Li JZ, Absher DM, Tang H, Southwick AM, Casto AM, Ramachandran S, et al.Worldwide human relationships inferred from genome-wide patterns of variation. Science. 2008; 319:1100–4.
Article
CAS
PubMed
Google Scholar
Beissinger TM, Wang L, Crosby K, Durvasula A, Hufford MB, Ross-Ibarra J. Recent demography drives changes in linked selection across the maize genome. Nat Plants. 2016; 2:16084.
Article
PubMed
Google Scholar
Doebley JF, Gaut BS, Smith BD. The molecular genetics of crop domestication. Cell. 2006; 127:1309–21.
Article
CAS
PubMed
Google Scholar
Gignoux CR, Henn BM, Mountain JL. Rapid, global demographic expansions after the origins of agriculture. Proc Natl Acad Sci. 2011; 108:6044–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hufford MB, Lubinksy P, Pyhäjärvi T, Devengenzo MT, Ellstrand NC, Ross-Ibarra J. The genomic signature of crop-wild introgression in maize. PLoS Genet. 2013; 9:e1003477.
Article
CAS
PubMed
PubMed Central
Google Scholar
Prufer K, Racimo F, Patterson N, Jay F, Sankararaman S, Sawyer S, et al.The complete genome sequence of a Neanderthal from the Altai Mountains. Nature. 2014; 505:43–9.
Article
PubMed
Google Scholar
Simons YB, Turchin MC, Pritchard JK, Sella G. The deleterious mutation load is insensitive to recent population history. Nat Genet. 2014; 46:220–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Do R, Balick D, Li H, Adzhubei I, Sunyaev S, Reich D. No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans. Nat Genet. 2015; 47:126–31.
Article
CAS
PubMed
PubMed Central
Google Scholar
Harris K, Nielsen R. The genetic cost of Neanderthal introgression. Genetics. 2016; 203:881–91.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fu W, Gittelman RM, Bamshad MJ, Akey JM. Characteristics of neutral and deleterious protein-coding variation among individuals and populations. Am J Human Genet. 2014; 95:421–36.
Article
CAS
Google Scholar
Zhang M, Zhou L, Bawa R, Suren H, Holliday J. Recombination rate variation, hitchhiking, and demographic history shape deleterious load in poplar. Mol Biol Evol. 2016; 33:2899–910.
Article
CAS
PubMed
Google Scholar
Marsden CD, Ortega-Del Vecchyo D, O’Brien DP, Taylor JF, Ramirez O, Vilà C, et al.Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs. Proc Natl Acad Sci. 2016; 113:152–7.
Article
CAS
PubMed
Google Scholar
Simons YB, Sella G. The impact of recent population history on the deleterious mutation load in humans and close evolutionary relatives. Curr Opin Genet Dev. 2016; 41:150–8.
Article
CAS
PubMed
Google Scholar
Liu Q, Zhou Y, Morrell PL, Gaut BS. Deleterious variants in Asian rice and the potential cost of domestication. Mol Biol Evol. 2017; 34:908–924.
Article
PubMed
Google Scholar
Slatkin M, Excoffier L. Serial founder effects during range expansion: a spatial analog of genetic drift. Genetics. 2012; 191:171–81.
Article
CAS
PubMed
PubMed Central
Google Scholar
Austerlitz F, Jung-Muller B, Godelle B, Gouyon PH. Evolution of coalescence times, genetic diversity and structure during colonization. Theor Popul Biol. 1997; 51:148–64.
Article
Google Scholar
Ramachandran S, Deshpande O, Roseman CC, Rosenberg NA, Feldman MW, Cavalli-Sforza LL. Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. Proc Natl Acad Sci of the U S A. 2005; 102:15942–7.
Article
CAS
Google Scholar
Henn BM, Botigué LR, Bustamante CD, Clark AG, Gravel S. Estimating the mutation load in human genomes. Nat Rev Genet. 2015; 16:333–43.
Article
CAS
PubMed
PubMed Central
Google Scholar
Juric I, Aeschbacher S, Coop G. The strength of selection against Neanderthal introgression. PLoS Genet. 2016; 12:1–25.
