Clinal distribution of human genomic diversity across the Netherlands despite archaeological evidence for genetic discontinuities in Dutch population history

Abstract

BackgroundThe 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.MethodsWe 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.ResultsWe 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.ConclusionsConsidering 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.

High Y-chromosomal diversity and low relatedness between paternal lineages on a communal scale in the Western European Low Countries during the surname establishment

“…The observed clinal distribution of the Y-chromosomal diversity despite archaeological and historical evidence for genetic discontinuities in Western Europe suggests that future human population genetic studies-especially on a micro-geographic scale-always have to pay attention to recent demographic history in interpreting genetic clines in the light of prehistoric events. This is a conclusion which was already made based on the genetic population structure in the Netherlands by genome-wide analyses (Lao et al, 2013).…”

Simultaneous Analysis of Hundreds of Y-Chromosomal SNPs for High-Resolution Paternal Lineage Classification using Targeted Semiconductor Sequencing

“…To further exemplify the potential of the newly developed method to resolve broad haplogroups, 21 samples from Dutch European individuals described elsewhere [Lao et al., ] and all belonging to the common haplogroup R1b1a2 (R‐M269) were typed with our tool. These 21 R1b1a2 samples were resolved into 11 different R1b1a2 subhaplogroups or unique paternal lineages (Table ).…”

“…If more samples will be typed with our tool in the future, more markers may prove to be recurrent, which could be valuable information for future marker ascertainment and is not likely to be observed with routinely used Y-SNP detection tools employing small Y-SNP panels. To further exemplify the potential of the newly developed method to resolve broad haplogroups, 21 samples from Dutch European individuals described elsewhere [Lao et al, 2013] and all belonging to the common haplogroup R1b1a2 (R-M269) were typed with our tool. These 21 R1b1a2 samples were resolved into 11 different R1b1a2 subhaplogroups or unique paternal lineages (Table 3).…”

“…Subsequently, the performance of the tool was demonstrated on a geographically diverse panel of DNA samples. In order to cover all major branches of the Y tree, we ascertained and used 21 DNA samples based on Y‐haplogroup information we previously obtained with other Y‐SNP tools [van Oven et al., ]; these 21 samples came from four different resources: the commercially available ECACC panel (http://www.phe-culturecollections.org.uk/products/dna/ethnicdna.jsp), individuals from the Netherlands [Lao et al., ], volunteers with informed consent from the department, and samples from Papua New Guinea [Kayser et al., ]. For sensitivity testing, three samples with Y chromosomes that originated from three continents, namely Europe (haplogroup R), East Asia (haplogroup O), and sub‐Saharan Africa (haplogroup E), were used.…”

The black legend on the Spanish presence in the low countries: Verifying shared beliefs on genetic ancestry

“…The individuals in the Low Countries can be placed exactly between the genomes from autochthonous individuals of France, Germany, Denmark, and the UK when looking at two‐dimensional summaries of genetic variation in Europeans (Lao et al, ; Novembre et al, ). Also more in‐depth genomic analyses show a clear North‐South cline within the Netherlands, which is part of the much broader cline over the European continent in accordance to their geographical position (Abdellaoui et al, ; Francioli et al, ; Lao et al, ). Moreover, no admixture history between both populations is yet inferred by genomic data and appropriate statistical methods to date (Hellenthal et al, ).…”