Costas Triantaphyllidis

Tracing European Founder Lineages in the Near Eastern mtDNA Pool

Founder analysis is a method for analysis of nonrecombining DNA sequence data, with the aim of identification and dating of migrations into new territory. The method picks out founder sequence types in potential source populations and dates lineage clusters deriving from them in the settlement zone of interest. Here, using mtDNA, we apply the approach to the colonization of Europe, to estimate the proportion of modern lineages whose ancestors arrived during each major phase of settlement. To estimate the Palaeolithic and Neolithic contributions to European mtDNA diversity more accurately than was previously achievable, we have now extended the Near Eastern, European, and northern-Caucasus databases to 1,234, 2, 804, and 208 samples, respectively. Both back-migration into the source population and recurrent mutation in the source and derived populations represent major obstacles to this approach. We have developed phylogenetic criteria to take account of both these factors, and we suggest a way to account for multiple dispersals of common sequence types. We conclude that (i) there has been substantial back-migration into the Near East, (ii) the majority of extant mtDNA lineages entered Europe in several waves during the Upper Palaeolithic, (iii) there was a founder effect or bottleneck associated with the Last Glacial Maximum, 20,000 years ago, from which derives the largest fraction of surviving lineages, and (iv) the immigrant Neolithic component is likely to comprise less than one-quarter of the mtDNA pool of modern Europeans.

Origin, Diffusion, and Differentiation of Y-Chromosome Haplogroups E and J: Inferences on the Neolithization of Europe and Later Migratory Events in the Mediterranean Area

The phylogeography of Y-chromosome haplogroups E (Hg E) and J (Hg J) was investigated in >2400 subjects from 29 populations, mainly from Europe and the Mediterranean area but also from Africa and Asia. The observed 501 Hg E and 445 Hg J samples were subtyped using 36 binary markers and eight microsatellite loci. Spatial patterns reveal that (1). the two sister clades, J-M267 and J-M172, are distributed differentially within the Near East, North Africa, and Europe; (2). J-M267 was spread by two temporally distinct migratory episodes, the most recent one probably associated with the diffusion of Arab people; (3). E-M81 is typical of Berbers, and its presence in Iberia and Sicily is due to recent gene flow from North Africa; (4). J-M172(xM12) distribution is consistent with a Levantine/Anatolian dispersal route to southeastern Europe and may reflect the spread of Anatolian farmers; and (5). E-M78 (for which microsatellite data suggest an eastern African origin) and, to a lesser extent, J-M12(M102) lineages would trace the subsequent diffusion of people from the southern Balkans to the west. A 7%-22% contribution of Y chromosomes from Greece to southern Italy was estimated by admixture analysis.

Differential Y‐chromosome Anatolian Influences on the Greek and Cretan Neolithic

The earliest Neolithic sites of Europe are located in Crete and mainland Greece. A debate persists concerning whether these farmers originated in neighboring Anatolia and the role of maritime colonization. To address these issues 171 samples were collected from areas near three known early Neolithic settlements in Greece together with 193 samples from Crete. An analysis of Y‐chromosome haplogroups determined that the samples from the Greek Neolithic sites showed strong affinity to Balkan data, while Crete shows affinity with central/Mediterranean Anatolia. Haplogroup J2b‐M12 was frequent in Thessaly and Greek Macedonia while haplogroup J2a‐M410 was scarce. Alternatively, Crete, like Anatolia showed a high frequency of J2a‐M410 and a low frequency of J2b‐M12. This dichotomy parallels archaeobotanical evidence, specifically that while bread wheat (Triticum aestivum) is known from Neolithic Anatolia, Crete and southern Italy; it is absent from earliest Neolithic Greece. The expansion time of YSTR variation for haplogroup E3b1a2‐V13, in the Peloponnese was consistent with an indigenous Mesolithic presence. In turn, two distinctive haplogroups, J2a1h‐M319 and J2a1b1‐M92, have demographic properties consistent with Bronze Age expansions in Crete, arguably from NW/W Anatolia and Syro‐Palestine, while a later mainland (Mycenaean) contribution to Crete is indicated by relative frequencies of V13.

A study of karyotypes and heterochromatic associations in Artemia, with special reference to two N. Greek populations

The chromosomes of three stains of Artemia were studied, a bisexual diploid (A. franciscana, strain GSL), and two parthenogenetic tetraploids from Northern Greece. Routine karyotypes were constructed for the diploid and tetraploid forms, as well as a Giemsa C-banding karyotype of the bisexual form; some data are also presented on the chromosomal C-banding patterns of the parthenogenetic populations. The possible significance of various chromosomal configurations that have been observed, and their relationships to heterochromatin, are discussed.