Article
Google Scholar
Matsuoka Y, Vigouroux Y, Goodman MM, Sanchez GJ, Buckler E, Doebley J. A single domestication for maize shown by multilocus microsatellite genotyping. Proc Natl Acad Sci. 2002; 99:6080–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Piperno DR, Ranere AJ, Holst I, Iriarte J, Dickau R. Starch grain and phytolith evidence for early ninth millennium B.P. maize from the Central Balsas River Valley. Mexico. Proc Natl Acad Sci. 2009; 106:5019–24.
Article
CAS
PubMed
Google Scholar
van Heerwaarden J, Doebley J, Briggs WH, Glaubitz JC, Goodman MM, Gonzalez JdJS, et al.Genetic signals of origin, spread, and introgression in a large sample of maize landraces. Proc Natl Acad Sci. 2011; 108:1088–92.
Article
CAS
PubMed
Google Scholar
Wright SI, Bi IV, Schroeder SG, Yamasaki M, Doebley JF, McMullen MD, et al.The effects of artificial selection on the maize genome. Science. 2005; 308:1310–4.
Article
CAS
PubMed
Google Scholar
Hufford MB, Xu X, Van Heerwaarden J, Pyhäjärvi T, Chia JM, Cartwright RA, et al.Comparative population genomics of maize domestication and improvement. Nat Genet. 2012; 44:808–11.
Article
CAS
PubMed
PubMed Central
Google Scholar
Merrill WL, Hard RJ, Mabry JB, Fritz GJ, Adams KR, Roney JR, et al.The diffusion of maize to the southwestern United States and its impact. Proc Natl Acad Sci. 2009; 106:21019–26.
Article
CAS
PubMed
PubMed Central
Google Scholar
Grobman A, Bonavia D, Dillehay TD, Piperno DR, Iriarte J, Holst I. Preceramic maize from Paredones and Huaca Prieta, Peru. Proc Natl Acad Sci. 2012; 109:1755–9.
Article
CAS
PubMed
Google Scholar
Ross-Ibarra J, Tenaillon M, Gaut BS. Historical divergence and gene flow in the genus Zea. Genetics. 2009; 181:1399–413.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tenaillon MI, U’Ren J, Tenaillon O, Gaut BS. Selection versus demography: a multilocus investigation of the domestication process in maize. Mol Biol Evol. 2004; 21:1214–25.
Article
CAS
PubMed
Google Scholar
Van Etten J, Hijmans RJ. A geospatial modelling approach integrating archaeobotany and genetics to trace the origin and dispersal of domesticated plants. PLoS One. 2010; e12060:5.
Google Scholar
Races of maize. Available from:https://www.ars.usda.gov/midwest-area/ames/plant-introduction-research/docs/races-of-maize/. Accessed 15 Apr 2015.
Schiffels S, Durbin R. Inferring human population size and separation history from multiple genome sequences. Nat Genet. 2014; 46:919–25.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schrider DR, Shanku AG, Kern AD. Effects of linked selective sweeps on demographic inference and model selection. Genetics. 2016; 204:1207–23.
Article
PubMed
PubMed Central
Google Scholar
Hearne S, Chen C, Buckler E, Mitchell S. Unimputed GBS derived SNPs for maize landrace accessions represented in the SeeD-maize GWAS panel. CIMMYT. 2014. http://data.cimmyt.org/dvn/dv/seedsofdiscoverydvn/faces/study/StudyPage.xhtml?studyId=21%24tab=files.
Thompson EA. Identity by descent: variation in meiosis, across genomes, and in populations. Genetics. 2013; 194(2):301–26.
Article
CAS
PubMed
PubMed Central
Google Scholar
Durand EY, Patterson N, Reich D, Slatkin M. Testing for ancient admixture between closely related populations. Mol Biol Evol. 2011; 28:2239–52.
Article
CAS
PubMed
PubMed Central
Google Scholar
da Fonseca RR, Smith BD, Wales N, Cappellini E, Skoglund P, Fumagalli M, et al.The origin and evolution of maize in the American Southwest. Nat Plants. 2015; 1:14003.
