-
1
-
-
0025528844
-
Hybridization between pied and collared flycatchers-sexual selection and speciation theory
-
Alatalo RV, Eriksson D, Gustafsson L, Lundberg A. 1990. Hybridization between pied and collared flycatchers-sexual selection and speciation theory. J Evol Biol 3: 375-389.
-
(1990)
J Evol Biol
, vol.3
, pp. 375-389
-
-
Alatalo, R.V.1
Eriksson, D.2
Gustafsson, L.3
Lundberg, A.4
-
2
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215: 403-410.
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
3
-
-
84883557236
-
Divergence is focused on few genomic regions early in speciation: Incipient speciation in sunflower ecotypes
-
Andrew RL, Rieseberg LH. 2013. Divergence is focused on few genomic regions early in speciation: incipient speciation in sunflower ecotypes. Evolution 67: 2468-2482.
-
(2013)
Evolution
, vol.67
, pp. 2468-2482
-
-
Andrew, R.L.1
Rieseberg, L.H.2
-
4
-
-
77950628781
-
The recombination landscape of the zebra finch Taeniopygia guttata genome
-
Backström N, Forstmeier W, Schielzeth H, Mellenius H, Nam K, Bolund E, Webster MT, Öst T, Schneider M, Kempenaers B, et al. 2010. The recombination landscape of the zebra finch Taeniopygia guttata genome. Genome Res 20: 485-495.
-
(2010)
Genome Res
, vol.20
, pp. 485-495
-
-
Backström, N.1
Forstmeier, W.2
Schielzeth, H.3
Mellenius, H.4
Nam, K.5
Bolund, E.6
Webster, M.T.7
Öst, T.8
Schneider, M.9
Kempenaers, B.10
-
5
-
-
84871672493
-
Inferring the demographic history of European Ficedula flycatcher populations
-
Backström N, Sætre GP, Ellegren H. 2013. Inferring the demographic history of European Ficedula flycatcher populations. BMC Evol Biol 13: 2.
-
(2013)
BMC Evol Biol
, vol.13
, pp. 2
-
-
Backström, N.1
Sætre, G.P.2
Ellegren, H.3
-
6
-
-
0037226131
-
Automated de novo identification of repeat sequence families in sequenced genomes
-
Bao Z, Eddy SR. 2002. Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res 12: 1269-1276.
-
(2002)
Genome Res
, vol.12
, pp. 1269-1276
-
-
Bao, Z.1
Eddy, S.R.2
-
7
-
-
84933498486
-
Heredity and variation in modern lights
-
(ed. Seward AC). Cambridge University Press, Cambridge, UK
-
Bateson W. 1909. Heredity and variation in modern lights. In Darwin and modern science (ed. Seward AC), pp. 85-101. Cambridge University Press, Cambridge, UK.
-
Darwin and modern science
, pp. 85-101
-
-
Bateson, W.1
-
8
-
-
84886035850
-
Meiotic recombination in mammals: Localization and regulation
-
Baudat F, Imai Y, de Massy B. 2013. Meiotic recombination in mammals: localization and regulation. Nat Rev Genet 14: 794-806.
-
(2013)
Nat Rev Genet
, vol.14
, pp. 794-806
-
-
Baudat, F.1
Imai, Y.2
De Massy, B.3
-
9
-
-
0033555906
-
Tandem repeats finder: A program to analyze DNA sequences
-
Benson G. 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27: 573-580.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 573-580
-
-
Benson, G.1
-
10
-
-
28444481333
-
Amount of introgression in flycatcher hybrid zones reflects regional differences in pre and post-zygotic barriers to gene exchange
-
Borge T, Lindroos K, Nádvorník P, Syvänen AC, Sætre GP. 2005. Amount of introgression in flycatcher hybrid zones reflects regional differences in pre and post-zygotic barriers to gene exchange. J Evol Biol 18: 1416-1424.
-
(2005)
J Evol Biol
, vol.18
, pp. 1416-1424
-
-
Borge, T.1
Lindroos, K.2
Nádvorník, P.3
Syvänen, A.C.4
Sætre, G.P.5
-
11
-
-
0031901554
-
Measures of divergence between populations and the effect of forces that reduce variability
-
Charlesworth B. 1998.Measures of divergence between populations and the effect of forces that reduce variability. Mol Biol Evol 15: 538-543.
-
(1998)
Mol Biol Evol
, vol.15
, pp. 538-543
-
-
Charlesworth, B.1
-
12
-
-
84913592766
-
The relations between recombination rate and patterns of molecular variation and evolution in Drosophila
-
Charlesworth B, Campos JL. 2014. The relations between recombination rate and patterns of molecular variation and evolution in Drosophila. Annu Rev Genet 48: 383-403.
