Estimating population genetics and forensic efficiency of the GlobalFiler PCR amplification kit in the population of Sardinia (Italy).

We recently characterized an Alu-mediated recombination causing the loss of the complete HFE gene sequence. Here, we describe the case of a novel homozygous patient. We further show that HFE deletion results from a founder effect and that it represents the common cause of hemochromatosis in Sardinia. We recently reported the case of a 47-year old woman with a moderate iron overload due to an Alu-mediated recombination causing the loss of the complete HFE gene sequence.1 The same chromosomal alteration was identified by Pelucchi and co-workers in another woman. Despite a younger age at diagnosis (29 years), their patient showed a more impressive iron overload.2 A third case, a man, came to our attention. At the age of 44 he showed a transferrin saturation level of 80% and a serum ferritin level of 2080 μg/L. He was not genotyped for the p.C282Y and p.H63D variations because of an inability to amplify the HFE exons 2 and 4. We confirmed absence of the HFE gene in this patient but we were also interested in its origins. Indeed, the patient and both previously reported women were of Sardinian descent. The Sardinian population is genetically differentiated from the other Caucasian populations.3 It represents a genetic isolate where the p.C282Y mutation is considered as rare or even absent.4 This led us to assume that the HFE deleted allele was present at the population level and, related to a founder effect, was the common cause of hemochromatosis in this Mediterranean island. To characterize the contribution of the HFE deletion in the Sardinian population, we first established the frequency of this mutation in a sample set of 198 controls who originated from different districts of the island (90% of them were from South Sardinia, while the others originated from central and Northern parts of the island). Genotype analysis was performed using a rearrangement specific PCR, as previously described.1 The HFE deletion was detected at the heterozygous state in 4 subjects, giving a carrier frequency of 2.02% and an estimated homozygous frequency of 0.01% (one person in 10,000). We also looked for the p.C282Y mutation. It was identified at the heterozygous state in one of 193 subjects (0.52%). We next proceeded to analyze polymorphic microsatellite repeat markers flanking HFE. Based on results from the consanguineous family reported in our initial study,1 we selected a set of informative markers and defined a first chromosomal region of 12.049 megabases (Mb). This chromosomal region encompassed two HLA-class I loci which were added to the haplotypes analysis. Final results are summarized in Table 1 and Figure 1. A conserved haplotype of 3.150 Mb was deduced from the consideration of alleles shared by the 2 homozygous cases identified by us (P1, P2), and the 4 mutation carriers (MC 1–4). However, a recombination event could account for differences in HLA-A, HLA-B and D6S273 alleles of one of the study subjects (MC 3 in Table 1). This allowed us to consider a common haplotype of 7,359 Mb. Figure 1. Physical map of the chromosome 6 region flanking HFE. Distance between the D6S1621 and D6S2414 marker is indicated in grey; the arrow marks a possible ancestral haplotype. Distance between the D6S1621 and D6S1022 markers is indicated in black; the arrow ... Table 1. Allelic distribution of markers surrounding HFE. *The parentheses mark differences between the 6 individuals; these differences are probably related to a recombination event on chromosome 6 of the mutation carrier number 3. By their position on the same maritime routes, the histories of the West Mediterranean islands are very similar. Studies based on HLA polymorphisms have confirmed singularity of these populations, and have further revealed a close relationship between the Sardinian and Corsican populations. However, it must be pointed out that the HLA-A*2-B*58 haplotype is frequent in Sardinia (4.9%) and almost absent in the other West Mediterranean islands (Corsica and Balearic Islands). In fact, this haplotype could be of African origin.5 If so, comparing frequency of the HFE deleted allele (2%) to that of the HLA-A*2-B*58 haplotype (4.9%), one may assume that deletion of the HFE gene arose in the Sardinian population after contacts with African populations. But an African ancestry for the HFE deletion cannot be completely excluded. To conclude, we show that HFE deletion results from a founder effect rather than that of a mutational hotspot. We also demonstrate that, with an estimated homozygous frequency of one person in 10,000, HFE deletion is the common cause of hemochromatosis in Sardinia.

The genetic structure of Balearic islands (Corsica and Sardinia), situated on the same trans-Mediterranean maritime routes and having very similar histories, were compared and their position among the neighbouring Caucasian populations was inferred. For this purpose, three HLA loci (HLA-A, -B and -Cw) were typed at the DNA level in these populations and the allelic and haplotypic frequencies were estimated. Because previous studies have shown common genetic features in the Sardinians and Basques, HLA-Cw molecular typing was also performed in a sample of French Basques in order to establish the haplotypic structure of this population for a more accurate comparison with the three others. By its allelic composition, the Corsican population has an intermediate position between the two other islander populations. Its close relationship with the Sardinian population, however, was clearly revealed by the phylogenetic analysis which also suggests a proximity with eastern Mediterranean peoples, whereas the Balearic islands are more narrowly related to Spain and western Europe. Peculiarities were observed in the distributions of some common haplotypes in the populations of the islands that confirm the results of the phylogenetic analysis and could be related to their history. Noteworthy is the presence of the HLA-A30-Cw*0501-B18 haplotype at frequencies approximately 2% in Corsica and the Balearic islands, yet the estimated frequencies of this haplotype are much lower than in the Sardinian and Basque populations.

