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Thread: New DNA Papers

  1. #21
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    Yersinia pestis DNA from Skeletal Remains from the 6th Century AD Reveals Insights into Justinianic Plague
    http://www.plospathogens.org/article...l.ppat.1003349


    Plague is a notorious and fatal human disease caused by the bacterium Yersinia pestis that is endemic in many countries around the world. Three of the most devastating pandemics in human history have been associated with plague. The second pandemic originated in central Asia and peaked in Europe between 1348 and 1350 (a period of time known as the Black Death). The third pandemic began in the Yunnan province of China in the mid-1850s and subsequently spread to Africa, the Americas, Australia, Europe, and other parts of Asia. The second and third pandemics are well documented and scientifically proven. However, the first pandemic, which began in the 6th century and is also known as Justinianic Plague, is still a matter of controversy. Recently it has been suggested that Justinian's plague was not caused by Y. pestis. We detected Y. pestis DNA in samples obtained from multiple 6th century skeletons from Germany. This confirms that Justinianic Plague crossed the Alps and affected local populations there, including current day Bavaria. Furthermore, we used DNA fingerprinting approaches to determine Asia as the likely geographic origin for these strains

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     Jean M (05-20-2013)

  3. #22
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    Oscar Lao et al., Clinal distribution of human genomic diversity across the Netherlands despite archaeological evidence for genetic discontinuities in Dutch population history, Investigative Genetics 2013, 4 :9 http://www.investigativegenetics.com...4/1/9/abstract . Full paper free.

    Background

    The presence of a southeast to northwest gradient across Europe in human genetic diversity is a well-established observation and has recently been confirmed by genome-wide single nucleotide polymorphism (SNP) data. This pattern is traditionally explained by major prehistoric human migration events in Palaeolithic and Neolithic times. Here, we investigate whether (similar) spatial patterns in human genomic diversity also occur on a micro-geographic scale within Europe, such as in the Netherlands, and if so, whether these patterns could also be explained by more recent demographic events, such as those that occurred in Dutch population history.

    Methods

    We newly collected data on a total of 999 Dutch individuals sampled at 54 sites across the country at 443,816 autosomal SNPs using the Genome-Wide Human SNP Array 5.0 (Affymetrix). We studied the individual genetic relationships by means of classical multidimensional scaling (MDS) using different genetic distance matrices, spatial ancestry analysis (SPA), and ADMIXTURE software. We further performed dedicated analyses to search for spatial patterns in the genomic variation and conducted simulations (SPLATCHE2) to provide a historical interpretation of the observed spatial patterns.

    Results


    We detected a subtle but clearly noticeable genomic population substructure in the Dutch population, allowing differentiation of a north-eastern, central-western, central-northern and a southern group. Furthermore, we observed a statistically significant southeast to northwest cline in the distribution of genomic diversity across the Netherlands, similar to earlier findings from across Europe. Simulation analyses indicate that this genomic gradient could similarly be caused by ancient as well as by the more recent events in Dutch history.

    Conclusions

    Considering the strong archaeological evidence for genetic discontinuity in the Netherlands, we interpret the observed clinal pattern of genomic diversity as being caused by recent rather than ancient events in Dutch population history. We therefore suggest that future human population genetic studies pay more attention to recent demographic history in interpreting genetic clines. Furthermore, our study demonstrates that genetic population substructure is detectable on a small geographic scale in Europe despite recent demographic events, a finding we consider potentially relevant for future epidemiological and forensic studies.

