-
2
-
-
0037043719
-
Evolution, consequences and future of plant and animal domestication
-
COI: 1:CAS:528:DC%2BD38XlvVyltbY%3D
-
Diamond, J. Evolution, consequences and future of plant and animal domestication. Nature 418, 700–707 (2002).
-
(2002)
Nature
, vol.418
, pp. 700-707
-
-
Diamond, J.1
-
3
-
-
84949461386
-
The accumulation of deleterious mutations as a consequence of domestication and improvement in sunflowers and other compositae crops
-
COI: 1:CAS:528:DC%2BC28Xht12hs7rE
-
Renaut, S. & Rieseberg, L. H. The accumulation of deleterious mutations as a consequence of domestication and improvement in sunflowers and other compositae crops. Mol. Biol. Evol. 32, 2273–2283 (2015).
-
(2015)
Mol. Biol. Evol.
, vol.32
, pp. 2273-2283
-
-
Renaut, S.1
Rieseberg, L.H.2
-
4
-
-
84903278682
-
Domestication genomics: evidence from animals
-
COI: 1:CAS:528:DC%2BC2MXkt1Shtbk%3D
-
Wang, G. D., Xie, H. B., Peng, M. S., Irwin, D. & Zhang, Y. P. Domestication genomics: evidence from animals. Annu Rev. Anim. Biosci. 2, 65–84 (2014).
-
(2014)
Annu Rev. Anim. Biosci.
, vol.2
, pp. 65-84
-
-
Wang, G.D.1
Xie, H.B.2
Peng, M.S.3
Irwin, D.4
Zhang, Y.P.5
-
5
-
-
0004045481
-
-
Thames and Hudson, New York
-
Coe, S. D., Coe, M. D. & Huxtable, R. J. The true history of chocolate. (Thames and Hudson, New York, 1996).
-
(1996)
The True History of Chocolate
-
-
Coe, S.D.1
Coe, M.D.2
Huxtable, R.J.3
-
7
-
-
0000437961
-
Notes on the nomenclature, classification and possible relationships of cocoa populations
-
Cheesman, E. E. Notes on the nomenclature, classification and possible relationships of cocoa populations. Trop. Agric. 21, 144–159 (1944).
-
(1944)
Trop. Agric.
, vol.21
, pp. 144-159
-
-
Cheesman, E.E.1
-
8
-
-
0036858841
-
Cacao domestication I: the origin of the cacao cultivated by the Mayas
-
COI: 1:CAS:528:DC%2BD38XotFWksL0%3D
-
Motamayor, J. C. et al. Cacao domestication I: the origin of the cacao cultivated by the Mayas. Hered. (Edinb.) 89, 380–386 (2002).
-
(2002)
Hered. (Edinb.)
, vol.89
, pp. 380-386
-
-
Motamayor, J.C.1
-
9
-
-
79957674360
-
Cacao use and the San Lorenzo Olmec
-
COI: 1:CAS:528:DC%2BC3MXntVGqtLg%3D
-
Powis, T. G., Cyphers, A., Gaikwad, N. W., Grivetti, L. & Cheong, K. Cacao use and the San Lorenzo Olmec. P Natl. Acad. Sci. USA 108, 8595–8600 (2011).
-
(2011)
P Natl. Acad. Sci. USA
, vol.108
, pp. 8595-8600
-
-
Powis, T.G.1
Cyphers, A.2
Gaikwad, N.W.3
Grivetti, L.4
Cheong, K.5
-
10
-
-
53249115350
-
Geographic and genetic population differentiation of the Amazonian chocolate tree (Theobroma cacao L)
-
Motamayor, J. C. et al. Geographic and genetic population differentiation of the Amazonian chocolate tree (Theobroma cacao L). PLoS One 3, e3311 (2008).
-
(2008)
PLoS One
, vol.3
-
-
Motamayor, J.C.1
-
11
-
-
84869070362
-
Insight into the wild origin, migration and domestication history of the fine flavour Nacional Theobroma cacao L. variety from Ecuador
-
Loor Solorzano, R. G. et al. Insight into the wild origin, migration and domestication history of the fine flavour Nacional Theobroma cacao L. variety from Ecuador. PLoS One 7, e48438 (2012).
