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Journal Article Archive 2016-10-14T01:03:42+00:00

Journal Article Archive

A time transect of exomes from a Native American population before and after European contact

Journal: Nature Communications | Year: 2016

Abstract:

A major factor for the population decline of Native Americans after European contact has been attributed to infectious disease susceptibility. To investigate whether a pre-existing genetic component contributed to this phenomenon, here we analyse 50 exomes of a continuous population from the Northwest Coast of North America, dating from before and after European contact. We model the population collapse after European contact, inferring a 57% reduction in effective population size. We also identify signatures of positive selection on immune-related genes in the ancient but not the modern group, with the strongest signal deriving from the human leucocyte antigen (HLA) gene HLA-DQA1. The modern individuals show a marked frequency decrease in the same alleles, likely due to the environmental change associated with European colonization, whereby negative selection may have acted on the same gene after contact. The evident shift in selection pressures correlates to the regional European-borne epidemics of the 1800s.

Peoples: Native Americans | Places: North America | Topics: Effective population size, European-borne epidemics, HLA-DQA1, Negative selection, and Positive selection | DNA Type: Autosomal DNA and X-DNA

A Unified Approach to Genotype Imputation and Haplotype-Phase Inference for Large Data Sets of Trios and Unrelated Individuals

Journal: American Journal of Human Genetics | Year: 2009

Abstract:

We present methods for imputing data for ungenotyped markers and for inferring haplotype phase in large data sets of unrelated individuals and parent-offspring trios. Our methods make use of known haplotype phase when it is available, and our methods are computationally efficient so that the full information in large reference panels with thousands of individuals is utilized. We demonstrate that substantial gains in imputation accuracy accrue with increasingly large reference panel sizes, particularly when imputing low-frequency variants, and that unphased reference panels can provide highly accurate genotype imputation. We place our methodology in a unified framework that enables the simultaneous use of unphased and phased data from trios and unrelated individuals in a single analysis. For unrelated individuals, our imputation methods produce well-calibrated posterior genotype probabilities and highly accurate allele-frequency estimates. For trios, our haplotype-inference method is four orders of magnitude faster than the gold-standard PHASE program and has excellent accuracy. Our methods enable genotype imputation to be performed with unphased trio or unrelated reference panels, thus accounting for haplotype-phase uncertainty in the reference panel. We present a useful measure of imputation accuracy, allelic R(2), and show that this measure can be estimated accurately from posterior genotype probabilities. Our methods are implemented in version 3.0 of the BEAGLE software package.

Peoples: | Places: | Topics: | DNA Type:

A western Eurasian male is found in 2000-year-old elite Xiongnu cemetery in Northeast Mongolia

Journal: American Journal of Physical Anthropology | Year: 2010

Abstract:

We analyzed mitochondrial DNA (mtDNA), Y-chromosome single nucleotide polymorphisms (Y-SNP), and autosomal short tandem repeats (STR) of three skeletons found in a 2,000-year-old Xiongnu elite cemetery in Duurlig Nars of Northeast Mongolia. This study is one of the first reports of the detailed genetic analysis of ancient human remains using the three types of genetic markers. The DNA analyses revealed that one subject was an ancient male skeleton with maternal U2e1 and paternal R1a1 haplogroups. This is the first genetic evidence that a male of distinctive Indo-European lineages (R1a1) was present in the Xiongnu of Mongolia. This might indicate an Indo-European migration into Northeast Asia 2,000 years ago. Other specimens are a female with mtDNA haplogroup D4 and a male with Y-SNP haplogroup C3 and mtDNA haplogroup D4. Those haplogroups are common in Northeast Asia. There was no close kinship among them. The genetic evidence of U2e1 and R1a1 may help to clarify the migration patterns of Indo-Europeans and ancient East-West contacts of the Xiongnu Empire. Artifacts in the tombs suggested that the Xiongnu had a system of the social stratification. The West Eurasian male might show the racial tolerance of the Xiongnu Empire and some insight into the Xiongnu society. Am J Phys Anthropol, 2010. copyright 2010 Wiley-Liss, Inc.

