-
1
-
-
84865475040
-
Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty
-
COI: 1:CAS:528:DC%2BC38Xht1KjsbvL, PID: 22403239
-
Baele G, Lemey P, Bedford T et al (2012) Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. Mol Biol Evol 29:2157–2167. doi:10.1093/molbev/mss084
-
(2012)
Mol Biol Evol
, vol.29
, pp. 2157-2167
-
-
Baele, G.1
Lemey, P.2
Bedford, T.3
-
2
-
-
84877663836
-
Accurate model selection of relaxed molecular clocks in bayesian phylogenetics
-
COI: 1:CAS:528:DC%2BC3sXhtFGlsLw%3D, PID: 23090976
-
Baele G, Li WLS, Drummond AJ et al (2013) Accurate model selection of relaxed molecular clocks in bayesian phylogenetics. Mol Biol Evol 30:239–243. doi:10.1093/molbev/mss243
-
(2013)
Mol Biol Evol
, vol.30
, pp. 239-243
-
-
Baele, G.1
Li, W.L.S.2
Drummond, A.J.3
-
3
-
-
84873734497
-
Ancient substructure in early mtDNA lineages of southern Africa
-
COI: 1:CAS:528:DC%2BC3sXht1Gisbw%3D, PID: 23332919
-
Barbieri C, Vicente M, Rocha J et al (2013) Ancient substructure in early mtDNA lineages of southern Africa. Am J Hum Genet 92:285–292. doi:10.1016/j.ajhg.2012.12.010
-
(2013)
Am J Hum Genet
, vol.92
, pp. 285-292
-
-
Barbieri, C.1
Vicente, M.2
Rocha, J.3
-
4
-
-
84893971805
-
Unraveling the complex maternal history of Southern African Khoisan populations
-
PID: 24323467
-
Barbieri C, Güldemann T, Naumann C et al (2014a) Unraveling the complex maternal history of Southern African Khoisan populations. Am J Phys Anthropol 153:435–448. doi:10.1002/ajpa.22441
-
(2014)
Am J Phys Anthropol
, vol.153
, pp. 435-448
-
-
Barbieri, C.1
Güldemann, T.2
Naumann, C.3
-
5
-
-
84902531850
-
Migration and interaction in a contact zone: mtDNA variation among Bantu-speakers in southern Africa
-
PID: 24901532
-
Barbieri C, Vicente M, Oliveira S et al (2014b) Migration and interaction in a contact zone: mtDNA variation among Bantu-speakers in southern Africa. PLoS One 9:e99117
-
(2014)
PLoS One
, vol.9
, pp. e99117
-
-
Barbieri, C.1
Vicente, M.2
Oliveira, S.3
-
6
-
-
79959648730
-
Signatures of the preagricultural peopling processes in sub-Saharan Africa as revealed by the phylogeography of early Y chromosome lineages
-
COI: 1:CAS:528:DC%2BC3MXhtFShu7bO, PID: 21478374
-
Batini C, Ferri G, Destro-Bisol G et al (2011) Signatures of the preagricultural peopling processes in sub-Saharan Africa as revealed by the phylogeography of early Y chromosome lineages. Mol Biol Evol 28:2603–2613
-
(2011)
Mol Biol Evol
, vol.28
, pp. 2603-2613
-
-
Batini, C.1
Ferri, G.2
Destro-Bisol, G.3
-
7
-
-
67649345681
-
Genetic and demographic implications of the Bantu expansion: insights from human paternal lineages
-
COI: 1:CAS:528:DC%2BD1MXntlGju7s%3D, PID: 19369595
-
Berniell-Lee G, Calafell F, Bosch E et al (2009) Genetic and demographic implications of the Bantu expansion: insights from human paternal lineages. Mol Biol Evol 26:1581–1589. doi:10.1093/molbev/msp069
-
(2009)
Mol Biol Evol
, vol.26
, pp. 1581-1589
-
-
Berniell-Lee, G.1
