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

Journal Article Archive

Western Eurasian genetic influences in the Indonesian Archipelago

Journal: Quaternary International | Year: 2016


Western Eurasia, notably the Near East and South Asia (Indian sub-continent), has interacted with Indonesia through Indian Ocean trade (the Maritime Silk Route) for more than 2000 years. The Indianization, and later Islamization, of Indonesia was enacted largely through trading activities, but also spread with help from the many Indianized and Islamic kingdoms that reigned over parts of the Indonesian archipelago during this time. Western Eurasian interaction left behind not only imported trade goods and cultural features, but also genetic traces. To locate the primary areas of Western Eurasian genetic influence in Indonesia, we have assembled published uniparental genetic data from ∼2900 Indonesian individuals. Frequency distributions show that Western Eurasian paternal lineages are found more commonly than Western Eurasian maternal lineages. Furthermore, the origins of these paternal lineages are more diverse than the corresponding maternal lineages, predominantly tracing back to South West and South Asia, and the Indian sub-continent, respectively. Indianized kingdoms in the Indonesian archipelago likely played a major role in dispersing Western Eurasian lineages, as these kingdoms overlap geographically with the current distribution of individuals carrying Western Eurasian genetic markers. Our data highlight the important role of these Western Eurasian migrants in contributing to the complexity of genetic diversity across the Indonesian archipelago today.

Peoples: - | Places: Indonesia, South Asia, and Western Eurasia | Topics: Indian Ocean trade, Indianization, and Islamization | DNA Type: mtDNA and Y-DNA

What is an adverse” environment? Interactions of rearing experiences and MAOA genotype in rhesus monkeys”

Journal: Biological psychiatry | Year: 2009


Studies have been inconsistent in demonstrating that early adversity and specific genotype can be joint risk factors for poor behavioral outcomes. Using a rhesus monkey model, we examined how social context and different forms of early adversity influence whether a specific genotype (polymorphism in the promoter region of monoamine oxidase A [MAOA]) affects display of aggressive, fearful, and anxious behaviors.

Rhesus monkey infants (n = 473) were exposed to brief social challenge at age 3–4 months. Infants were reared 1) with mothers and up to 150 other animals in large cages; 2) with mothers in smaller social groups; 3) with mother and access to, at most, one other mother–infant pair; and 4) without mother but with access to a same-age peer in a nursery.

No effects of genotype were found for infants reared by mothers in large social cages, although several genotype by rearing environment interactions were evident. Animals reared in smaller social groups were more likely to display aggression, which was especially true of animals possessing the low-activity MAOA genotype. In addition, animals with low-activity genotypes that had experienced restricted mother rearing showed more anxious behavior (scratch, yawn).

Among mother-reared animals, broader contextual features, associated with the social environment and experience of the mother, can affect the extent to which genotype contributes to behavioral expression under conditions of challenge. Results also suggest that different forms of early adverse experience can affect the types of responses displayed by animals of different genotypes.

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

What's in a name? Y chromosomes, surnames and the genetic genealogy revolution

Journal: Trends in Genetics | Year: 2009


Heritable surnames are highly diverse cultural markers of coancestry in human populations. A patrilineal surname is inherited in the same way as the non-recombining region of the Y chromosome and there should, therefore, be a correlation between the two. Studies of Y haplotypes within surnames, mostly of the British Isles, reveal high levels of coancestry among surname cohorts and the influence of confounding factors, including multiple founders for names, non-paternities and genetic drift. Combining molecular genetics and surname analysis illuminates population structure and history, has potential applications in forensic studies and, in the form of [`]genetic genealogy', is an area of rapidly growing interest for the public.

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

Who were the Paleo-Eskimo Saqqaq?