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     Ian B (05-22-2013)

  5. #23
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    Increasing phylogenetic resolution still informative for Y chromosomal studies on West-European populations

    http://www.fsigenetics.com/article/S...101-4/abstract

    Some quick observations:

    - This is the first paper to test Z-series SNPs. Included are Z18, Z381 and Z195.
    - Different from prior Belgian studies by the same group, L21 (M529 in the paper), L2, L20 and L48 were also tested.
    - Their previously observed U106 North-South gradient is really made up of both L48 and Z381
    - A drastic West-East gradient is observed for L48
    - A less drastic West-East gradient is also observed for L21. However, this gradient almost vanishes in the genealogical dataset and a movement from Northern France during the late 16th century is given as its cause.
    - Z195 was found at 3.3%. DF27 was not tested.
    - P312* still makes up 10.9%. I imagine that this will be heavily reduced once DF19, DF27*, and perhaps some unknown P312* lineages are tested.

    Abstract
    Many Y-chromosomal lineages which are defined in the latest phylogenetic tree of the human Y chromosome by the Y Chromosome Consortium (YCC) in 2008 are distributed in (Western) Europe due to the fact that a large number of phylogeographic studies focus on this area. Therefore, the question arises whether newly discovered polymorphisms on the Y chromosome will still be interesting to study Western Europeans on a population genetic level. To address this question, the West-European region of Flanders (Belgium) was selected as study area since more than 1000 Y chromosomes from this area have previously been genotyped at the highest resolution of the 2008 YCC-tree and coupled to in-depth genealogical data. Based on these data the temporal changes of the population genetic pattern over the last centuries within Flanders were studied and the effects of several past gene flow events were identified. In the present study a set of recently reported novel Y-SNPs were genotyped to further characterize all those Flemish Y chromosomes that belong to haplogroups G, R-M269 and T. Based on this extended Y-SNP set the discrimination power increased drastically as previous large (sub-)haplogroups are now subdivided in several non-marginal groups. Next, the previously observed population structure within Flanders appeared to be the result of different gradients of independent sub-haplogroups. Moreover, for the first time within Flanders a significant East–West gradient was observed in the frequency of two R-M269 lineages, and this gradient is still present when considering the current residence of the DNA donors. Our results thus suggest that an update of the Y-chromosomal tree based on new polymorphisms is still useful to increase the discrimination power based on Y-SNPs and to study population genetic patterns in more detail, even in an already well-studied region such as Western Europe.
    Paternal: R1b-U152 >> L2 >> FGC10543 >> PR5365, Pietro Rocca, b. 1559, Agira, Sicily, Italy
    Maternal: H4a1-T152C!, Maria Coto, b. ~1864, Galicia, Spain
    Mother's Paternal: J1+ FGC4745/FGC4766+ PF5019+, Gerardo Caprio, b. 1879, Caposele, Avellino, Campania, Italy
    Father's Maternal: T2b-C150T, Francisca Santa Cruz, b.1916, Garganchon, Burgos, Spain
    Paternal Great (x3) Grandfather: R1b-U106 >> L48 >> CTS2509, Filippo Ensabella, b.~1836, Agira, Sicily, Italy

  6. #24
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    Kinship and mobility in 11th-Century A.D. Gammertingen, Germany: an interdisciplinary approach, Journal of Archaeological Science, Available online 15 May 2013
    http://www.sciencedirect.com/science...05440313001623

    Excavation in and around a Medieval church in Gammertingen, Germany, revealed the skeletal remains of eight individuals dating to the 10th and 11th century AD. Archaeologists hypothesized that the individuals were the first members of a family later known as the Counts of Gammertingen, a medieval high nobility family. In an interdisciplinary approach, Strontium isotope and ancient DNA techniques were performed in order to test the hypothesis that the church was used as a family burial site and to investigate the provenance of family members. Seven of the eight individuals can be placed in a three-generation genealogy. The isotope analyses establish that the eighth individual had a different birthplace and possibly became a member of the Counts of Gammertingen through marriage. Further, genetic data revealed that distant relatives of the paternal lineage are still present in this area today. Thus, the combined results lead to a very detailed knowledge about a 1000-year old noble family.
    I do not have (or really need) the full paper. There is a family tree built from mtDNA haplogroups T, H* and K.
    Last edited by Jean M; 05-29-2013 at 06:37 PM.