Calafell, F.2
Bosch, E.3
-
8
-
-
0033358608
-
Variation in short tandem repeats is deeply structured by genetic background on the human Y chromosome
-
COI: 1:CAS:528:DC%2BD3cXjvFemtQ%3D%3D, PID: 10577916
-
Bosch E, Calafell F, Santos FR et al (1999) Variation in short tandem repeats is deeply structured by genetic background on the human Y chromosome. Am J Hum Genet 65:1623–1638
-
(1999)
Am J Hum Genet
, vol.65
, pp. 1623-1638
-
-
Bosch, E.1
Calafell, F.2
Santos, F.R.3
-
9
-
-
84995280090
-
Paternal age and genetic load
-
PID: 25019186
-
Cochran G, Harpending H (2013) Paternal age and genetic load. Hum Biol 85:515–528. doi:10.3378/027.085.0401
-
(2013)
Hum Biol
, vol.85
, pp. 515-528
-
-
Cochran, G.1
Harpending, H.2
-
10
-
-
79958787832
-
A revised root for the human Y chromosomal phylogenetic tree: the origin of patrilineal diversity in Africa
-
COI: 1:CAS:528:DC%2BC3MXnsVOrsbk%3D, PID: 21601174
-
Cruciani F, Trombetta B, Massaia A et al (2011) A revised root for the human Y chromosomal phylogenetic tree: the origin of patrilineal diversity in Africa. Am J Hum Genet 88:814–818. doi:10.1016/j.ajhg.2011.05.002
-
(2011)
Am J Hum Genet
, vol.88
, pp. 814-818
-
-
Cruciani, F.1
Trombetta, B.2
Massaia, A.3
-
11
-
-
84864453108
-
jModelTest 2: more models, new heuristics and parallel computing
-
COI: 1:CAS:528:DC%2BC38XhtFWmsbfP, PID: 22847109
-
Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9:772. doi:10.1038/nmeth.2109
-
(2012)
Nat Methods
, vol.9
, pp. 772
-
-
Darriba, D.1
Taboada, G.L.2
Doallo, R.3
Posada, D.4
-
12
-
-
79952171953
-
Y-chromosomal variation in sub-Saharan Africa: insights into the history of Niger-Congo groups
-
PID: 21109585
-
de Filippo C, Barbieri C, Whitten M et al (2011) Y-chromosomal variation in sub-Saharan Africa: insights into the history of Niger-Congo groups. Mol Biol Evol 28:1255–1269. doi:10.1093/molbev/msq312
-
(2011)
Mol Biol Evol
, vol.28
, pp. 1255-1269
-
-
de Filippo, C.1
Barbieri, C.2
Whitten, M.3
-
13
-
-
79955483667
-
A framework for variation discovery and genotyping using next-generation DNA sequencing data
-
COI: 1:CAS:528:DC%2BC3MXksFWguro%3D, PID: 21478889
-
DePristo MA, Banks E, Poplin R et al (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43:491–498. doi:10.1038/ng.806
-
(2011)
Nat Genet
, vol.43
, pp. 491-498
-
-
DePristo, M.A.1
Banks, E.2
Poplin, R.3
-
14
-
-
17744381574
-
Bayesian coalescent inference of past population dynamics from molecular sequences
-
COI: 1:CAS:528:DC%2BD2MXjvVKitb4%3D, PID: 15703244
-
Drummond AJ, Rambaut A, Shapiro B, Pybus OG (2005) Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol 22:1185–1192
-
(2005)
Mol Biol Evol
, vol.22
, pp. 1185-1192
-
-
Drummond, A.J.1
Rambaut, A.2
Shapiro, B.3
Pybus, O.G.4
-
15
-
-
84864530626
-
Bayesian phylogenetics with BEAUti and the BEAST 1.7
-
COI: 1:CAS:528:DC%2BC38XhtFagu7fO, PID: 22367748
-
Drummond AJ, Suchard MA, Xie D, Rambaut A (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 29:1969–1973. doi:10.1093/molbev/mss075