-
(2014)
Annu Rev Genet
, vol.48
, pp. 383-403
-
-
Charlesworth, B.1
Campos, J.L.2
-
13
-
-
0027305597
-
The effect of deleterious mutations on neutral molecular variation
-
Charlesworth B, Morgan MT, Charlesworth D. 1993. The effect of deleterious mutations on neutral molecular variation. Genetics 134: 1289-1303.
-
(1993)
Genetics
, vol.134
, pp. 1289-1303
-
-
Charlesworth, B.1
Morgan, M.T.2
Charlesworth, D.3
-
14
-
-
84903376433
-
Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow
-
Cruickshank TE, Hahn MW. 2014. Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow. Mol Ecol 23: 3133-3157.
-
(2014)
Mol Ecol
, vol.23
, pp. 3133-3157
-
-
Cruickshank, T.E.1
Hahn, M.W.2
-
15
-
-
51549089796
-
A genealogical approach to quantifying lineage divergence
-
Cummings MP, Neel MC, Shaw KL. 2008. A genealogical approach to quantifying lineage divergence. Evolution 62: 2411-2422.
-
(2008)
Evolution
, vol.62
, pp. 2411-2422
-
-
Cummings, M.P.1
Neel, M.C.2
Shaw, K.L.3
-
16
-
-
84875230189
-
Genomic signatures of selection at linked sites: Unifying the disparity among species
-
Cutter AD, Payseur BA. 2013. Genomic signatures of selection at linked sites: unifying the disparity among species. Nat Rev Genet 14: 262-274.
-
(2013)
Nat Rev Genet
, vol.14
, pp. 262-274
-
-
Cutter, A.D.1
Payseur, B.A.2
-
17
-
-
79955483667
-
A framework for variation discovery and genotyping using next-generation DNA sequencing data
-
DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, et al. 2011. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43: 491-498.
-
(2011)
Nat Genet
, vol.43
, pp. 491-498
-
-
DePristo, M.A.1
Banks, E.2
Poplin, R.3
Garimella, K.V.4
Maguire, J.R.5
Hartl, C.6
Philippakis, A.A.7
Del Angel, G.8
Rivas, M.A.9
Hanna, M.10
-
19
-
-
79961039058
-
Testing for ancient admixture between closely related populations
-
Durand EY, Patterson N, Reich D, Slatkin M. 2011. Testing for ancient admixture between closely related populations. Mol Biol Evol 28: 2239-2252.
-
(2011)
Mol Biol Evol
, vol.28
, pp. 2239-2252
-
-
Durand, E.Y.1
Patterson, N.2
Reich, D.3
Slatkin, M.4
-
20
-
-
0001077032
-
Nonparametric estimates of standard error: The jackknife, the bootstrap and other methods
-
Efron B. 1981. Nonparametric estimates of standard error: the jackknife, the bootstrap and other methods. Biometrika 68: 589-599.
-
(1981)
Biometrika
, vol.68
, pp. 589-599
-
-
Efron, B.1
-
21
-
-
77950630372
-
Evolutionary stasis: The stable chromosomes of birds
-
Ellegren H. 2010. Evolutionary stasis: the stable chromosomes of birds. Trends Ecol Evol 25: 283-291.
-
(2010)
Trends Ecol Evol
, vol.25
, pp. 283-291
-
-
Ellegren, H.1
-
22
-
-
84870297139
-
The genomic landscape of species divergence in Ficedula flycatchers
-
Ellegren H, Smeds L, Burri R, Olason PI, Backström N, Kawakami T, Kunstner A, Makinen H, Nadachowska-Brzyska K, Qvarnstrom A, et al. 2012. The genomic landscape of species divergence in Ficedula flycatchers. Nature 491: 756-760.
-
(2012)
Nature
, vol.491
, pp. 756-760
-
-
Ellegren, H.1
Smeds, L.2
Burri, R.3
Olason, P.I.4
Backström, N.5
Kawakami, T.6
Kunstner, A.7
Makinen, H.8
Nadachowska-Brzyska, K.9
Qvarnstrom, A.10
-
23
-
-
84901393253
-
Genome-wide signals of positive selection in human evolution
-
Enard D, Messer PW, Petrov DA. 2014. Genome-wide signals of positive selection in human evolution. Genome Res 24: 885-895.
-
(2014)
Genome Res
, vol.24
, pp. 885-895
-
-
Enard, D.1
Messer, P.W.2
Petrov, D.A.3
-
24
-
-
0033911640
-
Hitchhiking under positive Darwinian selection
-
Fay JC, Wu CI. 2000. Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
-
(2000)
Genetics
, vol.155
, pp. 1405-1413
-
-
Fay, J.C.1
Wu, C.I.2
-
25
-
-
18244405773
-
Mayr, Dobzhansky, and Bush and the complexities of sympatric speciation in Rhagoletis
-
Feder JL, Xie X, Rull J, Velez S, Forbes A, Leung B, Dambroski H, Filchak KE, Aluja M. 2005. Mayr, Dobzhansky, and Bush and the complexities of sympatric speciation in Rhagoletis. Proc Natl Acad Sci 102: 6573-6580.
