Discordant patterns of mtDNA and ethno-linguistic variation in 14 Iranian Ethnic groups.

BACKGROUND/AIMS: Present-day Iran has long represented a natural hub for the expansion of human genes and cultures. That being so, the overlapping of prehistoric and more recent demographic events interacting at different time scales with geographical and cultural barriers has yielded a tangled patchwork of anthropological types within this narrow area. This study aims to comprehensively evaluate this ethnic mosaic by depicting a fine-grained picture of the Iranian mitochondrial landscape. METHODS: mtDNA variability at both HVS-I and coding regions was surveyed in 718 unrelated individuals belonging to 14 Iranian ethnic groups characterized by different languages, religions and patterns of subsistence. RESULTS: A discordant pattern of high ethno-linguistic and low mtDNA heterogeneity was observed for the whole examined Iranian sample. Geographical factors and cultural/linguistic differences actually represented barriers to matrilineal gene flow only for the Baloch, Lur from Yasouj, Zoroastrian and Jewish groups, for which unusual reduced levels of mtDNA variability and high inter-population distances were found. CONCLUSION: Deep rooting genealogies and endogamy in a few of the examined ethnic groups might have preserved ancestral lineages that can be representative of Proto-Indo-Iranian or prehistoric mitochondrial profiles which survived relatively recent external contributions to the Iranian gene pool.

Molecular phylogeography of the asp viper Vipera aspis (Linnaeus, 1758) in Italy: evidence for introgressive hybridization and mitochondrial DNA capture.

Owing to its temperature dependence and low vagility, the asp viper (Vipera aspis) is an interesting model species to study the effects of Pleistocene climatic fluctuations on vertebrate genomes. We genotyped 102 specimens from the whole Italian distribution range at three mitochondrial DNA regions (2278 characters, total) and six microsatellite DNA loci (Short Tandem Repeats, STR). The molecular phylogeny was constructed according to Bayesian, Neighbour Joining, Maximum Parsimony and Maximum Likelihood procedures. All methods grouped individuals of the three morphological subspecies (V. a. aspis, V. a. francisciredi, V. a. hugyi) into five different haploclades. Specimens assigned to hugyi clustered in two highly differentiated clades, one being sister group to the complex comprising the second clade of hugyi (i.e., a paraphyletic status), plus two clades of francisciredi. The Bayesian clustering of the STR variability disclosed only two groups, the first including aspis and francisciredi, the second all hugyi. Introgressive hybridization and capture of francisciredi-like lineages in the hugyi mitochondrial genome were suggested to explain the discordance between mitochondrial and nuclear data. The phylogeographic pattern was compatible with population contractions in three glacial refuges. Plausibility of derived hypothesis was checked using coalescence simulations as post hoc tests. Long-term drift and serial founder effects, rather than selection, appeared the main factors affecting the genetic make-up of the Italian asp viper.

Ethnogenomic diversity of Caucasus, Daghestan.

Autosomal short-tandem repeats (STRs) were typed in ethnic populations of Kubachians, Dargins, Avars, Lezgins, Kumiks, and Nogais of the Caucasus (Daghestan, Russia) at the University of Utah. Daghestan ethnic populations demonstrated differences in STR allele frequency distributions, but these differences were much lower among these ethnic groups compared to worldwide ethnic groups. The observed genetic diversity was low while F(ST) values were high, both of which provided supporting evidence for small population sizes and high levels of isolation among the ethnic groups. An analysis of genetic distance from the three major continents, encompassing Daghestan populations and groups, reveals three distinct clusters: all populations of African affiliation, European and Daghestan populations except the Nogais, and Asian populations with ethnic Nogais.

Y chromosomal haplogroup J as a signature of the post-neolithic colonization of Europe.

