-
1
-
-
77956397064
-
A new model for extinction and recolonisation in two dimensions: Quantifying phylogeography
-
Barton, N. H., J. Kelleher, and A. M. Etheridge, 2010 A new model for extinction and recolonisation in two dimensions: quantifying phylogeography. Evolution 64(9): 2701-2715.
-
(2010)
Evolution
, vol.64
, Issue.9
, pp. 2701-2715
-
-
Barton, N.H.1
Kelleher, J.2
Etheridge, A.M.3
-
2
-
-
84908206474
-
Descartes rule of signs and the identifiability of population demographic models from genomic variation data
-
Bhaskar, A., and Y. S. Song, 2014 Descartes rule of signs and the identifiability of population demographic models from genomic variation data. Ann. Stat. 42(6): 2469-2493.
-
(2014)
Ann. Stat
, vol.42
, Issue.6
, pp. 2469-2493
-
-
Bhaskar, A.1
Song, Y.S.2
-
3
-
-
84937029830
-
Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations
-
(in press)
-
Bosse, M., H. J. Megens, O. Madsen, R. P. Crooijmans, O. A. Ryder et al., 2015 Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations. Genome Res. (in press).
-
(2015)
Genome Res
-
-
Bosse, M.1
Megens, H.J.2
Madsen, O.3
Crooijmans, R.P.4
Ryder, O.A.5
-
4
-
-
84856553089
-
The joint allele frequency spectrum of multiple populations: A coalescent theory approach
-
Chen, H., 2012 The joint allele frequency spectrum of multiple populations: a coalescent theory approach. Theor. Popul. Biol. 81(2): 179-195.
-
(2012)
Theor. Popul. Biol
, vol.81
, Issue.2
, pp. 179-195
-
-
Chen, H.1
-
5
-
-
78951476873
-
The confounding effects of population structure, genetic diversity and the sampling scheme on the detection and quantification of population size changes
-
Chikhi, L., V. C. Sousa, P. Luisi, B. Goossens, and M. A. Beaumont, 2010 The confounding effects of population structure, genetic diversity and the sampling scheme on the detection and quantification of population size changes. Genetics 186: 983-995.
-
(2010)
Genetics
, vol.186
, pp. 983-995
-
-
Chikhi, L.1
Sousa, V.C.2
Luisi, P.3
Goossens, B.4
Beaumont, M.A.5
-
6
-
-
84866077853
-
Patterns of neutral diversity under general models of selective sweeps
-
Coop, G., and P. L. Ralph, 2012 Patterns of neutral diversity under general models of selective sweeps. Genetics 192: 205-224.
-
(2012)
Genetics
, vol.192
, pp. 205-224
-
-
Coop, G.1
Ralph, P.L.2
-
7
-
-
79959435199
-
Genome-wide genetic marker discovery and genotyping using next-generation sequencing
-
Davey, J. W., P. A. Hohenlohe, P. D. Etter, J. Q. Boone, J. M. Catchen et al., 2011 Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat. Rev. Genet. 12(7): 499-510.
-
(2011)
Nat. Rev. Genet
, vol.12
, Issue.7
, pp. 499-510
-
-
Davey, J.W.1
Hohenlohe, P.A.2
Etter, P.D.3
Boone, J.Q.4
Catchen, J.M.5
-
8
-
-
0004128472
-
-
Cambridge University Press, Cambridge, UK
-
Edwards, A. W. F., 1972 Likelihood. Cambridge University Press, Cambridge, UK.
-
(1972)
Likelihood
-
-
Edwards, A.W.F.1
-
9
-
-
84887312794
-
Robust demographic inference from genomic and SNP data
-
Excoffier, L., I. Dupanloup, E. Huerta-Sánchez, V. C. Sousa, and M. Foll, 2013 Robust demographic inference from genomic and SNP data. PLoS Genet. 9(10): e1003905.
-
(2013)
PLoS Genet
, vol.9
, Issue.10
-
-
Excoffier, L.1
Dupanloup, I.2
Huerta-Sánchez, E.3
Sousa, V.C.4
Foll, M.5
-
10
-
-
0002339122
-
The number of evolutionary trees
-
Felsenstein, J., 1978 The number of evolutionary trees. Mol. Phylogenet. Evol. 27(1): 27-33.