-
(2005)
Proc Natl Acad Sci
, vol.102
, pp. 6573-6580
-
-
Feder, J.L.1
Xie, X.2
Rull, J.3
Velez, S.4
Forbes, A.5
Leung, B.6
Dambroski, H.7
Filchak, K.E.8
Aluja, M.9
-
26
-
-
84862499260
-
The genomics of speciation-with-geneflow
-
Feder JL, Egan SP, Nosil P. 2012. The genomics of speciation-with-geneflow. Trends Genet 28: 342-350.
-
(2012)
Trends Genet
, vol.28
, pp. 342-350
-
-
Feder, J.L.1
Egan, S.P.2
Nosil, P.3
-
27
-
-
84913601872
-
Genome-wide congealing and rapid transitions across the speciation continuum during speciation with gene flow
-
Feder JL, Nosil P, Wacholder AC, Egan SP, Berlocher SH, Flaxman SM. 2014. Genome-wide congealing and rapid transitions across the speciation continuum during speciation with gene flow. J Hered 105: 810-820.
-
(2014)
J Hered
, vol.105
, pp. 810-820
-
-
Feder, J.L.1
Nosil, P.2
Wacholder, A.C.3
Egan, S.P.4
Berlocher, S.H.5
Flaxman, S.M.6
-
28
-
-
84883551749
-
Genetic hitchhiking and the dynamic buildup of genomic divergence during speciation with gene flow
-
Flaxman SM, Feder JL, Nosil P. 2013. Genetic hitchhiking and the dynamic buildup of genomic divergence during speciation with gene flow. Evolution 67: 2577-2591.
-
(2013)
Evolution
, vol.67
, pp. 2577-2591
-
-
Flaxman, S.M.1
Feder, J.L.2
Nosil, P.3
-
29
-
-
84900332666
-
NgsTools: Methods for population genetics analyses from next-generation sequencing data
-
Fumagalli M, Vieira FG, Linderoth T, Nielsen R. 2014. ngsTools: methods for population genetics analyses from next-generation sequencing data. Bioinformatics 30: 1486-1487.
-
(2014)
Bioinformatics
, vol.30
, pp. 1486-1487
-
-
Fumagalli, M.1
Vieira, F.G.2
Linderoth, T.3
Nielsen, R.4
-
31
-
-
14844359279
-
HIERFSTAT, a package for R to compute and test hierarchical F-statistics
-
Goudet J. 2005. HIERFSTAT, a package for R to compute and test hierarchical F-statistics. Mol Ecol Notes 5: 184-186.
-
(2005)
Mol Ecol Notes
, vol.5
, pp. 184-186
-
-
Goudet, J.1
-
32
-
-
77952136530
-
A draft sequence of the Neandertal genome
-
Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, et al. 2010. A draft sequence of the Neandertal genome. Science 328: 710-722.
-
(2010)
Science
, vol.328
, pp. 710-722
-
-
Green, R.E.1
Krause, J.2
Briggs, A.W.3
Maricic, T.4
Stenzel, U.5
Kircher, M.6
Patterson, N.7
Li, H.8
Zhai, W.9
Fritz, M.H.10
-
33
-
-
61849153558
-
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, et al. 2009. A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate. Genome Res 19: 510-519.
-
(2009)
Genome Res
, vol.19
, pp. 510-519
-
-
Groenen, M.A.1
Wahlberg, P.2
Foglio, M.3
Cheng, H.H.4
Megens, H.J.5
Crooijmans, R.P.6
Besnier, F.7
Lathrop, M.8
Muir, W.M.9
Wong, G.K.10
-
34
-
-
33744816190
-
Genomic islands of differentiation between house mouse subspecies
-
Harr B. 2006. Genomic islands of differentiation between house mouse subspecies. Genome Res 16: 730-737.
-
(2006)
Genome Res
, vol.16
, pp. 730-737
-
-
Harr, B.1
-
36
-
-
84859462157
-
The genomic basis of adaptive evolution in threespine sticklebacks
-
Jones FC, Grabherr MG, Chan YF, Russell P, Mauceli E, Johnson J, Swofford R, Pirun M, Zody MC, White S, et al. 2012. The genomic basis of adaptive evolution in threespine sticklebacks. Nature 484: 55-61.
-
(2012)
Nature
, vol.484
, pp. 55-61
-
-
Jones, F.C.1
Grabherr, M.G.2
Chan, Y.F.3
Russell, P.4
Mauceli, E.5
Johnson, J.6
Swofford, R.7
Pirun, M.8
Zody, M.C.9
White, S.10
-
37
-
-
77954209892
-
The Newick utilities: High-throughput phylogenetic tree processing in the UNIX shell
-
Junier T, Zdobnov EM. 2010. The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell. Bioinformatics 26: 1669-1670.
