Genetic Genealogy Comes of Age: Perspectives on the Use of Deep-Rooted Pedigrees in Human Population Genetics.

UZ Leuven, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium
American Journal of Physical Anthropology (Impact Factor: 2.38). 04/2013; 150(4). DOI: 10.1002/ajpa.22233
Source: PubMed


In this article, we promote the implementation of extensive genealogical data in population genetic studies. Genealogical records can provide valuable information on the origin of DNA donors in a population genetic study, going beyond the commonly collected data such as residence, birthplace, language, and self-reported ethnicity. Recent studies demonstrated that extended genealogical data added to surname analysis can be crucial to detect signals of (past) population stratification and to interpret the population structure in a more objective manner. Moreover, when in-depth pedigree data are combined with haploid markers, it is even possible to disentangle signals of temporal differentiation within a population genetic structure during the last centuries. Obtaining genealogical data for all DNA donors in a population genetic study is a labor-intensive task but the vastly growing (genetic) genealogical databases, due to the broad interest of the public, are making this job more time-efficient if there is a guarantee for sufficient data quality. At the end, we discuss the advantages and pitfalls of using genealogy within sampling campaigns and we provide guidelines for future population genetic studies. Am J Phys Anthropol, 2013. © 2013 Wiley Periodicals, Inc.

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Available from: Maarten H D Larmuseau, Oct 02, 2015
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    • "Extensive genealogical data, on the other hand, are rare and their collection is considerably time-consuming. A small but increasing number of studies has shown that surname-and pedigree-based samplings can reveal otherwise hidden genetic structures (Larmuseau et al., 2013 and references therein). As recently observed (Boattini et al., 2013), the genetic history of Italy is particularly complicated in comparison with other European countries. "
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    ABSTRACT: Social and cultural factors had a critical role in determining the genetic structure of Europe. Therefore, socially stratified populations may help to focus on specific episodes of European demographic history. In this study, we use uniparental markers to analyse the genetic structure of Partecipanza in San Giovanni in Persiceto (Northern Italy), a peculiar institution whose origins date back to the Middle Ages and whose members form the patrilineal descent of a group of founder families. From a maternal point of view (mtDNA), Partecipanza is genetically homogeneous with the rest of the population. However, we observed a significant differentiation for Y-chromosomes. In addition, by comparing 17 Y-STR profiles with deep-rooted paternal pedigrees, we estimated a Y-STR mutation rate equal to 3.90 * 10(-3) mutations per STR per generation and an average generation duration time of 33.38 years. When we used these values for tentative dating, we estimated 1300-600 years ago for the origins of the Partecipanza. These results, together with a peculiar Y-chromosomal composition and historical evidence, suggest that Germanic populations (Lombards in particular) settled in the area during the Migration Period (400-800 AD, approximately) and may have had an important role in the foundation of this community.Heredity advance online publication, 10 September 2014; doi:10.1038/hdy.2014.77.
    Heredity 09/2014; 114(2). DOI:10.1038/hdy.2014.77 · 3.81 Impact Factor
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    • "To have a representative East–West range for Flanders, the region 'Belgian Brabant' was defined as the sum of the regions Antwerp and Vlaams-Waals Brabant. For GD an ideal autochthonous sample of the population needs to fulfill several extra criteria according to the recommendations for sampling on micro-geographical scale defined in Larmuseau et al. [15]. First, pairs of DNA-donors with a common documented ancestor in paternal lineage but with a different Y-chromosomal sub-haplogroup or Y-STR-haplotypes with more than six differences (out of 38 Y-STRs) were excluded from the dataset. "
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    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.
    Forensic Science International: Genetics 05/2013; DOI:10.1016/j.fsigen.2013.04.002 · 4.60 Impact Factor
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    ABSTRACT: The Y-chromosomal phylogenetic tree has a wide variety of important forensic applications and therefore it needs to be state-of-the-art. Nevertheless, since the last ‘official’ published tree many publications reported additional Y-chromosomal lineages and other phylogenetic topologies. Therefore, it is difficult for forensic scientists to interpret those reports and use an up-to-date tree and corresponding nomenclature in their daily work. Whole genome sequencing (WGS) data is useful to verify and optimise the current phylogenetic tree for haploid markers. The AMY-tree software is the first open access program which analyses WGS data for Y-chromosomal phylogenetic applications. Here, all published information is collected in a phylogenetic tree and the correctness of this tree is checked based on the first large analysis of 747 WGS samples with AMY-tree. The obtained result is one phylogenetic tree with all peer-reviewed reported Y-SNPs without the observed recurrent and ambiguous mutations. Nevertheless, the results showed that currently only the genomes of a limited set of Y-chromosomal (sub-)haplogroups is available and that many newly reported Y-SNPs based on WGS projects are false positives, even with high sequencing coverage methods. This study demonstrates the usefulness of AMY-tree in the process of checking the quality of the present Y-hromosomal tree and it accentuates the difficulties to enlarge this tree based on only WGS methods.
    Forensic Science International: Genetics 04/2013; DOI:10.1016/j.fsigen.2013.03.010 · 4.60 Impact Factor
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