Peoples: - | Places: - | Topics: - | DNA Type: Y-DNA

A Worldwide Survey of Human Male Demographic History Based on Y-SNP and Y-STR Data from the HGDP–CEPH Populations

Journal: Molecular Biology and Evolution | Year: 2010

Abstract:

We have investigated human male demographic history using 590 males from 51 populations in the Human Genome Diversity Project – Centre d”Etude du Polymorphisme Humain worldwide panel, typed with 37 Y-chromosomal Single Nucleotide Polymorphisms and 65 Y-chromosomal Short Tandem Repeats and analyzed with the program Bayesian Analysis of Trees With Internal Node Generation. The general patterns we observe show a gradient from the oldest population time to the most recent common ancestors (TMRCAs) and expansion times together with the largest effective population sizes in Africa, to the youngest times and smallest effective population sizes in the Americas. These parameters are significantly negatively correlated with distance from East Africa, and the patterns are consistent with most other studies of human variation and history. In contrast, growth rate showed a weaker correlation in the opposite direction. Y-lineage diversity and TMRCA also decrease with distance from East Africa, supporting a model of expansion with serial founder events starting from this source. A number of individual populations diverge from these general patterns, including previously documented examples such as recent expansions of the Yoruba in Africa, Basques in Europe, and Yakut in Northern Asia. However, some unexpected demographic histories were also found, including low growth rates in the Hazara and Kalash from Pakistan and recent expansion of the Mozabites in North Africa.

Peoples: - | Places: - | Topics: - | DNA Type: Y-DNA

A Y-Chromosome Signature of Hegemony in Gaelic Ireland

Journal: American Journal of Human Genetics | Year: 2006

Abstract:

Seventeen-marker simple tandem repeat genetic analysis of Irish Y chromosomes reveals a previously unnoted modal haplotype that peaks in frequency in the northwestern part of the island. It shows a significant association with surnames purported to have descended from the most important and enduring dynasty of early medieval Ireland, the Ui Neill. This suggests that such phylogenetic predominance is a biological record of past hegemony and supports the veracity of semimythological early genealogies. The fact that about one in five males sampled in northwestern Ireland is likely a patrilineal descendent of a single early medieval ancestor is a powerful illustration of the potential link between prolificacy and power and of how Y-chromosome phylogeography can be influenced by social selection.

Peoples: - | Places: - | Topics: - | DNA Type: Y-DNA

A Y-STR database of Iranian and Azerbaijanian minority populations

Journal: Forensic Science International: Genetics | Year: 2009

Abstract:

Seventeen Y-chromosomal short tandem repeats (Y-STR) DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a, DYS385b, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4 were studied in five minor linguistic groups from Iran (Arabs, Gilaki, Mazandarani, Bakhtiari and Southern Talysh) and one from Azerbaijan (Northern Talysh) with the goal of constructing of a representative Y-STR database for this region in Southwest Asia. Analysis of Molecular Variance (AMOVA) reveals non-significant or low genetic distances between the Iranian Gilaki, Mazandarani, Bakhtiari and non-Iranian Turkish, Azerbaijanian, Armenian and Kurd populations, but larger genetic distances to both Talysh populations, the Iranian Arabs, Georgian and Kazakh populations.