-
(2010)
Bioinformatics
, vol.26
, pp. 1669-1670
-
-
Junier, T.1
Zdobnov, E.M.2
-
38
-
-
45949107473
-
Recent developments in the MAFFT multiple sequence alignment program
-
Katoh K, Toh H. 2008. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 9: 286-298.
-
(2008)
Brief Bioinform
, vol.9
, pp. 286-298
-
-
Katoh, K.1
Toh, H.2
-
39
-
-
84905459089
-
Estimation of linkage disequilibrium and interspecific gene flow in Ficedula flycatchers by a newly developed 50k single-nucleotide polymorphism array
-
Kawakami T, Backström N, Burri R, Husby A, Olason P, Rice AM, Ålund M, Qvarnström A, Ellegren H. 2014a. Estimation of linkage disequilibrium and interspecific gene flow in Ficedula flycatchers by a newly developed 50k single-nucleotide polymorphism array. Mol Ecol Res 14: 1248-1260.
-
(2014)
Mol Ecol Res
, vol.14
, pp. 1248-1260
-
-
Kawakami, T.1
Backström, N.2
Burri, R.3
Husby, A.4
Olason, P.5
Rice, A.M.6
Ålund, M.7
Qvarnström, A.8
Ellegren, H.9
-
40
-
-
84905465421
-
A high-density linkage map enables a second- generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution
-
Kawakami T, Smeds L, Backström N, Husby A, Qvarnström A, Mugal CF, Olason P, Ellegren H. 2014b. A high-density linkage map enables a second- generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution. Mol Ecol 23: 4035-4058.
-
(2014)
Mol Ecol
, vol.23
, pp. 4035-4058
-
-
Kawakami, T.1
Smeds, L.2
Backström, N.3
Husby, A.4
Qvarnström, A.5
Mugal, C.F.6
Olason, P.7
Ellegren, H.8
-
42
-
-
84887616256
-
Hybridization reveals the evolving genomic architecture of speciation
-
Kronforst MR, Hansen ME, Crawford NG, Gallant JR, Zhang W, Kulathinal RJ, Kapan DD, Mullen SP. 2013. Hybridization reveals the evolving genomic architecture of speciation. Cell Rep 5: 666-677.
-
(2013)
Cell Rep
, vol.5
, pp. 666-677
-
-
Kronforst, M.R.1
Hansen, M.E.2
Crawford, N.G.3
Gallant, J.R.4
Zhang, W.5
Kulathinal, R.J.6
Kapan, D.D.7
Mullen, S.P.8
-
43
-
-
68249090481
-
The genomics of speciation in Drosophila: Diversity, divergence, and introgression estimated using lowcoverage genome sequencing
-
Kulathinal RJ, Stevison LS, Noor MAF. 2009. The genomics of speciation in Drosophila: diversity, divergence, and introgression estimated using lowcoverage genome sequencing. PLoS Genet 5: e1000550.
-
(2009)
PLoS Genet
, vol.5
, pp. e1000550
-
-
Kulathinal, R.J.1
Stevison, L.S.2
Noor, M.A.F.3
-
44
-
-
84884748768
-
Transposable element evolution in Heliconius suggests genome diversity within lepidoptera
-
Lavoie CA, Platt RN II, Novick PA, Counterman BA, Ray DA. 2013. Transposable element evolution in Heliconius suggests genome diversity within lepidoptera. Mobile DNA 4: 21.
-
(2013)
Mobile DNA
, vol.4
, pp. 21
-
-
Lavoie, C.A.1
Platt, R.N.I.I.2
Novick, P.A.3
Counterman, B.A.4
Ray, D.A.5
-
45
-
-
77958184872
-
Widespread divergence between incipient Anopheles gambiae species revealed by whole genome sequences
-
Lawniczak MK, Emrich SJ, Holloway AK, Regier AP, Olson M, White B, Redmond S, Fulton L, Appelbaum E, Godfrey J, et al. 2010. Widespread divergence between incipient Anopheles gambiae species revealed by whole genome sequences. Science 330: 512-514.
-
(2010)
Science
, vol.330
, pp. 512-514
-
-
Lawniczak, M.K.1
Emrich, S.J.2
Holloway, A.K.3
Regier, A.P.4
Olson, M.5
White, B.6
Redmond, S.7
Fulton, L.8
Appelbaum, E.9
Godfrey, J.10
-
46
-
-
67649884743
-
Fast and accurate short read alignment with Burrows- Wheeler transform
-
Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows- Wheeler transform. Bioinformatics 25: 1754-1760.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
47
-
-
68549104404
-
1000 Genome Project Data Processing Subgroup. 2009. The sequence alignment/map format and SAMtools
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25: 2078-2079.
-
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
Marth, G.7
Abecasis, G.8
Durbin, R.9
-
48
-
-
77957686501
-
A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
-
Liu L, Yu L, Edwards S. 2010. A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evol Biol 10: 302.