Journal: Vavilov Institute of General Genetics | Year: 2015


Complete sequencing Y-chromosome data from four samples from Koryak village of Evensk North Eastern District Magadan region (KrkG11, KrkG13, KrkG14, KrkG55). The four samples have 37 SNPs in common with the paleo-Eskimo sample. The resulting subclade has been assigned the label Q-YP1500 / YP11467-YP1503 in the YFull service experimental tree. Thus, the structure of Q-F746 subclades is as follows: Q-F746 / NWT01 ……….Q-YP1500 / YP1467-YP1503 (Paleo-Eskimo and Koryak Saqqaq) ……….Q-M120

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

Whole-exome sequencing in an isolated population from the Dalmatian island of Vis

Journal: European Journal of Human Genetics | Year: 2016


We have whole-exome sequenced 176 individuals from the isolated population of the island of Vis in Croatia in order to describe exonic variation architecture. We found 290 577 single nucleotide variants (SNVs), 65% of which are singletons, low frequency or rare variants. A total of 25 430 (9%) SNVs are novel, previously not catalogued in NHLBI GO Exome Sequencing Project, UK10K-Generation Scotland, 1000Genomes Project, ExAC or NCBI Reference Assembly dbSNP. The majority of these variants (76%) are singletons. Comparable to data obtained from UK10K-Generation Scotland that were sequenced and analysed using the same protocols, we detected an enrichment of potentially damaging variants (non-synonymous and loss-of-function) in the low frequency and common variant categories. On average 115 (range 93–140) genotypes with loss-of-function variants, 23 (15–34) of which were homozygous, were identified per person. The landscape of loss-of-function variants across an exome revealed that variants mainly accumulated in genes on the xenobiotic-related pathways, of which majority coded for enzymes. The frequency of loss-of-function variants was additionally increased in Vis runs of homozygosity regions where variants mainly affected signalling pathways. This work confirms the isolate status of Vis population by means of whole-exome sequence and reveals the pattern of loss-of-function mutations, which resembles the trails of adaptive evolution that were found in other species. By cataloguing the exomic variants and describing the allelic structure of the Vis population, this study will serve as a valuable resource for future genetic studies of human diseases, population genetics and evolution in this population.

Peoples: Dalmatians | Places: Croatia and Vis | Topics: evolution, human diseases, and population genetics | DNA Type: Autosomal DNA

Whole-genome view of the consequences of a population bottleneck using 2926 genome sequences from Finland and United Kingdom

Journal: European Journal of Human Genetics | Year: 2017


Isolated populations with enrichment of variants due to recent population bottlenecks provide a powerful resource for identifying disease-associated genetic variants and genes. As a model of an isolate population, we sequenced the genomes of 1463 Finnish individuals as part of the Sequencing Initiative Suomi (SISu) Project. We compared the genomic profiles of the 1463 Finns to a sample of 1463 British individuals that were sequenced in parallel as part of the UK10K Project. Whereas there were no major differences in the allele frequency of common variants, a significant depletion of variants in the rare frequency spectrum was observed in Finns when comparing the two populations. On the other hand, we observed >2.1 million variants that were twice as frequent among Finns compared with Britons and 800 000 variants that were more than 10 times more frequent in Finns. Furthermore, in Finns we observed a relative proportional enrichment of variants in the minor allele frequency range between 2 and 5% (P<2.2 × 10−16). When stratified by their functional annotations, loss-of-function variants showed the highest proportional enrichment in Finns (P=0.0291). In the non-coding part of the genome, variants in conserved regions (P=0.002) and promoters (P=0.01) were also significantly enriched in the Finnish samples. These functional categories represent the highest a priori power for downstream association studies of rare variants using population isolates.