-
(2012)
PLoS One
, vol.7
-
-
Loor Solorzano, R.G.1
-
12
-
-
37649008913
-
Chemical and archaeological evidence for the earliest cacao beverages
-
COI: 1:CAS:528:DC%2BD2sXhsVSru7nM
-
Henderson, J. S., Joyce, R. A., Hall, G. R., Hurst, W. J. & McGovern, P. E. Chemical and archaeological evidence for the earliest cacao beverages. P Natl. Acad. Sci. USA 104, 18937–18940 (2007).
-
(2007)
P Natl. Acad. Sci. USA
, vol.104
, pp. 18937-18940
-
-
Henderson, J.S.1
Joyce, R.A.2
Hall, G.R.3
Hurst, W.J.4
McGovern, P.E.5
-
13
-
-
0141454836
-
Cacao domestication II: progenitor germplasm of the Trinitario cacao cultivar
-
COI: 1:CAS:528:DC%2BD3sXms1Cruro%3D
-
Motamayor, J. C., Risterucci, A. M., Heath, M. & Lanaud, C. Cacao domestication II: progenitor germplasm of the Trinitario cacao cultivar. Heredity 91, 322–330 (2003).
-
(2003)
Heredity
, vol.91
, pp. 322-330
-
-
Motamayor, J.C.1
Risterucci, A.M.2
Heath, M.3
Lanaud, C.4
-
14
-
-
0038807950
-
-
D. Stone, Harvard University Press, Cambridge
-
Schultes, R. E. In Pre-Columbian plant migration, papers of the peabody museum of archaeology and ethnology, Vol. 76 (ed D. Stone) 69–83 (Harvard University Press, Cambridge, 1984).
-
(1984)
Pre-Columbian Plant Migration, Papers of the Peabody Museum of Archaeology and Ethnology
, vol.76
, pp. 69-83
-
-
Schultes, R.E.1
-
15
-
-
79956142463
-
Dissecting genetic structure in farmer selections of theobroma cacao in the Peruvian Amazon: implications for on farm conservation and rehabilitation
-
Zhang, D. et al. Dissecting genetic structure in farmer selections of theobroma cacao in the Peruvian Amazon: implications for on farm conservation and rehabilitation. Trop. Plant Biol. 4, 106–116 (2011).
-
(2011)
Trop. Plant Biol.
, vol.4
, pp. 106-116
-
-
Zhang, D.1
-
16
-
-
84856690246
-
Genetic diversity and spatial structure in a new distinct Theobroma cacao L. population in Bolivia
-
Zhang, D. et al. Genetic diversity and spatial structure in a new distinct Theobroma cacao L. population in Bolivia. Genet. Resour. Crop Evol. 59, 239–252 (2011).
-
(2011)
Genet. Resour. Crop Evol.
, vol.59
, pp. 239-252
-
-
Zhang, D.1
-
17
-
-
84981331913
-
The age of chocolate: a diversification history of Theobroma and Malvaceae
-
Richardson, J. E., Whitlock, B. A., A.W., M. & Madriñan, S. The age of chocolate: a diversification history of Theobroma and Malvaceae. Front. Ecol. Evol. 3, 120 (2015).
-
(2015)
Front. Ecol. Evol.
, vol.3
, pp. 120
-
-
Richardson, J.E.1
Whitlock, B.A.2
A.W, M.3
Madriñan, S.4
-
18
-
-
84857367657
-
Morphological characterization of leaf, flower, fruit and seed traits among Brazilian Theobroma L. species
-
Carvalho Santos, R., Pires, J. L. & Correa, R. X. Morphological characterization of leaf, flower, fruit and seed traits among Brazilian Theobroma L. species. Genet. Resour. Crop Evol. 59, 327–345 (2012).
-
(2012)
Genet. Resour. Crop Evol.
, vol.59
, pp. 327-345
-
-
Carvalho Santos, R.1
Pires, J.L.2
Correa, R.X.3
-
19
-
-
33344458581
-
The accumulation of deleterious mutations in rice genomes: a hypothesis on the cost of domestication
-
COI: 1:CAS:528:DC%2BD28XhvVWit7o%3D
-
Lu, J. et al. The accumulation of deleterious mutations in rice genomes: a hypothesis on the cost of domestication. Trends Genet. 22, 126–131 (2006).