-
(2010)
BMC Evol Biol
, vol.10
, pp. 302
-
-
Liu, L.1
Yu, L.2
Edwards, S.3
-
50
-
-
84886085175
-
Genome-wide evidence for speciation with gene flow in Heliconius butterflies
-
Martin SH, Dasmahapatra KK, Nadeau NJ, Salazar C, Walters JR, Simpson F, Blaxter M, Manica A, Mallet J, Jiggins CD. 2013. Genome-wide evidence for speciation with gene flow in Heliconius butterflies. Genome Res 23: 1817-1828.
-
(2013)
Genome Res
, vol.23
, pp. 1817-1828
-
-
Martin, S.H.1
Dasmahapatra, K.K.2
Nadeau, N.J.3
Salazar, C.4
Walters, J.R.5
Simpson, F.6
Blaxter, M.7
Manica, A.8
Mallet, J.9
Jiggins, C.D.10
-
51
-
-
77956295988
-
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
-
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, et al. 2010. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20: 1297-1303.
-
(2010)
Genome Res
, vol.20
, pp. 1297-1303
-
-
McKenna, A.1
Hanna, M.2
Banks, E.3
Sivachenko, A.4
Cibulskis, K.5
Kernytsky, A.6
Garimella, K.7
Altshuler, D.8
Gabriel, S.9
Daly, M.10
-
52
-
-
0002084648
-
Bearing of the Drosophila work on systematics
-
(ed. Huxley J). Clarendon Press, Oxford, UK.
-
Muller HJ. 1940. Bearing of the Drosophila work on systematics. In The new systematics (ed. Huxley J). Clarendon Press, Oxford, UK.
-
(1940)
The New Systematics
-
-
Muller, H.J.1
-
53
-
-
0036889393
-
Variation in recombination rate across the genome: Evidence and implications
-
Nachman MW. 2002. Variation in recombination rate across the genome: evidence and implications. Curr Opin Genet Dev 12: 657-663.
-
(2002)
Curr Opin Genet Dev
, vol.12
, pp. 657-663
-
-
Nachman, M.W.1
-
54
-
-
84255162277
-
Recombination rate variation and speciation: Theoretical predictions and empirical results from rabbits and mice
-
Nachman MW, Payseur BA. 2012. Recombination rate variation and speciation: theoretical predictions and empirical results from rabbits and mice. Philos Trans R Soc Lond B Biol Sci 367: 409-421.
-
(2012)
Philos Trans R Soc Lond B Biol Sci
, vol.367
, pp. 409-421
-
-
Nachman, M.W.1
Payseur, B.A.2
-
55
-
-
84888261459
-
Demographic divergence history of pied flycatcher and collared flycatcher inferred from whole-genome re-sequencing data
-
Nadachowska-Brzyska K, Burri R, Olason PI, Kawakami T, Smeds L, Ellegren H. 2013. Demographic divergence history of pied flycatcher and collared flycatcher inferred from whole-genome re-sequencing data. PLoS Genet 9: e1003942.
-
(2013)
PLoS Genet
, vol.9
, pp. e1003942
-
-
Nadachowska-Brzyska, K.1
Burri, R.2
Olason, P.I.3
Kawakami, T.4
Smeds, L.5
Ellegren, H.6
-
56
-
-
84255162312
-
Genomic islands of divergence in hybridizing Heliconius butterflies identified by large-scale targeted sequencing
-
Nadeau NJ, Whibley A, Jones RT, Davey JW, Dasmahapatra KK, Baxter SW, Quail MA, Joron M, ffrench-Constant RH, Blaxter ML, et al. 2012. Genomic islands of divergence in hybridizing Heliconius butterflies identified by large-scale targeted sequencing. Philos Trans R Soc Lond B Biol Sci 367: 343-353.
-
(2012)
Philos Trans R Soc Lond B Biol Sci
, vol.367
, pp. 343-353
-
-
Nadeau, N.J.1
Whibley, A.2
Jones, R.T.3
Davey, J.W.4
Dasmahapatra, K.K.5
Baxter, S.W.6
Quail, M.A.7
Joron, M.8
Ffrench-Constant, R.H.9
Blaxter, M.L.10
-
57
-
-
84946127857
-
Resolving evolutionary relationships in closely related species with whole-genome sequencing data
-
Nater A, Burri R, Kawakami T, Smeds L, Ellegren H. 2015. Resolving evolutionary relationships in closely related species with whole-genome sequencing data. Syst Biol doi: 10.1093/sysbio/syv045.
-
(2015)
Syst Biol
-
-
Nater, A.1
Burri, R.2
Kawakami, T.3
Smeds, L.4
Ellegren, H.5
-
58
-
-
84864273210
-
SNP calling, genotype calling, and sample allele frequency estimation from New- Generation Sequencing data
-
Nielsen R, Korneliussen T, Albrechtsen A, Li Y, Wang J. 2012. SNP calling, genotype calling, and sample allele frequency estimation from New- Generation Sequencing data. PLoS One 7: e37558.
