Nancy Vanderheyden

Pig Domestication and Human-Mediated Dispersal in Western Eurasia Revealed through Ancient DNA and Geometric Morphometrics

Zooarcheological evidence suggests that pigs were domesticated in Southwest Asia ∼8,500 BC. They then spread across the Middle and Near East and westward into Europe alongside early agriculturalists. European pigs were either domesticated independently or more likely appeared so as a result of admixture between introduced pigs and European wild boar. As a result, European wild boar mtDNA lineages replaced Near Eastern/Anatolian mtDNA signatures in Europe and subsequently replaced indigenous domestic pig lineages in Anatolia. The specific details of these processes, however, remain unknown. To address questions related to early pig domestication, dispersal, and turnover in the Near East, we analyzed ancient mitochondrial DNA and dental geometric morphometric variation in 393 ancient pig specimens representing 48 archeological sites (from the Pre-Pottery Neolithic to the Medieval period) from Armenia, Cyprus, Georgia, Iran, Syria, and Turkey. Our results reveal the first genetic signatures of early domestic pigs in the Near Eastern Neolithic core zone. We also demonstrate that these early pigs differed genetically from those in western Anatolia that were introduced to Europe during the Neolithic expansion. In addition, we present a significantly more refined chronology for the introduction of European domestic pigs into Asia Minor that took place during the Bronze Age, at least 900 years earlier than previously detected. By the 5th century AD, European signatures completely replaced the endemic lineages possibly coinciding with the widespread demographic and societal changes that occurred during the Anatolian Bronze and Iron Ages.

Low historical rates of cuckoldry in a Western European human population traced by Y-chromosome and genealogical data

Recent evidence suggests that seeking out extra-pair paternity (EPP) can be a viable alternative reproductive strategy for both males and females in many pair-bonded species, including humans. Accurate data on EPP rates in humans, however, are scant and mostly restricted to extant populations. Here, we provide the first large-scale, unbiased genetic study of historical EPP rates in a Western European human population based on combining Y-chromosomal data to infer genetic patrilineages with genealogical and surname data, which reflect known historical presumed paternity. Using two independent methods, we estimate that over the last few centuries, EPP rates in Flanders (Belgium) were only around 1–2% per generation. This figure is substantially lower than the 8–30% per generation reported in some behavioural studies on historical EPP rates, but comparable with the rates reported by other genetic studies of contemporary Western European populations. These results suggest that human EPP rates have not changed substantially during the last 400 years in Flanders and imply that legal genealogies rarely differ from the biological ones. This result has significant implications for a diverse set of fields, including human population genetics, historical demography, forensic science and human sociobiology.

Micro-geographic distribution of Y-chromosomal variation in the central-western European region Brabant

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).

In the name of the migrant father—Analysis of surname origins identifies genetic admixture events undetectable from genealogical records

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.

Temporal differentiation across a West-European Y-chromosomal cline: genealogy as a tool in human population genetics

The pattern of population genetic variation and allele frequencies within a species are unstable and are changing over time according to different evolutionary factors. For humans, it is possible to combine detailed patrilineal genealogical records with deep Y-chromosome (Y-chr) genotyping to disentangle signals of historical population genetic structures because of the exponential increase in genetic genealogical data. To test this approach, we studied the temporal pattern of the ‘autochthonous’ micro-geographical genetic structure in the region of Brabant in Belgium and the Netherlands (Northwest Europe). Genealogical data of 881 individuals from Northwest Europe were collected, from which 634 family trees showed a residence within Brabant for at least one generation. The Y-chr genetic variation of the 634 participants was investigated using 110 Y-SNPs and 38 Y-STRs and linked to particular locations within Brabant on specific time periods based on genealogical records. Significant temporal variation in the Y-chr distribution was detected through a north–south gradient in the frequencies distribution of sub-haplogroup R1b1b2a1 (R-U106), next to an opposite trend for R1b1b2a2g (R-U152). The gradient on R-U106 faded in time and even became totally invisible during the Industrial Revolution in the first half of the nineteenth century. Therefore, genealogical data for at least 200 years are required to study small-scale ‘autochthonous’ population structure in Western Europe.

