Genetic differentiation between and within Northern Native American language groups: an argument for the expansion of the Native American CODIS database

References

• Budowle B, Shea B, Niezgoda S, et al. CODIS STR loci data from 41 sample populations. J Forensic Sci. 2001;46:453–489.
   PubMed Web of Science ®Google Scholar
• Gray RD, Atkinson QD, Greenhill SJ. Language evolution and human history: what a difference a date makes. Philos Trans R Soc B Biol Sci. 2011;366:1090–1100.
   Web of Science ®Google Scholar
• Zegura SL, Karafet TM, Zhivotovsky LA, et al. High-resolution SNPs and microsatellite haplotypes point to a single, recent entry of Native American Y chromosomes into the Americas. Mol Biol Evol. 2004;21:164–175.
   PubMed Web of Science ®Google Scholar
• Dimmendaal GJ. Historical linguistics and the comparative study of African languages. Amsterdam (The Netherlands): John Benjamins; 2011.
   Google Scholar
• Wang S, Lewis CM, Jakobsson M, et al. Genetic variation and population structure in Native Americans. PLoS Genet. 2007;3:e185.
   PubMed Web of Science ®Google Scholar
• Creanza N, Ruhlen M, Pemberton TJ, et al. A comparison of worldwide phonemic and genetic variation in human populations. Proc Natl Acad Sci U S A. 2015;112:1265–1272.
   PubMed Web of Science ®Google Scholar
• Rowe BM, Levine DP. A concise introduction to linguistics. USA: Routledge; 2015.
   Google Scholar
• Campbell L. American Indian languages: the historical linguistics of Native America. Oxford (UK): Oxford University Press; 1997.
   Google Scholar
• Hammer MF, Redd AJ. Forensic applications of Y chromosome STRs and SNPs, national criminal justice re­ference service NCJ publication number 211979, 2006.
   Google Scholar
• Redd AJ, Agellon AB, Kearney VA, et al. Forensic value of 14 novel STRs on the human Y chromosome. Forensic Sci Int. 2002;130:97–111.
   PubMed Web of Science ®Google Scholar
• Redd AJ, Chamberlain VF, Kearney VF, et al. Genetic structure among 38 populations from the United States based on 11 U.S. core Y chromosome STRs. J Forensic Sci. 2006;51:580–585.
   PubMed Web of Science ®Google Scholar
• Lorenz JG, Smith DG. Distribution of sequence variation in the mtDNA control region of Native North Americans. Hum Biol. 1997;69:749–776.
   PubMed Web of Science ®Google Scholar
• Smith DG. Examining the farming/language dispersal hypothesis. Am J of Hum Geneti. 2005;76:190–192.
   Google Scholar
• Kemp BM, Gonzalez-Oliver A, Malhi RS, et al. Evaluating the farming/language dispersal hypothesis with genetic variation exhibited by populations in the Southwest and Mesoamerica. Proc Natl Acad Sci USA. 2010;107:6759–6764.
   PubMed Web of Science ®Google Scholar
• Lorenz JG, Smith DG. Distribution of four founding mtDNA haplogroups among Native North Americans. Am J Phys Anthropol. 1996;101:307–323.
   PubMed Web of Science ®Google Scholar
• Tamm E, Kivisild T, Reidla M, et al. Beringian standstill and spread of Native American founders. PLoS One. 2007;2:e829.
   PubMed Web of Science ®Google Scholar
• Barbujani G. DNA variation and language affinities. Am J Hum Genet. 1997;61:1011–1014.
   PubMed Web of Science ®Google Scholar
• Smith DG, Lorenz J, Rolfs BK, et al. Implications of the distribution of albumin Naskapi and albumin Mexico for new world prehistory. Am J Phys Anthropol. 2000;111:557–572.
   PubMed Web of Science ®Google Scholar
• Greenberg JH, Turner CG, Zegura SL. The settlement of the Americas: a comparison of the linguistic, dental, and genetic evidence. Current Anthropology. 1986 doi:10.1086/203472.
   Google Scholar
• Cavalli-Sforza LL, Piazza A, Menozzi P, et al. Reconstruction of human evolution: bringing toge­ther genetic, archaeological, and linguistic data. Proc Natl Acad Sci USA. 1988;85:6002–6006.
   PubMed Web of Science ®Google Scholar
• Eshleman JA, Malhi RS, Johnson JR, et al. Mitochondrial DNA and prehistoric settlements: native migrations on the Western edge of North America. Hum Biol. 2004;76:55–75.
   PubMed Web of Science ®Google Scholar
• Forster P, Harding R, Torroni A, et al. Origin and evolution of Native American mtDNA variation: a reappraisal. Am J Hum Genet. 1996;59:935–945.
   PubMed Web of Science ®Google Scholar
• Wilson AC, Cann RL, Carr SM, et al. Mitochondrial DNA and two perspectives on evolutionary genetics. Biol J Linnean Soc. 1985;26:375–400.
   Web of Science ®Google Scholar
• Schroeder KB, Schurr TG, Long JC, et al. A private allele ubiquitous in the Americas. Biol Lett. 2007;3:218–223.
   PubMed Web of Science ®Google Scholar
• Roewer L, Nothnagel M, Gusmao L, et al. Continent-wide decoupling of Y-chromosomal gene­tic variation from language and geography in Native South Americans. PLoS Genet. 2013;9:e1003460.
