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Volumn 1, Issue 1, 2018, Pages

Population genomic analyses of the chocolate tree, Theobroma cacao L., provide insights into its domestication process

(18)  Cornejo, Omar E a,b   Yee, Muh Ching b,c   Dominguez, Victor d   Andrews, Mary d   Sockell, Alexandra b   Strandberg, Erika b   Livingstone, Donald e,f   Stack, Conrad e   Romero, Alberto e   Umaharan, Pathmanathan g   Royaert, Stefan e   Tawari, Nilesh R h   Ng, Pauline h   Gutierrez, Osman i   Phillips, Wilbert j   Mockaitis, Keithanne d   Bustamante, Carlos D b   Motamayor, Juan C e  


Author keywords

[No Author keywords available]

Indexed keywords


EID: 85055136884     PISSN: None     EISSN: 23993642     Source Type: Journal    
DOI: 10.1038/s42003-018-0168-6     Document Type: Article
Times cited : (71)

References (85)
  • 2
    • 0037043719 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 7
    • 0000437961 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 10
    • 53249115350 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 15
    • 79956142463 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 26
    • 84869026948 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • & 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 59
    • 84979619789 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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


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