-
(2012)
Mol Biol Evol
, vol.29
, pp. 1969-1973
-
-
Drummond, A.J.1
Suchard, M.A.2
Xie, D.3
Rambaut, A.4
-
16
-
-
84881048484
-
Low-pass DNA sequencing of 1200 Sardinians reconstructs European Y-chromosome phylogeny
-
COI: 1:CAS:528:DC%2BC3sXhtFyjsr3O, PID: 23908240
-
Francalacci P, Morelli L, Angius A et al (2013) Low-pass DNA sequencing of 1200 Sardinians reconstructs European Y-chromosome phylogeny. Science 341:565–569. doi:10.1126/science.1237947
-
(2013)
Science
, vol.341
, pp. 565-569
-
-
Francalacci, P.1
Morelli, L.2
Angius, A.3
-
17
-
-
84887109646
-
Population growth inflates the per-individual number of deleterious mutations and reduces their mean effect
-
PID: 23979573
-
Gazave E, Chang D, Clark AG, Keinan A (2013) Population growth inflates the per-individual number of deleterious mutations and reduces their mean effect. Genetics 195:969–978. doi:10.1534/genetics.113.153973
-
(2013)
Genetics
, vol.195
, pp. 969-978
-
-
Gazave, E.1
Chang, D.2
Clark, A.G.3
Keinan, A.4
-
18
-
-
84927738893
-
The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades
-
PID: 25468874
-
Hallast P, Batini C, Zadik D et al (2015) The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades. Mol Biol Evol 32:661–673. doi:10.1093/molbev/msu327
-
(2015)
Mol Biol Evol
, vol.32
, pp. 661-673
-
-
Hallast, P.1
Batini, C.2
Zadik, D.3
-
19
-
-
84964033297
-
-
Heibl C (2013) PHYLOCH: R language tree plotting tools and interfaces to diverse phylogenetic software packages
-
Heibl C (2013) PHYLOCH: R language tree plotting tools and interfaces to diverse phylogenetic software packages. http://www.christophheibl.de/Rpackages.html
-
-
-
-
20
-
-
84929132937
-
The Y-chromosome point mutation rate in humans
-
COI: 1:CAS:528:DC%2BC2MXltFWkt7k%3D, PID: 25807285
-
Helgason A, Einarsson AW, Guðmundsdóttir VB et al (2015) The Y-chromosome point mutation rate in humans. Nat Genet 47:453–457. doi:10.1038/ng.3171
-
(2015)
Nat Genet
, vol.47
, pp. 453-457
-
-
Helgason, A.1
Einarsson, A.W.2
Guðmundsdóttir, V.B.3
-
22
-
-
0036184745
-
Generating samples under a Wright-Fisher neutral model of genetic variation
-
COI: 1:CAS:528:DC%2BD38XitFentrw%3D, PID: 11847089
-
Hudson RR (2002) Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18:337–338. doi:10.1093/bioinformatics/18.2.337
-
(2002)
Bioinformatics
, vol.18
, pp. 337-338
-
-
Hudson, R.R.1
-
24
-
-
0000732090
-
Evolution of protein molecules
-
COI: 1:CAS:528:DyaE3cXjvVOqug%3D%3D
-
Jukes TH, Cantor CR (1969) Evolution of protein molecules. Mamm protein Metab 3:21–132
-
(1969)
Mamm protein Metab
, vol.3
, pp. 21-132
-
-
Jukes, T.H.1
Cantor, C.R.2
-
25
-
-
43149087535
-
New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree
-
COI: 1:CAS:528:DC%2BD1cXlslChsLk%3D, PID: 18385274
-
Karafet TM, Mendez FL, Meilerman MB et al (2008) New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree. Genome Res 18:830–838. doi:10.1101/gr.7172008
-