Genetic differentiation and phylogenetic relationships among Greek Salmo trutta L. (brown trout) populations as revealed by RFLP analysis of PCR amplified mitochondrial DNA segments.

The genetic differentiation and phylogenetic relationships of 13 populations (11 from Greece, one from Albania and one from France) of brown trout (Salmo trutta L.) were investigated at the mtDNA level. RFLP analysis of four segments of mitochondrial DNA (D-loop, cytochrome b and ND-5/6) amplified by PCR was used. Seven of 14 restriction endonucleases were found to detect variability in the ND-5/6 regions, whereas four and two out of 17 and 16 were polymorphic in the D-loop and cytochrome b, respectively. Eleven different haplotypes were observed. The observed interpopulation diversity was very high (mean = 1.65 per cent), whereas the intrapopulation diversity was low in most cases (mean = 0.063 per cent). Five phylogenetic assemblages were identified. The results demonstrate that Greece is one of the regions where brown trout display very high levels of genetic diversity. Most populations were genetically very distinct, possessing private mtDNA genotypes. Therefore, they represent unique gene pools which may warrant individual recognition for conservation and management. The genetic relationships among populations suggested by mtDNA data were not in accordance with allozyme data. This study illustrates the importance of considering the historical biogeography of a species in order to understand its population genetic structure. It also reinforces the view that mtDNA analysis represents a powerful tool to study past and present demographic phenomena.

Genetic Identification and Phylogeny of Three Species of the Genus Trachurus Based on Mitochondrial DNA Analysis

The genetic identification and the phylogenetic relationships of 3 European species of the genus Trachurus (T. trachurus, T. mediterraneus, and T. picturatus) across their geographical distribution, have been investigated by mitochondrial DNA analysis. Both cytochrome b and 16S ribosomal DNA sequence analysis revealed the existence of several species-specific positions that distinguish the 3 studied species. Genetic distances between the species indicated that T. mediterraneus and T. picturatus are more closely related than T. trachurus. Similar topologies have been produced by neighbor-joining, maximum-likelihood, and maximum-parsimony trees, and they were in accordance with previous taxonomic classification. Internucleotide and intranucleotide diversity of T. picturatus was 2 times higher than that of T. mediterraneus and T. trachurus, possibly owing to the low levels of fishing pressure for T. picturatus. This is the first report of the phylogenetic relationships of the 3 Trachurus species and provides a possible scenario of the time of divergence related to the closure of the Gibraltar Straits. In addition, the present results can be used for genetic identification of the 3 species, even from the early stage of eggs, and for detection of commercial fraud.

Genetic divergence and phylogenetic relationships among Salmo trutta L. (brown trout) populations from Greece and other European countries

In order to clarify the genetic structure and the phylogenetic relationships among brown trout (Salmo trutta) populations from Greece and other European countries starch gel electrophoresis was used. The populations come from various rivers from Greece and other European countries, flowing to the Atlantic or to the Mediterranean. Eleven enzymic systems were investigated. These correspond to 26 putative loci. A high degree of genetic polymorphism was found. The percentage of polymorphic loci ranged from 3.8 to 34.6 and the degree of expected heterozygosity from 0.016 to 0.1. F-statistics and clustering analyses indicated the existence of a high degree of differentiation. This differentiation is mainly between the Atlantic and the Mediterranean populations. Furthermore the Mediterranean populations seem to be divided into two groups. One includes the western Mediterranean populations and populations from western Greece and the other north-eastern Greek populations. The latter seem to be related to other Balkan populations and probably to Danubian or Black Sea populations. These results support the idea of two different lineages of Mediterranean brown trout populations, one of which is probably of aboriginal origin.

The coming of the Greeks to Provence and Corsica: Y-chromosome models of archaic Greek colonization of the western Mediterranean