Peoples: - | Places: - | Topics: - | DNA Type: Y-DNA

Accumulation of mutations over the entire mitochondrial genome of breast cancer cells obtained by tissue microdissection

Journal: Breast cancer research and treatment | Year: 2010

Abstract:

Peoples: | Places: | Topics: | DNA Type: mtDNA

Adaptive evolution of the Homo mitochondrial genome

Journal: Molecular Biology | Year: 2011

Abstract:

Adaptive evolution of 12 protein-coding mitochondrial genes in members of genus Homo (Denisova hominin ( H . sp. Altai ), Neanderthals ( H. neanderthalensis ) and modern humans ( H. sapiens )) has been evaluated by assessing the pattern of changes in the physicochemical properties of amino acid replacements during primate evolution. It has been found that molecular adaptation (positive destabilizing selection) in Homo becomes apparent in the form of 12 radical amino acid replacements accompanied with statistically significant ( P < 0.001) changes of physicochemical properties that probably had functional consequences. These replacements occurred at the stage of a common ancestor of Homo (in CO2 and CytB genes) as well as with the appearance of the common ancestor of Neanderthals and modern humans (in CO1 and ND5 genes). Radical amino acid replacements were mainly revealed in the cytochrome c oxidase complex IV and cytochrome bc 1 complex III, thus coinciding with the general trend of increasing nonsynonymous changes in mtDNA genes coding subunits of complexes' III and IV proteins in anthropoid primates.

Peoples: - | Places: - | Topics: - | DNA Type: mtDNA

Adaptive selection of an incretin gene in Eurasian populations

Journal: Genome Research | Year: 2011

Abstract:

Diversities in human physiology have been partially shaped by adaptation to natural environments and changing cultures. Recent genomic analyses have revealed single nucleotide polymorphisms (SNPs) that are associated with adaptations in immune responses, obvious changes in human body forms, or adaptations to extreme climates in select human populations. Here, we report that the human GIP locus was differentially selected among human populations based on the analysis of a nonsynonymous SNP (rs2291725). Comparative and functional analyses showed that the human GIP gene encodes a cryptic glucose-dependent insulinotropic polypeptide (GIP) isoform (GIP55S or GIP55G) that encompasses the SNP and is resistant to serum degradation relative to the known mature GIP peptide. Importantly, we found that GIP55G, which is encoded by the derived allele, exhibits a higher bioactivity compared with GIP55S, which is derived from the ancestral allele. Haplotype structure analysis suggests that the derived allele at rs2291725 arose to dominance in East Asians ?8100 yr ago due to positive selection. The combined results suggested that rs2291725 represents a functional mutation and may contribute to the population genetics observation. Given that GIP signaling plays a critical role in homeostasis regulation at both the enteroinsular and enteroadipocyte axes, our study highlights the importance of understanding adaptations in energy-balance regulation in the face of the emerging diabetes and obesity epidemics.

Peoples: | Places: | Topics: | DNA Type:

Additional analysis of mtDNA from the Tommy and Mine Canyon sites

Journal: Journal of Archaeological Science: Reports | Year: 2017

Abstract:

Ancient mitochondrial DNA analysis of samples from the Chaco outlier Tommy and Mine Canyon sites (dating to PII and PIII, respectively, and located near Farmington, New Mexico) originally revealed distinctly different haplogroup frequency distributions from one another. An additional twelve samples were added to those already published (Snow et al., 2010), bringing the total number of individuals with mitochondrial DNA data to 60. The additional samples diminished this difference but maintained the statistically significant distinction between the sites, pointing to a potential sampling bias at the Mine Canyon Site that might explain some, but not all, of the difference. The sites were compared with those from both modern and prehistoric populations in the desert Southwest and Mexico to better understand the regional context of the inhabitants, as well as inter-regional relationships, demonstrating that the Tommy Site fits well within the general Southwestern pattern, while the Mine Canyon Site stands out due to its higher than normal frequency of haplogroup A2. Thirteen burials from a kiva structure at the Mine Canyon Site are compared to the remainder of the excavated burials from the site in terms of mtDNA, burial position, pathology, and grave goods. The statistically significant differences of the kiva burials are discussed in terms of possible evidence of site abandonment, disease, slavery, and witchcraft.

Peoples: Native Americans | Places: Mine Canyon Site, North America Southwest, and Tommy Site | Topics: disease, site abandonment, slavery, and witchcraft | DNA Type: Ancient DNA and mtDNA

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