-
(2006)
Trends Genet.
, vol.22
, pp. 126-131
-
-
Lu, J.1
-
20
-
-
85044618290
-
Genetic costs of domestication and improvement
-
Moyers, B. T., Morrell, P. L. & McKay, J. K. Genetic costs of domestication and improvement. J. Hered. 109, 103–116 (2018).
-
(2018)
J. Hered.
, vol.109
, pp. 103-116
-
-
Moyers, B.T.1
Morrell, P.L.2
McKay, J.K.3
-
21
-
-
84878362237
-
The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color
-
Motamayor, J. C. et al. The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. Genome Biol. 14, r53 (2013).
-
(2013)
Genome Biol.
, vol.14
-
-
Motamayor, J.C.1
-
22
-
-
84978218359
-
Electronic address, m. n. g. o. a. a. & Genomes, C. 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana
-
Genomes Consortium. Electronic address, m. n. g. o. a. a. & Genomes, C. 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell 166, 481–491 (2016).
-
(2016)
Cell
, vol.166
, pp. 481-491
-
-
-
23
-
-
22744434580
-
The pattern of polymorphism in Arabidopsis thaliana
-
Nordborg, M. et al. The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol. 3, e196 (2005).
-
(2005)
PLoS Biol.
, vol.3
-
-
Nordborg, M.1
-
24
-
-
69749099417
-
Fast model-based estimation of ancestry in unrelated individuals
-
COI: 1:CAS:528:DC%2BD1MXhtFCjsLvL
-
Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009).
-
(2009)
Genome Res.
, vol.19
, pp. 1655-1664
-
-
Alexander, D.H.1
Novembre, J.2
Lange, K.3
-
25
-
-
77952289967
-
Origin and domestication of native Amazonian crops
-
Clement, C. R., de Cristo-Araújo, M., d’Eeckenbrugge, G. C., Alves Pereira, A. & Picanço-Rodrigues, D. Origin and domestication of native Amazonian crops. Diversity 2, 72–106 (2010).
-
(2010)
Diversity
, vol.2
, pp. 72-106
-
-
Clement, C.R.1
de Cristo-Araújo, M.2
d’Eeckenbrugge, G.C.3
Alves Pereira, A.4
Picanço-Rodrigues, D.5
-
26
-
-
84869026948
-
Inference of population splits and mixtures from genome-wide allele frequency data
-
COI: 1:CAS:528:DC%2BC38Xhsl2jsLfE
-
Pickrell, J. K. & Pritchard, J. K. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS. Genet. 8, e1002967 (2012).
-
(2012)
PLoS. Genet.
, vol.8
-
-
Pickrell, J.K.1
Pritchard, J.K.2
-
27
-
-
84868148259
-
Present spatial diversity patterns of Theobroma cacao L. in the neotropics reflect genetic differentiation in pleistocene refugia followed by human-influenced dispersal
-
COI: 1:CAS:528:DC%2BC38Xhs1Gjtb7M
-
Thomas, E. et al. Present spatial diversity patterns of Theobroma cacao L. in the neotropics reflect genetic differentiation in pleistocene refugia followed by human-influenced dispersal. PLoS One 7, e47676 (2012).
-
(2012)
PLoS One
, vol.7
-
-
Thomas, E.1
-
28
-
-
79960914105
-
Inference of human population history from individual whole-genome sequences
-
COI: 1:CAS:528:DC%2BC3MXoslymt7s%3D
-
Li, H. & Durbin, R. Inference of human population history from individual whole-genome sequences. Nature 475, 493–496 (2011).
-
(2011)
Nature
, vol.475
, pp. 493-496
-
-
Li, H.1
Durbin, R.2
-
29
-
-
85007071697
-
Robust and scalable inference of population history from hundreds of unphased whole genomes
-
COI: 1:CAS:528:DC%2BC28XitFCgu7%2FE
-
Terhorst, J., Kamm, J. A. & Song, Y. S. Robust and scalable inference of population history from hundreds of unphased whole genomes. Nat. Genet. 49, 303–309 (2017).