  7. #25
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    Cornelius A. Rietveld et al., GWAS of 126,559 Individuals Identifies Genetic Variants Associated with Educational Attainment, Science, Published Online May 30 2013

    A genome-wide association study of educational attainment was conducted in a discovery sample of 101,069 individuals and a replication sample of 25,490. Three independent SNPs are genome-wide significant (rs9320913, rs11584700, rs4851266), and all three replicate. Estimated effects sizes are small (R2 ≈ 0.02%), approximately 1 month of schooling per allele. A linear polygenic score from all measured SNPs accounts for ≈ 2% of the variance in both educational attainment and cognitive function. Genes in the region of the loci have previously been associated with health, cognitive, and central nervous system phenotypes, and bioinformatics analyses suggest the involvement of the anterior caudate nucleus. These findings provide promising candidate SNPs for follow-up work, and our effect size estimates can anchor power analyses in social-science genetics.

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  9. #26
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    Chuan-Chao Wang and Hui Li, Inferring human history in East Asia from Y chromosomes, Investigative Genetics 2013, 4:11.
    http://www.investigativegenetics.com.../1/11/abstract


    East Asia harbors substantial genetic, physical, cultural and linguistic diversity, but the detailed structures and interrelationships of those aspects remain enigmatic. This question has begun to be addressed by a rapid accumulation of molecular anthropological studies of the populations in and around East Asia, especially by Y chromosome studies. The current Y chromosome evidence suggests multiple early migrations of modern humans from Africa via Southeast Asia to East Asia. After the initial settlements, the northward migrations during the Paleolithic Age shaped the genetic structure in East Asia. Subsequently, recent admixtures between Central Asian immigrants and northern East Asians enlarged the genetic divergence between southern and northern East Asia populations. Cultural practices, such as languages, agriculture, military affairs and social prestige, also have impacts on the genetic patterns in East Asia. Furthermore, application of Y chromosome analyses in the family genealogy studies offers successful showcases of the utility of genetics in studying the ancient history.

  10. #27
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    Gene flow from North Africa contributes to differential human genetic diversity in southern Europe

    http://www.pnas.org/content/early/20...23110.abstract

    Laura R. Botiguéa,, Brenna M. Hennb, Simon Gravelb, Brian K. Maplesb, Christopher R. Gignouxc, Erik Coronad, Gil Atzmonf, Edward Burnsf, Harry Ostrerg, Carlos Floresi, Jaume Bertranpetita, David Comasa, and Carlos D. Bustamanteb, Edited by Mary-Claire King, University of Washington, Seattle, WA, and approved May 1, 2013 (received for review April 5, 2013)

    Abstract
    Human genetic diversity in southern Europe is higher than in other regions of the continent. This difference has been attributed to postglacial expansions, the demic diffusion of agriculture from the Near East, and gene flow from Africa. Using SNP data from 2,099 individuals in 43 populations, we show that estimates of recent shared ancestry between Europe and Africa are substantially increased when gene flow from North Africans, rather than Sub-Saharan Africans, is considered. The gradient of North African ancestry accounts for previous observations of low levels of sharing with Sub-Saharan Africa and is independent of recent gene flow from the Near East. The source of genetic diversity in southern Europe has important biomedical implications; we find that most disease risk alleles from genome-wide association studies follow expected patterns of divergence between Europe and North Africa, with the principal exception of multiple sclerosis.
    Paternal: R1b-U152 >> L2 >> FGC10543 >> PR5365, Pietro Rocca, b. 1559, Agira, Sicily, Italy
    Maternal: H4a1-T152C!, Maria Coto, b. ~1864, Galicia, Spain
    Mother's Paternal: J1+ FGC4745/FGC4766+ PF5019+, Gerardo Caprio, b. 1879, Caposele, Avellino, Campania, Italy
    Father's Maternal: T2b-C150T, Francisca Santa Cruz, b.1916, Garganchon, Burgos, Spain
    Paternal Great (x3) Grandfather: R1b-U106 >> L48 >> CTS2509, Filippo Ensabella, b.~1836, Agira, Sicily, Italy