(2008)
Genome Res
, vol.18
, pp. 830-838
-
-
Karafet, T.M.1
Mendez, F.L.2
Meilerman, M.B.3
-
26
-
-
84927713385
-
A recent bottleneck of Y chromosome diversity coincides with a global change in culture
-
COI: 1:CAS:528:DC%2BC2MXmvFCgu70%3D, PID: 25770088
-
Karmin M, Saag L, Vicente M et al (2015) A recent bottleneck of Y chromosome diversity coincides with a global change in culture. Genome Res 25:459–466
-
(2015)
Genome Res
, vol.25
, pp. 459-466
-
-
Karmin, M.1
Saag, L.2
Vicente, M.3
-
27
-
-
84950934893
-
Bayes factors
-
Kass RE, Raftery AE (1995) Bayes factors. J Am Stat Assoc 90:773–795. doi:10.1080/01621459.1995.10476572
-
(1995)
J Am Stat Assoc
, vol.90
, pp. 773-795
-
-
Kass, R.E.1
Raftery, A.E.2
-
28
-
-
84865208871
-
Rate of de novo mutations and the importance of father’s age to disease risk
-
COI: 1:CAS:528:DC%2BC38Xht1emtrbO, PID: 22914163
-
Kong A, Frigge ML, Masson G et al (2012) Rate of de novo mutations and the importance of father’s age to disease risk. Nature 488:471–475. doi:10.1038/nature11396
-
(2012)
Nature
, vol.488
, pp. 471-475
-
-
Kong, A.1
Frigge, M.L.2
Masson, G.3
-
29
-
-
84908128676
-
Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences
-
PID: 25254093
-
Lippold S, Xu H, Ko A et al (2014) Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences. Investig Genet 5:13. doi:10.1186/2041-2223-5-13
-
(2014)
Investig Genet
, vol.5
, pp. 13
-
-
Lippold, S.1
Xu, H.2
Ko, A.3
-
30
-
-
84876407035
-
An African American paternal lineage adds an extremely ancient root to the human Y chromosome phylogenetic tree
-
COI: 1:CAS:528:DC%2BC3sXjtl2isbY%3D, PID: 23453668
-
Mendez FL, Krahn T, Schrack B et al (2013) An African American paternal lineage adds an extremely ancient root to the human Y chromosome phylogenetic tree. Am J Hum Genet 92:454–459. doi:10.1016/j.ajhg.2013.02.002
-
(2013)
Am J Hum Genet
, vol.92
, pp. 454-459
-
-
Mendez, F.L.1
Krahn, T.2
Schrack, B.3
-
31
-
-
0033504552
-
The parsimony ratchet, a new method for rapid parsimony analysis
-
Nixon K (1999) The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics 15:407–414. doi:10.1006/clad.1999.0121
-
(1999)
Cladistics
, vol.15
, pp. 407-414
-
-
Nixon, K.1
-
33
-
-
84881043944
-
Sequencing Y chromosomes resolves discrepancy in time to common ancestor of males versus females
-
COI: 1:CAS:528:DC%2BC3sXhtFyjsr3N, PID: 23908239
-
Poznik GD, Henn BM, Yee M-C et al (2013) Sequencing Y chromosomes resolves discrepancy in time to common ancestor of males versus females. Science 341:562–565. doi:10.1126/science.1237619
-
(2013)
Science
, vol.341
, pp. 562-565
-
-
Poznik, G.D.1
Henn, B.M.2
Yee, M.-C.3
-
34
-
-
33646832209
-
Evaluation of saliva as a source of human DNA for population and association studies
-
COI: 1:CAS:528:DC%2BD28XltFCrs74%3D, PID: 16620753
-
Quinque D, Kittler R, Kayser M et al (2006) Evaluation of saliva as a source of human DNA for population and association studies. Anal Biochem 353:272–277
-
(2006)
