Reconstructing the Origins and Migrations of Diasporic Populations: The Case of the European Gypsies

The sociohistorical study of Gypsies/Sinti/Roma has been dominated by the "Gypsy-lorist" paradigm. According to this paradigm, these itinerant people belong to a unitary ethnic group of South Asian origin whose cultural practices have been preserved over the centuries. Recently, this perspective has come under criticism for perpetuating the image of Gypsies as an isolate within the wider context of the development of European societies, and, in particular, for placing too much importance on the external origin of Gypsy cultural and linguistic practices. This article attempts to place the available biological anthropological data for Roma origins and population history (from molecular genetic and clinical studies) in the wider ethnohistorical and linguistic context, and assesses their potential impact for an integrationist approach to Gypsy studies. These data suggest that, while the "Gypsy-lorist" paradigm is problematic, Gypsy populations share a common biological origin, a reality that should not be ignored.     

湖羊6号染色体微卫星标记多样性与产羔数的关系

选择位于绵羊6号染色体上FecB基因紧密连锁的6个微卫星标记, 即LSCV043、BMS2508、GC101、300U、Bulge5和471U, 分析其在湖羊中的遗传多样性以及和产羔数的关系。结果表明, 6个微卫星位点均属多态性位点, 共检测到34个等位基因、53种基因型。LSCV043、BMS2508和300U属高度多态位点, 其多态信息含量分别为0.6674、0.6035和0.5615。对不同基因型群体的产羔率进行统计分析, LSCV043基因型为107 bp/123 bp所对应的总体产羔数明显高于110 bp/123 bp基因型群体所对应的产羔数(P<0.05); BMS2508基因型为154 bp/154 bp、154 bp/170 bp和154 bp/200 bp所对应的群体第一胎产羔数明显高于170 bp/170 bp所对应的产羔数(P<0.05), 基因型170 bp/170 bp的群体总体产羔数均低于该位点的其他基因型(P<0.05); 其他位点各基因型之间产羔数均无显著差异。     

Autosomal genetic diversity in non‐breed horses from eastern Eurasia provides insights into historical population movements

Many events in the history of eastern Eurasia, including the process of domestication itself, the initial spread of domestic horses and subsequent movements, are believed to have affected the genetic structure of domestic horse populations in this area. We investigated levels of within‐ and between‐population genetic diversity in ‘non‐breed horses’ (working horses sampled in remote areas) from 17 locations in Asia and parts of Eastern Europe, using 26 autosomal microsatellite loci. Non‐breed horses have not been subject to the same intensity of artificial selection and closed breeding as have most breed animals and are thus expected to better reflect the population history of domestic horses. Despite geographic distances of between 300 and 7000 km between sampling locations, pairwise F _ST was very low (range: <0.001 to ?0.033), suggesting historically high levels of gene flow. Our analyses of non‐breed horses revealed a pattern of isolation by distance and a significant decline in genetic diversity (expected heterozygosity and allelic richness) from east to west, consistent with a westward expansion of horses out of East Asia. Although the timing of this putative expansion is unclear, our results highlight the benefit of studying animals that do not belong to particular breeds when investigating aspects of a population's history.     

Global diversity and genetic contributions of chicken populations from African,Asian and European regions

Genetic diversity and population structure of 113 chicken populations from Africa, Asia and Europe were studied using 29 microsatellite markers. Among these, three populations of wild chickens and nine commercial purebreds were used as reference populations for comparison. Compared to commercial lines and chickens sampled from the European region, high mean numbers of alleles and a high degree of heterozygosity were found in Asian and African chickens as well as in Red Junglefowl. Population differentiation (F_ST) was higher among European breeds and commercial lines than among African, Asian and Red Junglefowl populations. Neighbour‐Net genetic clustering and structure analysis revealed two main groups of Asian and north‐west European breeds, whereas African populations overlap with other breeds from Eastern Europe and the Mediterranean region. Broilers and brown egg layers were situated between the Asian and north‐west European clusters. structure analysis confirmed a lower degree of population stratification in African and Asian chickens than in European breeds. High genetic differentiation and low genetic contributions to global diversity have been observed for single European breeds. Populations with low genetic variability have also shown a low genetic contribution to a core set of diversity in attaining maximum genetic variation present from the total populations. This may indicate that conservation measures in Europe should pay special attention to preserving as many single chicken breeds as possible to maintain maximum genetic diversity given that higher genetic variations come from differentiation between breeds.     