-
(1978)
Mol. Phylogenet. Evol
, vol.27
, Issue.1
, pp. 27-33
-
-
Felsenstein, J.1
-
12
-
-
84884581710
-
Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus
-
Frantz, L., J. Schraiber, O. Madsen, H. J. Megens, M. Bosse et al., 2013 Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus. Genome Biol. 14(9): R107.
-
(2013)
Genome Biol
, vol.14
, Issue.9
-
-
Frantz, L.1
Schraiber, J.2
Madsen, O.3
Megens, H.J.4
Bosse, M.5
-
13
-
-
84928321268
-
Testing models of speciation from genome sequences: Divergence and asymmetric admixture in island South-East Asian Sus species during the plio-pleistocene climatic fluctuations
-
Frantz, L. A. F., O. Madsen, H. J. Megens, M. A. M. Groenen, and K. Lohse, 2014 Testing models of speciation from genome sequences: divergence and asymmetric admixture in island South-East Asian Sus species during the plio-pleistocene climatic fluctuations. Mol. Ecol. 23(22): 5566-5574.
-
(2014)
Mol. Ecol
, vol.23
, Issue.22
, pp. 5566-5574
-
-
Frantz, L.A.F.1
Madsen, O.2
Megens, H.J.3
Groenen, M.A.M.4
Lohse, K.5
-
14
-
-
0027453041
-
Statistical tests of neutrality of mutations
-
Fu, Y. X., and W. H. Li, 1993 Statistical tests of neutrality of mutations. Genetics 133: 693-709.
-
(1993)
Genetics
, vol.133
, pp. 693-709
-
-
Fu, Y.X.1
Li, W.H.2
-
15
-
-
0034086970
-
Detecting bottlenecks and selective sweeps from DNA sequence polymorphism
-
Galtier, N., F. Depaulis, and N. H. Barton, 2000 Detecting bottlenecks and selective sweeps from DNA sequence polymorphism. Genetics 155: 981-987.
-
(2000)
Genetics
, vol.155
, pp. 981-987
-
-
Galtier, N.1
Depaulis, F.2
Barton, N.H.3
-
16
-
-
84878716362
-
Inferring population size changes with sequence and SNP data: Lessons from human bottlenecks
-
Gattepaille, L. M., M. Jakobsson, and M. G. Blum, 2013 Inferring population size changes with sequence and SNP data: lessons from human bottlenecks. Heredity 110(5): 409-419.
-
(2013)
Heredity
, vol.110
, Issue.5
, pp. 409-419
-
-
Gattepaille, L.M.1
Jakobsson, M.2
Blum, M.G.3
-
17
-
-
0001301442
-
The age of a mutation in the general coalescent tree
-
Griffiths, R., and S. Tavaré, 1998 The age of a mutation in the general coalescent tree. Stoch. Models 14(1-2): 273-295.
-
(1998)
Stoch. Models
, vol.14
, Issue.1-2
, pp. 273-295
-
-
Griffiths, R.1
Tavaré, S.2
-
18
-
-
84869003221
-
Analyses of pig genomes provide insight into porcine demography and evolution
-
Groenen, M. A. M., A. L. Archibald, and H. Uenishi, C. K. Tuggle, Y. Takeuchiet al., 2012 Analyses of pig genomes provide insight into porcine demography and evolution. Nature 491(7424): 393-398.
-
(2012)
Nature
, vol.491
, Issue.7424
, pp. 393-398
-
-
Groenen, M.A.M.1
Archibald, A.L.2
Uenishi, H.3
Tuggle, C.K.4
Takeuchi, Y.5
-
19
-
-
80053386624
-
Bayesian inference of ancient human demography from individual genome sequences
-
Gronau, I., M. Hubisz, B. Gulko, C. Danko, and A. Siepel, 2011 Bayesian inference of ancient human demography from individual genome sequences. Nat. Genet. 43(10): 1031-1035.
-
(2011)
Nat. Genet
, vol.43
, Issue.10
, pp. 1031-1035
-
-
Gronau, I.1
Hubisz, M.2
Gulko, B.3
Danko, C.4
Siepel, A.5
-
20
-
-
73449149044
-
Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data
-
Gutenkunst, R. N., R. D. Hernandez, S. H. Williamson, and C. D. Bustamante, 2009 Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet. 5(10): e1000695.
-
(2009)
PLoS Genet
, vol.5
, Issue.10
-
-
Gutenkunst, R.N.1
Hernandez, R.D.2
Williamson, S.H.3
Bustamante, C.D.4
-
21
-
-
22344444998
-
Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations
-
Haddrill, P. R., K. R. Thornton, B. Charlesworth, and P. Andolfatto, 2005 Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations. Genome Res. 15(6): 790-799.
