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Cuveliers E.L.,Charles University | Volckaert F.A.M.,Charles University | Rijnsdorp A.D.,Institute for Marine Resources and Ecological Studies | Rijnsdorp A.D.,Wageningen University | And 4 more authors.
Molecular Ecology | Year: 2011

Heavy fishing and other anthropogenic influences can have profound impact on a species' resilience to harvesting. Besides the decrease in the census and effective population size, strong declines in mature adults and recruiting individuals may lead to almost irreversible genetic changes in life-history traits. Here, we investigated the evolution of genetic diversity and effective population size in the heavily exploited sole (Solea solea), through the analysis of historical DNA from a collection of 1379 sole otoliths dating back from 1957. Despite documented shifts in life-history traits, neutral genetic diversity inferred from 11 microsatellite markers showed a remarkable stability over a period of 50 years of heavy fishing. Using simulations and corrections for fisheries induced demographic variation, both single-sample estimates and temporal estimates of effective population size (N e) were always higher than 1000, suggesting that despite the severe census size decrease over a 50-year period of harvesting, genetic drift is probably not strong enough to significantly decrease the neutral diversity of this species in the North Sea. However, the inferred ratio of effective population size to the census size (N e/N c) appears very small (10 -5), suggesting that overall only a low proportion of adults contribute to the next generation. The high N e level together with the low N e/N c ratio is probably caused by a combination of an equalized reproductive output of younger cohorts, a decrease in generation time and a large variance in reproductive success typical for marine species. Because strong evolutionary changes in age and size at first maturation have been observed for sole, changes in adaptive genetic variation should be further monitored to detect the evolutionary consequences of human-induced selection. © 2011 Blackwell Publishing Ltd.

Pinceel T.,Catholic University of Leuven | Brendonck L.,Catholic University of Leuven | Larmuseau M.H.D.,Catholic University of Leuven | Larmuseau M.H.D.,Laboratory of Forensic Genetics and Molecular Archaeology | And 3 more authors.
Freshwater Biology | Year: 2013

Over the past 65 my, the Australian continent experienced a pronounced shift from predominantly wet, tropical, conditions to a much drier climate. Little is known, however, about the effect of this important continent-wide event on freshwater organisms and ecosystems. Fairy shrimps (Crustacea; Anostraca) are ancient and specialist inhabitants of temporary and saline aquatic habitats that typically prevail under semiarid conditions. Therefore, they present suitable evolutionary models to study scenarios of historic environmental change and the impact of a drying climate on aquatic ecosystems in particular. Focussing on both macro- and micro-evolution in the fairy shrimp genus Branchinella and using mitochondrial DNA data (16S and COI), we evaluated whether patterns of contemporary genetic variation reflect historic climate change. There is a close match between episodes of Cenozoic climate change and macro-evolutionary diversification in Australian fairy shrimps, presumably mediated by a progressive increase in the abundance and diversity of temporary aquatic habitats on the continent. Micro-evolutionary patterns reflect both range expansion and recent contraction, linked to extreme drying events during the Pleistocene glacial periods. This study effectively illustrates the potential long-term effects of environmental change on the diversity and the evolutionary trajectories of the fauna of temporary waters. Moreover, it demonstrates the importance of adaptation to new environments and non-adaptive processes, such as divergence in isolation, for explaining extant diversity patterns in this particular environment. © 2013 John Wiley & Sons Ltd.

Van Geystelen A.,Laboratory of Forensic Genetics and Molecular Archaeology | Van Geystelen A.,Catholic University of Leuven | Decorte R.,Laboratory of Forensic Genetics and Molecular Archaeology | Decorte R.,Catholic University of Leuven | And 2 more authors.
Forensic Science International: Genetics | Year: 2013

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-chromosomal tree and it accentuates the difficulties to enlarge this tree based on only WGS methods. © 2013 Elsevier Ireland Ltd.

Van Geystelen A.,Laboratory of Forensic Genetics and Molecular Archaeology | Van Geystelen A.,Catholic University of Leuven | Decorte R.,Laboratory of Forensic Genetics and Molecular Archaeology | Decorte R.,Catholic University of Leuven | And 2 more authors.
BMC Genomics | Year: 2013

Background: Due to the rapid progress of next-generation sequencing (NGS) facilities, an explosion of human whole genome data will become available in the coming years. These data can be used to optimize and to increase the resolution of the phylogenetic Y chromosomal tree. Moreover, the exponential growth of known Y chromosomal lineages will require an automatic determination of the phylogenetic position of an individual based on whole genome SNP calling data and an up to date Y chromosomal tree.Results: We present an automated approach, 'AMY-tree', which is able to determine the phylogenetic position of a Y chromosome using a whole genome SNP profile, independently from the NGS platform and SNP calling program, whereby mistakes in the SNP calling or phylogenetic Y chromosomal tree are taken into account. Moreover, AMY-tree indicates ambiguities within the present phylogenetic tree and points out new Y-SNPs which may be phylogenetically relevant. The AMY-tree software package was validated successfully on 118 whole genome SNP profiles of 109 males with different origins. Moreover, support was found for an unknown recurrent mutation, wrong reported mutation conversions and a large amount of new interesting Y-SNPs.Conclusions: Therefore, AMY-tree is a useful tool to determine the Y lineage of a sample based on SNP calling, to identify Y-SNPs with yet unknown phylogenetic position and to optimize the Y chromosomal phylogenetic tree in the future. AMY-tree will not add lineages to the existing phylogenetic tree of the Y-chromosome but it is the first step to analyse whole genome SNP profiles in a phylogenetic framework. © 2013 Van Geystelen et al.; licensee BioMed Central Ltd.

