Not all isolates are equal: linkage disequilibrium analysis on Xq13.3 reveals different patterns in Sardinian sub-populations

Recent studies indicate that, whereas the Sardinian population as a whole is comparable to outbred populations for linkage disequilibrium (LD) mapping of common variants, LD in Sardinian sub-isolates is more extended, making these populations particularly suitable for this approach. To evaluate the extent of LD between microsatellite markers, we compared different sub-populations within Sardinia selected on the basis of their geographical position and isolation: two small isolated villages (Talana, Urzulei), two larger but remote areas (Ogliastra, Nuoro province) and a cohort of samples representing the wider Sardinian population. LD analysis was carried out by using six microsatellite markers that are located on Xq13.3 and that have been extensively studied in different populations. We found different extents and patterns of LD in the sub-population samples depending on their degree of isolation and demographic history. All LD measurements and haplotype analyses indicate that there is a decreasing trend from Talana (the most inbred population, LD up to 9.5-11.5 Mb) to the more outbred Sardinian population (LD only for intervals <2 Mb). In one village (Talana), five haplotype classes accounting for 80% of the entire sample perfectly matched five Ogliastra clusters, supporting the origin of the village from the Ogliastra genetic pool. In contrast, the other village (Urzulei) showed a different pattern of haplotypes with a closer relationship to the Nuoro region sub-population. LD analyses therefore show that even neighbouring isolate villages may differ in their genetic background. Here, we highlight the importance of selecting appropriate populations and/or sub-populations for the analysis of complex traits. Isolated sub-populations showing different extents of LD can provide a powerful method for mapping complex traits by LD scanning at relatively low marker density.     

Blood lead levels in children from Sardinian villages at high risk of environmental crisis

This study reports blood lead levels measured in 1998 in children from three Sardinian villages: Portoscuso, Sant'Antioco, and Sestu. Portoscuso is located about 2 km from one of the most important industrial complexes in Sardinia. Sant'Antioco, together with the villages of Carbonia, Gonnesa, Portoscuso and San Giovanni Suergiu, is in the Sulcis-Iglesiente zone, defined as an “area of high risk of environmental crisis” on the basis of the Decree of the Italian Council of Ministers dated November 30, 1990. Sestu, a semi-urban centre about 10 km from Cagliari (the island's capital), can be considered not exposed to lead pollution. Blood lead concentration was determined in heparinized venous blood samples by graphite furnace atomic absorption spectrophotometry. Comparing the mean blood lead levels for the boys of Portoscuso measured in 1993 (9.27 μg/dl) and 1998 (11.30 μg/dl), we found an increase of 21.90%, whereas the mean values for the girls are practically identical in 1993 (7.35 μg/dl) and 1998 (7.39 μg/dl). In contrast, in the boys and girls of Sestu, the mean blood lead levels decrease from 1993 to 1998 by 55.62% and 29.09% respectively (from 6.71 μg/dl to 4.09 μg/dl in the boys; from 4.71 μg/dl to 3.34 μg/dl in the girls). In the Sant'Antioco children, we found a 52.65% decrease from 1987 (8.30 μg/dl reported for a sample not subdivided by sex)) to 1998 (3.93 μg/dl for males and females combined). Our results confirm the findings of previous investigations of blood lead levels in children from Sardinian villages with different environmental risks of lead pollution: the children of Portoscuso present higher blood lead levels than other groups of Sardinian children.     

Genetic differentiation among Sardinian villages.

The present study reports an analysis of genetic differentiation among 14 Sardinian villages located mainly in the center of the island. Chi-square tests show significant genetic heterogeneity among villages, and analyses by F- and R- statistics indicate an essentially random pattern of differentiation for all alleles. Using the kinship methods of Morton, a matrix, R, with elements rij describing the correlations between the gene frequencies of villages i and j is obtained. Use of Malécot's formula relating the rij to the geographic distances between villages shows a rapid decline of kinship with increasing distance but reveals essentially no relationship for distances over 40 km. Rotation of a two-dimensional reduction of the kinship matrix to maximum congruence with the geographic distances indicates that about 25% of the genetic distances can be accounted for by the geographic location of the villages. Isolation due in part to cultural factors, genetic drift, and special local or regional patterns of villages associations appear to be involved in the pattern of genetic variation.     

