Revealing the Genetic Impact of the Ottoman Occupation on Ethnic Groups of East-Central Europe and on the Roma Population of the Area

Founder lineages in the Iberian Roma mitogenomes recapitulate the Roma diaspora and show the effects of demographic bottlenecks

The Roma are the largest ethnic minority in Europe. With a Northwestern Indian origin around ~ 1.5 kya, they travelled throughout West Asia until their arrival in Europe around the eleventh century CE. Their diaspora through Europe is characterized by population bottlenecks and founder events which have contributed to their present day genetic and cultural diversity. In our study, we focus on the effects of founder effects in the mitochondrial DNA (mtDNA) pool of Iberian Roma by producing and analyzing 144 novel whole mtDNA sequences of Iberian Roma. Over 60% of their mtDNA pool is composed by founder lineages of South Asian origin or acquired by gene flow during their diaspora in the Middle East or locally in Europe in Europe. The TMRCA of these lineages predates the historical record of the Roma arrival in Spain. The abundance of founder lineages is in contrast with ~ 0.7% of autochthonous founder lineages present in the non-Roma Iberian population. Within those founder lineages, we found a substantial amount of South Asian M5a1b1a1 haplotypes and high frequencies of West Eurasian founder lineages (U3b1c, J2b1c, J1c1b, J1b3a, H88, among others), which we characterized phylogenetically and put in phylogeographical context. Besides, we found no evidence of genetic substructure of Roma within the Iberian Peninsula. These results show the magnitude of founder effects in the Iberian Roma and further explain the Roma history and genetic diversity from a matrilineal point of view.

Why do we pick similar mates, or do we?

Humans often mate with those resembling themselves, a phenomenon described as positive assortative mating (PAM). The causes of this attract broad interest, but there is little agreement on the topic. This may be because empirical studies and reviews sometimes focus on just a few explanations, often based on disciplinary conventions. This review presents an interdisciplinary conceptual framework on the causes of PAM in humans, drawing on human and non-human biology, the social sciences, and the humanities. Viewing causality holistically, we first discuss the proximate causes (i.e. the 'how') of PAM, considering three mechanisms: stratification, convergence and mate choice. We also outline methods to control for confounders when studying mate choice. We then discuss ultimate explanations (i.e. 'the why') for PAM, including adaptive and non-adaptive processes. We conclude by suggesting a focus on interdisciplinarity in future research.

The genetic structure of the Turkish population reveals high levels of variation and admixture

The construction of population-based variomes has contributed substantially to our understanding of the genetic basis of human inherited disease. Here, we investigated the genetic structure of Turkey from 3,362 unrelated subjects whose whole exomes (n = 2,589) or whole genomes (n = 773) were sequenced to generate a Turkish (TR) Variome that should serve to facilitate disease gene discovery in Turkey. Consistent with the history of present-day Turkey as a crossroads between Europe and Asia, we found extensive admixture between Balkan, Caucasus, Middle Eastern, and European populations with a closer genetic relationship of the TR population to Europeans than hitherto appreciated. We determined that 50% of TR individuals had high inbreeding coefficients (≥0.0156) with runs of homozygosity longer than 4 Mb being found exclusively in the TR population when compared to 1000 Genomes Project populations. We also found that 28% of exome and 49% of genome variants in the very rare range (allele frequency < 0.005) are unique to the modern TR population. We annotated these variants based on their functional consequences to establish a TR Variome containing alleles of potential medical relevance, a repository of homozygous loss-of-function variants and a TR reference panel for genotype imputation using high-quality haplotypes, to facilitate genome-wide association studies. In addition to providing information on the genetic structure of the modern TR population, these data provide an invaluable resource for future studies to identify variants that are associated with specific phenotypes as well as establishing the phenotypic consequences of mutations in specific genes.

Evaluation of the Ion AmpliSeq™ PhenoTrivium Panel: MPS-Based Assay for Ancestry and Phenotype Predictions Challenged by Casework Samples

As the field of forensic DNA analysis has started to transition from genetics to genomics, new methods to aid in crime scene investigations have arisen. The development of informative single nucleotide polymorphism (SNP) markers has led the forensic community to question if DNA can be a reliable "eye-witness" and whether the data it provides can shed light on unknown perpetrators. We have developed an assay called the Ion AmpliSeq™ PhenoTrivium Panel, which combines three groups of markers: 41 phenotype- and 163 ancestry-informative autosomal SNPs together with 120 lineage-specific Y-SNPs. Here, we report the results of testing the assay's sensitivity and the predictions obtained for known reference samples. Moreover, we present the outcome of a blind study performed on real casework samples in order to understand the value and reliability of the information that would be provided to police investigators. Furthermore, we evaluated the accuracy of admixture prediction in Converge™ Software. The results show the panel to be a robust and sensitive assay which can be used to analyze casework samples. We conclude that the combination of the obtained predictions of phenotype, biogeographical ancestry, and male lineage can serve as a potential lead in challenging police investigations such as cold cases or cases with no suspect.

