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Journal Article Archive

The relationship between surname frequency and Y chromosome variation in Spain

Journal: European Journal of Human Genetics | Year: 2016


In most societies, surnames are passed down from fathers to sons, just like the Y chromosome. It follows that, theoretically, men sharing the same surnames would also be expected to share related Y chromosomes. Previous investigations have explored such relationships, but so far, the only detailed studies that have been conducted are on samples from the British Isles. In order to provide additional insights into the correlation between surnames and Y chromosomes, we focused on the Spanish population by analysing Y chromosomes from 2121 male volunteers representing 37 surnames. The results suggest that the degree of coancestry within Spanish surnames is highly dependent on surname frequency, in overall agreement with British but not Irish surname studies. Furthermore, a reanalysis of comparative data for all three populations showed that Irish surnames have much greater and older surname descent clusters than Spanish and British ones, suggesting that Irish surnames may have considerably earlier origins than Spanish or British ones. Overall, despite closer geographical ties between Ireland and Britain, our analysis points to substantial similarities in surname origin and development between Britain and Spain, while possibly hinting at unique demographic or social events shaping Irish surname foundation and development.

Peoples: Spanish | Places: Spain | Topics: Surnames | DNA Type: Y-DNA

The role of complex I genes in MELAS: A novel heteroplasmic mutation 3380G>A in ND1 of mtDNA

Journal: Neuromuscular Disorders | Year: 2008


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

The Role of Selection in the Evolution of Human Mitochondrial Genomes

Journal: Genetics | Year: 2006


High mutation rate in mammalian mitochondrial DNA generates a highly divergent pool of alleles even within species that have dispersed and expanded in size recently. Phylogenetic analysis of 277 human mitochondrial genomes revealed a significant (P < 0.01) excess of rRNA and nonsynonymous base substitutions among hotspots of recurrent mutation. Most hotspots involved transitions from guanine to adenine that, with thymine-to-cytosine transitions, illustrate the asymmetric bias in codon usage at synonymous sites on the heavy-strand DNA. The mitochondrion-encoded tRNAThr varied significantly more than any other tRNA gene. Threonine and valine codons were involved in 259 of the 414 amino acid replacements observed. The ratio of nonsynonymous changes from and to threonine and valine differed significantly (P = 0.003) between populations with neutral (22/58) and populations with significantly negative Tajima's D values (70/76), independent of their geographic location. In contrast to a recent suggestion that the excess of nonsilent mutations is characteristic of Arctic populations, implying their role in cold adaptation, we demonstrate that the surplus of nonsynonymous mutations is a general feature of the young branches of the phylogenetic tree, affecting also those that are found only in Africa. We introduce a new calibration method of the mutation rate of synonymous transitions to estimate the coalescent times of mtDNA haplogroups.

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

The scale and nature of Viking settlement in Ireland from Y-chromosome admixture analysis

Journal: European Journal of Human Genetics | Year: 2006


The Vikings (or Norse) played a prominent role in Irish history but, despite this, their genetic legacy in Ireland, which may provide insights into the nature and scale of their immigration, is largely unexplored. Irish surnames, some of which are thought to have Norse roots, are paternally inherited in a similar manner to Y-chromosomes. The correspondence of Scandinavian patrilineal ancestry in a cohort of Irish men bearing surnames of putative Norse origin was examined using both slow mutating unique event polymorphisms and relatively rapidly changing short tandem repeat Y-chromosome markers. Irish and Scandinavian admixture proportions were explored for both systems using six different admixture estimators, allowing a parallel investigation of the impact of method and marker type in Y-chromosome admixture analysis. Admixture proportion estimates in the putative Norse surname group were highly consistent and detected little trace of Scandinavian ancestry. In addition, there is scant evidence of Scandinavian Y-chromosome introgression in a general Irish population sample. Although conclusions are largely dependent on the accurate identification of Norse surnames, the findings are consistent with a relatively small number of Norse settlers (and descendents) migrating to Ireland during the Viking period (ca. AD 800–1200) suggesting that Norse colonial settlements might have been largely composed of indigenous Irish. This observation adds to previous genetic studies that point to a flexible Viking settlement approach across North Atlantic Europe.

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

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

Journal: Nature | Year: 2016


Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.

Peoples: - | Places: - | Topics: Genome diversity | DNA Type: Autosomal DNA, X-DNA, and Y-DNA

The SNP for ID browser: an online tool for query and display of frequency data from the SNP for ID project

Journal: International journal of legal medicine | Year: 2008


The SNPforID browser is a web-based tool for the query and visualization of the SNP allele frequency data generated by the SNPforID consortium (http://www.snpforid.org/). From this project, validated panels of single nucleotide polymorphisms (SNPs) for a variety of forensic applications have been generated with the browser concentrating on the single-tube identification SNP set comprising 52 markers. A web interface allows the visitor to review the allele frequencies of the studied markers from all the available populations used by SNPforID to validate global SNP variability. The interface has been designed to offer the useful facility of combining populations into appropriate geographic groups for visual comparison of populations individually or amongst user-defined groupings and with equivalent HapMap data.