Seasonality of marriages in sardinian pastoral and agricultural communities in the nineteenth century

The study of marriage seasonality of populations with different socioeconomic backgrounds may contribute to the better understanding their reproductive behaviours. This study analyses the monthly distribution of marriages in the 19th century in four agricultural villages and four pastoral villages on the island of Sardinia (Italy). The data were derived from 7340 marriage acts (3571 for the four agricultural villages and 3769 for the four pastoral villages). The aim is to ascertain whether the Sardinian agricultural and pastoral communities followed the matrimonial models reported for contemporary Italy and Europe and whether there was a change in the monthly distribution of marriages between the two halves of the 19th century. The results suggest that the marriage seasonality of the Sardinian farmers and shepherds was very similar to the patterns shown in the 19th century by Italian and European agricultural and pastoral communities. The Sardinian farmers preferred to marry in autumn-winter, while the Sardinian shepherds had a very high concentration of marriages in summer-autumn. Both communities avoided marriages in the Advent and Easter periods and in the month of May (dedicated to the Virgin Mary), and the farmers also in August (also dedicated to the Virgin Mary). Despite a certain seasonal stability, there was a significant change in the monthly distribution of marriages between the two halves of the 19th century in both the agricultural and pastoral communities, probably due to a series of laws that transformed the centuries-old socioeconomic system of Sardinia in the second half of the century.     

Evolution of marital structure in 20 Sardinian villages from 1800 to 1974

This paper reports the data for endogamy, exogamy and consanguinity in 20 Sardinian villages from 1800 to 1974, divided into generational periods (25 years). The data are taken from the records of 48,262 marriages celebrated in the parishes of 20 Sardinian villages. The results for Spearman's rank correlation coefficient indicate significant positive correlations of endogamy with consanguinity (r(s) = 0.6551, percentage of consanguineous marriages; r(s) = 0.5477, Bernstein's alpha), with altitude (r(s) = 0.6386), with population size (r(s) = 0.2519), as well as a significant negative correlation of endogamy with time (r(s) = -0.4210). In addition, consanguinity shows a significant positive correlation with altitude (r(s) = 0.5717, percentage of consanguineous marriages; r(s) = 0.6295, Bernstein's alpha) and a significant negative correlation with time (r(s) = -0.2363, percentage of consanguineous marriages); the negative correlation between the mean level of consanguinity (alpha) and time is statistically not significant. In the single parishes, the levels of endogamy and consanguinity are generally higher in the mountain villages than in those situated in the hill and plain areas. Finally, it is hypothesized that, in the time period considered, the level of consanguinity and especially of endogamy were largely determined by isolation.     

Identifying native animals in crossbred populations: the case of the Sardinian goat population

The aim of this work was to develop a strategy for using a genetic analysis for identifying native animals in regions where local breeds have been crossed with improved breeds and then compare that strategy to the overall morphology and breeding histories of the herds for identifying these animals. The experiment included the Sardinian goat population, which is a crossbred of native animals with the Maltese breed. Whole herds were assigned to Maltese (five herds; 49 animals), crossbred (18 herds; 117 animals) or Sardinian (12 herds; 164 animals) groups. For the genetic analysis, genotypes of 22 microsatellites were determined on 330 animals, and basic measurements of genetic diversity were calculated. Genetic variability in the microsatellites was different in the three groups. High positive F _IS showed that inbreeding existed in the subpopulations. The index of genetic differentiation, Nei's standard genetic distance and Reynolds' genetic distance were calculated and found to be significantly different between the three groups. The Sardinian and Maltese groups were the most distant whereas the crossbred group was closer to the Sardinian group. The proportion of the genome derived from two ancestral populations (native Sardinian and Maltese) was assessed using the structure software. Animals were assigned to three clusters on the basis of native Sardinian thresholds. A good correspondence between the empirical (morphology and breeding histories) and the objective genetic analysis was found. Both approaches indicate the presence of three different subpopulations in the Sardinian goat population.     