The role of the Vlax Roma in shaping the European Romani maternal genetic history

The Roma are comprised of many founder groups of common Indian origins but different socio-cultural characteristics. The Vlax Roma are one of the founder Roma populations characterized by a period of bondage in the historic Romanian principalities, and by the archaic Romanian language. Demographic history suggests different migration routes of Roma populations, especially after their arrival in Mesopotamia and the eastern boundary of the Byzantine Empire. Although various genetic studies of uniparental genetic markers showed a connection between Roma genetic legacy and their migration routes, precise sampling of Roma populations elucidates this relationship in more detail. In this study, we analyzed mitochondrial DNA of 384 Croatian Vlax Roma from two geographic locations in the context of 734 European Roma samples. Our results show that Roma migration routes are marked with two Near-Eastern haplogroups, X2 and U3, whose inverse proportional incidence clearly separates the Balkan and the Vlax Roma from other Roma populations that reached Europe as part of the first migration wave. Spatial and temporal characteristics of these haplogroups indicate a possibility of their admixture with Roma populations before arrival in Europe. Distribution of haplogroup M35 indicates that all Vlax Roma populations descend from one single founder population that might even reach back to the original ancestral Indian population. Founder effects followed by strict endogamy rules can be traced from India to contemporary small, local communities, as in the case of two Croatian Vlax Roma populations that show clear population differentiation despite similar origins and shared demographic history.     

Population genetic diversity and species relationships in the genus Rhinanthus L. based on microsatellite markers

The genus Rhinanthus L. is complex, containing many taxonomically unresolved taxa. In this paper we studied genetic variation and species relationships in 15 populations of six Rhinanthus species from three sections. For this purpose, we developed new microsatellite primers for R. osiliensis and used them to investigate genetic variation in two narrow endemics (R. osiliensis, R. javorkae) and in four widespread species (R. rumelicus R. wagneri, R. angustifolius and R. minor). Species‐specific private alleles were found in all species except R. osiliensis and R. angustifolius. The Bulgarian endemic R. javorkae showed the lowest genetic variation, followed by widespread R. minor and Estonian endemic R. osiliensis. Rhinanthus javorkae and R. minor were genetically most differentiated. Section Cleistolemus is weakly structured genetically, indicating close affinity between R. osiliensis, R. rumelicus, R. wagneri and R. angustifolius.     

Inferring ancient Agave cultivation practices from contemporary genetic patterns

Several Agave species have played an important ethnobotanical role since prehistory in Mesoamerica and semiarid areas to the north, including central Arizona. We examined genetic variation in relict Agave parryi populations northeast of the Mogollon Rim in Arizona, remnants from anthropogenic manipulation over 600 years ago. We used both allozymes and microsatellites to compare genetic variability and structure in anthropogenically manipulated populations with putative wild populations, to assess whether they were actively cultivated or the result of inadvertent manipulation, and to determine probable source locations for anthropogenic populations. Wild populations were more genetically diverse than anthropogenic populations, with greater expected heterozygosity, polymorphic loci, effective number of alleles and allelic richness. Anthropogenic populations exhibited many traits indicative of past active cultivation: fixed heterozygosity for several loci in all populations (nonexistent in wild populations); fewer multilocus genotypes, which differed by fewer alleles; and greater differentiation among populations than was characteristic of wild populations. Furthermore, manipulated populations date from a period when changes in the cultural context may have favoured active cultivation near dwellings. Patterns of genetic similarity among populations suggest a complex anthropogenic history. Anthropogenic populations were not simply derived from the closest wild A. parryi stock; instead they evidently came from more distant, often more diverse, wild populations, perhaps obtained through trade networks in existence at the time of cultivation.     

Microsatellite markers isolated from a polyploid saltbush, Atriplex nummularia Lindl. (Chenopodiaceae)

Atriplex nummularia is a polyploid Australian saltbush which has been identified as a suitable species for use in the rehabilitation of agricultural land affected by salinity. We isolated 12 polymorphic loci for a preliminary assessment of genetic variability and structure within the species as a basis for a breeding programme. Preliminary screening of loci in 40 individuals from two populations revealed multibanded genotypes consisting of up to seven alleles in a single individual, with up to 29 alleles observed at a single locus. The multibanded patterns are consistent with the polyploid status of this species.     

Characterization of polymorphic microsatellite markers,isolated from ginger (Zingiber officinale Rosc.)

The present study reports isolation and characterization of eight polymorphic microsatellite markers for Zingiber officinale Rosc. (Ginger). A total of 34 alleles were detected across the 20 accessions, with an average of 4.3 alleles per locus. Values for observed and expected heterozygosities ranged from 0 to 1.0 and from 0.23 to 0.67, respectively. The heterozygote deficits were observed at three loci. At the significance threshold (P < 0.05) of the eight loci, seven were found to have deviated from Hardy–Weinberg equilibrium, whereas significant linkage disequilibria were observed between 10 pairs of loci. Our data indicate the existence of moderate level of genetic diversity among the ginger accessions genotyped with eight markers.     

