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

Journal Article Archive

Whole-mtDNA Genome Sequence Analysis of Ancient African Lineages

Journal: Nature Communications | Year: 2006

Abstract:

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

Abstract:

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

Abstract:

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.

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

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

Journal: European Journal of Human Genetics | Year: 2004

Abstract:

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.

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

Y chromosomal deletion pattern in Koreans inhabiting Jeju Island

Journal: Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur | Year: 2017

Abstract:

Mutations occur in Y chromosome genes similar to autosomal genes. However, unlike autosomal genes, Y chromosome genes do not undergo recombination, which produce distinctive characteristics and distribution patterns in different geographic regions. Therefore, detailed analysis of mutations of Y chromosome genes might provide information for personal identification or analysis of phylogenetic history. In Y-STR (short tandem repeat) analysis tests on 668 habitants of Jeju Island, the largest island in the Korean peninsula located apart from the mainland, a deletion at DYS448 was found in 10 samples. The length of deletion was estimated by confirming specific Sequence Tagged Site (STS) markers ranging from G66018 to sY1201. Patterns found were similar to those of the Kalmyks, a tribe that has had strong social and genetic influences in Jeju Island in the past. Historically from 1273 on, Jeju Island was governed by Mongolian for about one hundred years. The results of this study suggest such historical aspects affected the genetic composition of people living in Jeju Island. Furthermore, previous reports showed that Y chromosomal deletions and region specific Y chromosomal mutations depended on regional differences. This study may be useful for a better understanding of the genetic structure of Jeju habitants as well as Korean population for the purpose of forensic practice and population genetics.

Peoples: Koreans and Mongolians | Places: Jeju Island and Korean peninsula | Topics: Y-DNA | DNA Type: Y-DNA

Y chromosomal heritage of Croatian population and its island isolates

Journal: European Journal of Human Genetics | Year: 2003

Abstract:

Y chromosome variation in 457 Croatian samples was studied using 16 SNPs/indel and eight STR loci. High frequency of haplogroup I in Croatian populations and the phylogeographic pattern in its background STR diversity over Europe make Adriatic coast one likely source of the recolonization of Europe following the Last Glacial Maximum. The higher frequency of I in the southern island populations is contrasted with higher frequency of group R1a chromosomes in the northern island of Krk and in the mainland. R1a frequency, while low in Greeks and Albanians, is highest in Polish, Ukrainian and Russian populations and could be a sign of the Slavic impact in the Balkan region. Haplogroups J, G and E that can be related to the spread of farming characterize the minor part (12.5%) of the Croatian paternal lineages. In one of the southern island (Hvar) populations, we found a relatively high frequency (14%) of lineages belonging to P*(xM173) cluster, which is unusual for European populations. Interestingly, the same population also harbored mitochondrial haplogroup F that is virtually absent in European populations – indicating a connection with Central Asian populations, possibly the Avars.

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

Y Chromosomal STR Locus DYS385 in Azoospermic and Fertile Men from the Aegean Region of Turkey: Is there any Forensic Relevance?

Journal: Balkan Journal of Medical Genetics | Year: 2008

Abstract:

The DYS385 locus, consisting of two linked short tandem repeat (STR) subloci, is the polymorphic marker on the Y chromosome. The distribution of DYS385 genotypes was studied in 51 fertile and 49 azoospermic male individuals from the Aegean Region of Turkey. Genotype 14-17 was the most frequently observed genotype, and the gene diversity value of the Aegean population (n = 100) was 0.946 in this study. Results of the analyses show that there is a statistically significant difference between azoospermic and fertile males in terms of the DYS385 polymorphism. In addition, the results demonstrate that the DYS385 locus is very useful for human identification in forensic cases and paternity tests in the Aegean Region of Turkey.