-
(2017)
Nat. Genet.
, vol.49
, pp. 303-309
-
-
Terhorst, J.1
Kamm, J.A.2
Song, Y.S.3
-
30
-
-
0035808596
-
2concentrations over the last glacial termination
-
COI: 1:CAS:528:DC%2BD3MXisV2qsQ%3D%3D
-
2concentrations over the last glacial termination. Science 291, 112–114 (2001).
-
(2001)
Science
, vol.291
, pp. 112-114
-
-
Monnin, E.1
-
31
-
-
33644955631
-
South American climate during the Last Glacial Maximum: Delayed onset of the South American monsoon
-
Cook, K. & Vizy, E. South American climate during the Last Glacial Maximum: delayed onset of the South American monsoon. J. Geophys. Res. 111, D02110 (2006).
-
(2006)
J. Geophys. Res.
, vol.111
-
-
Cook, K.1
Vizy, E.2
-
32
-
-
84978381006
-
Estimating the global conservation status of more than 15,000 Amazonian tree species
-
Ter Steege, H. et al. Estimating the global conservation status of more than 15,000 Amazonian tree species. Sci. Adv. 1, e1500936 (2015).
-
(2015)
Sci. Adv.
, vol.1
-
-
Ter Steege, H.1
-
33
-
-
73449149044
-
Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data
-
Gutenkunst, R. N., Hernandez, R. D., Williamson, S. H. & Bustamante, C. D. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS. Genet. 5, e1000695 (2009).
-
(2009)
PLoS. Genet.
, vol.5
-
-
Gutenkunst, R.N.1
Hernandez, R.D.2
Williamson, S.H.3
Bustamante, C.D.4
-
34
-
-
85014943325
-
Persistent effects of pre-Columbian plant domestication on Amazonian forest composition
-
COI: 1:CAS:528:DC%2BC2sXjsVCgsLs%3D
-
Levis, C. et al. Persistent effects of pre-Columbian plant domestication on Amazonian forest composition. Science 355, 925–931 (2017).
-
(2017)
Science
, vol.355
, pp. 925-931
-
-
Levis, C.1
-
35
-
-
79957774983
-
The origins of cacao use in Mesoamerica
-
Powis, T. G. The origins of cacao use in Mesoamerica. Mexicon 30, 35–38 (2002).
-
(2002)
Mexicon
, vol.30
, pp. 35-38
-
-
Powis, T.G.1
-
36
-
-
84893961036
-
The genome of a late Pleistocene human from a Clovis burial site in western Montana
-
COI: 1:CAS:528:DC%2BC2cXisValu7w%3D
-
Rasmussen, M. et al. The genome of a late Pleistocene human from a Clovis burial site in western Montana. Nature 506, 225–229 (2014).
-
(2014)
Nature
, vol.506
, pp. 225-229
-
-
Rasmussen, M.1
-
37
-
-
84939864401
-
POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans
-
Raghavan, M. et al. POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans. Science 349, aab3884 (2015).
-
(2015)
Science
, vol.349
, pp. aab3884
-
-
Raghavan, M.1
-
38
-
-
85018226075
-
Tracing the peopling of the world through genomics
-
COI: 1:CAS:528:DC%2BC2sXht1Olu70%3D
-
Nielsen, R. et al. Tracing the peopling of the world through genomics. Nature 541, 302–310 (2017).
-
(2017)
Nature
, vol.541
, pp. 302-310
-
-
Nielsen, R.1
-
39
-
-
84964240074
-
Post-invasion demography of prehistoric humans in South America
-
COI: 1:CAS:528:DC%2BC28Xlsl2gtLk%3D
-
Goldberg, A., Mychajliw, A. M. & Hadly, E. A. Post-invasion demography of prehistoric humans in South America. Nature 532, 232–235 (2016).
-
(2016)
Nature
, vol.532
, pp. 232-235
-
-
Goldberg, A.1
Mychajliw, A.M.2
Hadly, E.A.3
-
40
-
-
33745831743
-
The presence of Leuco-Anthocyanins in Criollo Cacao
-
COI: 1:CAS:528:DyaA1MXltFaqsw%3D%3D
-
Knapp, A. W. T. L. & Hearne, J. F. The presence of Leuco-Anthocyanins in Criollo Cacao. Analyst 64, 475–480 (1939).