Article
PubMed
Google Scholar
Martin SH, Davey JW, Jiggins CD. Evaluating the use of ABBA–BABA statistics to locate introgressed loci. Mol Biol Evol. 2015; 32:244–57.
Article
CAS
PubMed
Google Scholar
Navarro JAR, Willcox M, Burgueño J, Romay C, Swarts K, Trachsel S, et al.A study of allelic diversity underlying flowering-time adaptation in maize landraces. Nat Genet. 2017; 49:476–80.
Article
Google Scholar
Buckler ES, Holland JB, Bradbury PJ, Acharya CB, Brown PJ, Browne C, et al.The genetic architecture of maize flowering time. Science. 2009; 325(5941):714–8.
Article
CAS
PubMed
Google Scholar
Cooper GM, Stone EA, Asimenos G, Green ED, Batzoglou S, Sidow A. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res. 2005; 15:901–13.
Article
CAS
PubMed
PubMed Central
Google Scholar
Renaut S, Rieseberg LH. The accumulation of deleterious mutations as a consequence of domestication and improvement in sunflowers and other Compositae crops. Mol Biol Evol. 2015; 32:2273–83.
Article
CAS
PubMed
Google Scholar
Günther T, Schmid KJ. Deleterious amino acid polymorphisms in Arabidopsis thaliana and rice. Theor Appl Genet. 2010; 121:157–68.
Article
PubMed
Google Scholar
Kono TJ, Fu F, Mohammadi M, Hoffman PJ, Liu C, Stupar RM, et al.The role of deleterious substitutions in crop genomes. Mol Biol Evol. 2016; 33:2307–17.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhu Q, Zheng X, Luo J, Gaut BS, Ge S. Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice. Mol Biol Evol. 2007; 24:875–88.
Article
CAS
PubMed
Google Scholar
Lam HM, Xu X, Liu X, Chen W, Yang G, Wong FL, et al.Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet. 2010; 42:1053–9.
Article
CAS
PubMed
Google Scholar
Zhou Y, Massonnet M, Sanjak J, Cantu D, Gaut BS. Evolutionary genomics of grape (Vitis vinifera ssp. vinifera) domestication. Proc Natl Acad Sci. 2017; 114:11715–11720. doi:10.1073/pnas.1709257114.
Article
CAS
PubMed
Google Scholar
Meyer RS, Choi JY, Sanches M, Plessis A, Flowers JM, Amas J, et al.Domestication history and geographical adaptation inferred from a SNP map of African rice. Nat Genet. 2016; 48:1083–8.
Article
CAS
PubMed
Google Scholar
Gaut BS, Díez CM, Morrell PL. Genomics and the contrasting dynamics of annual and perennial domestication. Trends Genet. 2015; 31:709–19.
Article
CAS
PubMed
Google Scholar
Eyre-Walker A, Gaut RL, Hilton H, Feldman DL, Gaut BS. Investigation of the bottleneck leading to the domestication of maize. Proc Natl Acad Sci. 1998; 95:4441–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nielsen R, Beaumont MA. Statistical inferences in phylogeography. Mol Ecol. 2009; 18:1034–47.
Article
CAS
PubMed
Google Scholar
Mazet O, Rodriguez W, Grusea S, Boitard S, Chikhi L. On the importance of being structured: instantaneous coalescence rates and human evolution—lessons for ancestral population size inference?Heredity. 2016; 116:362.
Article
CAS
PubMed
Google Scholar
Whitlock MC, McCauley DE. Some population genetic consequences of colony formation and extinction: genetic correlations within founding groups. Evolution. 1990; 44(7):1717–24.
Article
PubMed
Google Scholar
Vigouroux Y, Glaubitz JC, Matsuoka Y, Goodman MM, Sánchez J, Doebley J. Population structure and genetic diversity of New World maize races assessed by DNA microsatellites. Am J Bot. 2008; 95:1240–53.
Article
PubMed
Google Scholar
Takuno S, Ralph P, Swarts K, Elshire RJ, Glaubitz JC, Buckler ES, et al.Independent molecular basis of convergent highland adaptation in maize. Genetics. 2015; 200:1297–312.