Sampling strategies are crucial issues in population genetics and anthropological studies. The sampling choice is related to the research question and the type of markers used. In this research, we compared two different sampling strategies in the Sardinian linguistic isolate of Carloforte (Italy). A first sampling (N = 49) was carried out through grandparents criterion: individuals selected for the study were born and resident in Carloforte, and unrelated for at least three generations. A second sampling (N = 50) was based on founders surnames (FS): selected participants were proved to be descendants of the village founders, and to have no ancestors in common, at least up to the grandparental generation. The group selected through FS showed a greater gene diversity, which was confirmed by both network and haplogroup analysis. Among the shared haplogroups, we find clear differences in their frequencies. Sampling through grandparents criterion showed essentially the same haplogroups found in Sardinia, and with similar frequencies. Interesting results came from genetic tree. The FS sampling clustered with Northern African populations and it is located very far from Italian and Sardinian populations, whereas the grandparents criterion sampling clustered with Italian populations and it is located close to the other Sardinian populations. Results showed that different sampling strategies can lead to contrasting results. As sampling through grandparents criterion is influenced by recent gene flow, we hypothesize that the difference observed with the two sampling strategies is due to the merging of Carloforte with Sardinian populations.

fshr: a fish sex-determining locus shows variable incomplete penetrance across flathead grey mullet populations.

Salicornia is a highly taxonomically problematic genus due to the reduced morphological observable characters. Ten Eurasian species are currently recognized: S. alpini, S. europaea, S. fruticosa, S. hispanica, S. lagascae, S. perennans, S. perennis, S. persica, S. procumbens, and S. pruinosa. In addition, eleven subspecies are accepted, mainly based on their distribution areas. Along the Venetian coasts and in Sardinia, in the past, an endemic species called S. veneta was recognized, but this name was later synonymized with S. procumbens subsp. procumbens. The aim of the present research is investigating different Italian Salicornia populations by a molecular point of view, using the nuclear ribosomal external transcribed spacer ETS and the plastid psbA-trnH intergenic spacer. A particular focus is on the comparison between Venetian (including those occurring in locus classicus of S. veneta) and Sardinian S. procumbens and other Italian populations of this species. The molecular analyses based on the plastid marker highlight that the Italian S. procumbens populations form two well distinct groups. In particular, some of the Venetian (Locus classicus of S. veneta) and all the Sardinian specimens are genetically distinct (=plastid haplotype 1) from the other investigated populations (=plastid haplotype 2). This indicates that the psbA-trnH haplotype 1 glassworts represent a distinct entity, which we suppose to coincide with the former S. veneta. Therefore, we suggest to recognize this taxonomic entity at the subspecies rank, as S. procumbens subsp. veneta comb. and stat. nov. However, contrary to the results found with the plastid psbA-trnH intergenic spacer, the ETS locus does not show a separation into two distinct clades for S. procumbens, probably due to a different evolution of the two loci. Nevertheless, in the ETS phylogenetic reconstruction, the Sardinian specimens (=ribotypes 2 and 3) are placed, together with a Moroccan sample, in a subclade separated from all the other S. procumbens. These results suggest that the Sardinian populations can represent a subspecies/incipient speciation process, probably due to geographic isolation. In the light of this, morphometric analyses (k-means, MANOVA, PCA, DA, and Box-Plot) have been carried out on the Sardinian and Venetian populations to verify if this distinction is detectable also by a morphological point of view. The morphometric analyses highlight the existence of two groups, concerning both the nuclear and plastid trees. Six characters were found to be diagnostic.

Since human skulls may be used as a benchmark of the evolutionary process, the aim of the present study is to assess the cranial affinity of Sardinian populations from different chronological periods, with a standard index to evaluate its benefits for orthodontic purposes. Craniometric variables from four throughout cephalograms (anterior and lateral) of 72 units from historical Sardinian populations, two prehistoric, one medieval, and one modern were compared to the Bolton standard. A one-way analysis of variance (ANOVA) was performed for means comparison. A hierarchical cluster analysis and the bootstrap technique for the reliability of the dendrogram were used. Length data revealed statistically significant results (p < 0.01). Usually, the medieval population showed higher mean values compared to the other groups; the prehistoric population presented the highest value of Euclidean distance when compared to the medieval; the modern showed no affinity to prehistoric populations nor to the Bolton standard. The length and the breadth of the neurocranium, maxillary–alveolar length, orbital height, maximum cranial breadth, and external palate breadth contributed to the dissimilarity among populations. The dissimilarities in the craniometric measurements of Sardinian populations are remarkable. Therefore, the main outcome showed that the craniometric standards of the Bolton standard are not applicable across the Sardinian population.