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

The study of human Y chromosome variation through ancient DNA

Journal: Human Genetics | Year: 2017


High throughput sequencing methods have completely transformed the study of human Y chromosome variation by offering a genome-scale view on genetic variation retrieved from ancient human remains in context of a growing number of high coverage whole Y chromosome sequence data from living populations from across the world. The ancient Y chromosome sequences are providing us the first exciting glimpses into the past variation of male-specific compartment of the genome and the opportunity to evaluate models based on previously made inferences from patterns of genetic variation in living populations. Analyses of the ancient Y chromosome sequences are challenging not only because of issues generally related to ancient DNA work, such as DNA damage-induced mutations and low content of endogenous DNA in most human remains, but also because of specific properties of the Y chromosome, such as its highly repetitive nature and high homology with the X chromosome. Shotgun sequencing of uniquely mapping regions of the Y chromosomes to sufficiently high coverage is still challenging and costly in poorly preserved samples. To increase the coverage of specific target SNPs capture-based methods have been developed and used in recent years to generate Y chromosome sequence data from hundreds of prehistoric skeletal remains. Besides the prospects of testing directly as how much genetic change in a given time period has accompanied changes in material culture the sequencing of ancient Y chromosomes allows us also to better understand the rate at which mutations accumulate and get fixed over time. This review considers genome-scale evidence on ancient Y chromosome diversity that has recently started to accumulate in geographic areas favourable to DNA preservation. More specifically the review focuses on examples of regional continuity and change of the Y chromosome haplogroups in North Eurasia and in the New World.

Peoples: - | Places: - | Topics: ancient Y chromosome diversity and Y-chromosome | DNA Type: Ancient DNA and Y-DNA

The Tatar Descendants of the Golden Horde Mokhshi Ulus Population

Journal: The Russian Journal of Genetic Genealogy (Русская версия) | Year: 2014


This Article is dedicated to the origin of Tatar Mirzas referring to such lineages as the Akchurins, Kashaevs, Kudashevs, Muratovs, Engalychevs, Enikeevs, Isheevs, Sedekhmetevs, Dashkins, Diveevs, Mansyrevs, Syundyukovs, Efaevs, etc. This Tatar Group origin concept is backed up by historical sources, genealogical notes and genetic results. Mokhshi settlement is known to appear in the early 14th century; the first coins minted there refer to 1313. The ruins of the Golden Horde Mokhshi settlement are currently located near the present-day Narovchat village in Penza Region [15, 106]. In Russian Annals this settlement was known under Naruchad’ name. According to V.L. Egorov, Mokhshi was an administrative centre of the ulus (territory, region)
where “the Mordvinian tribes habited”. To the west this ulus comprised
the Tsna, Moksha, and Vad river basins; to the east, it was limited by the
left bank of the Sura river, as well as by the Alatyr’ and Pyana river basins.

Peoples: Akchurins, Dashkins, Diveevs, Efaevs, Engalychevs, Enikeevs, Isheevs, Kashaevs, Kudashevs, Mansyrevs, Muratovs, Sedekhmetevs, Syundyukovs, and Tatar Mirzas | Places: Penza Region | Topics: | DNA Type: Y-DNA

The time and place of European admixture in Ashkenazi Jewish history

Journal: PLoS ONE | Year: 2017


The Ashkenazi Jewish (AJ) population is important in genetics due to its high rate of Mendelian disorders. AJ appeared in Europe in the 10th century, and their ancestry is thought to comprise European (EU) and Middle-Eastern (ME) components. However, both the time and place of admixture are subject to debate. Here, we attempt to characterize the AJ admixture history using a careful application of new and existing methods on a large AJ sample. Our main approach was based on local ancestry inference, in which we first classified each AJ genomic segment as EU or ME, and then compared allele frequencies along the EU segments to those of different EU populations. The contribution of each EU source was also estimated using GLOBETROTTER and haplotype sharing. The time of admixture was inferred based on multiple statistics, including ME segment lengths, the total EU ancestry per chromosome, and the correlation of ancestries along the chromosome. The major source of EU ancestry in AJ was found to be Southern Europe (≈60–80% of EU ancestry), with the rest being likely Eastern European. The inferred admixture time was ≈30 generations ago, but multiple lines of evidence suggest that it represents an average over two or more events, pre- and post-dating the founder event experienced by AJ in late medieval times. The time of the pre-bottleneck admixture event, which was likely Southern European, was estimated to ≈25–50 generations ago.

Peoples: Ashkenazi Jews and Jewish peoples | Places: Europe and Middle East | Topics: admixture | DNA Type: Autosomal DNA

The trans-Saharan slave trade – clues from interpolation analyses and high-resolution characterization of mitochondrial DNA lineages

Journal: BMC Evolutionary Biology | Year: 2010


A proportion of 1/4 to 1/2 of North African female pool is made of typical sub-Saharan lineages, in higher frequencies as geographic proximity to sub-Saharan Africa increases. The Sahara was a strong geographical barrier against gene flow, at least since 5,000 years ago, when desertification affected a larger region, but the Arab trans-Saharan slave trade could have facilitate enormously this migration of lineages. Till now, the genetic consequences of these forced trans-Saharan movements of people have not been ascertained.RESULTS:The distribution of the main L haplogroups in North Africa clearly reflects the known trans-Saharan slave routes: West is dominated by L1b, L2b, L2c, L2d, L3b and L3d; the Center by L3e and some L3f and L3w; the East by L0a, L3h, L3i, L3x and, in common with the Center, L3f and L3w; while, L2a is almost everywhere. Ages for the haplogroups observed in both sides of the Saharan desert testify the recent origin (holocenic) of these haplogroups in sub-Saharan Africa, claiming a recent introduction in North Africa, further strengthened by the no detection of local expansions.CONCLUSIONS:The interpolation analyses and complete sequencing of present mtDNA sub-Saharan lineages observed in North Africa support the genetic impact of recent trans-Saharan migrations, namely the slave trade initiated by the Arab conquest of North Africa in the seventh century. Sub-Saharan people did not leave traces in the North African maternal gene pool for the time of its settlement, some 40,000 years ago.

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

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