Richard Villems - Academia.edu (original) (raw)

Papers by Richard Villems

Numerous studies of mitochondrial and Y chromosomal biallelic markers have resolved major prehist... more Numerous studies of mitochondrial and Y chromosomal biallelic markers have resolved major prehistoric routes of the settling of Europe and proved that the majority of European gene pool has Paleolithic genes. In order to determine the extent of Paleolithic vs. Neolithic impact among Croatian maternal and paternal lineages, we analyzed biallelic markers diagnostic for main Eurasian haplogroups in 457 Croatian Y chromosomes and 721 mitochondrial DNA of inhabitants from various Croatian regions (mainland and four eastern Adriatic islands: north-Krk ; south-Brac, Hvar and Korcula). If Y chromosomal haplogroups: J-12f2, G-201, E-SRY4064 and mitochondrial J and T1 are considered as major Neolithic markers, the majority of females and males in the investigated population are carrying Paleolithic haplogroups. Overall, frequency of mitochondrial Neolithic markers is 11.5% whereas Y chromosomal Neolithic impact is 13.1%. When investigated populations are analyzed separately, the highest mitochondrial Neolithic impact is noticed in mainland population whereas the lowest is on the island of Korcula. For Y chromosomal markers, the lowest Neolithic impact is noticed in mainland population and the highest on the islands of Krk and Korcula. We will discuss these results in the light of evolutionary forces that could cause these differences as well as in the light of archeological data that can prove material evidence of Paleolithic and Neolithic legacy in the investigated area, both mainland and islands.

A battery of biallelic and microsatellite markers was typed in 457 Croatian Y chromosomes. Analys... more A battery of biallelic and microsatellite markers was typed in 457 Croatian Y chromosomes. Analysis of biallelic markers allowed to characterize nine different haplogroups. European-specific haplogroup I was found at the highest frequency (48.4%), followed by haplogroup R1a (24.7%). High frequency of M170 mutation, its microsatellite diversity as well as the finding that its frequency is significantly higher in three southern Adriatic islands compared to the mainland population and the northern island of Krk, makes it likely that the Adriatic coast can be considered as a geographic origin for this mutation. Its higher frequency in the southern islands population is in contrast to higher frequency of group R1a chromosomes in the northern island of Krk and in the mainland population. As Croats belong to a Slavic linguistic family, R1a speaks in favor of possible Slavic genetic impact into their Y-chromosomal pool. Indeed, this haplogroup, while frequently found in Slavic populations (e.g. in Poles, Ukrainians and Russians), is low in Croatian non-Slavic neighbors like Albanians and Greeks. This finding is in concordance with currently favored view that the spread of variants of the European mtDNA and Y chromosome pool is explained rather by geographic proximity than by linguistic affinity. On the other hand, haplogroups E, G, and J that have been suggested by other authors to be related to the spread of farming, encompass a minor part of the Croatian paternal lineages. Their summary frequency (9%) corresponds to that observed among the western European populations – an observation that does not support an assumption that the Adriatic region received a more sizable share of putative Neolithic demic diffusion from the Near East. In sum, clear and meaningful in terms of ethnogenesis pattern and gradients of the distribution of Y chromosome variants in Croatia, uniparentally inherited genetic loci prove their usefulness in understanding of the demographic history of human populations.

Oxford University Press eBooks, May 1, 2012

In the coverage of the genetic pool of Europe, some major cavities were left, hence to fill one o... more In the coverage of the genetic pool of Europe, some major cavities were left, hence to fill one of them, namely the French mtDNA pool we collected 868 samples from twelve different locations of France. Those samples were sequenced for the hypervariable segment I (HVS- I) and then typed for SNPs in the coding region, either by RFLP or 5' nuclease allelic discrimination, in order to assign them to the right haplogroup. Then the mtDNA gene pools of French Basques and Bretons were compared in terms of frequency and composition with relevant neighbouring populations. The French Basques’ mtDNA pool shares some common cardinal features with that of the Spanish Basques, represented in the high prevalence of haplogroup H. However, the French Basques do show a number of distinct features, most notably expressed in the much higher frequency of haplogroups linked with the Neolithic diffusion in Europe. In Brittany, Finiste ; ; re shows closer affinities with Britain and Scandinavia than the...

