Dulik, Matthew

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Now showing 1 - 7 of 7
  • Publication
    Y-Chromosome Variation in Altaian Kazakhs Reveals a Common Paternal Gene Pool for Kazakhs and the Influence of Mongolian Expansions
    (2011-03-11) Dulik, Matthew C; Schurr, Theodore G; Osipova, Ludmila P
    Kazakh populations have traditionally lived as nomadic pastoralists that seasonally migrate across the steppe and surrounding mountain ranges in Kazakhstan and southern Siberia. To clarify their population history from a paternal perspective, we analyzed the non-recombining portion of the Y-chromosome from Kazakh populations living in southern Altai Republic, Russia, using a high-resolution analysis of 60 biallelic markers and 17 STRs. We noted distinct differences in the patterns of genetic variation between maternal and paternal genetic systems in the Altaian Kazakhs. While they possess a variety of East and West Eurasian mtDNA haplogroups, only three East Eurasian paternal haplogroups appear at significant frequencies (C3*, C3c and O3a3c*). In addition, the Y-STR data revealed low genetic diversity within these lineages. Analysis of the combined biallelic and STR data also demonstrated genetic differences among Kazakh populations from across Central Asia. The observed differences between Altaian Kazakhs and indigenous Kazakhs were not the result of admixture between Altaian Kazakhs and indigenous Altaians. Overall, the shared paternal ancestry of Kazakhs differentiates them from other Central Asian populations. In addition, all of them showed evidence of genetic influence by the 13th century CE Mongol Empire. Ultimately, the social and cultural traditions of the Kazakhs shaped their current pattern of genetic variation.
  • Publication
    Evaluation of Group Genetic Ancestry of Populations From Philadelphia and Dakar in the Context of Sex-Biased Admixture in the Americas
    (2009-11-25) Dulik, Matthew C; Stefflova, Klara; Pai, Athma A; Walker, Amy H; Schurr, Theodore G; Zeigler-Johnson, Charnita M; Rebbeck, Timothy R; Gueye, Serigne M
    Background Population history can be reflected in group genetic ancestry, where genomic variation captured by the mitochondrial DNA (mtDNA) and non-recombining portion of the Y chromosome (NRY) can separate female- and male-specific admixture processes. Genetic ancestry may influence genetic association studies due to differences in individual admixture within recently admixed populations like African Americans. Principal Findings We evaluated the genetic ancestry of Senegalese as well as European Americans and African Americans from Philadelphia. Senegalese mtDNA consisted of ~12% U haplotypes (U6 and U5b1b haplotypes, common in North Africa) while the NRY haplotypes belonged solely to haplogroup E. In Philadelphia, we observed varying degrees of admixture. While African Americans have 9–10% mtDNAs and ~31% NRYs of European origin, these results are not mirrored in the mtDNA/NRY pools of European Americans: they have less than 7% mtDNAs and less than 2% NRYs from non-European sources. Additionally, there is <2% Native American contribution to Philadelphian African American ancestry and the admixture from combined mtDNA/NRY estimates is consistent with the admixture derived from autosomal genetic data. To further dissect these estimates, we have analyzed our samples in the context of different demographic groups in the Americas. Conclusions We found that sex-biased admixture in African-derived populations is present throughout the Americas, with continual influence of European males, while Native American females contribute mainly to populations of the Caribbean and South America. The high non-European female contribution to the pool of European-derived populations is consistently characteristic of Iberian colonization. These data suggest that genomic data correlate well with historical records of colonization in the Americas.
  • Publication
    Russian Old Believers: Genetic Consequences of Their Persecution and Exile, as Shown by Mitochondrial DNA Evidence
    (2008-06-01) Dulik, Matthew C; Rubinstein, Samara; Gokcumen, Omer; Zhadanov, Sergey I; Osipova, Ludmila P; Cocca, Maggie; Mehta, Nishi; Gubina, Marina; Schurr, Theodore G; Posukh, Olga
    In 1653, the Patriarch Nikon modified liturgical practices to bring the Russian Orthodox Church in line with those of the Eastern (Greek) Orthodox Church, from which it had split 200 years earlier. The Old Believers (staroveri) rejected these changes and continued to worship using the earlier practices. These actions resulted in their persecution by the Russian Orthodox Church, which forced them into exile across Siberia. Given their history, we investigate whether populations of Old Believers have diverged genetically from other Slavic populations as a result of their isolation. We also examine whether the three Old Believer populations analyzed in this study are part of a single gene pool (founder population) or are instead derived from heterogeneous sources. As part of this analysis, we survey the mitochondrial DNAs (mtDNAs) of 189 Russian Old Believer individuals from three populations in Siberia and 201 ethnic Russians from different parts of Siberia for phylogenetically informative mutations in the coding and noncoding regions. Our results indicate that the Old Believers have not significantly diverged genetically from other Slavic populations over the 200-300 years of their isolation in Siberia. However, they do show some unique patterns of mtDNA variation relative to other Slavic groups, such as a high frequency of subhaplogroup U4, a surprisingly low frequency of haplogroup H, and low frequencies of the rare East Eurasian subhaplogroup D5.