Pitfalls in the analysis of mitochondrial DNA from ancient specimens and the consequences for forensic DNA analysis: the historical case of the putative heart of Louis XVII

Abstract Amplification of mtDNA D-loop fragments with a length of 200 bp or more from ancient and even from fairly recent biological samples, can lead to erroneous results. This was clearly illustrated in our investigation of the putative heart of Louis XVII. By selecting different sets of primers which amplified shorter fragments of mtDNA (length 109 bp–201 bp), authentic polymorphisms could be visualised which remained undetected with the more classical primers for fragment sizes > 210 bp. Here we have extended those findings to other biological materials. A competitive PCR assay for quantitation of the amount of mtDNA for different fragment lengths, using a 10 bp deletion construct, was applied to ancient material and on a set of hairs of various ages of sampling (1966 up to the present). The results showed that DNA degradation started a few years after sampling. In the DNA extracts of the older hair shafts (1983–1995), the proportion of the number of short fragments to the number of long fragments is on average 4 in contrast to the most recent hair shafts. The numbers of amplifiable mtDNA copies for the hairs from 1975 and older were too small to show a clear difference. Use of long PCR fragments in such cases can yield misleading results. Use of short PCR fragments for the analysis of mtDNA from shed hair, in combination with a competitive PCR assay to determine the state of degradation, should improve the reliability of forensic mtDNA analysis considerably.

Recent radiation within Y-chromosomal haplogroup R-M269 resulted in high Y-STR haplotype resemblance.

Y‐chromosomal short tandem repeats (Y‐STRs) are often used in addition to Y‐chromosomal single‐nucleotide polymorphisms (Y‐SNP) to detect subtle patterns in a population genetic structure. There are, however, indications for Y‐STR haplotype resemblance across different subhaplogroups within haplogroup R1b1b2 (R‐M269) which may lead to erosion in the observation of the population genetic pattern. Hence the question arises whether Y‐STR haplotypes are still informative beyond high‐resolution Y‐SNP genotyping for population genetic studies. To address this question, we genotyped the Y chromosomes of more than 1000 males originating from the West‐European regions of Flanders (Belgium), North‐Brabant and Limburg (the Netherlands) at the highest resolution of the current Y‐SNP tree together with 38 commonly used Y‐STRs. We observed high resemblance of Y‐STR haplotypes between males belonging to different subhaplogroups of haplogroup R‐M269. Several subhaplogroups within R‐M269 could not be distinguished from each other based on differences in Y‐STR haplotype variation. The most likely hypothesis to explain this similarity of Y‐STR haplotypes within the population of R‐M269 members is a recent radiation where various subhaplogroups originated within a relatively short time period. We conclude that high‐resolution Y‐SNP typing rather than Y‐STR typing might be more useful to study population genetic patterns in (Western) Europe.

Deep Into the Roots of the Libyan Tuareg: A Genetic Survey of Their Paternal Heritage.

Recent genetic studies of the Tuareg have begun to uncover the origin of this semi-nomadic northwest African people and their relationship with African populations. For centuries they were caravan traders plying the trade routes between the Mediterranean coast and south-Saharan Africa. Their origin most likely coincides with the fall of the Garamantes who inhabited the Fezzan (Libya) between the 1st millennium BC and the 5th century AD. In this study we report novel data on the Y-chromosome variation in the Libyan Tuareg from Al Awaynat and Tahala, two villages in Fezzan, whose maternal genetic pool was previously characterized. High-resolution investigation of 37 Y-chromosome STR loci and analysis of 35 bi-allelic markers in 47 individuals revealed a predominant northwest African component (E-M81, haplogroup E1b1b1b) which likely originated in the second half of the Holocene in the same ancestral population that contributed to the maternal pool of the Libyan Tuareg. A significant paternal contribution from south-Saharan Africa (E-U175, haplogroup E1b1a8) was also detected, which may likely be due to recent secondary introduction, possibly through slavery practices or fusion between different tribal groups. The difference in haplogroup composition between the villages of Al Awaynat and Tahala suggests that founder effects and drift played a significant role in shaping the genetic pool of the Libyan Tuareg.

Identification and sequence analysis of discordant phenotypes between AmpFlSTR SGM Plus™ and PowerPlex® 16

During duplicate analysis of buccal swabs from 1,377 individuals with 2 commercial short tandem repeat (STR) kits, we observed 8 discordant phenotypes with SGM Plus™ (SGM, second generation multiplex) for the STRs THO1 (2), vWA (4) and D18S51 (2), and 1 discrepancy with PowerPlex® 16 for D18S51. One individual even showed two discrepancies (vWA and THO1) for SGM Plus™. In each case, the difference observed was due to the non-amplification or allele dropout of the second allele in a heterozygous genotype. Sequence analysis revealed each time the presence of a mutation that probably coincided with the primer-binding site. Primer-binding site mutations for vWA and D18S51 have been reported previously, while the mutation for THO1 (C-to-T substitution at position 1286 of GenBank sequence D00269) is reported here for the first time. While the frequency of these silent alleles remains low (0.58% in our study), it is suggested that appropriate measures should be taken for database comparisons and that allelic dropout should be further investigated by sequence analysis and be reported to the forensic community.

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

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.