-
(2005)
Genome Res
, vol.15
, Issue.6
, pp. 790-799
-
-
Haddrill, P.R.1
Thornton, K.R.2
Charlesworth, B.3
Andolfatto, P.4
-
22
-
-
84879671007
-
Inferring demographic history from a spectrum of shared haplotype lengths
-
Harris, K., and R. Nielsen, 2013 Inferring demographic history from a spectrum of shared haplotype lengths. PLoS Genet. 9(6): e1003521.
-
(2013)
PLoS Genet
, vol.9
, Issue.6
-
-
Harris, K.1
Nielsen, R.2
-
23
-
-
84891529646
-
Likelihood-based inference of population history from low-coverage de novo genome assemblies
-
Hearn, J., G. N. Stone, L. Bunnefeld, J. A. Nicholls, N. H. Barton et al., 2014 Likelihood-based inference of population history from low-coverage de novo genome assemblies. Mol. Ecol. 23(1): 198-211.
-
(2014)
Mol. Ecol
, vol.23
, Issue.1
, pp. 198-211
-
-
Hearn, J.1
Stone, G.N.2
Bunnefeld, L.3
Nicholls, J.A.4
Barton, N.H.5
-
24
-
-
3142714474
-
Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis
-
Hey, J., and R. Nielsen, 2004 Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167: 747-760.
-
(2004)
Genetics
, vol.167
, pp. 747-760
-
-
Hey, J.1
Nielsen, R.2
-
25
-
-
0036184745
-
Generating samples under a Wright-Fisher neutral model of genetic variation
-
Hudson, R. R., 2002 Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338.
-
(2002)
Bioinformatics
, vol.18
, pp. 337-338
-
-
Hudson, R.R.1
-
26
-
-
84911437070
-
Maximum-likelihood inference of population size contractions from microsatellite data
-
Leblois, R., P. Pudlo, J. Néron, F. Bertaux, C. Reddy Beeravolu et al., 2014 Maximum-likelihood inference of population size contractions from microsatellite data. Mol. Biol. Evol. 31(10): 2805-2823.
-
(2014)
Mol. Biol. Evol
, vol.31
, Issue.10
, pp. 2805-2823
-
-
Leblois, R.1
Pudlo, P.2
Néron, J.3
Bertaux, F.4
Reddy Beeravolu, C.5
-
27
-
-
79960914105
-
Inference of human population history from individual whole-genome sequences
-
Li, H., and R. Durbin, 2011 Inference of human population history from individual whole-genome sequences. Nature 475(7357): 493-496.
-
(2011)
Nature
, vol.475
, Issue.7357
, pp. 493-496
-
-
Li, H.1
Durbin, R.2
-
28
-
-
68549104404
-
1000 Genome Project Data Processing Subgroup et al., 2009 The sequence alignment/map format and samtools
-
Li, H., B. Handsaker, A. Wysoker, and T. Fennell; 1000 Genome Project Data Processing Subgroup et al., 2009 The sequence alignment/map format and samtools. Bioinformatics 25(16): 2078-2079.
-
Bioinformatics
, vol.25
, Issue.16
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
-
29
-
-
84901303939
-
Neanderthal admixture in Eurasia confirmed by maximum-likelihood analysis of three genomes
-
Lohse, K., and L. A. F. Frantz, 2014 Neanderthal admixture in Eurasia confirmed by maximum-likelihood analysis of three genomes. Genetics 196: 1241-1251.
-
(2014)
Genetics
, vol.196
, pp. 1241-1251
-
-
Lohse, K.1
Frantz, L.A.F.2
-
30
-
-
81255210687
-
A general method for calculating likelihoods under the coalescent process
-
Lohse, K., R. J. Harrison, and N. H. Barton, 2011 A general method for calculating likelihoods under the coalescent process. Genetics 58: 977-987.
-
(2011)
Genetics
, vol.58
, pp. 977-987
-
-
Lohse, K.1
Harrison, R.J.2
Barton, N.H.3
-
32
-
-
20044366577
-
New phylogenetic perspectives among species of southeast asian wild pig (Sus sp.) based on mtDNA sequences and morphometric data
-
Lucchini, V., E. Meijaard, C. H. Diong, C. P. Groves, and E. Randi, 2005 New phylogenetic perspectives among species of southeast asian wild pig (Sus sp.) based on mtDNA sequences and morphometric data. J. Zool. 266(1): 25-35.
