Cryptic Distant Relatives Are Common in Both Isolated and Cosmopolitan Genetic Samples

Although a few hundred single nucleotide polymorphisms (SNPs) suffice to infer close familial relationships, high density genome-wide SNP data make possible the inference of more distant relationships such as 2nd to 9th cousinships. In order to characterize the relationship between genetic similarity and degree of kinship given a timeframe of 100–300 years, we analyzed the sharing of DNA inferred to be identical by descent (IBD) in a subset of individuals from the 23andMe customer database (n = 22,757) and from the Human Genome Diversity Panel (HGDP-CEPH, n = 952). With data from 121 populations, we show that the average amount of DNA shared IBD in most ethnolinguistically-defined populations, for example Native American groups, Finns and Ashkenazi Jews, differs from continentally-defined populations by several orders of magnitude. Via extensive pedigree-based simulations, we determined bounds for predicted degrees of relationship given the amount of genomic IBD sharing in both endogamous and ‘unrelated’ population samples. Using these bounds as a guide, we detected tens of thousands of 2nd to 9th degree cousin pairs within a heterogenous set of 5,000 Europeans. The ubiquity of distant relatives, detected via IBD segments, in both ethnolinguistic populations and in large ‘unrelated’ populations samples has important implications for genetic genealogy, forensics and genotype/phenotype mapping studies

Evidence for Positive Selection on a Number of MicroRNA Regulatory Interactions during Recent Human Evolution

MicroRNA (miRNA)–mediated gene regulation is of critical functional importance in animals and is thought to be largely constrained during evolution. However, little is known regarding evolutionary changes of the miRNA network and their role in human evolution. Here we show that a number of miRNA binding sites display high levels of population differentiation in humans and thus are likely targets of local adaptation. In a subset we demonstrate that allelic differences modulate miRNA regulation in mammalian cells, including an interaction between miR-155 and TYRP1, an important melanosomal enzyme associated with human pigmentary differences. We identify alternate alleles of TYRP1 that induce or disrupt miR-155 regulation and demonstrate that these alleles are selected with different modes among human populations, causing a strong negative correlation between the frequency of miR-155 regulation of TYRP1 in human populations and their latitude of residence. We propose that local adaptation of microRNA regulation acts as a rheostat to optimize TYRP1 expression in response to differential UV radiation. Our findings illustrate the evolutionary plasticity of the microRNA regulatory network in recent human evolution

Autosomal STR Variation in a Basque Population: Vizcaya Province

We have characterized 68 unrelated Basque individuals from Vizcaya, Spain, for 13 tetrameric short tandem repeat (STR) loci: CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, TH01, TPOX, and VWA. Interpopulational analyses were also performed for 21 European and North African population data sets for nine of the STRs typed in the Basque sample. Heterozygosity values for the Vizcayan Basques were found to be high, ranging from 0.662 to 0.882, and none of the STR loci significantly deviated from Hardy-Weinberg equilibrium. Based on the comparative population data set, the average GST score is 0.7%, indicating a low degree of genetic differentiation. However, neighbor-joining trees and multidimensional-scaling plots of DA genetic distances indicate that the Vizcayan Basques are an outlier relative to both neighboring Iberians and North African populations

Autosomal STR Variation in a Basque Population: Vizcaya Province

This is the publisher's version, also available electronically through http://digitalcommons.wayne.edu/humbiol/vol78/iss5/5/.We have characterized 68 unrelated Basque individuals from Vizcaya, Spain, for 13 tetrameric short tandem repeat (STR) loci: CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, TH01, TPOX, and VWA. Interpopulational analyses were also performed for 21 European and North African population data sets for nine of the STRs typed in the Basque sample. Heterozygosity values for the Vizcayan Basques were found to be high, ranging from 0.662 to 0.882, and none of the STR loci significantly deviated from Hardy-Weinberg equilibrium. Based on the comparative population data set, the average GST score is 0.7%, indicating a low degree of genetic differentiation. However, neighbor-joining trees and multidimensional-scaling plots of DA genetic distances indicate that the Vizcayan Basques are an outlier relative to both neighboring Iberians and North African populations .This research was sponsored by the National Geographic Society through grant 6935-00

Surname Distributions and Their Association with Y-Chromosome Markers in the Aleutian Islands

We examine surname distribution, origin, and association with Y-chromosome haplogroups in native communities from the Aleutian archipelago. The underlying hypothesis is that surnames and Y-chromosome haplogroups should be associated because both are paternally inherited markers. We used Lasker’s coefficient of relationship through isonymy (Rib) to identify the distribution of 143 surnames in the Aleutian Islands. The geographic distribution of surnames was explored both through frequency distribution and through the use of Mantel tests. Multidimensional scaling, chi-square, and Mantel tests were used to examine the relationship between surname and Y-chromosome markers. Overall, we observed that the distribution of surnames in the Aleutian archipelago is culturally driven rather than being one of paternal inheritance. Surnames follow a gradient from east to west, with high frequencies of Russian surnames found in western Aleut communities and high levels of non-Russian surnames found in eastern Aleut communities. A nonsignificant correlation (r = –0.0132; P = 0.436) was found between distance matrices based on haplogroups of the nonrecombining portion of the Y chromosome and surnames, although an association was found between non-Russian surnames and the predominantly non-Russian haplogroups (R1b, I1a, and I). Pay-Per-View Download To access this article as a PDF pay-per-view download via BioOne, please click here