  • Publication
    Hasanlu IVB: An Ancient DNA Pilot Project
    (2015-01-01) Dulik, Matthew C; Schurr, Theodore G; Lorenz, Joseph G
  • Publication
    Neolithic Mitochondrial Haplogroup H Genomes and the Genetic Origins of Europeans
    (2013-04-23) Dulik, Matthew; Gaieski, Jill Bennett; Schurr, Theodore G; Genographic Consortium
    Haplogroup H dominates present-day Western European mitochondrial DNA variability (>40%), yet was less common (~19%) among Early Neolithic farmers (~5450 BC) and virtually absent in Mesolithic hunter-gatherers. Here we investigate this major component of the maternal population history of modern Europeans and sequence 39 complete haplogroup H mitochondrial genomes from ancient human remains. We then compare this â real-timeâ genetic data with cultural changes taking place between the Early Neolithic (~5450 BC) and Bronze Age (~2200 BC) in Central Europe. Our results reveal that the current diversity and distribution of haplogroup H were largely established by the Mid Neolithic (~4000 BC), but with substantial genetic contributions from subsequent pan-European cultures such as the Bell Beakers expanding out of Iberia in the Late Neolithic (~2800 BC). Dated haplogroup H genomes allow us to reconstruct the recent evolutionary history of haplogroup H and reveal a mutation rate 45% higher than current estimates for human mitochondria.
  • Publication
    A Molecular Anthropological Study of Altaian Histories Utilizing Population Genetics and Phylogeography
    (2011-05-16) Dulik, Matthew
    This dissertation explores the genetic histories of several populations living in the Altai Republic of Russia. It employs an approach combining methods from population genetics and phylogeography to characterize genetic diversity in these populations, and places the results in a molecular anthropological context. Previously, researchers used anthropological, historical, ethnographic and linguistic evidence to categorize the indigenous inhabitants of the Altai into two groups – northern and southern Altaians. Genetic data obtained in this study were therefore used to determine whether these anthropological groupings resulted from historical processes involving different source populations, and if the observed geographical and anthropological separation between northern and southern Altaians also represented a genetic boundary between them. These comparisons were made by examining mitochondrial DNA (mtDNA) coding region single nucleotide polymorphisms (SNPs), control region sequences (including HVS1), and several complete mitochondrial genomes. Variation in the non-recombining portion of the Y-chromosome (NRY) was characterized with biallelic markers and short tandem repeat (STR) haplotypes. Overall, this work provided a high-resolution data set for both unipaternally inherited genetic marker systems. The resulting data were analyzed using both population genetic and phylogeographic methods. Northern Altaians (Chelkan, Kumandin and Tubalar) were distinctive from the southern Altaians (Altai-kizhi) with both genetic systems, yet the Tubalar consistently showed evidence of admixture with southern Altaians, reflecting differences in the origin and population history of northern and southern groups as well as between ethnic northern Altaian populations. These results complement the observation of cultural differences as noted by anthropological/ethnographic research on Altaian populations. These differences likely reinforced and maintained the genetic differences between ethnic groups (i.e., a cultural barrier to genetic exchange). Therefore, biological and cultural lines of evidence suggest separate origins for northern and southern Altaians. Phylogeographic analysis of mtDNA and NRY haplotypes examined the impact of different historical events on genetic diversity in Altaians, including Neolithic expansions, the introduction of Kurgan cultures, the spread of Altaic-speakers, and the intrusion of the Mongol Empire. These insights also allowed for a greater understanding of the peopling of Siberia itself. The cultures of Altaian peoples ultimately helped to shape their current genetic variation.
  • Publication
    Mitochondrial Genome Sequence Analysis: A Custom Bioinformatics Pipeline Substantially Improves Affymetrix MitoChip v2.0 Call Rate and Accuracy
    (2011-10-19) Schurr, Theodore G; Dulik, Matthew C; Xie, Hongbo M; Perin, Juan C; Baur, Joseph A; Zhadanov, Sergey I; King, Michael P; Schug, Jonathan; Place, Emily; Clarke, Colleen; Grauer, Michael; Santani, Avni; Albano, Anthony; Kim, Cecilia; Procaccio, Vincent; Hakonarson, Hakon; Gai, Xiaowu; Falk, Marni J
    Background Mitochondrial genome sequence analysis is critical to the diagnostic evaluation of mitochondrial disease. Existing methodologies differ widely in throughput, complexity, cost efficiency, and sensitivity of heteroplasmy detection. Affymetrix MitoChip v2.0, which uses a sequencing-by-genotyping technology, allows potentially accurate and high-throughput sequencing of the entire human mitochondrial genome to be completed in a cost-effective fashion. However, the relatively low call rate achieved using existing software tools has limited the wide adoption of this platform for either clinical or research applications. Here, we report the design and development of a custom bioinformatics software pipeline that achieves a much improved call rate and accuracy for the Affymetrix MitoChip v2.0 platform. We used this custom pipeline to analyze MitoChip v2.0 data from 24 DNA samples representing a broad range of tissue types (18 whole blood, 3 skeletal muscle, 3 cell lines), mutations (a 5.8 kilobase pair deletion and 6 known heteroplasmic mutations), and haplogroup origins. All results were compared to those obtained by at least one other mitochondrial DNA sequence analysis method, including Sanger sequencing, denaturing HPLC-based heteroduplex analysis, and/or the Illumina Genome Analyzer II next generation sequencing platform. Results An average call rate of 99.75% was achieved across all samples with our custom pipeline. Comparison of calls for 15 samples characterized previously by Sanger sequencing revealed a total of 29 discordant calls, which translates to an estimated 0.012% for the base call error rate. We successfully identified 4 known heteroplasmic mutations and 24 other potential heteroplasmic mutations across 20 samples that passed quality control. Conclusions Affymetrix MitoChip v2.0 analysis using our optimized MitoChip Filtering Protocol (MFP) bioinformatics pipeline now offers the high sensitivity and accuracy needed for reliable, high-throughput and cost-efficient whole mitochondrial genome sequencing. This approach provides a viable alternative of potential utility for both clinical diagnostic and research applications to traditional Sanger and other emerging sequencing technologies for whole mitochondrial genome analysis.