-
(2005)
J. Zool
, vol.266
, Issue.1
, pp. 25-35
-
-
Lucchini, V.1
Meijaard, E.2
Diong, C.H.3
Groves, C.P.4
Randi, E.5
-
33
-
-
1642282195
-
The allele frequency spectrum in genome-wide human variation data reveals signals of differential demographic history in three large world populations
-
Marth, G. T., E. Czabarka, J. Murvai, and S. T. Sherry, 2004 The allele frequency spectrum in genome-wide human variation data reveals signals of differential demographic history in three large world populations. Genetics 166: 351-372.
-
(2004)
Genetics
, vol.166
, pp. 351-372
-
-
Marth, G.T.1
Czabarka, E.2
Murvai, J.3
Sherry, S.T.4
-
35
-
-
84873084821
-
Applications of next-generation sequencing to phylogeography and phylogenetics
-
McCormack, J. E., S. M. Hird, A. J. Zellmer, B. C. Carstens, and R. T. Brumfield, 2013 Applications of next-generation sequencing to phylogeography and phylogenetics. Mol. Phylogenet. Evol. 66: 526-538.
-
(2013)
Mol. Phylogenet. Evol
, vol.66
, pp. 526-538
-
-
McCormack, J.E.1
Hird, S.M.2
Zellmer, A.J.3
Carstens, B.C.4
Brumfield, R.T.5
-
36
-
-
84899534182
-
Killer whale nuclear genome and mtDNA reveal widespread population bottleneck during the last glacial maximum
-
Moura, A. E., C. Janse van Rensburg, M. Pilot, A. Tehrani, and P. B. Best et al., 2014 Killer whale nuclear genome and mtDNA reveal widespread population bottleneck during the last glacial maximum. Mol. Biol. Evol. 31(5): 1121-1131.
-
(2014)
Mol. Biol. Evol
, vol.31
, Issue.5
, pp. 1121-1131
-
-
Moura, A.E.1
Janse van Rensburg, C.2
Pilot, M.3
Tehrani, A.4
Best, P.B.5
-
37
-
-
61649119281
-
Statistical inferences in phylogeography
-
Nielsen, R., and M. A. Beaumont, 2009 Statistical inferences in phylogeography. Mol. Ecol. 18(6): 1034-1047.
-
(2009)
Mol. Ecol
, vol.18
, Issue.6
, pp. 1034-1047
-
-
Nielsen, R.1
Beaumont, M.A.2
-
38
-
-
0032231870
-
On the probability of Neanderthal ancestry
-
Nordborg, M., 1998 On the probability of Neanderthal ancestry. Am. J. Hum. Genet. 63(4): 1237-1240.
-
(1998)
Am. J. Hum. Genet
, vol.63
, Issue.4
, pp. 1237-1240
-
-
Nordborg, M.1
-
39
-
-
84879835308
-
Evolutionary dynamics of copy number variation in pig genomes in the context of adaptation and domestication
-
Paudel, Y., O. Madsen, H. J. Megens, L. Frantz, M. Bosse et al., 2013 Evolutionary dynamics of copy number variation in pig genomes in the context of adaptation and domestication. BMC Genomics 14(1): 449.
-
(2013)
BMC Genomics
, vol.14
, Issue.1
, pp. 449
-
-
Paudel, Y.1
Madsen, O.2
Megens, H.J.3
Frantz, L.4
Bosse, M.5
-
40
-
-
0141566652
-
New explicit expressions for relative frequencies of single-nucleotide polymorphisms with application to statistical inference on population growth
-
Polanski, A., and M. Kimmel, 2003 New explicit expressions for relative frequencies of single-nucleotide polymorphisms with application to statistical inference on population growth. Genetics 165: 427-436.
-
(2003)
Genetics
, vol.165
, pp. 427-436
-
-
Polanski, A.1
Kimmel, M.2
-
41
-
-
0001915002
-
Information and the accuracy attainable in the estimation of statistical parameters
-
Rao, C. R., 1945 Information and the accuracy attainable in the estimation of statistical parameters. Bull. Calcutta Math. Soc. 37: 81-89.