-
(1939)
Analyst
, vol.64
, pp. 475-480
-
-
Knapp, A.W.T.L.1
Hearne, J.F.2
-
41
-
-
51749120796
-
Flavor formation and character in cocoa and chocolate: a critical review
-
Afoakawa, E. O., Peterson, A., Fowler, M. & Ryan, A. Flavor formation and character in cocoa and chocolate: a critical review. Crit. Rev. Food Sci. Nutr. 48, 840–857 (2008).
-
(2008)
Crit. Rev. Food Sci. Nutr.
, vol.48
, pp. 840-857
-
-
Afoakawa, E.O.1
Peterson, A.2
Fowler, M.3
Ryan, A.4
-
42
-
-
84955747459
-
Flavor chemistry of cocoa and cocoa products—an overview
-
COI: 1:CAS:528:DC%2BC2MXitVKjs7bI
-
Aprotosoaie, A. C., Luca, S. V. & Miron, A. Flavor chemistry of cocoa and cocoa products—an overview. Compr. Rev. Food Sci. adn Food Saf. 15, 73–91 (2016).
-
(2016)
Compr. Rev. Food Sci. adn Food Saf.
, vol.15
, pp. 73-91
-
-
Aprotosoaie, A.C.1
Luca, S.V.2
Miron, A.3
-
43
-
-
84938408730
-
& Bispo, E. d. S. Bioactive compounds in different cocoa (Theobroma cacao, L) cultivars during fermentation
-
Cruz, J. F. M., Leite, P. B. & Soares, S. E. & Bispo, E. d. S. Bioactive compounds in different cocoa (Theobroma cacao, L) cultivars during fermentation. Food Sci. Technol. (Camp.) 35, 279–284 (2015).
-
(2015)
Food Sci. Technol. (Camp.)
, vol.35
, pp. 279-284
-
-
Cruz, J.F.M.1
Leite, P.B.2
Soares, S.E.3
-
44
-
-
77955523100
-
Influence of cocoa beans fermentation and drying on the polyphenol content and sensory acceptance
-
Efraim, P. et al. Influence of cocoa beans fermentation and drying on the polyphenol content and sensory acceptance. Ciência e Tecnol. De. Aliment. 30, 142–150 (2010).
-
(2010)
Ciência e Tecnol. De. Aliment.
, vol.30
, pp. 142-150
-
-
Efraim, P.1
-
45
-
-
77649260327
-
Population differentiation as a test for selective sweeps
-
COI: 1:CAS:528:DC%2BC3cXjtlCkur8%3D
-
Chen, H., Patterson, N. & Reich, D. Population differentiation as a test for selective sweeps. Genome Res. 20, 393–402 (2010).
-
(2010)
Genome Res.
, vol.20
, pp. 393-402
-
-
Chen, H.1
Patterson, N.2
Reich, D.3
-
46
-
-
0036000026
-
Laccase down-regulation causes alterations in phenolic metabolism and cell wall structure in poplar
-
COI: 1:CAS:528:DC%2BD38XjvFSnu7s%3D
-
Ranocha, P. et al. Laccase down-regulation causes alterations in phenolic metabolism and cell wall structure in poplar. Plant Physiol. 129, 145–155 (2002).
-
(2002)
Plant Physiol.
, vol.129
, pp. 145-155
-
-
Ranocha, P.1
-
47
-
-
84859817791
-
Laccase-catalysed oxidations of naturally occurring phenols: from in vivo biosynthetic pathways to green synthetic applications
-
Jeon, J. R., Baldrian, P., Murugesan, K. & Chang, Y. S. Laccase-catalysed oxidations of naturally occurring phenols: from in vivo biosynthetic pathways to green synthetic applications. Microb. Biotechnol. 5, 318–332 (2012).
-
(2012)
Microb. Biotechnol.