Article
PubMed
PubMed Central
Google Scholar
Pearsall, DM. Plant domestication and the shift to agriculture in the Andes In: Silverman H, Isbell WH, editors. The handbook of South American archaeology. New York: Springer: 2008. p. 105–20.
Google Scholar
Ross-Ibarra J, Tenaillon M, Gaut BS. Historical divergence and gene flow in the genus Zea. Genetics. 2009; 181:1399–413.
Article
CAS
PubMed
PubMed Central
Google Scholar
Piperno DR, Moreno JE, Iriarte J, Holst I, Lachniet M, Jones JG, et al.Late Pleistocene and Holocene environmental history of the Iguala valley, central Balsas watershed of Mexico. Proc Natl Acad Sci. 2007; 104:11874–81.
Article
CAS
PubMed
PubMed Central
Google Scholar
Correa-Metrio A, Lozano-García S, Xelhuantzi-López S, Sosa-Nájera S, Metcalfe SE. Vegetation in western Central Mexico during the last 50000 years: modern analogs and climate in the Zacapu Basin. J Quat Sci. 2012; 27:509–18.
Article
Google Scholar
Poets AM, Fang Z, Clegg MT, Morrell PL. Barley landraces are characterized by geographically heterogeneous genomic origins. Genome Biol. 2015; 16:1.
Article
Google Scholar
Bredeson JV, Lyons JB, Prochnik SE, Wu GA, Ha CM, Edsinger-Gonzales E, et al.Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity. Nat Biotechnol. 2016; 34:562–70.
Article
CAS
PubMed
Google Scholar
Miao B, Wang Z, Li Y. Genomic analysis reveals hypoxia adaptation in the Tibetan Mastiff by introgression of the grey wolf from the Tibetan Plateau. Mol Biol Evol. 2016; 34:734–43.
Google Scholar
Doebley J, Goodman MM, Stuber CW. Patterns of isozyme variation between maize and Mexican annual teosinte. Econ Bot. 1987; 41(2):234–46.
Article
Google Scholar
Yang J, Mezmouk S, Baumgarten A, Buckler ES, Guill KE, McMullen MD, et al. Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize. PLoS Genetics. 2017; 13:e1007019.
Article
PubMed
PubMed Central
Google Scholar
Gerke JP, Edwards JW, Guill KE, Ross-Ibarra J, McMullen MD. The genomic impacts of drift and selection for hybrid performance in maize. Genetics. 2015; 201(3):1201–11.
Article
PubMed
PubMed Central
Google Scholar
Lu J, Tang T, Tang H, Huang J, Shi S, Wu CI. The accumulation of deleterious mutations in rice genomes: a hypothesis on the cost of domestication. Trends Genet. 2006; 22:126–31.
Article
CAS
PubMed
Google Scholar
Schubert M, Jónsson H, Chang D, Der Sarkissian C, Ermini L, Ginolhac A, et al.Prehistoric genomes reveal the genetic foundation and cost of horse domestication. Proc Natl Acad Sci. 2014; 111:E5661—9.
PubMed
Google Scholar
Ramu P, Esuma W, Kawuki R, Rabbi IY, Egesi C, Bredeson JV, et al.Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation. Nat Genet. 2017; 49:959–63.
Article
CAS
PubMed
Google Scholar
Liu Q, Zhou Y, Morrell PL, Gaut BS. Deleterious variants in Asian rice and the potential cost of domestication. Mol Biol Evol. 2017; 34:908–24.
Article
PubMed
Google Scholar
McQuillan R, Eklund N, Pirastu N, Kuningas M, McEvoy BP, Esko T, et al. Evidence of inbreeding depression on human height. PLoS Genet. 2012; 8:e1002655.
Article
CAS
PubMed
PubMed Central
Google Scholar
Agrawal AF, Whitlock MC. Inferences about the distribution of dominance drawn from yeast gene knockout data. Genetics. 2011; 187:553–66.
Article
CAS
PubMed
PubMed Central
Google Scholar
Manna F, Martin G, Lenormand T. Fitness landscapes: an alternative theory for the dominance of mutation. Genetics. 2011; 189:923–37.
Article
PubMed
PubMed Central
Google Scholar
Doyle JJ. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull. 1987; 19:11–15.