Adenosine deaminase polymorphism in sardinia

Summary Red blood cell adenosine deaminase and G-6-PD polymorphisms have been studied in the populations of 17 Sardinian villages located at various altitudes. A total of 1615 individuals of both sexes, with age between 7 and 14 years were examined.The negative relationship between Gd^Med gene frequency and altitude was confirmed.Adenosine deaminase polymorphism showed a considerable variability among the villages examined: ADA² frequency ranged from 0.025 to 0.106. The ADA² frequency was negatively related (p< 0.05) with Gd^Med gene frequency.

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Zusammenfassung Die Erythrocyten-Adenosin-Desaminase und Glucose-6-Phosphat-Dehydrogenase-Polymorphismen sind in Stichproben aus der Bevölkerung von 17 Dörfern auf Sardinien untersucht worden. Diese sind in verschiedener Höhe über dem Meer im zentralen Teil der Insel gelegen.Die negative Häufigkeitsbeziehung zwischen der Genfrequenz Gd^Med und der Höhenlage der Dörfer konnte bestätigt werden.Der Adenosin-Desaminase-Polymorphismus zeigt eine beträchtliche Variabilität zwischen den verschiedenen Dorfpopulationen. Die ADA²-Frequenz liegt zwischen 0,025 und 0,106. Die ADA²-Frequenz steht in negativer Beziehung (p< 0,05) zur Gd^Med-Frequenz.

     

Further data on a 9.1-kb insertion-deletion polymorphism: survey of Mediterranean populations

We report the distribution of a previously described 9.1-kb insertion-deletion polymorphism located on chromosome 22. We analyzed 1,844 individuals sampled from 26 Mediterranean populations in mainland Italy, Sicily, Sardinia, Tunisia, Libya, Morocco, Egypt, Greece, and Albania. The 9.1 kb - allele is the prevalent allele in the North African (range, 0.53-0.56), Greek (0.51), and Albanian (0.66) populations, whereas the 9.1 kb + allele is most frequent in a mainland Italian town (0.55) and in all Sicilian and Sardinian towns and villages thus far tested, with marked fluctuation ranges of 0.53-0.78 and 0.56-0.80, respectively. In tests for Hardy-Weinberg equilibrium the genotype frequencies observed in Athens and in four of the nine towns in Sicily (but in none of the towns in Sardinia) departed highly significantly from the expected values. Identical results were found in the same towns for a second insertion-deletion polymorphism located on chromosome 22ql13 at a distance compatible with a low incidence of recombination. The data, which are in good agreement with the different histories of the two islands (Sardinia and Sicily), are consistent with a west-east differentiation in Sicily and support the evidence for ancient gene flow from the Iberian peninsula to Sardinia.     

Craniofacial morphometric variation and the biological history of the peopling of Sardinia

The aim of this work is to explore the pattern of craniofacial morphometric variation and the relationships among five prehistoric Sardinian groups dated from Late Neolithic to the Nuragic Period (Middle and Late Bronze Age), in order to formulate hypotheses on the peopling history of Sardinia. Biological relationships with coeval populations of central peninsular Italy were also analysed to detect influences from and towards extra-Sardinian sources. Furthermore, comparison with samples of contemporary populations from Sardinia and from continental Italy provided an indication of the trend leading to the final part of the peopling history. Finally, Upper Palaeolithic and Mesolithic samples were included in the analyses to compare the prehistoric Sardinians with some of their potential continental ancestors. The analysis is based on multivariate techniques including Mahalanobis D² distance, non-parametric multidimensional scaling (MDS) and principal component analysis (PCA). The results showed the tendency to progressive differentiation between Sardinian groups and peninsular Italian groups, with the possible exception of a discontinuity showed by the Bonnànaro (Early Bronze Age) Sardinian sample. Several aspects of the morphological results were found to agree with the current genetic evidence available for the present-day Sardinian population and a Nuragic sample: (1) biological divergence between the Sardinian and peninsular Italian populations; (2) similarity/continuity among Neolithic, Bronze Age and recent Sardinians; (3) biological separation between the Nuragic and Etruscan populations; (4) contribution of a Palaeo-Mesolithic gene pool to the genetic structure of current Sardinians.     