-
(2012)
PLoS One
, vol.7
, pp. e37558
-
-
Nielsen, R.1
Korneliussen, T.2
Albrechtsen, A.3
Li, Y.4
Wang, J.5
-
59
-
-
70450233628
-
Islands of speciation or mirages in the desert? Examining the role of restricted recombination in maintaining species
-
Noor MA, Bennett SM. 2009. Islands of speciation or mirages in the desert? Examining the role of restricted recombination in maintaining species. Heredity 103: 439-444.
-
(2009)
Heredity
, vol.103
, pp. 439-444
-
-
Noor, M.A.1
Bennett, S.M.2
-
60
-
-
42449144387
-
Speciation with gene flow could be common
-
Nosil P. 2008. Speciation with gene flow could be common. Mol Ecol 17: 2103-2106.
-
(2008)
Mol Ecol
, vol.17
, pp. 2103-2106
-
-
Nosil, P.1
-
61
-
-
39749135589
-
Heterogeneous genomic differentiation between walking-stick ecotypes: Isolation by adaptation" and multiple roles for divergent selection
-
Nosil P, Egan SP, Funk DJ. 2008. Heterogeneous genomic differentiation between walking-stick ecotypes: "isolation by adaptation" and multiple roles for divergent selection. Evolution 62: 316-336.
-
(2008)
Evolution
, vol.62
, pp. 316-336
-
-
Nosil, P.1
Egan, S.P.2
Funk, D.J.3
-
62
-
-
84869057650
-
Ancient admixture in human history
-
Patterson NJ, Moorjani P, Luo Y, Mallick S, Rohland N, Zhan Y, Genschoreck T, Webster T, Reich D. 2012. Ancient admixture in human history. Genetics 192: 1065-1093.
-
(2012)
Genetics
, vol.192
, pp. 1065-1093
-
-
Patterson, N.J.1
Moorjani, P.2
Luo, Y.3
Mallick, S.4
Rohland, N.5
Zhan, Y.6
Genschoreck, T.7
Webster, T.8
Reich, D.9
-
63
-
-
84905900226
-
Disputed islands
-
Pennisi E. 2014. Disputed islands. Science 345: 611-613.
-
(2014)
Science
, vol.345
, pp. 611-613
-
-
Pennisi, E.1
-
64
-
-
29144455282
-
De novo identification of repeat families in large genomes
-
Price AL, Jones NC, Pevzner PA. 2005. De novo identification of repeat families in large genomes. Bioinformatics 21: i351-i358.
-
(2005)
Bioinformatics
, vol.21
, pp. i351-i358
-
-
Price, A.L.1
Jones, N.C.2
Pevzner, P.A.3
-
65
-
-
70349472875
-
Reconstructing Indian population history
-
Reich D, Thangaraj K, Patterson N, Price AL, Singh L. 2009. Reconstructing Indian population history. Nature 461: 489-494.
-
(2009)
Nature
, vol.461
, pp. 489-494
-
-
Reich, D.1
Thangaraj, K.2
Patterson, N.3
Price, A.L.4
Singh, L.5
-
66
-
-
84878589154
-
Genomic islands of divergence are not affected by geography of speciation in sunflowers
-
Renaut S, Grassa CJ, Yeaman S, Moyers BT, Lai Z, Kane NC, Bowers JE, Burke JM, Rieseberg LH. 2013. Genomic islands of divergence are not affected by geography of speciation in sunflowers. Nat Commun 4: 1827.
-
(2013)
Nat Commun
, vol.4
, pp. 1827
-
-
Renaut, S.1
Grassa, C.J.2
Yeaman, S.3
Moyers, B.T.4
Lai, Z.5
Kane, N.C.6
Bowers, J.E.7
Burke, J.M.8
Rieseberg, L.H.9
-
67
-
-
84891821460
-
Shared selective pressure and local genomic landscape lead to repeatable patterns of genomic divergence in sunflowers
-
Renaut S, Owens GL, Rieseberg LH. 2014. Shared selective pressure and local genomic landscape lead to repeatable patterns of genomic divergence in sunflowers. Mol Ecol 23: 311-324.
-
(2014)
Mol Ecol
, vol.23
, pp. 311-324
-
-
Renaut, S.1
Owens, G.L.2
Rieseberg, L.H.3
-
68
-
-
84862025426
-
Genome divergence during evolutionary diversification as revealed in replicate lake-stream stickleback population pairs
-
Roesti M, Hendry AP, Salzburger W, Berner D. 2012. Genome divergence during evolutionary diversification as revealed in replicate lake-stream stickleback population pairs. Mol Ecol 21: 2852-2862.
