello D, Lu F, Murphy B, Ferriera S, Wang G, Zheng X, White TJ, Sninsky JJ, Adams MD, Cargill M., Science 302(5652), 2003
PMID: 14671302
Positive selection, relaxation, and acceleration in the evolution of the human and chimp genome.
Arbiza L, Dopazo J, Dopazo H., PLoS Comput. Biol. 2(4), 2006
PMID: 16683019
Patterns of positive selection in six Mammalian genomes.
Kosiol C, Vinar T, da Fonseca RR, Hubisz MJ, Bustamante CD, Nielsen R, Siepel A., PLoS Genet. 4(8), 2008
PMID: 18670650
Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species.
Kunstner A, Wolf JB, Backstrom N, Whitney O, Balakrishnan CN, Day L, Edwards SV, Janes DE, Schlinger BA, Wilson RK, Jarvis ED, Warren WC, Ellegren H., Mol. Ecol. 19 Suppl 1(), 2010
PMID: 20331785
Dynamics of the vocal imitation process: how a zebra finch learns its song.
Tchernichovski O, Mitra PP, Lints T, Nottebohm F., Science 291(5513), 2001
PMID: 11283361
How sleep affects the developmental learning of bird song.
Deregnaucourt S, Mitra PP, Feher O, Pytte C, Tchernichovski O., Nature 433(7027), 2005
PMID: 15716944
A specialized forebrain circuit for vocal babbling in the juvenile songbird.
Aronov D, Andalman AS, Fee MS., Science 320(5876), 2008
PMID: 18451295
Song presentation induces gene expression in the songbird forebrain.
Mello CV, Vicario DS, Clayton DF., Proc. Natl. Acad. Sci. U.S.A. 89(15), 1992
PMID: 1495970
Motor-driven gene expression.
Jarvis ED, Nottebohm F., Proc. Natl. Acad. Sci. U.S.A. 94(8), 1997
PMID: 9108111
For whom the bird sings: context-dependent gene expression.
Jarvis ED, Scharff C, Grossman MR, Ramos JA, Nottebohm F., Neuron 21(4), 1998
PMID: 9808464
A molecular neuroethological approach for identifying and characterizing a cascade of behaviorally regulated genes.
Wada K, Howard JT, McConnell P, Whitney O, Lints T, Rivas MV, Horita H, Patterson MA, White SA, Scharff C, Haesler S, Zhao S, Sakaguchi H, Hagiwara M, Shiraki T, Hirozane-Kishikawa T, Skene P, Hayashizaki Y, Carninci P, Jarvis ED., Proc. Natl. Acad. Sci. U.S.A. 103(41), 2006
PMID: 17018643
Discrete molecular states in the brain accompany changing responses to a vocal signal.
Dong S, Replogle KL, Hasadsri L, Imai BS, Yau PM, Rodriguez-Zas S, Southey BR, Sweedler JV, Clayton DF., Proc. Natl. Acad. Sci. U.S.A. 106(27), 2009
PMID: 19541599
ASPM is a major determinant of cerebral cortical size.
Bond J, Roberts E, Mochida GH, Hampshire DJ, Scott S, Askham JM, Springell K, Mahadevan M, Crow YJ, Markham AF, Walsh CA, Woods CG., Nat. Genet. 32(2), 2002
PMID: 12355089
Microcephalin, a gene regulating brain size, continues to evolve adaptively in humans.
Evans PD, Gilbert SL, Mekel-Bobrov N, Vallender EJ, Anderson JR, Vaez-Azizi LM, Tishkoff SA, Hudson RR, Lahn BT., Science 309(5741), 2005
PMID: 16151009
Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens.
Mekel-Bobrov N, Gilbert SL, Evans PD, Vallender EJ, Anderson JR, Hudson RR, Tishkoff SA, Lahn BT., Science 309(5741), 2005
PMID: 16151010
Reconstructing the evolutionary history of microcephalin, a gene controlling human brain size.
Evans PD, Anderson JR, Vallender EJ, Choi SS, Lahn BT., Hum. Mol. Genet. 13(11), 2004
PMID: 15056607
Brain architecture and social complexity in modern and ancient birds.
Burish MJ, Kueh HY, Wang SS., Brain Behav. Evol. 63(2), 2003
PMID: 14685004
The ongoing adaptive evolution of ASPM and Microcephalin is not explained by increased intelligence.
Mekel-Bobrov N, Posthuma D, Gilbert SL, Lind P, Gosso MF, Luciano M, Harris SE, Bates TC, Polderman TJ, Whalley LJ, Fox H, Starr JM, Evans PD, Montgomery GW, Fernandes C, Heutink P, Martin NG, Boomsma DI, Deary IJ, Wright MJ, de Geus EJ, Lahn BT., Hum. Mol. Genet. 16(6), 2007
PMID: 17220170
NMDA receptor trafficking in synaptic plasticity and neuropsychiatric disorders.
Lau CG, Zukin RS., Nat. Rev. Neurosci. 8(6), 2007
PMID: 17514195
Hippocampal specialization of food-storing birds.
Krebs JR, Sherry DF, Healy SD, Perry VH, Vaccarino AL., Proc. Natl. Acad. Sci. U.S.A. 86(4), 1989
PMID: 2919184