Russian Journal of Genetics, 2017

European Journal of Human Genetics, 2021

Scientific Reports, 2021

Human Y chromosome haplogroup J1-M267 is a common male lineage in West Asia. One high-frequency r... more Human Y chromosome haplogroup J1-M267 is a common male lineage in West Asia. One high-frequency region—encompassing the Arabian Peninsula, southern Mesopotamia, and the southern Levant—resides ~ 2000 km away from the other one found in the Caucasus. The region between them, although has a lower frequency, nevertheless demonstrates high genetic diversity. Studies associate this haplogroup with the spread of farming from the Fertile Crescent to Europe, the spread of mobile pastoralism in the desert regions of the Arabian Peninsula, the history of the Jews, and the spread of Islam. Here, we study past human male demography in West Asia with 172 high-coverage whole Y chromosome sequences and 889 genotyped samples of haplogroup J1-M267. We show that this haplogroup evolved ~ 20,000 years ago somewhere in northwestern Iran, the Caucasus, the Armenian Highland, and northern Mesopotamia. The major branch—J1a1a1-P58—evolved during the early Holocene ~ 9500 years ago somewhere in the Arabian ...

European Journal of Human Genetics, 2019

Kalmyks, the only Mongolic-speaking population in Europe, live in the southeast of the European P... more Kalmyks, the only Mongolic-speaking population in Europe, live in the southeast of the European Plain, in Russia. They adhere to Buddhism and speak a dialect of the Mongolian language. Historical and linguistic evidence, as well a shared clan names, suggests a common origin with Oirats of western Mongolia; yet, only a limited number of genetic studies have focused on this topic. Here we compare the paternal genetic relationship of Kalmyk clans with ethnographically related groups from Mongolia, Kyrgyzstan and China, within the context of their neighbouring populations. A phylogeny of 37 high-coverage Y-chromosome sequences, together with further genotyping of larger sample sets, reveals that all the Oirat-speaking populations studied here, including Kalmyks, share, as a dominant paternal lineage, Y-chromosomal haplogroup C3c1-M77, which is also present in several geographically distant native Siberian populations. We identify a subset of this clade, C3c1b-F6379, specifically enriche...

Russian Journal of Genetics, 2012

Genetic diversity has been analyzed in 22 ethnic groups of the Caucasus on the basis of data on Y... more Genetic diversity has been analyzed in 22 ethnic groups of the Caucasus on the basis of data on Y-chromosome and mitochondrial DNA (mtDNA) markers, as well as genome-wide data on autosomal single-nucleotide polymorphisms (SNPs). It has been found that the West Asian component is prevailing in all ethnic groups studied except for Nogays. This Near Eastern ancestral component has proved to be characteristic of Caucasian populations and almost entirely absent in their northern neighbors inhabiting the Eastern European Plain. Turkic-speaking populations, except Nogays, did not exhibit an increased proportion of Eastern Eurasian mtDNA or Y-chromosome haplogroups compared to some Abkhaz-Adyghe populations (Adygs and Kabardians). Genome-wide SNP analysis has also shown substantial differences of Nogays from all other Caucasian populations studied. However, the characteristic difference of Nogays from other populations of the Caucasus seems somewhat ambiguous in terms of the R1a1a-M17(M198) and R1b1b1-M73 haplogroups of the Y chromosome. The state of these haplogroups in Turkic-speaking populations of the Caucasus requires further study.

BMC Evolutionary Biology, 2013

BackgroundSakha – an area connecting South and Northeast Siberia – is significant for understandi... more BackgroundSakha – an area connecting South and Northeast Siberia – is significant for understanding the history of peopling of Northeast Eurasia and the Americas. Previous studies have shown a genetic contiguity between Siberia and East Asia and the key role of South Siberia in the colonization of Siberia.ResultsWe report the results of a high-resolution phylogenetic analysis of 701 mtDNAs and 318 Y chromosomes from five native populations of Sakha (Yakuts, Evenks, Evens, Yukaghirs and Dolgans) and of the analysis of more than 500,000 autosomal SNPs of 758 individuals from 55 populations, including 40 previously unpublished samples from Siberia. Phylogenetically terminal clades of East Asian mtDNA haplogroups C and D and Y-chromosome haplogroups N1c, N1b and C3, constituting the core of the gene pool of the native populations from Sakha, connect Sakha and South Siberia. Analysis of autosomal SNP data confirms the genetic continuity between Sakha and South Siberia. Maternal lineages ...