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  12. #28
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    BTW, Davidski commented on the study in his site and posted this graphic from the paper:



    Graphic 'C' is very similar to the distribution of Y-DNA haplogroup J in Europe.
    Paternal: R1b-U152 >> L2 >> FGC10543 >> PR5365, Pietro Rocca, b. 1559, Agira, Sicily, Italy
    Maternal: H4a1-T152C!, Maria Coto, b. ~1864, Galicia, Spain
    Mother's Paternal: J1+ FGC4745/FGC4766+ PF5019+, Gerardo Caprio, b. 1879, Caposele, Avellino, Campania, Italy
    Father's Maternal: T2b-C150T, Francisca Santa Cruz, b.1916, Garganchon, Burgos, Spain
    Paternal Great (x3) Grandfather: R1b-U106 >> L48 >> CTS2509, Filippo Ensabella, b.~1836, Agira, Sicily, Italy

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  14. #29
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    The Genome of the Netherlands: design, and project goals (Boomsma et al. 2013)

    Their plan is to fully sequence 1000 Dutch samples and provide the data for research. Of interest is...

    "The GoNL data can also be used to address questions related to the
    demographic history of the Dutch as in-depth information on both
    mitochondrial DNA and Y-chromosome will become available."

    http://www.nature.com/ejhg/journal/v...g2013118a.html

    Abstract:
    Within the Netherlands a national network of biobanks has been established (Biobanking and Biomolecular Research
    Infrastructure-Netherlands (BBMRI-NL)) as a national node of the European BBMRI. One of the aims of BBMRI-NL is to enrich
    biobanks with different types of molecular and phenotype data. Here, we describe the Genome of the Netherlands (GoNL), one
    of the projects within BBMRI-NL. GoNL is a whole-genome-sequencing project in a representative sample consisting of 250
    trio-families from all provinces in the Netherlands, which aims to characterize DNA sequence variation in the Dutch population.
    The parent–offspring trios include adult individuals ranging in age from 19 to 87 years (mean¼53 years; SD¼16 years) from
    birth cohorts 1910–1994. Sequencing was done on blood-derived DNA from uncultured cells and accomplished coverage was
    14–15x. The family-based design represents a unique resource to assess the frequency of regional variants, accurately
    reconstruct haplotypes by family-based phasing, characterize short indels and complex structural variants, and establish the
    rate of de novo mutational events. GoNL will also serve as a reference panel for imputation in the available genome-wide
    association studies in Dutch and other cohorts to refine association signals and uncover population-specific variants. GoNL
    will create a catalog of human genetic variation in this sample that is uniquely characterized with respect to micro-geographic
    location and a wide range of phenotypes. The resource will be made available to the research and medical community
    to guide the interpretation of sequencing projects. The present paper summarizes the global characteristics of the project.
    Paternal: R1b-U152 >> L2 >> FGC10543 >> PR5365, Pietro Rocca, b. 1559, Agira, Sicily, Italy
    Maternal: H4a1-T152C!, Maria Coto, b. ~1864, Galicia, Spain
    Mother's Paternal: J1+ FGC4745/FGC4766+ PF5019+, Gerardo Caprio, b. 1879, Caposele, Avellino, Campania, Italy
    Father's Maternal: T2b-C150T, Francisca Santa Cruz, b.1916, Garganchon, Burgos, Spain
    Paternal Great (x3) Grandfather: R1b-U106 >> L48 >> CTS2509, Filippo Ensabella, b.~1836, Agira, Sicily, Italy

  15. #30
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    This has probably already been posted but I just found it available on the net and it only came out last year

    http://books.google.co.uk/books?id=_...ed=0CFcQ6AEwBw

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