Mitochondrial DNA Diversity in Mennonite Communities from the Midwestern United States

This is the published version, also available here http://digitalcommons.wayne.edu/humbiol/vol82/iss3/2/We examined mitochondrial DNA (mtDNA) variation in six Mennonite communities from Kansas (Goessel, Lone Tree, Garden View, Meridian, and Garden City) and Nebraska (Henderson) to determine their genetic structure and its relationship to population history. Mitochondrial DNA haplogroup and haplotype information were obtained from blood samples from 118 individuals. Molecular genetic variation was analyzed using diversity measures, neutrality test statistics, spatial analysis of molecular variance (SAMOVA), and multidimensional scaling plots. The Mennonite samples exhibited eight western European mtDNA haplogroups: H, HV0, I, J, K, T, U, and X. Comparable to other populations of European descent, haplogroup H was the most frequent in all six communities and ranged from 35% in Lone Tree to 75% in Old Order Mennonites from Garden City. Fifty-eight different mtDNA haplotypes were found in these groups with only one shared among all six populations. Haplotype diversities varied from 0.81 in Goessel to 0.96 in Henderson and Garden View. Multivariate statistical analysis of these populations indicates that these Anabaptist communities formed new congregations by fissioning along familial lines. Population subdivision of these communities into congregations supports previously documented patterns of fission-fusion. These haploid molecular data provide a more accurate reflection of biological relationships between midwestern Mennonite communities than evidence based on classical genetic markers

Mitochondrial DNA Diversity in Mennonite Communities from the Midwestern United States

We examined mitochondrial DNA (mtDNA) variation in six Mennonite communities from Kansas (Goessel, Lone Tree, Garden View, Meridian, and Garden City) and Nebraska (Henderson) to determine their genetic structure and its relationship to population history. Mitochondrial DNA haplogroup and haplotype information were obtained from blood samples from 118 individuals. Molecular genetic variation was analyzed using diversity measures, neutrality test statistics, spatial analysis of molecular variance (SAMOVA), and multidimensional scaling plots. The Mennonite samples exhibited eight western European mtDNA haplogroups: H, HV0, I, J, K, T, U, and X. Comparable to other populations of European descent, haplogroup H was the most frequent in all six communities and ranged from 35% in Lone Tree to 75% in Old Order Mennonites from Garden City. Fifty-eight different mtDNA haplotypes were found in these groups with only one shared among all six populations. Haplotype diversities varied from 0.81 in Goessel to 0.96 in Henderson and Garden View. Multivariate statistical analysis of these populations indicates that these Anabaptist communities formed new congregations by fissioning along familial lines. Population subdivision of these communities into congregations supports previously documented patterns of fission-fusion. These haploid molecular data provide a more accurate reflection of biological relationships between midwestern Mennonite communities than evidence based on classical genetic markers

Applications of pooled DNA samples to the assessment of population affinities: short tandem repeats

Pooled DNA samples have been used in association studies of Mendelian disease genes. This method involves combining equal quantities of DNA from patients and control subjects into separate pools and comparing the pools for distributions of genetic markers. In this study identical quantities of DNA from 300 individuals representing 6 populations were pooled and amplified for 296 loci using the touchdown polymerase chain reaction (PCR) method. The purpose of this study is to test the efficacy of pooled DNA markers in the reconstruction of the genetic structure of human populations. The populations sampled included Chuvash, Buryats, Kizhi, Native Americans, South Africans, and New York City whites. To test the accuracy of the allele-frequency distributions, we genotyped the Buryats and New York samples individually for six microsatellite markers and compared their frequencies to the allele frequencies derived from the electropherogram peak heights for the pooled DNA, producing a correlation of 0.9811 with a variance of less than 0.04. Two-dimensional scaling of genetic distances among the six populations produced clusters that reflected known historical relationships. A distance matrix was created using all 296 loci, and matrices based on individual chromosomes were correlated against the total matrix. As expected, the largest chromosomes had the highest correlations with the total matrix, whereas one of the smallest chromosomes, chromosome 22, had the lowest correlation and differed most from the combined STR distance matrix.Michael H. Crawford, P Banerjee, Dario A. Demarchi, M Zlojutro, J McComb, Gregory Livshits, Maciej Henneberg, M. J. Mosher, Moses S. Schanfield, J. A. Knowle