Raeymaekers J.A.M.,Catholic University of Leuven | Raeymaekers J.A.M.,University of Basel | Konijnendijk N.,Catholic University of Leuven | Larmuseau M.H.D.,Catholic University of Leuven | And 4 more authors.
Molecular Ecology | Year: 2014

Genes with major phenotypic effects facilitate quantifying the contribution of genetic vs. plastic effects to adaptive divergence. A classical example is Ectodysplasin (Eda), the major gene controlling lateral plate phenotype in three-spined stickleback. Completely plated marine stickleback populations evolved repeatedly towards low-plated freshwater populations, representing a prime example of parallel evolution by natural selection. However, many populations remain polymorphic for lateral plate number. Possible explanations for this polymorphism include relaxation of selection, disruptive selection or a balance between divergent selection and gene flow. We investigated 15 polymorphic stickleback populations from brackish and freshwater habitats in coastal North-western Europe. At each site, we tracked changes in allele frequency at the Eda gene between subadults in fall, adults in spring and juveniles in summer. Eda genotypes were also compared for body size and reproductive investment. We observed a fitness advantage for the Eda allele for the low morph in freshwater and for the allele for the complete morph in brackish water. Despite these results, the differentiation at the Eda gene was poorly correlated with habitat characteristics. Neutral population structure was the best predictor of spatial variation in lateral plate number, suggestive of a substantial effect of gene flow. A meta-analysis revealed that the signature of selection at Eda was weak compared to similar studies in stickleback. We conclude that a balance between divergent selection and gene flow can maintain stickleback populations polymorphic for lateral plate number and that ecologically relevant genes may not always contribute much to local adaptation, even when targeted by selection. © 2013 John Wiley & Sons Ltd.

Larmuseau M.H.D.,Laboratory of Forensic Genetics and Molecular Archaeology | Larmuseau M.H.D.,Catholic University of Leuven | Vanderheyden N.,Laboratory of Forensic Genetics and Molecular Archaeology | Jacobs M.,Laboratory of Forensic Genetics and Molecular Archaeology | And 4 more authors.
Forensic Science International: Genetics | Year: 2011

One of the future issues in the forensic application of the haploid Y-chromosome (Y-chr) is surveying the distribution of the Y-chr variation on a micro-geographical scale. Studies on such a scale require observing Y-chr variation on a high resolution, high sampling efforts and reliable genealogical data of all DNA-donors. In the current study we optimised this framework by surveying the micro-geographical distribution of the Y-chr variation in the central-western European region named Brabant. The Duchy of Brabant was a historical region in the Low Countries containing three contemporary Belgian provinces and one Dutch province (Noord-Brabant). 477 males from five a priori defined regions within Brabant were selected based on their genealogical ancestry (known pedigree at least before 1800). The Y-haplotypes were determined based on 37 Y-STR loci and the finest possible level of substructuring was defined according to the latest published Y-chr phylogenetic tree. In total, eight Y-haplogroups and 32 different subhaplogroups were observed, whereby 70% of all participants belonged to only four subhaplogroups: R1b1b2a1 (R-U106), R1b1b2a2* (R-P312*), R1b1b2a2g (R-U152) and I1* (I-M253*). Significant micro-geographical differentiation within Brabant was detected between the Dutch (Noord-Brabant) vs. the Flemish regions based on the differences in (sub)haplogroup frequencies but not based on Y-STR variation within the main subhaplogroups. A clear gradient was found with higher frequencies of R1b1b2 (R-M269) chromosomes in the northern vs. southern regions, mainly related to a trend in the frequency of R1b1b2a1 (R-U106). © 2010 Elsevier Ireland Ltd.