Google Scholar
Li H, Durbin R. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics. 2010; 26:589–95.
Article
PubMed
PubMed Central
Google Scholar
Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, et al.The B73 maize genome: complexity, diversity, and dynamics. Science. 2009; 326:1112–5.
Article
CAS
PubMed
Google Scholar
DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, et al.A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011; 43:491–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, et al.The variant call format and VCFtools. Bioinformatics. 2011; 27:2156–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Browning SR, Browning BL. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet. 2007; 81:1084–97.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chia JM, Song C, Bradbury PJ, Costich D, de Leon N, Doebley J, et al.Maize HapMap2 identifies extant variation from a genome in flux. Nat Genet. 2012; 44:803–7.
Article
CAS
PubMed
Google Scholar
Fumagalli M, Vieira FG, Korneliussen TS, Linderoth T, Huerta-Sánchez E, Albrechtsen A, et al.Quantifying population genetic differentiation from next-generation sequencing data. Genetics. 2013; 195:979–92.
Article
PubMed
PubMed Central
Google Scholar
Fumagalli M, Vieira FG, Linderoth T, Nielsen R. ngsTools: methods for population genetics analyses from next-generation sequencing data. Bioinformatics. 2014; 30:1486–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Korneliussen TS, Albrechtsen A, Nielsen R. ANGSD: analysis of next generation sequencing data. BMC Bioinformatics. 2014; 15:356.
Article
PubMed
PubMed Central
Google Scholar
Skotte L, Korneliussen TS, Albrechtsen A. Estimating individual admixture proportions from next generation sequencing data. Genetics. 2013; 195:693–702.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schliep KP. phangorn: phylogenetic analysis in R. Bioinformatics. 2011; 27:592–3.
Article
CAS
PubMed
Google Scholar
Korneliussen TS, Moltke I, Albrechtsen A, Nielsen R. Calculation of Tajima’s D and other neutrality test statistics from low depth next-generation sequencing data. BMC Bioinformatics. 2013; 14:289.
Article
PubMed
PubMed Central
Google Scholar
Vieira FG, Fumagalli M, Albrechtsen A, Nielsen R. Estimating inbreeding coefficients from NGS data: impact on genotype calling and allele frequency estimation. Genome Res. 2013; 23:1852–61.
Article
CAS
PubMed
PubMed Central
Google Scholar
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, et al.PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007; 81:559–75.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ogut F, Bian Y, Bradbury PJ, Holland JB. Joint-multiple family linkage analysis predicts within-family variation better than single-family analysis of the maize nested association mapping population. Heredity. 2015; 114:552–63.
Article
CAS
PubMed
PubMed Central
Google Scholar
De Mita S, Siol M. EggLib: processing, analysis and simulation tools for population genetics and genomics. BMC Genet. 2012; 13:27.
Article
PubMed
PubMed Central
Google Scholar
Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S. Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Comput Biol. 2010; 6:e1001025.
Article
PubMed
PubMed Central
Google Scholar
Rodgers-Melnick E, Bradbury PJ, Elshire RJ, Glaubitz JC, Acharya CB, Mitchell SE, et al.Recombination in diverse maize is stable, predictable, and associated with genetic load. Proc Natl Acad Sci. 2015; 112:3823–8.
CAS
PubMed
PubMed Central
Google Scholar
Bukowski R, Guo X, Lu Y, Zou C, He B, Rong Z, et al.Construction of the third generation Zea mays haplotype map. bioRxiv. 2015;:026963.
Wang L, Beissinger TM, Lorant A, Ross-Ibarra C, Ross-Ibarra J, Hufford M. The interplay of demography and selection during maize domestication and expansion. github. 2017. Available from: https://doi.org/10.5281/zenodo.1013415. Accessed 15 Oct 2017.
Wang L, Beissinger TM, Lorant A, Ross-Ibarra C, Ross-Ibarra J, Hufford M. The interplay of demography and selection during maize domestication and expansion. NCBI SRA; 2017. BioProject Accession: PRJNA300309; SRP065483. Available from: https://www.ncbi.nlm.nih.gov/bioproject/300309?log%24=activity. Accessed 15 Oct 2017.