Adaptation to past malarial endemia and susceptibility to common diseases in modern populations: a study of adenosine deaminase and MN blood group genetic polymorphisms

We carried out a study of adenosine deaminase (ADA) and MN blood group genetic polymorphisms in relation to past malarial morbidity in Sardinia and in relation to susceptibility to allergic asthma (a Th2 disorder) and Crohn's disease (a Th1 disorder) in the population of Rome. Eight hundred and eight schoolchildren, aged 7--14 years from 14 Sardinian villages located in the central area of the island, were considered. One hundred and twenty-two children with allergic asthma and 39 adult patients with Crohn's disease from the population of Rome were also studied. The data suggest an interaction between the two systems concerning resistance/susceptibility, both to malaria and to the diseases considered. In Sardinia, the frequency of the *L(M)/ADA*2 gametic type is negatively correlated with past malarial endemia, suggesting an increased susceptibility to malaria leading to its decrease in areas with high malarial endemia. In Rome, this gametic type is correlated negatively to allergic asthma and positively to Crohn's disease, suggesting a protective effect against allergic asthma and increased susceptibility to Crohn's disease.     

Analysis of HLA-DRB1 polymorphism in the Gidra of Papua New Guinea

The genetic structure of the Gidra-speaking population inhabiting 13 villages in Papua New Guinea was investigated, based on the analysis of HLA-DRB1 polymorphism. Nei's fixation indices (F(IS), F(IT), and F(ST)) showed that the Gidra villages were genetically differentiated. The genetic distances significantly correlated with the geographic distances among the 13 villages. Thus, it is likely that a low intervillage migration rate has been maintained since the Gidra community was established. Correspondence analysis revealed that the Gidra, who belong to non-Austronesian-speaking groups, are genetically located at the intermediate point between the Aboriginal Australian groups and the Austronesian-speaking groups. Moreover, the HLA-DRB1*0802 allele, which has been observed in only two Polynesian groups (Austronesian-speaking groups) of Oceanian populations, was also found in the Gidra. These results suggest that the admixture of Austronesian and indigenous non-Austronesian groups beyond the linguistic boundary occurred partly in Papua New Guinea before Austronesian groups spread to the Pacific.     

Allozymic characterization of Sardinian Bacillus rossius (Rossi) and B. atticus Brunner (Insecta Phasmatodea)

The allozymic characterization of newly discovered populations of B. atticus and B. rossius is given. Most Sardinian B. rossius demes belong to the subspecies B. r. rossius, Southeastern populations are B. r. redtenbacheri, while the central ones appear to be intermediate. Like all Italian B. atticus, also Sardinian demes belong to B. a. caprai. The presence of B. atticus alleles in syntopic B. rossius populations is explained through gene introgression due to past hybridization events between the two taxa.     

Genetic markers and insulin-dependent diabetes mellitus (IDDM) in Sardinia.

The distributions of some genetic markers in 106 Sardinian individuals with insulin-dependent diabetes mellitus (IDDM) and in a control sample of 186 nondiabetic Sardinians were studied. A strong association of IDDM with some phenotypes of ACP, PGM1, C3 and GC genetic markers was found. In the IDDM patients there is a significant increase of ACP B, ACP B-C, PGM1 1S-1F and GC 1S-2 phenotypes. Particularly the individuals with the ACP B, PGM1 1S-1F and GC 1S-2 phenotypes show the highest values of the relative risk (RR) and the attributable risk (AR) and seem to be more susceptible to IDDM disease.     

Phylogeography and Pleistocene refugia of the Little Owl Athene noctua inferred from mtDNA sequence data