, vol.5
, pp. 318-332
-
-
Jeon, J.R.1
Baldrian, P.2
Murugesan, K.3
Chang, Y.S.4
-
48
-
-
84922657796
-
Involvement of an extracellular fungus laccase in the flavonoid metabolism in Citrus fruits inoculated with Alternaria alternata
-
COI: 1:CAS:528:DC%2BC2MXis1ejtr8%3D
-
Diaz, L., Del Rio, J. A., Perez-Gilabert, M. & Ortuno, A. Involvement of an extracellular fungus laccase in the flavonoid metabolism in Citrus fruits inoculated with Alternaria alternata. Plant. Physiol. Biochem. 89, 11–17 (2015).
-
(2015)
Plant. Physiol. Biochem.
, vol.89
, pp. 11-17
-
-
Diaz, L.1
Del Rio, J.A.2
Perez-Gilabert, M.3
Ortuno, A.4
-
49
-
-
34447546660
-
The distribution of fitness effects of new mutations
-
COI: 1:CAS:528:DC%2BD2sXnvVekt7s%3D
-
Eyre-Walker, A. & Keightley, P. D. The distribution of fitness effects of new mutations. Nat. Rev. Genet. 8, 610–618 (2007).
-
(2007)
Nat. Rev. Genet.
, vol.8
, pp. 610-618
-
-
Eyre-Walker, A.1
Keightley, P.D.2
-
50
-
-
33644956987
-
The mutation load in small populations
-
COI: 1:STN:280:DyaF2c%2FivFertQ%3D%3D, PID: 14071753
-
Kimura, M., Maruyama, T. & Crow, J. F. The mutation load in small populations. Genetics 48, 1303–1312 (1963).
-
(1963)
Genetics
, vol.48
, pp. 1303-1312
-
-
Kimura, M.1
Maruyama, T.2
Crow, J.F.3
-
51
-
-
77951544989
-
The population genetics of mutations: good, bad and in different
-
Loewe, L. & Hill, W. G. The population genetics of mutations: good, bad and in different. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 365, 1153–1167 (2010).
-
(2010)
Philos. Trans. R. Soc. Lond. B. Biol. Sci.
, vol.365
, pp. 1153-1167
-
-
Loewe, L.1
Hill, W.G.2
-
52
-
-
0001400708
-
The effect of variation on fitness
-
Haldane, J. B. S. The effect of variation on fitness. Am. Nat. 71, 337–349 (1937).
-
(1937)
Am. Nat.
, vol.71
, pp. 337-349
-
-
Haldane, J.B.S.1
-
53
-
-
84953215554
-
Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs
-
COI: 1:CAS:528:DC%2BC2MXitVylsr%2FJ
-
Marsden, C. D. et al. Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs. P Natl. Acad. Sci. USA 113, 152–157 (2016).
-
(2016)
P Natl. Acad. Sci. USA
, vol.113
, pp. 152-157
-
-
Marsden, C.D.1
-
54
-
-
0001507896
-
Coefficients of inbreeding and relationship
-
Wright, S. Coefficients of inbreeding and relationship. Am. Nat. 56, 330–338 (1922).
-
(1922)
Am. Nat.
, vol.56
, pp. 330-338
-
-
Wright, S.1
-
55
-
-
0023468755
-
Inbreeding depression and its evolutionary consequences
-
Charlesworth, D. & Charlesworth, B. Inbreeding depression and its evolutionary consequences. Annu. Rev. Ecol. Syst. 18, 237–268 (1987).
-
(1987)
Annu. Rev. Ecol. Syst.
, vol.18
, pp. 237-268
-
-
Charlesworth, D.1
Charlesworth, B.2
-
56
-
-
0022236684
-
The evolution of self-fertilization and inbreeding depression in plants.1. genetic models
-
Lande, R. & Schemske, D. W. The evolution of self-fertilization and inbreeding depression in plants.1. genetic models. Evolution 39, 24–40 (1985).
-
(1985)
Evolution
, vol.39
, pp. 24-40
-
-
Lande, R.1
Schemske, D.W.2
-
57
-
-
0043122919
-
SIFT: predicting amino acid changes that affect protein function
-
Ng, P. & Henikoff, S. SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res. 3, 3812–3814 (2003).
-
(2003)
Nucleic Acids Res.