Dissection of ancestral genetic contributions to Creole goat populations

Goats have played a key role as source of nourishment for humans in their expansion all over the world in long land and sea trips. This has guaranteed a place for this species in the important and rapid episode of livestock expansion triggered by Columbus’ arrival in the Americas in the late 1400s. The aims of this study are to provide a comprehensive perspective on genetic diversity in American goat populations and to assess their origins and evolutionary trajectories. This was achieved by combining data from autosomal neutral genetic markers obtained in more than two thousand samples that encompass a wide range of Iberian, African and Creole goat breeds. In general, even though Creole populations differ clearly from each other, they lack a strong geographical pattern of differentiation, such that populations of different admixed ancestry share relatively close locations throughout the large geographical range included in this study. Important Iberian signatures were detected in most Creole populations studied, and many of them, particularly the Cuban Creole, also revealed an important contribution of African breeds. On the other hand, the Brazilian breeds showed a particular genetic structure and were clearly separated from the other Creole populations, with some influence from Cape Verde goats. These results provide a comprehensive characterisation of the present structure of goat genetic diversity, and a dissection of the Iberian and African influences that gave origin to different Creole caprine breeds, disentangling an important part of their evolutionary history. Creole breeds constitute an important reservoir of genetic diversity that justifies the development of appropriate management systems aimed at improving performance without loss of genomic diversity.     

A genetic analysis of the Italian Salernitano horse

Salernitano (SAL) is an ancient Italian horse breed developed over the course of the ages together with Napoletano and, during the 20th century, by crossing with Thoroughbred horse lines. Excellent in hurdle jumping, this breed is currently facing a concrete risk of extinction due to the lack of appropriate management strategies. This research is the first SAL genetic characterization that aims to set up the basic knowledge for a conservation plan. A representative sample of 61 SALs was analyzed by means of a set of 16 microsatellites markers (short tandem repeats (STRs)). The sequence of hypervariable D-loop mtDNA region was also performed on a subset of 24 mares in order to study the maternal diversity and obtain a complete picture of the internal genetic variation. All the molecular data were analyzed together with those obtained from three Sicilian horse breeds investigated in a previous research (Siciliano, Sanfratellano and Sicilian Oriental Purebred). STRs markers revealed a moderate level of genetic diversity in SAL (alleles/locus 5.1, He 0.67) and confirmed the hunch of genetic erosion. Autosomal variability highlighted a very light deficit of homozygotes (FIS=−0.067). Experimental D-loop sequences were compared by multiple alignments with those retrieved from biological databases and revealed two unreported haplotypes. The phylogenetic network, which was built on mtDNA sequences, included various cosmopolitan and European horses and showed SAL haplotypes distributed among different mtDNA lineages.     

Twelve new microsatellite markers for gilted seabream (Sparus aurata L.): characterization,polymorphism and linkage

Twelve new microsatellite markers were isolated from the gilted seabream Sparus aurata L., a seawater fish distributed throughout the Mediterranean Sea and on the East Atlantic Coast and exploited in both fisheries and aquaculture. Characterization in 16 individuals from a hatchery population from France reveals three to 17 alleles and a mean expected heterozygosity of 0.752. Inheritance and linkage were assessed in a bi‐parental cross, and using polymorphism and linkage information, two PCR‐multiplex were developed for routine analysis of Sparus aurata populations.     

European pig genetic diversity: a minireview

An evaluation of the European pig diversity has been carried on by several countries, with the support of the European Union over the period of 1994 to 2000. This article presents an overview of the results of this investigation, focussing on two genetic marker techniques, namely microsatellites (MS) and amplification of fragment length polymorphism (AFLP). Nearly 200 loci were characterised on about 50 individuals from each of 59 to 71 breeds, according to the marker considered. The analysis of diversity, based on genetic distances, led to similar conclusions for the two marker types (MS and AFLP), in spite of a markedly lower total diversity of AFLP compared to MS. The analysis of the MS loci showed that the allelic diversity pattern among breeds was quasi-independent from the diversity pattern based on allele frequencies. Genetic distances showed no particular clustering of local with international breeds, confirming the genetic uniqueness of the European local breeds compared to mainstream international breeds. The taxonomy of the local breeds revealed a cluster of the Iberian type breeds, in contrast with a wider dispersal of the breeds from other countries. Phylogeny often disagreed with documented breeds' history, showing the complex migration/admixture patterns which underlie the breeds' relationships. Methodologies developed in this investigation as well as the database and the DNA depository created should provide support for further innovative research in the field of domestic animal diversity management.     