Larmuseau M.H.D.,Laboratory of Forensic Genetics and Molecular Archaeology | Larmuseau M.H.D.,Catholic University of Leuven | Vanoverbeke J.,Catholic University of Leuven | Gielis G.,University of Arts | And 4 more authors.
Heredity | Year: 2012

Patrilineal heritable surnames are widely used to select autochthonous participants for studies on small-scale population genetic patterns owing to the unique link between the surname and a genetic marker, the Y-chromosome (Y-chr). Today, the question arises as to whether the surname origin will be informative on top of in-depth genealogical pedigrees. Admixture events that happened in the period after giving heritable surnames but before the start of genealogical records may be informative about the additional value of the surname origin. In this context, an interesting historical event is the demic migration from French-speaking regions in Northern France to the depopulated and Dutch-speaking region Flanders at the end of the sixteenth century. Y-chr subhaplogroups of individuals with a French/Roman surname that could be associated with this migration event were compared with those of a group with autochthonous Flemish surnames. Although these groups could not be differentiated based on in-depth genealogical data, they were significantly genetically different from each other. Moreover, the observed genetic divergence was related to the differences in the distributions of main Y-subhaplogroups between contemporary populations from Northern France and Flanders. Therefore, these results indicate that the surname origin can be an important feature on top of in-depth genealogical results to select autochthonous participants for a regional population genetic study based on Y-chromosomes. © 2012 Macmillan Publishers Limited All rights reserved.

Larmuseau M.H.D.,Laboratory of Forensic Genetics and Molecular Archaeology | Larmuseau M.H.D.,Catholic University of Leuven | Van Geystelen A.,Catholic University of Leuven | Kayser M.,Rotterdam University | And 3 more authors.
Forensic Science International: Genetics | Year: 2015

Currently, several different Y-chromosomal phylogenies and haplogroup nomenclatures are presented in scientific literature and at conferences demonstrating the present diversity in Y-chromosomal phylogenetic trees and Y-SNP sets used within forensic and anthropological research. This situation can be ascribed to the exponential growth of the number of Y-SNPs discovered due to mostly next-generation sequencing (NGS) studies. As Y-SNPs and their respective phylogenetic positions are important in forensics, such as for male lineage characterization and paternal bio-geographic ancestry inference, there is a need for forensic geneticists to know how to deal with these newly identified Y-SNPs and phylogenies, especially since these phylogenies are often created with other aims than to carry out forensic genetic research. Therefore, we give here an overview of four categories of currently used Y-chromosomal phylogenies and the associated Y-SNP sets in scientific research in the current NGS era. We compare these categories based on the construction method, their advantages and disadvantages, the disciplines wherein the phylogenetic tree can be used, and their specific relevance for forensic geneticists. Based on this overview, it is clear that an up-to-date reduced tree with a consensus Y-SNP set and a stable nomenclature will be the most appropriate reference resource for forensic research. Initiatives to reach such an international consensus are therefore highly recommended. © 2014 Elsevier Ireland Ltd. All rights reserved.

Larmuseau M.H.D.,Laboratory of Forensic Genetics and Molecular Archaeology | Larmuseau M.H.D.,Catholic University of Leuven | Van Geystelen A.,Laboratory of Forensic Genetics and Molecular Archaeology | Van Oven M.,Rotterdam University | And 2 more authors.
American Journal of Physical Anthropology | Year: 2013

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. © 2013 Wiley Periodicals, Inc.

Larmuseau M.H.D.,Laboratory of Forensic Genetics and Molecular Archaeology | Larmuseau M.H.D.,Catholic University of Leuven | Vanderheyden N.,Laboratory of Forensic Genetics and Molecular Archaeology | Van Geystelen A.,Catholic University of Leuven | And 2 more authors.
Forensic Science International: Genetics | Year: 2014

The analysis of human short tandem repeats of the Y-chromosome (Y-STRs) provides a powerful tool in forensic cases for male sex identification, male lineage identification and identification of the geographical origin of male lineages. As the commonly used 12 and 17 Y-STR multiplexes do not discriminate between some unrelated males, additional Y-STRs were implemented in the PowerPlex® Y23 System to supplement the existing commercial Y-STR kits. Until today, the forensic value of a (near) 23 versus 17 Y-STR haplotype match between an unknown DNA donor and a certain biological sample in a database is not yet well studied. This will be of huge interest for cases where an autosomal DNA profile yields no match to a DNA database and the database is used for familial searching (male relative(s) of the offender) or for the estimation of the geographical origin of the offender. In order to value (near) 23 Y-STR haplotype matches in a local sample from Western Europe, we selected the region of Flanders (Belgium) due to the already present knowledge on its Y-chromosomal variants. Many Y-chromosomes of this region were previously genotyped with Y-SNPs at a high resolution of the most recently updated Y-chromosomal tree and the deep-rooted genealogy of each DNA donor was already established. By comparing (near) matches of 23 versus 17 Y-STR haplotypes between patrilineal-unrelated males, a substantial lower number of uninformative (near) 23 Y-STR haplotype matches has been observed compared to 17 Y-STR haplotypes. Furthermore, the use of SNP data was informative to discriminate >60% of unrelated males with an (near) identical 17 Y-STR match while SNP data was only necessary to discriminate about 10% of unrelated males with a 23 Y-STR haplotype that differed at only two Y-STRs. This shows the higher value of the Y23 haplotype within familial DNA searching and the estimation of the geographical origin of a DNA donor. Therefore, the use of the PowerPlex® Y23 System instead of the commonly used 12 and 17 Y-STRs by the forensic community is recommended as it will increase the efficiency of Y-STRs in forensic casework. © 2014 Elsevier Ireland Ltd.

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