In order to attain a finer reconstruction of the peopling of southern and central-eastern Europe from the Levant, we determined the frequencies of eight lineages internal to the Y chromosomal haplogroup J, defined by biallelic markers, in 22 population samples obtained with a fine-grained sampling scheme. Our results partially resolve a major multifurcation of lineages within the haplogroup. Analyses of molecular variance show that the area covered by haplogroup J dispersal is characterized by a significant degree of molecular radiation for unique event polymorphisms within the haplogroup, with a higher incidence of the most derived sub-haplogroups on the northern Mediterranean coast, from Turkey westward; here, J diversity is not simply a subset of that present in the area in which this haplogroup first originated. Dating estimates, based on simple tandem repeat loci (STR) diversity within each lineage, confirmed the presence of a major population structuring at the time of spread of haplogroup J in Europe and a punctuation in the peopling of this continent in the post-Neolithic, compatible with the expansion of the Greek world. We also present here, for the first time, a novel method for comparative dating of lineages, free of assumptions of STR mutation rates.

Clinal patterns of human Y chromosomal diversity in continental Italy and Greece are dominated by drift and founder effects.

We explored the spatial distribution of human Y chromosomal diversity on a microgeographic scale, by typing 30 population samples from closely spaced locations in Italy and Greece for 9 haplogroups and their internal microsatellite variation. We confirm a significant difference in the composition of the Y chromosomal gene pools of the two countries. However, within each country, heterogeneity is not organized along the lines of clinal variation deduced from studies on larger spatial scales. Microsatellite data indicate that local increases of haplogroup frequencies can be often explained by a limited number of founders. We conclude that local founder or drift effects are the main determinants in shaping the microgeographic Y chromosomal diversity.

Peopling of three Mediterranean islands (Corsica, Sardinia, and Sicily) inferred by Y-chromosome biallelic variability.

An informative set of biallelic polymorphisms was used to study the structure of Y-chromosome variability in a sample from the Mediterranean islands of Corsica and Sicily, and compared with data on Sardinia to gain insights into the ethnogenesis of these island populations. The results were interpreted in a broader Mediterranean context by including in the analysis neighboring populations previously studied with the same methodology. All samples studied were enclosed in the comparable spectrum of European Y-chromosome variability. Pronounced differences were observed between the islands as well as in the percentages of haplotypes previously shown to have distinctive patterns of continental phylogeography. Approximately 60% of the Sicilian haplotypes are also prevalent in Southern Italy and Greece. Conversely, the Corsican sample had elevated levels of alternative haplotypes common in Northern Italy. Sardinia showed a haplotype ratio similar to that observed in Corsica, but with a remarkable difference in the presence of a lineage defined by marker M26, which approaches 35% in Sardinia but seems absent in Corsica. Although geographically adjacent, the data suggest different colonization histories and a minimal amount of recent gene flow between them. Our results identify possible ancestral continental sources of the various island populations and underscore the influence of founder effect and genetic drift. The Y-chromosome data are consistent with comparable mtDNA data at the RFLP haplogroup level of resolution, as well as linguistic and historic knowledge.

The STR-based genetic profile of the population from Corsica island (France).

Short tandem repeats (STR) at loci HumFES/FPS, HumVWA, HumCSF1PO, HumTH01, HumFXIIIA01, HumTPOX, HumCD4, D3S1358 are markers of choice for population genetics and validated systems for forensic use. In this report, we analysed their allele frequency distribution in a sample of native blood donors from the two departments of Corsica island (France). Deviations from the Hardy-Weinberg rule and heterozygosity values consistently suggested a spatial differentiation of allele and genotype frequencies across the island. Pairwise comparisons showed that Corsican gene pool presents a high level of heterogeneity between departments and substantially differs from that of neighbouring and historically-related populations. The results suggest the use of local databases to calculate a priori statistics in human identity testing.

Microsatellite variation in Central Africa: an analysis of intrapopulational and interpopulational genetic diversity.