Pleistocene glaciations greatly affected the distribution of genetic diversity in animal populations. The Little Owl is widely distributed in temperate regions and could have survived the last glaciations in southern refugia. To describe the phylogeographical structure of European populations, we sequenced the mitochondrial cytochrome c oxidase I (COI) and control region (CR1) in 326 individuals sampled from 22 locations. Phylogenetic analyses of COI identified two deeply divergent clades: a western haplogroup distributed in western and northwestern Europe, and an eastern haplogroup distributed in southeastern Europe. Faster evolving CR1 sequences supported the divergence between these two main clades, and identified three subgroups within the eastern clade: Balkan, southern Italian and Sardinian. Divergence times estimated from COI with fossil calibrations indicate that the western and eastern haplogroups split 2.01–1.71 Mya. Slightly different times for splits were found using the standard 2% rate and 7.3% mtDNA neutral substitution rate. CR1 sequences dated the origin of endemic Sardinian haplotypes at 1.04–0.26 Mya and the split between southern Italian and Balkan haplogroups at 0.72–0.21 Mya, coincident with the onset of two Pleistocene glaciations. Admixture of mtDNA haplotypes was detected in northern Italy and in central Europe. These findings support a model of southern Mediterranean and Balkan refugia, with postglacial expansion and secondary contacts for Little Owl populations. Central and northern Europe was predominantly recolonized by Little Owls from Iberia, whereas expansion out of the Balkans was more limited. Northward expansion of the Italian haplogroup was probably prevented by the Alps, and the Sardinian haplotypes remained confined to the island. Results showed a clear genetic pattern differentiating putative subspecies. Genetic distances between haplogroups were comparable with those recorded between different avian species.     

Nuclear and chloroplast microsatellite diversity in Phaseolus vulgaris L. from Sardinia (Italy)

Studies of the level and the structure of the genetic diversity of local varieties of Phaseolus vulgaris are of fundamental importance, both for the management of genetic resources and to improve our understanding of the pathways of dissemination and the evolution of this species in Europe. We have here characterized 73 local bean populations from Sardinia (Italy) using seed traits and molecular markers (phaseolins, nuSSRs and cpSSRs). American landraces and commercial varieties were also included for comparison. We see that: (a) the Sardinian material is distinct from the commercial varieties considered; (b) the variation in the seed traits is high and it mostly occurs among populations (95%); (c) compared to the American sample and the commercial varieties, the Sardinian collection has a low level of diversity; (d) the majority (>95%) of the Sardinian individuals belong to the Andean gene pool; (e) the Sardinian material shows a strong genetic structure, both for cpSSRs and nuSSRs; (f) the nuSSRs and cpSSRs concur in differentiating between gene pools, but a lack of congruence between nuclear and chloroplast has been observed within gene pools; and (g) there are three putative hybrids between the Andean and Mesoamerican gene pools. Despite the relatively low level of diversity, which is probably due to a strong founder effect, the Sardinian landraces are worth being conserved and studied further because of their distinctiveness and because hybridization within and between the gene pools could generate variation that will be useful for breeding. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Effects of human perturbation on the genetic make-up of an island population: the case of the Sardinian wild boar

Game species are often manipulated by human beings, whose activities can deeply affect their genetic make-up and population structure. We focused on a geographically isolated wild boar population (Sardinia, Italy), which is classified, together with the Corsican population, as a separate subspecies (Sus scrofa meridionalis). Two hundred and ten wild boars collected across Sardinia were analysed with a set of 10 microsatellites and compared with 296 reference genotypes from continental wild populations and to a sample of domestic pigs. The Sardinian population showed remarkable diversity and a high proportion of private alleles, and strongly deviated from the equilibrium. A Bayesian cluster analysis of only the Sardinian sample revealed a partition into five subpopulations. However, two different Bayesian approaches to the assignment of individuals, accounting for different possible source populations, produced consistent results and proved the admixed nature of the Sardinian population. Indeed, introgressive hybridization with boars from multiple sources (Italian peninsula, central Europe, domestic stocks) was detected, although poor evidence of crossbreeding with free-ranging domestic pigs was unexpectedly found. After excluding individuals who carried exotic genes, the population re-entered Hardy-Weinberg proportions and a clear population structure with three subpopulations emerged. Therefore, the inclusion of introgressed animals in the Bayesian analysis implied an overestimation of the number of clusters. Nonetheless, two of them were consistent between analyses and corresponded to highly pure stocks, located, respectively, in north-west and south-west Sardinia. This work shows the critical importance of including adequate reference samples when studying the genetic structure of managed wild populations.     