Anal Biochem
, vol.353
, pp. 272-277
-
-
Quinque, D.1
Kittler, R.2
Kayser, M.3
-
35
-
-
84907095419
-
R: a language and environment for statistical computing
-
Vienna, Austria
-
R Core Team (2014) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org/
-
(2014)
R Foundation for Statistical Computing
-
-
Core Team, R.1
-
36
-
-
84964030471
-
-
Rambaut A, Drummond AJ (2009) Tracer V1.5. Accessed 30 May 2013
-
Rambaut A, Drummond AJ (2009) Tracer V1.5. http://beast.bio.ed.ac.uk/Tracer. Accessed 30 May 2013
-
-
-
-
37
-
-
84893816707
-
Natural selection reduced diversity on human Y chromosomes
-
Sayres MAW, Lohmueller KE, Nielsen R (2014) Natural selection reduced diversity on human Y chromosomes. PLoS Genet 10:e1004064. doi:10.1371/journal.pgen.1004064
-
(2014)
PLoS Genet
, vol.10
, pp. e1004064
-
-
Sayres, M.A.W.1
Lohmueller, K.E.2
Nielsen, R.3
-
38
-
-
79951548848
-
phangorn: phylogenetic analysis in R
-
COI: 1:CAS:528:DC%2BC3MXitVWhur0%3D, PID: 21169378
-
Schliep KP (2011) phangorn: phylogenetic analysis in R. Bioinformatics 27:592–593. doi:10.1093/bioinformatics/btq706
-
(2011)
Bioinformatics
, vol.27
, pp. 592-593
-
-
Schliep, K.P.1
-
39
-
-
84868705138
-
Molecular dissection of the basal clades in the human Y chromosome phylogenetic tree
-
PID: 23145109
-
Scozzari R, Massaia A, D’Atanasio E et al (2012) Molecular dissection of the basal clades in the human Y chromosome phylogenetic tree. PLoS One. doi:10.1371/journal.pone.0049170
-
(2012)
PLoS One
-
-
Scozzari, R.1
Massaia, A.2
D’Atanasio, E.3
-
40
-
-
84895510940
-
An unbiased resource of novel SNP markers provides a new chronology for the human y chromosome and reveals a deep phylogenetic structure in Africa
-
COI: 1:CAS:528:DC%2BC2cXkvVyqsLY%3D, PID: 24395829
-
Scozzari R, Massaia A, Trombetta B et al (2014) An unbiased resource of novel SNP markers provides a new chronology for the human Y chromosome and reveals a deep phylogenetic structure in Africa. Genome Res 24:535–544. doi:10.1101/gr.160788.113
-
(2014)
Genome Res
, vol.24
, pp. 535-544
-
-
Scozzari, R.1
Massaia, A.2
Trombetta, B.3
-
41
-
-
74549133571
-
A worldwide survey of human male demographic history based on Y-SNP and Y-STR data from the HGDP-CEPH populations
-
COI: 1:CAS:528:DC%2BC3cXntlGntg%3D%3D, PID: 19822636
-
Shi W, Ayub Q, Vermeulen M et al (2010) A worldwide survey of human male demographic history based on Y-SNP and Y-STR data from the HGDP-CEPH populations. Mol Biol Evol 27:385–393. doi:10.1093/molbev/msp243
-
(2010)
Mol Biol Evol
, vol.27
, pp. 385-393
-
-
Shi, W.1
Ayub, Q.2
Vermeulen, M.3
-
43
-
-
84866912512
-
A direct characterization of human mutation based on microsatellites
-
COI: 1:CAS:528:DC%2BC38Xht1Ght7bP, PID: 22922873
-
Sun JX, Helgason A, Masson G et al (2012) A direct characterization of human mutation based on microsatellites. Nat Genet 44:1161–1165. doi:10.1038/ng.2398
-
(2012)
Nat Genet
, vol.44
, pp. 1161-1165
-
-
Sun, J.X.1
Helgason, A.2
Masson, G.3
-