, vol.3
, pp. 3812-3814
-
-
Ng, P.1
Henikoff, S.2
-
58
-
-
84949459120
-
SIFT missense predictions for genomes
-
COI: 1:CAS:528:DC%2BC2MXhvFKht7fF
-
Vaser, R., Adusumalli, S., Leng, S. N., Sikic, M. & Ng, P. C. SIFT missense predictions for genomes. Nat. Protoc. 11, 1–9 (2016).
-
(2016)
Nat. Protoc.
, vol.11
, pp. 1-9
-
-
Vaser, R.1
Adusumalli, S.2
Leng, S.N.3
Sikic, M.4
Ng, P.C.5
-
59
-
-
84979619789
-
Recent demography drives changes in linked selection across the maize genome
-
Beissinger, T. M. et al. Recent demography drives changes in linked selection across the maize genome. Nat. Plants 2, 16084 (2016).
-
(2016)
Nat. Plants
, vol.2
, pp. 16084
-
-
Beissinger, T.M.1
-
60
-
-
84901608835
-
The impact of population demography and selection on the genetic architecture of complex traits
-
Lohmueller, K. E. The impact of population demography and selection on the genetic architecture of complex traits. PLoS. Genet. 10, e1004379 (2014).
-
(2014)
PLoS. Genet.
, vol.10
-
-
Lohmueller, K.E.1
-
61
-
-
85038390840
-
A larger chocolate chip-development of a 15K Theobroma cacao L. SNP array to create high-density linkage maps
-
Livingstone, D. et al. A larger chocolate chip-development of a 15K Theobroma cacao L. SNP array to create high-density linkage maps. Front Plant Sci. 8, 2008 (2017).
-
(2017)
Front Plant Sci.
, vol.8
, pp. 2008
-
-
Livingstone, D.1
-
64
-
-
80255127234
-
Cutadapt
-
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. J. 17, 10–12 (2011).
-
(2011)
EMBnet. J.
, vol.17
, pp. 10-12
-
-
Martin, M.1
-
65
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
COI: 1:CAS:528:DC%2BD1MXot1Cjtbo%3D
-
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
66
-
-
79958151996
-
BamTools: a C + + API and toolkit for analyzing and managing BAM files
-
COI: 1:CAS:528:DC%2BC3MXntFGktbc%3D
-
Barnett, D. W., Garrison, E. K., Quinlan, A. R., Stromberg, M. P. & Marth, G. T. BamTools: a C + + API and toolkit for analyzing and managing BAM files. Bioinformatics 27, 1691–1692 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 1691-1692
-
-
Barnett, D.W.1
Garrison, E.K.2
Quinlan, A.R.3
Stromberg, M.P.4
Marth, G.T.5
-
67
-
-
68549104404
-
The sequence alignment/map format and SAMtools
-
Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
-
69
-
-
77956295988
-
The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data
-
COI: 1:CAS:528:DC%2BC3cXhtFeru7jM
-
McKenna, A. et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).
-
(2010)
Genome Res.
, vol.20
, pp. 1297-1303
-
-
McKenna, A.1
-
70
-
-
84901984971
-
Joint variant and de novo mutation identification on pedigrees from high-throughput sequencing data
-
COI: 1:CAS:528:DC%2BC2cXoslOqsrs%3D
-
Cleary, J. G. et al. Joint variant and de novo mutation identification on pedigrees from high-throughput sequencing data. J. Comput. Biol. 21, 405–419 (2014).
-
(2014)
J. Comput. Biol.
, vol.21
, pp. 405-419
-
-
Cleary, J.G.1
-
71
-
-
84856478855
-
A linear complexity phasing method for thousands of genomes
-
Delaneau, O., Marchini, J. & Zagury, J. F. A linear complexity phasing method for thousands of genomes. Nat. Methods 9, 179–181 (2011).
-
(2011)
Nat. Methods
, vol.9
, pp. 179-181
-
-
Delaneau, O.1
Marchini, J.2
Zagury, J.F.3
-
72
-
-
84871952176
-
Improved whole-chromosome phasing for disease and population genetic studies
-
COI: 1:CAS:528:DC%2BC38XhvFShtbnN
-
Delaneau, O., Zagury, J. F. & Marchini, J. Improved whole-chromosome phasing for disease and population genetic studies. Nat. Methods 10, 5–6 (2013).