High prevalence of Opisthorchis viverrini infection in a riparian population in Takeo Province, Cambodia

Opisthorchis viverrini infection was found to be highly prevalent in 3 riverside villages (Ang Svay Chek A, B, and C) of the Prey Kabas District, Takeo Province. This area is located in the southern part of Cambodia, where the recovery of adult O. viverrini worms was recently reported. From May 2006 until May 2010, fecal examinations were performed on a total of 1,799 villagers using the Kato-Katz thick smear technique. In the 3 villages, the overall positive rate for helminth eggs ranged from 51.7 to 59.0% (av. 57.4%), and the percentage positive for O. viverrini was 46.4-50.6% (47.5%). Other helminths detected included hookworms (13.2%), echinostomes (2.9%), Trichuris trichiura (1.3%), Ascaris lumbricoides (0.6%), and Taenia spp. (0.06%). The prevalence of O. viverrini eggs appeared to reflect a lower infection in younger individuals (<20 years) than in the adult population (>20 years). Men (50.4%) revealed a significantly higher (P=0.02) prevalence than women (44.3%). The Ang Svay Chek villages of the Prey Kabas District, Takeo Province, Cambodia have been confirmed to be a highly endemic area for human O. viverrini infection.     

Distribution of Agrobiodiversity in Home Gardens along the Corrientes River,Peruvian Amazon

Distribution of Agrobiodiversity in Home Gardens along the Corrientes River, Peruvian Amazon. This paper examines crop species diversity in home gardens of traditional communities along a remote tributary in northeastern Peru. A large-scale survey was conducted of 300 gardens in 15 villages along a 150 km reach of the Corrientes River. Study villages vary notably in community size, ethnicity of residents (Achuar, Urarina, mestizo), and proximity to the regional town (Trompeteros) as well as to oil wells. Gardens were inventoried and interviews conducted with garden tenders to provide data on socioeconomic characteristics of the household and contextual conditions. Multiple regression analyses identified the determinants of species diversity. Results indicate high crop diversity—the highest yet reported for sites in the Amazon basin—particularly among the Achuar people. Garden species diversity is greatest in larger villages and, surprisingly, in those villages located nearer to the oil company. Within villages, households with larger land holdings (and gardens), more in-house labor, and garden tenders who are older and female tend to have more diverse gardens. A small number of households (15/300) were found to hold exceptional diversity, often older and land-wealthier households located on the outskirts of villages. These farmers held, on average, three times the number of species as a typical village garden and 60% of all species encountered in the study.     

Arundo micrantha,a new reed species for Italy,threatened in the freshwater habitat by the congeneric invasive A. donax

Arundo micrantha Lam., a reed species from southern Mediterranean area, has found in Sardinia. Its presence represents the first record for Italy and the third one for western Europe. Investigations on distribution and ecology of the Sardinian population have been carried out, with special focusing on synecology of the species. A. micrantha has found in 40 localities mainly distributed along temporary streams and permanent rivers in the central and southern part of the island. Most of Sardinian populations occurs on alluvial soils in Thermomediterranean bioclimatic context. The autonomy of Sardinian phytocoenoses was characterized with the definition of exclusive floristic taxa, biological and chorological elements, and syndinamic relationships with other assemblages. Comparing the community with other reed beds from the Mediterranean basin, a marked floristic differentiation arose between the phytocoenoses characterized by autochthonous Arundo species and those dominated by the invasive Arundo donax. Finally, management activities are proposed to ensure the conservation of this threatened autochthonous plant community in freshwater habitat.     

Typologie et provenance de l’obsidienne du site néolithique d’A Guaita (NW Cap Corse,Corse, France)

The provenance of a large fraction of the obsidians from the Neolithic site of A Guaita was determined for its three chronocultural layers, between the second half of the 6th millennium and the beginning of the 4th millennium. The elemental composition of 140 samples was obtained by scanning electron microscopy (SEM–EDS) and/or ion beam analysis (PIXE). One hundred and thirty-eight obsidians were found to come from Sardinia and the remaining two from Palmarola Island. This result confirms the almost unique presence of Sardinian obsidians in Corsica and extends this observation to the northern end of the island. The three main Sardinian obsidian types, SA, SB2, and SC, are represented at A Guaita, with a predominance of SB2 and SC. The occurrence of two obsidians from Palmarola suggests that occasional contacts with the Italian Peninsula were in effect from the 6th millennium, in agreement with previous data from ceramics.