-
(2012)
Mol Ecol
, vol.21
, pp. 2852-2862
-
-
Roesti, M.1
Hendry, A.P.2
Salzburger, W.3
Berner, D.4
-
69
-
-
77950253423
-
Ecology and genetics of speciation in Ficedula flycatchers
-
Sætre GP, Sæther SA. 2010. Ecology and genetics of speciation in Ficedula flycatchers. Mol Ecol 19: 1091-1106.
-
(2010)
Mol Ecol
, vol.19
, pp. 1091-1106
-
-
Sætre, G.P.1
Sæther, S.A.2
-
70
-
-
0039132779
-
Dynamics of a clinal hybrid zone and a comparison with island hybrid zones of flycatchers (Ficedula hypoleuca and F. Albicollis)
-
Sætre GP, Král K, Bures S, Ims RA. 1999. Dynamics of a clinal hybrid zone and a comparison with island hybrid zones of flycatchers (Ficedula hypoleuca and F. albicollis). J Zool 247: 53-64.
-
(1999)
J Zool
, vol.247
, pp. 53-64
-
-
Sætre, G.P.1
Král, K.2
Bures, S.3
Ims, R.A.4
-
71
-
-
33644974019
-
A fast and flexible statistical model for largescale population genotype data: Applications to inferring missing genotypes and haplotypic phase
-
Scheet P, Stephens M. 2006. A fast and flexible statistical model for largescale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet 78: 1611-1618.
-
(2006)
Am J Hum Genet
, vol.78
, pp. 1611-1618
-
-
Scheet, P.1
Stephens, M.2
-
72
-
-
84893015775
-
Genomics and the origin of species
-
Seehausen O, Butlin RK, Keller I, Wagner CE, Boughman JW, Hohenlohe PA, Peichel CL, Sætre GP, Bank C, Brannstrom A, et al. 2014. Genomics and the origin of species. Nat Rev Genet 15: 176-192.
-
(2014)
Nat Rev Genet
, vol.15
, pp. 176-192
-
-
Seehausen, O.1
Butlin, R.K.2
Keller, I.3
Wagner, C.E.4
Boughman, J.W.5
Hohenlohe, P.A.6
Peichel, C.L.7
Sætre, G.P.8
Bank, C.9
Brannstrom, A.10
-
74
-
-
84861923558
-
The spatial regulation of meiotic recombination hotspots: Are all DSB hotspots crossover hotspots?
-
Serrentino ME, Borde V. 2012. The spatial regulation of meiotic recombination hotspots: Are all DSB hotspots crossover hotspots? Exp Cell Res 318: 1347-1352.
-
(2012)
Exp Cell Res
, vol.318
, pp. 1347-1352
-
-
Serrentino, M.E.1
Borde, V.2
-
75
-
-
84913533096
-
Speciation continuum
-
Shaw KL, Mullen SP. 2014. Speciation continuum. J Hered 105: 741-742.
-
(2014)
J Hered
, vol.105
, pp. 741-742
-
-
Shaw, K.L.1
Mullen, S.P.2
-
76
-
-
14844285310
-
The genomic distribution of population substructure in four populations using 8, 525 autosomal SNPs
-
Shriver M, Kennedy G, Parra E, Lawson H, Sonpar V, Huang J, Akey J, Jones K. 2004. The genomic distribution of population substructure in four populations using 8, 525 autosomal SNPs. Human Genomics 1: 274-286.
-
(2004)
Human Genomics
, vol.1
, pp. 274-286
-
-
Shriver, M.1
Kennedy, G.2
Parra, E.3
Lawson, H.4
Sonpar, V.5
Huang, J.6
Akey, J.7
Jones, K.8
-
77
-
-
84900439893
-
Stick insect genomes reveal natural selection's role in parallel speciation
-
Soria-Carrasco V, Gompert Z, Comeault AA, Farkas TE, Parchman TL, Johnston JS, Buerkle CA, Feder JL, Bast J, Schwander T, et al. 2014. Stick insect genomes reveal natural selection's role in parallel speciation. Science 344: 738-742.
-
(2014)
Science
, vol.344
, pp. 738-742
-
-
Soria-Carrasco, V.1
Gompert, Z.2
Comeault, A.A.3
Farkas, T.E.4
Parchman, T.L.5
Johnston, J.S.6
Buerkle, C.A.7
Feder, J.L.8
Bast, J.9
Schwander, T.10
-
78
-
-
18644368714
-
The BioPerl Toolkit: Perl modules for the life sciences
-
Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JGR, Korf I, Lapp H, et al. 2002. The BioPerl Toolkit: Perl modules for the life sciences. Genome Res 12: 1611-1618.
-
(2002)
Genome Res
, vol.12
, pp. 1611-1618
-
-
Stajich, J.E.1
Block, D.2
Boulez, K.3
Brenner, S.E.4
Chervitz, S.A.5
Dagdigian, C.6
Fuellen, G.7
Gilbert, J.G.R.8
Korf, I.9
Lapp, H.10
-
79
-
-
84899553363
-
RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies
-
Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312-1313.