HGM 2002, Human …, 2002

Phylogeography of the non-recombining maternally inherited mitochondrial DNA (mtDNA) and paternal... more Phylogeography of the non-recombining maternally inherited mitochondrial DNA (mtDNA) and paternally inherited Y chromosome have been broadly used to shed light on different aspects of demographic history of human populations. Based on coalescence age calculations, more than 80% of maternal lineages present in extant populations are believed to belong to the Upper Palaeolithic gene pool. With the onset of the Last Glacial Maximum (LGM) ca 20 000 years ago the maternal lineages were compressed into refugia and started to re-expand together with the climate improvement ca 15 000 years ago. In order to investigate possible reflections of those processes in genetic pool of present European populations we have analysed more than 5000 mtDNA samples from different populations of Europe (from Baltic region to western Siberia) and Near East using the sequencing of the first hypervariable segment (HVS-I) of mtDNA control region and combined it with RFLP typing of informative coding region polymorphisms. The phylogenetic networks based on obtained data were further investigated following the phylogeographic analysis of individual lineage clusters (subhaplogroups). Here we will concentrate on the lineages within a major western Eurasian haplogroup U, particularly on its most frequent subclusters U5 and U4. U5 is one of the largest western Eurasian maternal lineage clades, present also in northwestern Africa, in Near and Middle East and in Central Asia. Its coalescence age is calculated as 45 00055 000 years BP. In its highest values U5 is present in some Finno-Ugric speaking populations (about half of Saami maternal lineages). The phylogenetic network for U5 reveals more than ten putative sub-founders, most of which coalescence ages are around 11 00013 000 years BP which is corresponding to a rapid warming of climate after LGM and to the re-occupation of northern Europe by humans. U4 is largely a northeastern-central European variety of mtDNA and a characteristic sample of clinal distribution of maternal lineages in Europe. Its coalescence age is calculated to 16 000 24 000 years BP. U4 is nearly absent in Indo-Iranian speaking populations (Iranians, Ossetes and Kurds) but is frequent in Finno-Ugric speaking populations and among Volga basin Turkic speakers. Although mostly European-specific, its frequency is highest (ca 16 %) among western Siberian people - Khantys. The subcluster U4a is shared by different European populations, but the subcluster U4b is characteristic mostly to Germanic speaking populations and absent in Finno-Ugric, Volga region and western Siberian people. The coalescence age calculations for U4 subclusters reveal different expansion times after LGM in different geographical regions. Following the phylogeographical approach of discussing the mtDNA data we conclude that the present-day distribution of maternal lineages is largely determined by demographic events after the LGM.

The phylogenetic analysis of Y chromosomal haplogroup O2a-M95 was crucial to determine the nested... more The phylogenetic analysis of Y chromosomal haplogroup O2a-M95 was crucial to determine the nested structure of South Asian branches within the larger tree, predominantly present in East and Southeast Asia. However, it had previously been unclear how many founders brought the haplogroup O2a-M95 to South Asia. On the basis of the updated Y chromosomal tree for haplogroup O2a-M95, we analysed 1,437 male samples from South Asia for various downstream markers, carefully selected from the extant phylogenetic tree. With this increased resolution, we were able to identify at least three founders downstream to haplogroup O2a-M95 who are likely to have been associated with the dispersal of Austroasiatic languages to South Asia. The fourth founder was exclusively present amongst Tibeto-Burman speakers of Manipur and Bangladesh. In sum, our new results suggest the arrival of Austroasiatic languages in South Asia during last five thousand years.

SSRN Electronic Journal, 2019

We sequenced genomes from a ~7,000 year old early farmer from Stuttgart in Germany, an ~8,000 yea... more We sequenced genomes from a ~7,000 year old early farmer from Stuttgart in Germany, an ~8,000 year old hunter-gatherer from Luxembourg, and seven ~8,000 year old hunter-gatherers from southern Sweden. We analyzed these data together with other ancient genomes and 2,345 contemporary humans to show that the great majority of present-day Europeans derive from at least three highly differentiated populations: West European Hunter-Gatherers (WHG), who contributed ancestry to all Europeans but not to Near Easterners; Ancient North Eurasians (ANE), who were most closely related to Upper Paleolithic Siberians and contributed to both Europeans and Near Easterners; and Early European Farmers (EEF), who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model these populations' deep relationships and show that EEF had ~44% ancestry from a "Basal Eurasian" lineage that split prior to the diversification of all other non-African lineages.

The Turkic peoples represent a diverse collection of ethnic groups defined by the Turkic language... more The Turkic peoples represent a diverse collection of ethnic groups defined by the Turkic languages. These groups have dispersed across a vast area, including Siberia, Northwest China, Central Asia, East Europe, the Caucasus, Anatolia, the Middle East, and Afghanistan. The origin and early dispersal history of the Turkic peoples is disputed, with candidates for their ancient homeland ranging from the Transcaspian steppe to Manchuria in Northeast Asia. Previous genetic studies have not identified a clear-cut unifying genetic signal for the Turkic peoples, which lends support for language replacement rather than demic diffusion as the model for the Turkic language's expansion. We addressed the genetic origin of 373 individuals from 22 Turkic-speaking populations, representing their current geographic range, by analyzing genome-wide high-density genotype data. Most of the Turkic peoples studied, except those in Central Asia, genetically resembled their geographic neighbors, in agree...