Recent Common Origin, Reduced Population Size, and Marked Admixture Have Shaped European Roma Genomes

The Roma Diaspora-traditionally known as Gypsies-remains among the least explored population migratory events in historical times. It involved the migration of Roma ancestors out-of-India through the plateaus of Western Asia ultimately reaching Europe. The demographic effects of the Diaspora-bottlenecks, endogamy, and gene flow-might have left marked molecular traces in the Roma genomes. Here, we analyze the whole-genome sequence of 46 Roma individuals pertaining to four migrant groups in six European countries. Our analyses revealed a strong, early founder effect followed by a drastic reduction of ∼44% in effective population size. The Roma common ancestors split from the Punjabi population, from Northwest India, some generations before the Diaspora started, <2,000 years ago. The initial bottleneck and subsequent endogamy are revealed by the occurrence of extensive runs of homozygosity and identity-by-descent segments in all Roma populations. Furthermore, we provide evidence of gene flow from Armenian and Anatolian groups in present-day Roma, although the primary contribution to Roma gene pool comes from non-Roma Europeans, which accounts for >50% of their genomes. The linguistic and historical differentiation of Roma in migrant groups is confirmed by the differential proportion, but not a differential source, of European admixture in the Roma groups, which shows a westward cline. In the present study, we found that despite the strong admixture Roma had in their diaspora, the signature of the initial bottleneck and the subsequent endogamy is still present in Roma genomes.

The shaping of immunological responses through natural selection after the Roma Diaspora

The Roma people are the largest transnational ethnic minority in Europe and can be considered the last human migration of South Asian origin into the continent. They left Northwest India approximately 1,000 years ago, reaching the Balkan Peninsula around the twelfth century and Romania in the fourteenth century. Here, we analyze whole-genome sequencing data of 40 Roma and 40 non-Roma individuals from Romania. We performed a genome-wide scan of selection comparing Roma, their local host population, and a Northwestern Indian population, to identify the selective pressures faced by the Roma mainly after they settled in Europe. We identify under recent selection several pathways implicated in immune responses, among them cellular metabolism pathways known to be rewired after immune stimulation. We validated the interaction between PIK3-mTOR-HIF-1α and cytokine response influenced by bacterial and fungal infections. Our results point to a significant role of these pathways for host defense against the most prevalent pathogens in Europe during the last millennium.

Investigating the genetic characteristics of the Csangos, a traditionally Hungarian speaking ethnic group residing in Romania

Csango people are an East-Central European ethnographic group living mostly in the historical region of Moldavia, Romania. Their traditional language, the Csango is an old Hungarian dialect, which is a severely endangered language due to language shift. Their origin is still disputed among experts and there are many hypotheses since the 19th century. Previous genetic studies found connection with ethnic groups living in Hungary and provided evidence which might support their Hungarian origin. Another study found Inner Asian Altaic ancestry in their genetic makeup. The goal of this study was to analyze the genetic characteristics of the Csango people by comparing their genetic characteristics to contemporary Eurasian populations based on genome-wide autosomal marker data. Our findings suggest that genetic affinity of Csangos to Hungarians is more significant than to Romanians. They also have a detectable connection with Central-Asian and Siberian Turkic ethnic groups. Besides the presumable Middle Eastern/Central-Asian Turkic ancestry, Csangos show ~4% Turkic ancestry from Central Asia/Siberia, which makes them unique in comparison to all other East-Central European populations investigated in this study. The admixture that resulted in this Turkic ancestry could have occurred 30-40 generations ago, which date interval corresponds to Hungarian historical events regarding their migration and the conquest of the Carpathian basin.

Perceived attractiveness of Czech faces across 10 cultures: Associations with sexual shape dimorphism, averageness, fluctuating asymmetry, and eye color

Research on the perception of faces typically assumes that there are some universal values of attractiveness which are shared across individuals and cultures. The perception of attractiveness may, however, vary across cultures due to local differences in both facial morphology and standards of beauty. To examine cross-cultural consensus in the ratings of attractiveness, we presented a set of 120 non-manipulated photographs of Czech faces to ten samples of raters from both European (Czech Republic, Estonia, Sweden, Romania, Turkey, Portugal) and non-European countries (Brazil, India, Cameroon, Namibia). We examined the relative contribution of three facial markers (sexual shape dimorphism, averageness, fluctuating asymmetry) to the perception of attractiveness as well as the possible influence of eye color, which is a locally specific trait. In general, we found that both male and female faces which were closer to the average and more feminine in shape were regarded as more attractive, while fluctuating asymmetry had no effect. Despite a high cross-cultural consensus on attractiveness standards, significant differences in the perception of attractiveness seem to be related to the level of socio-economic development (as measured by the Human Development Index, HDI). Attractiveness ratings by raters from low-HDI countries (India, Cameroon, Namibia) converged less with ratings from Czech Republic than ratings from high-HDI countries (European countries and Brazil). With respect to eye color, some local patterns emerged which we discuss as a consequence of negative frequency-dependent selection.