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

Y chromosome azoospermia factor region microdeletions and recurrent pregnancy loss

Journal: American Journal of Obstetrics and Gynecology | Year: 2008

Abstract:

This study was undertaken to determine the prevalence of Y-chromosome microdeletions in couples with recurrent pregnancy loss (RPL) as compared with fertile couples.
Study Design Forty-three men from couples with recurrent pregnancy loss, and 43 men from couples with a live birth and no history of miscarriages were recruited from Zekai Tahir Burak Woman Health, Education and Research Hospital. The DNA was tested for the presence of 4 sequence tagged sites (STSs) spanning 4 AZF regions: DYS220 (AZFb), DYS235, DYS236, and DYS237 (AZFd).
Results Seven (7) of the 43 men (16%) from couples with recurrent pregnancy loss had microdeletions in 1 or more of the 4 segments studied, whereas none of the fertile men had any microdeletions (P < .05). Their microdeletions were all found specifically at locus DYS 220 (AZFb).
Conclusion The prevalence of the Y chromosome microdeletion in AZF region was much higher in men from couples with recurrent pregnancy loss than men in fertile couples. This study showed that Y chromosome microdeletion in AZF region may be a possible etiologic factor of recurrent pregnancy loss.

Peoples: - | Places: - | Topics: AZF region and Y chromosome microdeletion | DNA Type: Y-DNA

Y chromosome diversity in a linguistic isolate (Mirandese, NE Portugal)

Journal: American Journal of Human Biology | Year: 2016

Abstract:

Objectives

The purpose of this study was to genetically characterize the male lineages of people who speak Mirandese, an interesting case of a linguistic relict that can still be found in the municipality of Miranda do Douro, NE Portugal. This region lies within the area of the Leonese dialects, which are remnants of the Romance dialects spoken in the Kingdom of Leon currently grouped in the Astur–Leonese linguistic continuum. We intended to disclose affinities with surrounding populations, namely from Spain where the Astur–Leonese is also spoken.

Methods

Eighty-eight unrelated males (58 from Miranda and 30 from Bragança, the broad Portuguese region where Miranda is located) were genotyped with the combined use of 17 Y chromosome short tandem repeats (Y-STRs) and a high resolution Y chromosome single nucleotide polymorphism (Y-SNPs) strategy. Moreover, 236 males from Miranda and neighboring regions, previously classified as R-M269, were also genotyped.

Results

R-P312 was the most frequent haplogroup in the Mirandese, followed by J-12f2.1 and T-M70. The male lineages J-12f2.1 and T-M70 were also well represented, and both were shared with descendants of Sephardic Jews. No signs of diversity reduction were detected.

Conclusions

Mirandese speakers display a Y chromosome gene pool that shows a subtle differentiation from neighboring populations, mainly attributable to the assimilation of lineages ascribed to be of Jewish ancestry. Although not revealing signs of geographic/linguistic isolation, no clear affinities with other Astur–Leonese populations were detected. The results suggest that in Miranda language sharing is not accompanied by significant gene flow between populations from both sides of the political border.

Peoples: Mirandese speakers | Places: Kingdom of Leon, Miranda do Douro, and Portugal | Topics: linguistic relicts | DNA Type: Y-DNA

Y chromosome diversity, human expansion, drift, and cultural evolution

Journal: Proceedings of the National Academy of Sciences | Year: 2009

Abstract:

The relative importance of the roles of adaptation and chance in determining genetic diversity and evolution has received attention in the last 50 years, but our understanding is still incomplete. All statements about the relative effects of evolutionary factors, especially drift, need confirmation by strong demographic observations, some of which are easier to obtain in a species like ours. Earlier quantitative studies on a variety of data have shown that the amount of genetic differentiation in living human populations indicates that the role of positive (or directional) selection is modest. We observe geographic peculiarities with some Y chromosome mutants, most probably due to a drift-related phenomenon called the surfing effect. We also compare the overall genetic diversity in Y chromosome DNA data with that of other chromosomes and their expectations under drift and natural selection, as well as the rate of fall of diversity within populations known as the serial founder effect during the recent ” Out of Africa” expansion of modern humans to the whole world. All these observations are difficult to explain without accepting a major relative role for drift in the course of human expansions. The increasing role of human creativity and the fast diffusion of inventions seem to have favored cultural solutions for many of the problems encountered in the expansion. We suggest that cultural evolution has been subrogating biologic evolution in providing natural selection advantages and reducing our dependence on genetic mutations, especially in the last phase of transition from food collection to food production.

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

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