Mitochondrial phylogeography of the Bedriaga’s rock lizard, Archaeolacerta bedriagae (Reptilia: Lacertidae) endemic to Corsica and Sardinia

Using mtDNA sequences and 12 microsatellite loci, we compare populations of Testudo graeca from Sardinia and North Africa. The observed pattern of almost no differentiation combined with reduced variation in the Sardinian population is consistent with introduction in prehistoric or historic times from what is now Tunisia and neighbouring Algeria. Furthermore, in the light of the recently published recommendation to eradicate the non-native T. graeca from Italy, we review recent studies on the archaeological and fossil record, on the phylogeography and population genetics of the three other chelonian species occurring in Sardinia (Emys orbicularis, T. hermanni, T. marginata). We conclude that the extant Sardinian populations of all four species are not native. However, they are and should be safeguarded under EC law (Council Regulation No 338/97 on the Protection of Species of Wild Fauna and Flora; Flora Fauna Habitat Directive: Appendix IV, Art. 12) because they serve as a back-up for the declining mainland populations. Moreover, these populations constitute an important part of the human-shaped natural heritage of the Mediterranean.

The distribution of beta-globin cluster haplotypes has been studied in the populations of Corsica (France) and Sardinia (Italy). The analysis was carried out using five restriction fragment length polymorphism markers on chromosome 11 inside the beta-globin cluster using the restriction enzymes HincII and HindIII. The results show a remarkable heterogeneity within the two islands. However, the presence of rare haplotypes common to the most conservative areas (Nuoro and Corte) of the two islands is particularly interesting. These data support the hypothesis of a common origin of the populations of Sardinia and Corsica during the middle and upper Paleolithic periods and could be interpreted as a founder effect.

Brown trout is a species complex (Salmo trutta complex, L., 1758) including both widespread invasive (non‐native hatchery strains) lineages and endangered local‐endemic lineages, among which is the Sardinian trout, the only native salmonid present in Sardinia. Multiple stressors (e.g. the spread of stocked brown trout of Atlantic origin, habitat alteration and climate change) combine to seriously threaten the persistence of wild native populations. In this study, the origin, population genetics and demography of wild Sardinian brown trout populations were extensively investigated. A total of 274 trout individuals collected from 12 hydro‐geographical basins were analysed using both mitochondrial (control region) and nuclear (LDH‐C1* locus and 10 microsatellites) markers. Although stocking activities have altered the native genetic makeup of some populations in the study area, several (almost) uncontaminated populations showing strong genetic structure were detected. Eroded intra‐population diversity, as well as small effective population size, sometimes associated with a bottleneck signal was also found. The genetic characteristics of Sardinian trout populations described in this study are probably due, at least partly, to the peculiarity of local environmental conditions at the margin of the ecological niche for salmonids. Based on the results of this study, the need for urgent measures of conservation aimed to ensure the near future viability of the last wild Sardinian trout populations was discussed.

The Endangered Corsican red deer Cervus elaphus corsicanus was extirpated from Corsica in the early 1970s, at which time the Sardinian population fell to <250 individuals. The Sardinian authorities agreed to protect this subspecies and to secure its reintroduction in Corsica, a natural choice, considering ethological and historical descriptions. Since the beginning of 1985, when the first deer destined for captive breeding and eventual reintroduction arrived in Corsica, the population increased from 13 Sardinian founders to 106 captive animals under constant monitoring in three enclosures (Quenza, Casabianda and Ania di Fium'Orbu). The sites of Quenza, Chisà and Santo Pietro di Venaco were selected by the Regional Nature Park of Corsica for the reintroduction into the wild that began in 1998. Currently the size of the whole Corsican population is c. 250 individuals. These deer are still closely monitored and studied, both in enclosures and in the wild, to secure the long-term conservation of this subspecies. The Corsican and Sardinian populations together now total slightly >1,000, and the subspecies could therefore be downgraded to Near Threatened on the IUCN Red List.