BackgroundThe process of Greek colonization of the central and western Mediterranean during the Archaic and Classical Eras has been understudied from the perspective of population genetics. To investigate the Y chromosomal demography of Greek colonization in the western Mediterranean, Y-chromosome data consisting of 29 YSNPs and 37 YSTRs were compared from 51 subjects from Provence, 58 subjects from Smyrna and 31 subjects whose paternal ancestry derives from Asia Minor Phokaia, the ancestral embarkation port to the 6th century BCE Greek colonies of Massalia (Marseilles) and Alalie (Aleria, Corsica).Results19% of the Phokaian and 12% of the Smyrnian representatives were derived for haplogroup E-V13, characteristic of the Greek and Balkan mainland, while 4% of the Provencal, 4.6% of East Corsican and 1.6% of West Corsican samples were derived for E-V13. An admixture analysis estimated that 17% of the Y-chromosomes of Provence may be attributed to Greek colonization. Using the following putative Neolithic Anatolian lineages: J2a-DYS445 = 6, G2a-M406 and J2a1b1-M92, the data predict a 0% Neolithic contribution to Provence from Anatolia. Estimates of colonial Greek vs. indigenous Celto-Ligurian demography predict a maximum of a 10% Greek contribution, suggesting a Greek male elite-dominant input into the Iron Age Provence population.ConclusionsGiven the origin of viniculture in Provence is ascribed to Massalia, these results suggest that E-V13 may trace the demographic and socio-cultural impact of Greek colonization in Mediterranean Europe, a contribution that appears to be considerably larger than that of a Neolithic pioneer colonization.

No Evidence from Genome-wide Data of a Khazar Origin for the Ashkenazi Jews

Abstract The origin and history of the Ashkenazi Jewish population have long been of great interest, and advances in high-throughput genetic analysis have recently provided a new approach for investigating these topics. We and others have argued on the basis of genome-wide data that the Ashkenazi Jewish population derives its ancestry from a combination of sources tracing to both Europe and the Middle East. It has been claimed, however, through a reanalysis of some of our data, that a large part of the ancestry of the Ashkenazi population originates with the Khazars, a Turkic-speaking group that lived to the north of the Caucasus region ∼1,000 years ago. Because the Khazar population has left no obvious modern descendants that could enable a clear test for a contribution to Ashkenazi Jewish ancestry, the Khazar hypothesis has been difficult to examine using genetics. Furthermore, because only limited genetic data have been available from the Caucasus region, and because these data have been concentrated in populations that are genetically close to populations from the Middle East, the attribution of any signal of Ashkenazi-Caucasus genetic similarity to Khazar ancestry rather than shared ancestral Middle Eastern ancestry has been problematic. Here, through integration of genotypes from newly collected samples with data from several of our past studies, we have assembled the largest data set available to date for assessment of Ashkenazi Jewish genetic origins. This data set contains genome-wide single-nucleotide polymorphisms in 1,774 samples from 106 Jewish and non-Jewish populations that span the possible regions of potential Ashkenazi ancestry: Europe, the Middle East, and the region historically associated with the Khazar Khaganate. The data set includes 261 samples from 15 populations from the Caucasus region and the region directly to its north, samples that have not previously been included alongside Ashkenazi Jewish samples in genomic studies. Employing a variety of standard techniques for the analysis of population-genetic structure, we found that Ashkenazi Jews share the greatest genetic ancestry with other Jewish populations and, among non-Jewish populations, with groups from Europe and the Middle East. No particular similarity of Ashkenazi Jews to populations from the Caucasus is evident, particularly populations that most closely represent the Khazar region. Thus, analysis of Ashkenazi Jews together with a large sample from the region of the Khazar Khaganate corroborates the earlier results that Ashkenazi Jews derive their ancestry primarily from populations of the Middle East and Europe, that they possess considerable shared ancestry with other Jewish populations, and that there is no indication of a significant genetic contribution either from within or from north of the Caucasus region.

Genetic structure and phylogeography of European catfish (Silurus glanis) populations

The genetic structure of Silurus glanis (Europe’s largest freshwater fish species) across most of its natural distribution was investigated using 10 microsatellite loci. The revealed levels of genetic diversity were much higher than previous allozyme and restriction fragment length polymorphism mitochondrial DNA analyses had shown; relative levels of variability among populations were however, in good agreement with the previous studies. Populations from large basins (Volga and Danube rivers) were the most polymorphic, while samples from the smaller Greek rivers, which are more prone to genetic bottleneck, exhibited the lowest levels of genetic diversity. Microsatellite multilocus genotyping permitted the assignment of individual fish to their population of origin with a score as high as 98.3%. Despite the great genetic differentiation of S. glanis populations, no consistent pattern of geographical structuring was revealed, in contrast to previous studies of European freshwater fish species. A model of isolation by distance seems more probable and a hypothesis of recent dispersion from only one glacial refugium is proposed. The discovery of the highest levels of microsatellite and mitochondrial diversity in the Volga sample and the presence of river connections, during the Pleistocene, between this area and all major areas of the present catfish distribution, place this refugium around the Ponto‐Caspian region. Combining these data with those from previous studies, a number of markers are now available to monitor wild and hatchery populations even at the individual level.