Genetic diversity and subdivision of 57 European and Middle-Eastern sheep breeds

The population structure and genetic diversity of 57 European and Middle Eastern marginal and cosmopolitan sheep breeds from 15 countries were analysed by typing 31 microsatellite markers. Mean unbiased expected heterozygosities ranged from 0.63 in British Exmoor Horn to 0.77 in Albanian Ruda. South-eastern European and Middle-Eastern sheep breeds were significantly more variable than northwestern and western European breeds. An overall heterozygote deficiency (f) across all loci was observed (P < 0.001), while genetic differentiation (theta) was 5.7%. Principal component analysis and Bayesian model-based clustering indicate a south-east to north-west cline, but also revealed distinct groups of Middle-Eastern fat-tailed sheep, south-eastern European sheep and north-western/western European sheep. Within the last group, two less-distinct clusters comprised the Merino-type and Alpine breeds respectively. The incomplete demarcations of most clusters probably reflects cross-breeding and/or upgrading.     

Characterization of microsatellite markers derived from sequence databases for the European flounder (Platichthys flesus)

The European flounder (Platichthys flesus; Pleuronectidae) is an important commercial fish species. Nevertheless, no microsatellites for this species have been published to date. The sequence of flounder genes present in the public database was searched for short tandem repeats. Out of 12 microsatellite pairs derived from Sequenced Databases, five amplified successfully with an expected heterozygosity ranging from 0.43 to 0.75. The average allele number of these microsatellites was 4.8 per locus with a range between two and nine.     

Using molecular markers and multivariate methods to study the genetic diversity of local European and Asian chicken breeds

French and Asian subsets of chicken breeds were first analysed using 22 microsatellites and then compared to the AVIANDIV European set using 14 loci. Positive correlations were observed between F _IT or F _ST and typological values or variance of markers using the multivariate analysis mcoa . The first axis of the multivariate representation separated Asian from European breeds, revealing breeds with Asian ancestor. Using all or 14 loci, correct assignation rate was always higher than 93%. The Weitzman index and the aggregate diversity D were calculated using 22 loci within French and Asian breeds. The French breed Coucou de Rennes and the Hua-Tung breed seemed to contribute the most to the global diversity of each subset. This approach on French-only breeds and then on French with AVIANDIV domestic breeds (14 loci) showed that the Marans breed contributed the most. The AVIANDIV framework could be useful to evaluate the genetic diversity of local breeds and to help in connecting national and regional conservation policies.     

Lack of concordance between genetic diversity estimates at the molecular and quantitative-trait levels

In many applications of population genetics, particularly in the field of conservation biology, estimates of molecular diversity are used as surrogate indicators of less easily acquired measures of genetic variation for quantitative traits. The general validity of this approach to inferring levels of quantitative genetic variation within populations is called into question by the demonstration that estimates of molecular and quantitative-genetic variation are essentially uncorrelated in natural populations of Daphnia, one of the few organisms for which multiple estimates of both quantities are available. On the other hand, molecular measures of population subdivision seem to give conservatively low estimates of the degree of genetic subdivision at the level of quantitative traits. This suggests that although molecular markers provide little information on the level of genetic variation for quantitative traits within populations, they may be valid indicators of population subdivision for such characters.     

Characterization of microsatellite markers in the shea tree (Vitellaria paradoxa C. F Gaertn) in Mali

In order to study the genetic diversity and structure in the population of Vitellaria paradoxa, we characterized eight polymorphic microsatellite loci. Primers to amplify these loci were tested on 169 individual trees representing a sample of the population of shea tree in Mali. The loci were all polymorphic with a number of alleles between three to nine and with observed level of heterozygosity ranging from 0.035 to 0.507. These markers will be useful for genetic and ecological studies of this species.     

Interpopulation genetic divergence in European grayling (Thymallus thymallus, Salmonidae) at a microgeographic scale: implications for conservation

In order to provide guidelines for conservationand management of the severely declining LakeSaimaa (eastern Finland) European grayling(Thymallus thymallus, Salmonidae), weinvestigated the microgeographic geneticstructure of three populations from the watersystem using 17 microsatellite loci andmitochondrial DNA polymerase chainreaction-restriction fragment lengthpolymorphism analysis. Microsatellites revealedlow levels of intrapopulation genetic diversityand substantial divergence between populationssampled from spawning sites separated by aslittle as 55 kilometers. Mitochondrial analysisindicated the occurrence of two compositehaplotypes within Lake Saimaa. The nucleotidesubstitution estimates between the haplotypessuggested their separation to markedly predatethe late Pleistocene period. The populationsexhibited marked frequency differences for thetwo mitochondrial haplotypes, reinforcing theview of limited interpopulation gene flowwithin Lake Saimaa. An individual basedmicrosatellite Neighbor-Joining dendrogramdemonstrated clustering of all the specimensaccording to their sampling origin. Individualassignment tests revealed 100% assignmentsuccess of individuals into their population oforigin and 100% exclusion (p <0.05) from all alternative referencepopulations. These findings exemplify that T. thymallus populations may be genetically highly structured over small geographical scales and provide a good starting point for the development of appropriate conservation strategies for Lake Saimaa grayling.