As a part of a research project on molecular variation in Central Africa, we have analyzed 10 microsatellites (CD4, CSFO, D3S1358, D18S51, D21S11, F13A1, FES, TH01, TPOX, and VWA) in the Bamileke and Ewondo from Cameroon and the Sanga and Mbenzele Pygmies from the Central African Republic (a total of 390 chromosomes). A statistically significant trend towards heterozygote deficiency was detected in the Mbenzele Pygmies. This was established through the use of powerful exact tests for the Hardy-Weinberg equilibrium. A certain degree of isolation and a small effective size may explain this finding. However, the lack of any substantial reduction in allelic diversity in the Mbenzele does not support the possibility that this group has a smaller effective size in evolutionary terms. A possible explanation based on ethnographic studies suggests that the gene flow from non-Pygmies to Pygmies could have been interrupted only in relatively recent times. The analysis of association between genotypes at pairs of independent loci indicates that the level of subheterogeneity is markedly lower in the Bamileke than in other sampled populations. This may be explained by the combined effect of larger population size, more rigid respect of clanic exogamy, and higher matrimonial mobility of the Bamileke. Finally, we have analyzed interpopulational relationships among our sampled populations and other Central African populations. The results are consistent with a previous study of protein loci (Spedini et al. 1999), which suggests the recent history of the Bamileke and Ewondo has led them to aquire a substantial genetic similarity. Furthermore, the Mbenzele Pygmies diverge from Biaka Pygmies, despite their common origin and geographical proximity. This is probably due to the differentiating effect of genetic drift, which is enhanced by the small effective size of Pygmy populations.

Correlations of quantitative chromosomal heteromorphisms and classic genetic markers to demogeographic data in Garfagnana valley (Tuscany, Italy).

The genetic structure and interrelationships of six populations of the Garfagnana valley (Tuscany, Italy) were examined using chromosomal heteromorphisms concurrently with blood group system, red cell isozyme, and serum protein polymorphisms, secretor status, and surname frequency data. We aimed to evaluate the relationship of cytogenetic polymorphisms to more classical sources of gene frequency data in a population with a well-known demographic scenario. The R matrix technique (Harpending and Jenkins 1973) was used to estimate kinship coefficients, and the Harpending-Ward model (1982) and its extensions for quantitative traits (Relethford and Blangero 1990) were used to detect differential systematic pressure among population subdivisions. Mantel statistics were used to assess the significance of the correlations between cytogenetic, genetic, isonymy, geographic, and migration matrices. The analyses consistently gave similar results for the DA/DAPI cytogenetic heteromorphism and most gene frequency data. Both sets of results depend on migration patterns and on geographic distance among population subdivisions. However, C cytogenetic heteromorphism and some separately analyzed genetic markers did not fit the demogeographic pattern. Overall, it appears that data from different levels of the genetic hierarchy (namely, DNA regions encoding for classical biochemical markers and the noncoding highly variable cytogenetic bands of heterochromatin) can be treated and compared using the same analytical tools.

Genomic reorganization and disrupted chromosomal synteny in the siamang (Hylobates syndactylus) revealed by fluorescence in situ hybridization.

We employed in situ hybridization ("chromosome painting") of chromosome-specific DNA libraries of all human chromosomes to establish homologies between the human and siamang karyotypes (Hylobates syndactylus, 2n = 50). Numerous intra- and interchromosomal rearrangements have led to a massive reorganization of the siamang karyotype. There have been a minimum of 33 translocations. The 24 siamang autosomes are composed of 60 recognizable segments that show DNA homology to regions of the 22 human autosomes. Only two autosomes have not been involved in translocations. The siamang presents a case, in a primate closely related to humans, in which chromosome morphology and synteny are highly disturbed in a manner similar to that encountered among rodents.

Cytogenetic analysis shows extensive genomic rearrangements between red howler (Alouatta seniculus, Linnaeus) subspecies.

A comparison of the G-banded karyotypes of two red howler subspecies, Alouatta seniculus arctoidea and A. s. sara, showed that they differed by at least 14 chromosomal rearrangements. Genomic reshuffling is so great that homologs between subspecies could not be found for some chromosome, while the assignment of homology for other chromosomes remains uncertain. The two red howlers, however, share an unusual X1X2Y1Y2/ X1X1X2X2 sex-chromosome system that resulted from a Y-autosome translocation, probably in a common ancestor. The great chromosomal variability resulting from rapid chromosomal evolution in howlers indicates that cytogenetic data could make an important contribution to resolving phylogenetic and conservation problems in this group of highly conspicuous New World Monkeys. © 1995 Wiley-Liss, Inc.

