Ancestry inference for a person using a panel of SNPs depends on the variation of frequencies of those SNPs around the world and the amount of reference data available for calculation/comparison. The Kidd Lab panel of 55 AISNPs has been incorporated in commercial kits by both Life Technologies and Illumina for massively parallel sequencing. Therefore, a larger set of reference populations will be useful for researchers using those kits. We have added reference population allele frequencies for 52 population samples to the 73 previously entered so that there are now allele frequencies publicly available in ALFRED and FROG-kb for a total of 125 population samples.
Microhaplotypes have become a new type of forensic marker with a great ability to identify and deconvolute mixtures because massively parallel sequencing (MPS) allows the alleles (haplotypes) of the multi-SNP loci to be determined directly for an individual. As originally defined, a microhaplotype locus is a short segment of DNA with two or more SNPs defining three or more haplotypes. The length is short enough, less than about 300 bp, that the read length of current MPS technology can produce a phase-known sequence of each chromosome of an individual. As part of the discovery phase of our studies, data on 130 microhaplotype loci with estimates of haplotype frequency data on 83 populations have been published. To provide a better picture of global allele frequency variation, we have now tested 13 more populations for 65 of the microhaplotype loci from among those with higher levels of inter-population gene frequency variation, including 8 loci not previously published. These loci provide clear distinctions among 6 biogeographic regions and provide some information distinguishing up to 10 clusters of populations.Electronic supplementary materialThe online version of this article (10.1007/s00414-017-1748-6) contains supplementary material, which is available to authorized users.
Genetic data on North Central Asian populations are underrepresented in the literature, especially autosomal markers. In the present study we use 812 single nucleotide polymorphisms that are distributed across all the human autosomes and that have been extensively studied at Yale to examine the affinities of two recently collected, samples of populations: rural and cosmopolitan Mongolians from Ulaanbaatar and nomadic, Turkic-speakingTsaatan from Mongolia near the Siberian border. We compare these two populations to one another and to a global set of populations and discuss their relationships to New World populations. Specifically, we analyze data on 521 autosomal loci (single SNPs and multi-SNP haplotypes) studied on 57Pre-print version. Visit http://digitalcommons.wayne.edu/humbiol after official publication to acquire the final version.populations representing all the major geographical regions of the world. We conclude that the North Central Asian populations we study are genetically distinct from all other populations in our study and may be close to the ancestral lineage leading to the New World populations.North Central Asian (NCA) populations have been studied by many investigators but are underrepresented in more comprehensive population genetic surveys, such as the HGDP (Cann et al. 2002;Rosenberg et al. 2002; Li et al. 2008) and Duggan et al. 2013;Fedorova et al. 2013;Hertzberg et al. 1989;Kemp et al. 2015;Kitchen et al. 2008;Kolman et al. 1996;Lell et al. 2002;Malyarchuk et al. 2011;Malyarchuk et al. 2013;Mulligan et al. 2008;Nasidze et al. 2005;Dulik et al. 2012;Shi et al. 2013; Starikovskaya et al. 2004;Sukernik et al. 2012;Raghavan et al. 2014a;Volodko et al. 2008;Zhong et al. 2011;Zhong et al. 2010), ancient DNA (aDNA, uniparental and autosomal) (Crubezy et al. 2010;Keyser-Tracqui et al. 2003, Keyser-Tracqui et al. 2006Malyarchuk et al. 2011;Raghavan et al. 2014b). Mitochondrial DNA haplogroups offer a fairly crude inference of continental ancestry, conveying only information regarding possibly one or two top ancestry components while losing other ancestry information (Emery et al. 2015). Other studies used contemporary autosomal DNA (Fedorova et al. 2013;Keyser-Tracqui et al. 2003;Keyser-Tracqui et al. 2006; Kidd et al. 2011a,b; Nasidze et al. 2006;Reich et al. 2012;Tian et al. 2008). These studies were excellent but many more autosomal markers must be investigated, particularly in sparsely studied populations such as Mongolians, especially OuterMongolians who have been less studied than Mongolians living in Chinese InnerMongolia whose demographic history is also somewhat different, to clarify population relationships.Progress in answering the questions posed above is underway though by no means are the answers definitive yet. In this report we shall review some of Pre-print version. Visit http://digitalcommons.wayne.edu/humbiol after official publication to acquire the final version.the relevant studies that include population data from North Central Asia and contribute our findings...
Population genetic studies of North Asian ethnic groups have focused on genetic variation of sex chromosomes and mitochondria. Studies of the extensive variation available from autosomal variation have appeared infrequently. We focus on relationships among population samples using new North Asia microhaplotype data. We combined genotypes from our laboratory on 58 microhaplotypes, distributed across 18 autosomes, on 3945 individuals from 75 populations with corresponding data extracted for 26 populations from the Thousand Genomes consortium and for 22 populations from the GenomeAsia 100 K project. A total of 7107 individuals in 122 total populations are analyzed using STRUCTURE, Principal Component Analysis, and phylogenetic tree analyses. North Asia populations sampled in Mongolia include: Buryats, Mongolians, Altai Kazakhs, and Tsaatans. Available Siberians include samples of Yakut, Khanty, and Komi Zyriane. Analyses of all 122 populations confirm many known relationships and show that most populations from North Asia form a cluster distinct from all other groups. Refinement of analyses on smaller subsets of populations reinforces the distinctiveness of North Asia and shows that the North Asia cluster identifies a region that is ancestral to Native Americans.
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