Peoples: Finns | Places: Finland and United Kingdom | Topics: Population isolates and Sequencing Initiative Suomi (SISu) Project | DNA Type: Autosomal DNA

Whole-mtDNA Genome Sequence Analysis of Ancient African Lineages

Journal: Nature Communications | Year: 2006


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

Why were Sardinians the shortest Europeans? A journey through genes, infections, nutrition, and sex

Journal: American Journal of Physical Anthropology | Year: 2017


Since ancient times the Mediterranean island of Sardinia has been known for harboring a population with an average body height shorter than almost every other ethnic group in Europe. After over a century of investigations, the cause(s) at the origin of this uniqueness are not yet clear. The shorter stature of Sardinians appears to have been documented since prehistoric times, as revealed by the analysis of skeletal remains discovered in archaeological sites on the island. Recently, a number of genetic, hormonal, environmental, infective and nutritional factors have been put forward to explain this unique anthropometric feature, which persisted for a long time, even when environmental and living conditions improved around 1960. Although some of the putative factors are supported by sound empirical evidence, weaker support is available for others. The recent advent of whole genome analysis techniques shed new light on specific variants at the origin of this short stature. However, the marked geographical variability of stature across time and space within the island, and the well-known presence of pockets of short height in the population of the southern districts, are still puzzling findings that have attracted the interest of anthropologists and geneticists. The purpose of this review is to focus on the state-of-the-art research on stature, as well as the factors that made Sardinians the shortest among Europeans.

Peoples: Sardinians | Places: Sardinia | Topics: Stature | DNA Type: Autosomal DNA

Widespread signatures of recent selection linked to nucleosome positioning in the human lineage

Journal: Genome Research | Year: 2011


In this study we investigated the strengths and modes of selection associated with nucleosome positioning in the human lineage through the comparison of interspecies and intraspecies rates of divergence. We identify significant evidence for both positive and negative selection linked to human nucleosome positioning for the first time, implicating a widespread and important role for DNA sequence in the location of well-positioned nucleosomes. Selection appears to be acting on particular base substitutions to maintain optimum GC compositions in core and linker regions, with, e.g., unexpectedly elevated rates of C?T substitutions during recent human evolution at linker regions 60–90 bp from the nucleosome dyad but significant depletion of the same substitutions within nucleosome core regions. These patterns are strikingly consistent with the known relationships between genomic sequence composition and nucleosome assembly. By stratifying nucleosomes according to the GC content of their genomic neighborhood, we also show that the strength and direction of selection detected is dictated by local GC content. Intriguingly these signatures of selection are not restricted to nucleosomes in close proximity to exons, suggesting the correct positioning of nucleosomes is not only important in and around coding regions. This analysis provides strong evidence that the genomic sequences associated with nucleosomes are not evolving neutrally, and suggests that underlying DNA sequence is an important factor in nucleosome positioning. Recent signatures of selection linked to genomic features as ubiquitous as the nucleosome have important implications for human genome evolution and disease.

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X-chromosome as a marker for population history: linkage disequilibrium and haplotype study in Eurasian populations

Journal: European Journal of Human Genetics | Year: 2004


Linkage disequilibrium (LD) structure is still unpredictable because the interplay of regional recombination rate and demographic history is poorly understood. We have compared the distribution of LD across two genomic regions differing in crossing-over activity – Xq13 (0.166 cM/Mb) and Xp22 (1.3 cM/Mb) – in 15 Eurasian populations. Demographic events predicted to increase the LD level – genetic drift, bottleneck and admixture – had a very strong impact on extent and patterns of regional LD across Xq13 compared to Xp22. The haplotype distribution of the DXS1225–DXS8082 microsatellites from Xq13 exhibiting strong association in all populations was remarkably influenced by population history. European populations shared one common haplotype with a frequency of 25–40%. The Volga-Ural populations studied, living at the geographic borderline of Europe, showed elevated LD as well as harboring a significant fraction of haplotypes originating from East Asia, thus reflecting their past migrations and admixture. In the young Kuusamo isolate from Finland, a bottleneck has led to allelic associations between loci and shifted the haplotype distribution, but has much less affected single microsatellite allele frequencies compared to the main Finnish population. The data show that the footprint of a demographic event is longer preserved in haplotype distribution within a region of low crossing-over rate, than in the information content of a single marker, or between actively recombining markers. As the knowledge of LD patterns is often chosen to assist association mapping of common disease, our conclusions emphasize the importance of understanding the history, structure and variation of a study population.

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