AUTHOR UNKNOWN, 1996
Blockade of NMDA receptors during song model exposure impairs song development in juvenile zebra finches.
Aamodt SM, Nordeen EJ, Nordeen KW., Neurobiol Learn Mem 65(1), 1996
PMID: 8673412
Androgens modulate NMDA receptor-mediated EPSCs in the zebra finch song system.
White SA, Livingston FS, Mooney R., J. Neurophysiol. 82(5), 1999
PMID: 10561401
Comparisons of dN/dS are time dependent for closely related bacterial genomes.
Rocha EP, Smith JM, Hurst LD, Holden MT, Cooper JE, Smith NH, Feil EJ., J. Theor. Biol. 239(2), 2005
PMID: 16239014
Quantitative prediction of molecular clock and ka/ks at short timescales.
Peterson GI, Masel J., Mol. Biol. Evol. 26(11), 2009
PMID: 19661199
Nonlinear dynamics of nonsynonymous (dN) and synonymous (dS) substitution rates affects inference of selection.
Wolf JB, Kunstner A, Nam K, Jakobsson M, Ellegren H., Genome Biol Evol 1(), 2009
PMID: 20333200
The evolutionary advantage of recombination.
Felsenstein J., Genetics 78(2), 1974
PMID: 4448362
Reduced efficacy of selection in regions of the Drosophila genome that lack crossing over.
Haddrill PR, Halligan DL, Tomaras D, Charlesworth B., Genome Biol. 8(2), 2007
PMID: 17284312
Evolution of protein-coding genes in Drosophila.
Larracuente AM, Sackton TB, Greenberg AJ, Wong A, Singh ND, Sturgill D, Zhang Y, Oliver B, Clark AG., Trends Genet. 24(3), 2008
PMID: 18249460
Comparative recombination rates in the rat, mouse, and human genomes.
Jensen-Seaman MI, Furey TS, Payseur BA, Lu Y, Roskin KM, Chen CF, Thomas MA, Haussler D, Jacob HJ., Genome Res. 14(4), 2004
PMID: 15059993
Absence of the TAP2 human recombination hotspot in chimpanzees.
Ptak SE, Roeder AD, Stephens M, Gilad Y, Paabo S, Przeworski M., PLoS Biol. 2(6), 2004
PMID: 15208713
Comparison of fine-scale recombination rates in humans and chimpanzees.
Winckler W, Myers SR, Richter DJ, Onofrio RC, McDonald GJ, Bontrop RE, McVean GA, Gabriel SB, Reich D, Donnelly P, Altshuler D., Science 308(5718), 2005
PMID: 15705809
The rise and fall of a human recombination hot spot.
Jeffreys AJ, Neumann R., Nat. Genet. 41(5), 2009
PMID: 19349985
A common sequence motif associated with recombination hot spots and genome instability in humans.
Myers S, Freeman C, Auton A, Donnelly P, McVean G., Nat. Genet. 40(9), 2008
PMID: 19165926
Biomart
AUTHOR UNKNOWN, 0
InParanoid 6: eukaryotic ortholog clusters with inparalogs.
Berglund AC, Sjolund E, Ostlund G, Sonnhammer EL., Nucleic Acids Res. 36(Database issue), 2007
PMID: 18055500
PAML 4: phylogenetic analysis by maximum likelihood.
Yang Z., Mol. Biol. Evol. 24(8), 2007
PMID: 17483113
A direct approach to false discovery rates.
AUTHOR UNKNOWN, 2002
GOstat: find statistically overrepresented Gene Ontologies within a group of genes.
Beissbarth T, Speed TP., Bioinformatics 20(9), 2004
PMID: 14962934
Controlling the false discovery rate: a practical and powerful approach to multiple testing.
AUTHOR UNKNOWN, 1995
OMIM Database
AUTHOR UNKNOWN, 0

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 20573239
PubMed | Europe PMC

Suchen in

Google Scholar