-
(2014)
Bioinformatics
, vol.30
, pp. 1312-1313
-
-
Stamatakis, A.1
-
80
-
-
0001656332
-
Haldane rule and sex biased gene flow between two hybridizing flycatcher species (Ficedula albicollis and F. Hypoleuca, Aves, Muscicapidae)
-
Tegelström H, Gelter HP. 1990. Haldane rule and sex biased gene flow between two hybridizing flycatcher species (Ficedula albicollis and F. hypoleuca, Aves, Muscicapidae). Evolution 44: 2012-2021.
-
(1990)
Evolution
, vol.44
, pp. 2012-2021
-
-
Tegelström, H.1
Gelter, H.P.2
-
81
-
-
77953625372
-
Genomic islands of speciation or genomic islands and speciation?
-
Turner TL, Hahn MW. 2010. Genomic islands of speciation or genomic islands and speciation? Mol Ecol 19: 848-850.
-
(2010)
Mol Ecol
, vol.19
, pp. 848-850
-
-
Turner, T.L.1
Hahn, M.W.2
-
82
-
-
24944471763
-
Genomic islands of speciation in Anopheles gambiae
-
Turner TL, HahnMW, Nuzhdin SV. 2005. Genomic islands of speciation in Anopheles gambiae. PLoS Biol 3: e285.
-
(2005)
PLoS Biol
, vol.3
, pp. e285
-
-
Turner, T.L.1
Hahn, M.W.2
Nuzhdin, S.V.3
-
83
-
-
52649091697
-
The genetic mosaic suggests a new role for hitchhiking in ecological speciation
-
Via S, West J. 2008. The genetic mosaic suggests a new role for hitchhiking in ecological speciation. Mol Ecol 17: 4334-4345.
-
(2008)
Mol Ecol
, vol.17
, pp. 4334-4345
-
-
Via, S.1
West, J.2
-
84
-
-
0021566877
-
Estimating F-statistics for the analysis of population structure
-
Weir BS, Cockerham CC. 1984. Estimating F-statistics for the analysis of population structure. Evolution 38: 1358-1370.
-
(1984)
Evolution
, vol.38
, pp. 1358-1370
-
-
Weir, B.S.1
Cockerham, C.C.2
-
85
-
-
77953363913
-
Genetic association of physically unlinked islands of genomic divergence in incipient species of Anopheles gambiae
-
White BJ, Cheng CD, Simard F, Costantini C, Besansky NJ. 2010. Genetic association of physically unlinked islands of genomic divergence in incipient species of Anopheles gambiae. Mol Ecol 19: 925-939.
-
(2010)
Mol Ecol
, vol.19
, pp. 925-939
-
-
White, B.J.1
Cheng, C.D.2
Simard, F.3
Costantini, C.4
Besansky, N.J.5
-
86
-
-
67649445924
-
Postzygotic isolation over multiple generations of hybrid descendants in a natural hybrid zone: How well do single-generation estimates reflect reproductive isolation?
-
Wiley C, Qvarnström A, Andersson G, Borge T, Sætre GP. 2009. Postzygotic isolation over multiple generations of hybrid descendants in a natural hybrid zone: How well do single-generation estimates reflect reproductive isolation? Evolution 63: 1731-1739.
-
(2009)
Evolution
, vol.63
, pp. 1731-1739
-
-
Wiley, C.1
Qvarnström, A.2
Andersson, G.3
Borge, T.4
Sætre, G.P.5
-
87
-
-
0031717743
-
Estimating hierarchical F-statistics
-
Yang RC. 1998. Estimating hierarchical F-statistics. Evolution 52: 950-956.
-
(1998)
Evolution
, vol.52
, pp. 950-956
-
-
Yang, R.C.1
-
88
-
-
77954319020
-
Sequencing of 50 human exomes reveals adaptation to high altitude
-
Yi X, Liang Y, Huerta-Sanchez E, Jin X, Cuo ZX, Pool JE, Xu X, Jiang H, Vinckenbosch N, Korneliussen TS, et al. 2010. Sequencing of 50 human exomes reveals adaptation to high altitude. Science 329: 75-78.
-
(2010)
Science
, vol.329
, pp. 75-78
-
-
Yi, X.1
Liang, Y.2
Huerta-Sanchez, E.3
Jin, X.4
Cuo, Z.X.5
Pool, J.E.6
Xu, X.7
Jiang, H.8
Vinckenbosch, N.9
Korneliussen, T.S.10
-
89
-
-
79951827545
-
The choice in meiosis-defining the factors that influence crossover or non-crossover formation
-
Youds JL, Boulton SJ. 2011. The choice in meiosis-defining the factors that influence crossover or non-crossover formation. J Cell Sci 124: 501-513.
-
(2011)
J Cell Sci
, vol.124
, pp. 501-513
-
-
Youds, J.L.1
Boulton, S.J.2
|