-
(1945)
Bull. Calcutta Math. Soc
, vol.37
, pp. 81-89
-
-
Rao, C.R.1
-
42
-
-
84863561074
-
Resequencing data provide no evidence for a human bottleneck in Africa during the penultimate glacial period
-
Sjödin, P. E., A. Sjöstrand, M. Jakobsson, and M. G. Blum, 2012 Resequencing data provide no evidence for a human bottleneck in Africa during the penultimate glacial period. Mol. Biol. Evol. 29(7): 1851-1860.
-
(2012)
Mol. Biol. Evol
, vol.29
, Issue.7
, pp. 1851-1860
-
-
Sjödin, P.E.1
Sjöstrand, A.2
Jakobsson, M.3
Blum, M.G.4
-
43
-
-
67849119548
-
The impact of sampling schemes on the site frequency spectrum in nonequilibrium subdivided populations
-
Städler, T., B. Haubold, C. Merino, W. Stephan, and P. Pfaffelhuber, 2009 The impact of sampling schemes on the site frequency spectrum in nonequilibrium subdivided populations. Genetics 182: 205-216.
-
(2009)
Genetics
, vol.182
, pp. 205-216
-
-
Städler, T.1
Haubold, B.2
Merino, C.3
Stephan, W.4
Pfaffelhuber, P.5
-
44
-
-
0021066244
-
Evolutionary relationships of DNA sequences in finite populations
-
Tajima, F., 1983 Evolutionary relationships of DNA sequences in finite populations. Genetics 105: 437-460.
-
(1983)
Genetics
, vol.105
, pp. 437-460
-
-
Tajima, F.1
-
45
-
-
0024313579
-
Statistical method for testing the neutral mutation hypothesis by DNA polymorphism
-
Tajima, F., 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
-
(1989)
Genetics
, vol.123
, pp. 585-595
-
-
Tajima, F.1
-
46
-
-
84934917155
-
Fundamental limits on the accuracy of demographic inference based on the sample frequency spectrum
-
Terhorst, J., and Y. S. Song, 2015 Fundamental limits on the accuracy of demographic inference based on the sample frequency spectrum. Proc. Natl. Acad. Sci. USA 112(25): 7677-7682.
-
(2015)
Proc. Natl. Acad. Sci. USA
, vol.112
, Issue.25
, pp. 7677-7682
-
-
Terhorst, J.1
Song, Y.S.2
-
47
-
-
84868704770
-
A high density recombination map of the pig reveals a correlation between sex-specific recombination and gc content
-
Tortereau, F., B. Servin, L. Frantz, H. J. Megens, D. Milan et al., 2012 A high density recombination map of the pig reveals a correlation between sex-specific recombination and gc content. BMC Genomics 13(1): 586.
-
(2012)
BMC Genomics
, vol.13
, Issue.1
, pp. 586
-
-
Tortereau, F.1
Servin, B.2
Frantz, L.3
Megens, H.J.4
Milan, D.5
-
48
-
-
29444451610
-
Interrogating multiple aspects of variation in a full resequencing data set to infer human population size changes
-
Voight, B. F., A. M. Adams, L. A. Frisse, Y. Qian, R. R. Hudson et al., 2005 Interrogating multiple aspects of variation in a full resequencing data set to infer human population size changes. Proc. Natl. Acad. Sci. USA 102(51): 18508-18513.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, Issue.51
, pp. 18508-18513
-
-
Voight, B.F.1
Adams, A.M.2
Frisse, L.A.3
Qian, Y.4
Hudson, R.R.5
-
49
-
-
0032047371
-
Segregating sites in Wright's island model
-
Wakeley, J., 1998 Segregating sites in Wright's island model. Theor. Popul. Biol. 53(2): 166-174.
-
(1998)
Theor. Popul. Biol
, vol.53
, Issue.2
, pp. 166-174
-
-
Wakeley, J.1
-
50
-
-
0032736182
-
Nonequilibrium migration in human history
-
Wakeley, J., 1999 Nonequilibrium migration in human history. Genetics 153: 1863-1871.
-
(1999)
Genetics
, vol.153
, pp. 1863-1871
-
-
Wakeley, J.1
-
51
-
-
0037277564
-
Estimating ancestral population sizes and divergence times
-
Wall, J. D., 2003 Estimating ancestral population sizes and divergence times. Genetics 163: 395-404.
-
(2003)
Genetics
, vol.163
, pp. 395-404
-
-
Wall, J.D.1
-
52
-
-
0036961518
-
Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci
-
Yang, Z., 2002 Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci. Genetics 162: 1811-1823.
-
(2002)
Genetics
, vol.162
, pp. 1811-1823
-
-
Yang, Z.1
|