The study focuses on the analysis of the SOMK1 skullcap, a Mesolithic human remain from Sardinia encased in a thick concretion. The aim is to address the challenges presented by the concretion, which prevents direct examination, in order to explore the individual's biological and cultural relevance, duly contextualized within a broader population dynamic. The SOMK1 skullcap was examined using a combination of chemical and digital techniques. The chemical analyses revealed that the red concretion encasing the skullcap was hematite-based and of cultural origin, thus preventing its removal. Computed tomography (CT) scans were used to virtually draw out and reconstruct the skullcap, enabling a detailed morphological analysis, as well as linear and geometric morphometric measurements. The analyses were contextualized by comparing SOMK1 against three samples, namely: island-dwelling hunter-gatherers dating to 800 CE, pre-Last Glacial Maximum (pre-LGM) European fossils, and Sardinian populations spanning from the Neolithic to modern times. Digital analyses showed a dolichocephalic calvarium with morphometric traits consistent with a male individual. The cranial morphology matches pre-LGM European populations, differing from the brachycephalic forms observed in some Neolithic Sardinian populations. These findings suggest a possible link to earlier European populations, emphasizing the differences with later Sardinian groups. This study shows how digital methods like CT scanning and virtual reconstruction effectively analyze human remains in concretion. The findings offer new insights into Mesolithic cranial morphology in the Mediterranean during the Early Holocene, enhancing our understanding of prehistoric Sardinia's population dynamics and cultural practices.

Over the last ten years the population of the Mediterranean island of Sardinia has been object of numerous studies in the fields of anthropology and population genetics. Its insularity, central position in the Mediterranean area and rich historical past have made the island a veritable laboratory for the study and understanding of those interacting evolutionary mechanisms which determine a population's genetic structure. Indeed, from work performed at different levels on genetic structure analysis there emerges an extremely complex picture of the relationships between Sardinian and other Italian and Mediterranean populations, but also of relationships within the Sardinian population itself The diversification from Mediterranean and Italian populations can be explained by Sardinia's historical and demographic past. Internal heterogeneity can be attributed, in part, to strict isolation and the accompanying high levels of endogamy and inbreeding, and in part to the endemic presence of malaria which exerted a strong selective pressure on some characteristics; determining, for example, the differentiation between the plains and the mountain areas. Finally, an influence on Sardinia's biological history not to be neglected could be attributed to the demographic events, which triggered off phenomena of genetic drift and to cultural factors.

Background STR (Short Tandem Repeat) markers are highly polymorphic markers, which are widely used in forensics DNA analysis and aid to ascertain unique genotype profiles of individuals and determine the genetic diversity of the given population. Aim In the present study, an attempt has been made to evaluate the population genetic diversity of the Ramgharia Sikh population of Punjab, India, using 21 autosomal STR loci (D3S1358, vWA, D16S539, CSF1PO, TPOX, D8S1179, D21S11, D18S51, D2S441, D19S433, TH01, FGA, D22S1045, D5S818, D13S317, D7S820, SE33, D10S1248, D1S1656, D12S391, and D2S1338) to augment the emerging forensic database related to the indigenous population of India. Subjects and methods For generation of the database, 200 (blood on FTA card) samples were obtained from genetically unrelated Ramgharia Sikhs residing in the state of Punjab. Twenty-one autosomal STR markers were analysed using the Globalfiler® PCR amplification kit. Results With the help of various statistical tools, a total of 232 alleles were observed and 11.048 ± 1.284 (mean ± standard deviation) alleles per locus were recorded. No locus deviated from Hardy Weinberg Equilibrium. SE33 locus was found to be the most polymorphic and exhibited the highest discrimination power, that is, 0.99. Moreover, results further indicated that Ramgharia Sikhs of Punjab showed a high affinity with Bhils of Madhya Pradesh (India). Thus, the studied population showed genetic proximity with the geographically close populations of India and showed significant genetic variations with distant populations, which was evident from the UPGMA tree and Principal Component Analysis plot. Conclusion Overall, the 21 autosomal STRs were found to be polymorphic in the Ramgharia population and suitable for forensic casework and studies on population genetics.

Background: From the genetic viewpoint, Sardinia is well differentiated from other surrounding populations. In spite of a common ancestral origin, substantial genetic heterogeneity is observed within the island. Matrimonial pattern, as well as past migration movements, may account for the complex genetic structure of Sardinia.Aim: To compare data from uniparental markers in order to highlight the migration pattern of male and female lineages and check their congruence with the demographic data.Subjects and methods: Genomic DNA was obtained from 279 unrelated males selected from three isolated villages and from three open populations representative of North, Central and South Sardinia. The hypervariable region 1 of mtDNA was sequenced and 17 Y-chromosome loci were genotyped. Parameters of within and among populations diversity were calculated and analysis of migration was performed.Results: When analysed as a whole population, demographic data show a balanced movement of males and females in Sardinia, unlike other Italian and European populations. Remarkably, when the island is divided into geographic areas, different migration patterns are clearly recognisable. Whereas North and Central Sardinia populations show a stronger male migration rate, the South Sardinia population shows a stronger female migration rate.Conclusion: Distinct migration patterns of male and female lineages affect the areas investigated differently. These past migration movements are major contributors to the complex genetic structure currently observed in the Sardinian population.