-
(2013)
Nat. Methods
, vol.10
, pp. 5-6
-
-
Delaneau, O.1
Zagury, J.F.2
Marchini, J.3
-
73
-
-
84876030710
-
Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift
-
Cingolani, P. et al. Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift. Front. Genet. 3, 35 (2012).
-
(2012)
Front. Genet.
, vol.3
, pp. 35
-
-
Cingolani, P.1
-
74
-
-
0016491430
-
On the number of segregating sites in genetical models without recombination
-
COI: 1:STN:280:DyaE2M7pvFSquw%3D%3D
-
Watterson, G. A. On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7, 256–276 (1975).
-
(1975)
Theor. Popul. Biol.
, vol.7
, pp. 256-276
-
-
Watterson, G.A.1
-
75
-
-
0005814023
-
Mathematical model for studying genetic variation in terms of restriction endonucleases
-
COI: 1:CAS:528:DyaL3cXitVWn
-
Nei, M. & Li, W.-H. Mathematical model for studying genetic variation in terms of restriction endonucleases. P Natl. Acad. Sci. USA 76, 5269–5273 (1979).
-
(1979)
P Natl. Acad. Sci. USA
, vol.76
, pp. 5269-5273
-
-
Nei, M.1
Li, W.H.2
-
76
-
-
79960405019
-
The variant call format and VCFtools
-
COI: 1:CAS:528:DC%2BC3MXptFCqt7w%3D
-
Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 2156-2158
-
-
Danecek, P.1
-
77
-
-
0034118493
-
Inference of population structure using multilocus genotype data
-
COI: 1:STN:280:DC%2BD3cvislKrtA%3D%3D, PID: 10835412
-
Pritchard, J. K., Stephens, M. & Donnelly, P. Inference of population structure using multilocus genotype data. Genetics 155, 945–959 (2000).
-
(2000)
Genetics
, vol.155
, pp. 945-959
-
-
Pritchard, J.K.1
Stephens, M.2
Donnelly, P.3
-
78
-
-
77954542018
-
The genome-wide structure of the Jewish people
-
COI: 1:CAS:528:DC%2BC3cXntF2mu78%3D
-
Behar, D. M. et al. The genome-wide structure of the Jewish people. Nature 466, 238–242 (2010).
-
(2010)
Nature
, vol.466
, pp. 238-242
-
-
Behar, D.M.1
-
79
-
-
34547861256
-
CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure
-
COI: 1:CAS:528:DC%2BD2sXpt1ahtbs%3D
-
Jakobsson, M. & Rosenberg, N. A. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23, 1801–1806 (2007).
-
(2007)
Bioinformatics
, vol.23
, pp. 1801-1806
-
-
Jakobsson, M.1
Rosenberg, N.A.2
-
81
-
-
0021566877
-
Estimating F-Statistics for the Analysis of Population Structure
-
Weir, B. S. & Cockerham, C. C. Estimating F-Statistics for the Analysis of Population Structure. Evolution 38, 10.2307/2408641 (1984).
-
(1984)
Evolution
, vol.38
, Issue.6
, pp. 1358
-
-
Weir, B.S.1
Cockerham, C.C.2
-
82
-
-
77955090647
-
Evolution of the mutation rate
-
Lynch, M. Evolution of the mutation rate. Trends Genet 26, 345–352, 10.1016/j.tig.2010.05.003 (2010).
-
(2010)
Trends in Genetics
, vol.26
, Issue.8
, pp. 345-352
-
-
Lynch, M.1
-
83
-
-
74849090833
-
The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana
-
COI: 1:CAS:528:DC%2BD1MXhs1WksrfN
-
Ossowski, S. et al. The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327, 92–94 (2010).
-
(2010)
Science
, vol.327
, pp. 92-94
-
-
Ossowski, S.1
-
84
-
-
85043343540
-
The rate and potential relevance of new mutations in a colonizing plant lineage
-
Exposito-Alonso, M. et al. The rate and potential relevance of new mutations in a colonizing plant lineage. PLoS. Genet. 14, e1007155 (2018).
-
(2018)
PLoS. Genet.
, vol.14
-
-
Exposito-Alonso, M.1
|