Genetic polymorphism in the Garfagnana population (Tuscany).

Blood group systems ABO, KEL, MN, RH, secretor status for ABH blood group substances, red cell enzymes ACP1, ESD, AK1, 6-PGD, PGM1 subtypes, serum markers GC, TF, PI, AHSG, ORM1 and chromosomal heteromorphism Q, C, DA/DAPI were examined in a population sample of the Garfagnana, a semi-isolated mountainous area in the province of Lucca (Tuscany, Italy). The total sample was subdivided and analysed according to the more recent historical events which have occurred in Garfagnana. The observed phenotype and gene frequencies were discussed in the context of other population samples from the same province and of the same region. As a whole, the results concur in pointing out a certain degree of heterogeneity within the area and a high differentiation from the rest of Tuscany. Such peculiar genetic features of the population have to be related to the historical, geographic and cultural isolation of the Garfagnana.

Paleoserology of the Christian population at Sayala (Lower Nubia): an evaluation of the reliability of the results.

A paleoserological study of human remains from the Christian cemeteries of Sayala (Lower Nubia, 6th-11th centuries A.D.) was carried out by applying two techniques (absorption-elution and haemagglutination-inhibition), on two types of substratum (bones and hair), in separate laboratories (Pisa and Prague). The aim of research was to evaluate the degree of repeatability of the results and the reliability of the final paleoserological diagnoses. The results indicated different degrees of repeatability depending on the differential sensitivity of the two techniques and on the nature of the substratum. The frequencies of concordant and discordant final diagnoses within and between the two laboratories and by the two methods were significantly different from those expected under the conditions of random distribution, indicating a consistency in results from different laboratories and methods. The reliability of the resulting gene and phenotype distributions is also supported by their consistency both with the theoretical Hardy-Weinberg equilibrium and with the present distribution of the ABO gene frequencies in Egyptian, Sudanese, and Nubian populations.

Variability of DA/DAPI and C heterochromatic regions: a population study.

DA/DAPI and C chromosomal heteromorphic sites (1q, 9q, 15p, 16q, Yq) in a sample of 136 unrelated individuals from the Garfagnana valley (Tuscany, Italy) have been analyzed quantitatively and qualitatively. The variations in length, between-homolog heteromorphisms, and intensity of fluorescence of the heterochromatic bands have been compared in two subsamples of the population (upper and middle valley) individualized according to geodemographic criteria. DA/DAPI heterochromatin differed significantly from C heterochromatin, showing a lower average amount and a higher variability at each site. This suggests a differential staining of DNA of the two banding systems. Furthermore, DA/DAPI heterochromatin was less uniformly distributed in the population than C heterochromatin and the regions 16q and Yq discriminated better between subsamples. The variations of DA/DAPI fluorescence at the 15p site demonstrated an excess of homomorphic individuals in the upper valley, which could be related to the mating structure of the population living in this area.

Reconstruction of genomic rearrangements in great apes and gibbons by chromosome painting.

The homology between hylobatid chromosomes and other primates has long remained elusive. We used chromosomal in situ suppression hybridization of all human chromosome-specific DNA libraries to "paint" the chromosomes of primates and establish homologies between the human, great ape (chimpanzee, gorilla, and orangutan), and gibbon karyotypes (Hylobates lar species group, 2n = 44). The hybridization patterns unequivocally demonstrate the high degree of chromosomal homology and synteny of great ape and human chromosomes. Relative to human, no translocations were detected in great apes, except for the well-known fusion-origin of human chromosome 2 and a 5;17 translocation in the gorilla. In contrast, numerous translocations were detected that have led to the massive reorganization of the gibbon karyotype: the 22 autosomal human chromosomes have been divided into 51 elements to compose the 21 gibbon autosomes. Molecular cytogenetics promises to finally allow hylobatids to be integrated into the overall picture of chromosomal evolution in the primates.