44
-
-
0030009791
-
High male:female ratio of germ-line mutations: an alternative explanation for postulated gestational lethality in males in X-linked dominant disorders
-
COI: 1:STN:280:DyaK283htlOksw%3D%3D, PID: 8651313
-
Thomas GH (1996) High male:female ratio of germ-line mutations: an alternative explanation for postulated gestational lethality in males in X-linked dominant disorders. Am J Hum Genet 58:1364–1368
-
(1996)
Am J Hum Genet
, vol.58
, pp. 1364-1368
-
-
Thomas, G.H.1
-
45
-
-
0033762701
-
Y chromosome sequence variation and the history of human populations
-
COI: 1:CAS:528:DC%2BD3cXotVWhtr4%3D, PID: 11062480
-
Underhill PA, Shen P, Lin AA et al (2000) Y chromosome sequence variation and the history of human populations. Nat Genet 26:358–361. doi:10.1038/81685
-
(2000)
Nat Genet
, vol.26
, pp. 358-361
-
-
Underhill, P.A.1
Shen, P.2
Lin, A.A.3
-
46
-
-
84891946246
-
Seeing the wood for the trees: a minimal reference phylogeny for the human Y chromosome
-
PID: 24166809
-
Van Oven M, Van Geystelen A, Kayser M et al (2014) Seeing the wood for the trees: a minimal reference phylogeny for the human Y chromosome. Hum Mutat 35:187–191. doi:10.1002/humu.22468
-
(2014)
Hum Mutat
, vol.35
, pp. 187-191
-
-
Van Oven, M.1
Van Geystelen, A.2
Kayser, M.3
-
47
-
-
84915819118
-
Variation in male reproductive longevity across traditional societies
-
PID: 25405763
-
Vinicius L, Mace R, Migliano A (2014) Variation in male reproductive longevity across traditional societies. PLoS One 9:e112236. doi:10.1371/journal.pone.0112236
-
(2014)
PLoS One
, vol.9
, pp. e112236
-
-
Vinicius, L.1
Mace, R.2
Migliano, A.3
-
48
-
-
84868692234
-
A calibrated human Y-chromosomal phylogeny based on resequencing
-
COI: 1:CAS:528:DC%2BC3sXitVemtLg%3D, PID: 23038768
-
Wei W, Ayub Q, Chen Y et al (2013) A calibrated human Y-chromosomal phylogeny based on resequencing. Genome Res 23:388–395. doi:10.1101/gr.143198.112
-
(2013)
Genome Res
, vol.23
, pp. 388-395
-
-
Wei, W.1
Ayub, Q.2
Chen, Y.3
-
49
-
-
21744451176
-
Contrasting patterns of Y chromosome and mtDNA variation in Africa: evidence for sex-biased demographic processes
-
COI: 1:CAS:528:DC%2BD2MXlsVWmsbY%3D, PID: 15856073
-
Wood ET, Stover DA, Ehret C et al (2005) Contrasting patterns of Y chromosome and mtDNA variation in Africa: evidence for sex-biased demographic processes. Eur J Hum Genet 13:867–876. doi:10.1038/sj.ejhg.5201408
-
(2005)
Eur J Hum Genet
, vol.13
, pp. 867-876
-
-
Wood, E.T.1
Stover, D.A.2
Ehret, C.3
-
50
-
-
69949140292
-
Human Y chromosome base-substitution mutation rate measured by direct sequencing in a deep-rooting pedigree
-
COI: 1:CAS:528:DC%2BD1MXhtFams77O, PID: 19716302
-
Xue Y, Wang Q, Long Q et al (2009) Human Y chromosome base-substitution mutation rate measured by direct sequencing in a deep-rooting pedigree. Curr Biol 19:1453–1457. doi:10.1016/j.cub.2009.07.032
-
(2009)
Curr Biol
, vol.19
, pp. 1453-1457
-
-
Xue, Y.1
Wang, Q.2
Long, Q.3
|