   PubMed Web of Science ®Google Scholar
• Szathmary EJ. Peopling of Northern North America: clues from genetic studies. Acta Anthropogenet. 1984;8:79–109.
   PubMedGoogle Scholar
• McCulloh KL, Ng J, Oldt RF, et al. The genetic structure of Native Americans in North America based on the Globalfiler• STRs. Leg Med (Tokyo). 2016;23:49–54.
   PubMed Web of Science ®Google Scholar
• Ng J, Oldt RF, McCulloh KL, et al. Native american population data based on the Globalfiler• autosomal STR loci. Forensic Sci Int Genet. 2016;24:e12–e13.
   PubMed Web of Science ®Google Scholar
• Rosenberg NA, Mahajan S, Gonzalez-Quevedo C, et al. Low levels of genetic divergence across geographically and linguistically diverse populations from India. PLoS Genet. 2006;2:e215.
   PubMed Web of Science ®Google Scholar
• Malhi RS, Schultz BA, Smith DG. Distribution of mitochondrial DNA lineages among Native American tribes of northeastern North America. Hum Biol. 2001;73:17–55.
   PubMed Web of Science ®Google Scholar
• Malhi RS, Breece KE, Shook BA, et al. Patterns of mtDNA diversity in northwestern North America. Hum Biol. 2004;76:33–54.
   PubMed Web of Science ®Google Scholar
• Moretti TR, Moreno LI, Smerick JB, et al. Population data on the expanded CODIS core STR loci for eleven populations of significance for forensic DNA analyses in the United States. Forensic Sci Int Genet. 2016;25:175–181.
   PubMed Web of Science ®Google Scholar
• Excoffier L, Laval G, Schneider S. Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform Online. 2007;1:47–50.
   PubMed Web of Science ®Google Scholar
• Szpiech ZA, Jakobsson M, Rosenberg NA. ADZE: a rarefaction approach for counting alleles private to combinations of populations. Bioinformatics. 2008;24:2498–2504.
   PubMed Web of Science ®Google Scholar
• Weir BS, Cockerham CC. Estimating F-statistics for the analysis of population structure. Evolution. 1984;38:1358–1370.
   PubMed Web of Science ®Google Scholar
• Raymond MaR, Rousset F. GENEPOP (version 1.2): population genetics software for exact tests and ecu­menicism. J Heredity. 1995;86:248–249.
   Web of Science ®Google Scholar
• Glaubitz JC. CONVERT: a user-friendly program to reformat diploid genotypic data for commonly used population genetic software packages. Mol Ecol. 2004;4:309–310.
   Web of Science ®Google Scholar
• Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics. 2000;155:945–959.
   PubMed Web of Science ®Google Scholar
• Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol. 2005;14:2611–2620.
   PubMed Web of Science ®Google Scholar
• Campbell J. The hero with a thousand faces. New York (NY): Bollingen Foundation Incorporated; 1949.
   Google Scholar
• Reich D, Patterson N, Campbell D, et al. Reconstructing Native American population history. Nature. 2012;488:370–374.
   PubMed Web of Science ®Google Scholar
• Budowle B, Chidambaram A, Strickland L, et al. Population studies on three Native Alaska population groups using STR loci. Forensic Sci Int. 2002;129:51–57.
   PubMed Web of Science ®Google Scholar
• Rosenberg NA, Pritchard JK, Weber JL, et al. Genetic structure of human populations. Science. 2002;298:2381–2385.
   PubMed Web of Science ®Google Scholar
• Rangel-Villalobos H, Martinez-Sevilla VM, Martinez-Cortes G, et al. Importance of the geographic barriers to promote gene drift and avoid pre- and post-Columbian gene flow in Mexican native groups: evidence from forensic STR loci. Am J Phys Anthropol. 2016;160:298–316.
   PubMed Web of Science ®Google Scholar
• Slatkin M, Barton NH. A comparison of three indirect methods for estimating average levels of gene flow. Evolution. 1989;43:1349–1368.
   PubMed Web of Science ®Google Scholar
• Bryc K, Durand EY, Macpherson JM, et al. The genetic ancestry of African Americans, Latinos, and European Americans across the United States. Am J Hum Genet. 2015;96:37–53.
   PubMed Web of Science ®Google Scholar
• Haynie HJ. Geography and spatial analysis in historical linguistics. Lang Linguistics Compass. 2014;8:344–357.
   Google Scholar
• Hunley K. Reassessment of global gene-language coevolution. Proc Natl Acad Sci USA. 2015;112:1919–1920.
   PubMed Web of Science ®Google Scholar
• Green L. Choctaw removal was really a “trail of tears”. Bishinik. 1978;Nov:8–9.
   Google Scholar
• Tubby R, Wells S. After removal: the Choctaw in Mississippi. Jackson (MS): University Press of Mississippi; 2004.
   Google Scholar
• Smith DG, Malhi RS, Eshleman J, et al. Distribution of mtDNA haplogroup X among Native North Americans. Am J Phys Anthropol. 1999;110:271–284.
   PubMed Web of Science ®Google Scholar
• Flickinger GM, Yarbrough KM. Dermatoglyphics of Apache and Navajo Indians. Am J Phys Anthropol. 1976;45:117–121.
   Web of Science ®Google Scholar
• Hunley K, Long JC. Gene flow across linguistic boundaries in Native North American populations. Proc Natl Acad Sci USA. 2005;102:1312–1317.
   PubMed Web of Science ®Google Scholar