Genetic Substructure Research Articles

Determination of Giardia duodenalis assemblages and multi-locus genotypes in patients with sporadic giardiasis from England.

BackgroundThe protozoan Giardia duodenalis is a common but highly diverse human parasite that comprises a complex of seven morphologically identical genetic assemblages, further divided into sub-assemblages. There is very little information available on the diversity of Giardia sub-assemblages and multi-locus genotypes infecting people in the United Kingdom. In this study we studied the molecular epidemiology of Giardia in symptomatic patients from North West England.MethodsWhole faecal DNA was extracted from the faecal samples of 406 Giardia cases and the parasites assemblage, sub-assemblage and multi-locus genotype were determined using PCR amplification, DNA sequencing and phylogenetic analysis of the beta-giardin, glutamate dehydrogenase, triose-phosphate isomerase and small-subunit ribosomal RNA genes. Information about age, gender and self-reported clinical outcomes was also collected from the patients to check for differences associated with the infecting Giardia assemblage.ResultsOur results showed a difference in the age prevalence of the two assemblages, with assemblage A being more common in older cases. Cases infected with assemblage B more often reported vomiting and a longer illness than cases infected with assemblage A. The majority of infections (64 %) were caused by assemblage B followed by assemblage A (33 %), while mixed-assemblage infections were rare (3 %). Assemblage A isolates mostly belonged to the sub-assemblage AII and showed completed identity with previously described isolates. The level of genetic sub-structuring was significantly higher in assemblage B isolates, since a higher proportion of novel assemblage B sequences was detected compared to assemblage A. A high number of assemblage B sequences showed heterogeneous nucleotide positions that prevented the unambiguous assignment to a specific sub-assemblage. Both previously described and novel multi-locus genotypes were described in both assemblages, and up to 17 different assemblage B multi-locus genotypes were found.ConclusionsWe have produced the first data on the parasite multi-locus genotypes in the UK and have demonstrated that the molecular diversity of Giardia is similar to other developed countries. Furthermore, we showed that the parasite assemblages infecting humans may be associated with patients of different ages and with different clinical outcomes.Electronic supplementary materialThe online version of this article (doi:10.1186/s13071-015-1059-z) contains supplementary material, which is available to authorized users.

Merino and Merino-derived sheep breeds: a genome-wide intercontinental study.

BackgroundMerino and Merino-derived sheep breeds have been widely distributed across the world, both as purebred and admixed populations. They represent an economically and historically important genetic resource which over time has been used as the basis for the development of new breeds. In order to examine the genetic influence of Merino in the context of a global collection of domestic sheep breeds, we analyzed genotype data that were obtained with the OvineSNP50 BeadChip (Illumina) for 671 individuals from 37 populations, including a subset of breeds from the Sheep HapMap dataset.ResultsBased on a multi-dimensional scaling analysis, we highlighted four main clusters in this dataset, which corresponded to wild sheep, mouflon, primitive North European breeds and modern sheep (including Merino), respectively. The neighbor-network analysis further differentiated North-European and Mediterranean domestic breeds, with subclusters of Merino and Merino-derived breeds, other Spanish breeds and other Italian breeds. Model-based clustering, migration analysis and haplotype sharing indicated that genetic exchange occurred between archaic populations and also that a more recent Merino-mediated gene flow to several Merino-derived populations around the world took place. The close relationship between Spanish Merino and other Spanish breeds was consistent with an Iberian origin for the Merino breed, with possible earlier contributions from other Mediterranean stocks. The Merino populations from Australia, New Zealand and China were clearly separated from their European ancestors. We observed a genetic substructuring in the Spanish Merino population, which reflects recent herd management practices.ConclusionsOur data suggest that intensive gene flow, founder effects and geographic isolation are the main factors that determined the genetic makeup of current Merino and Merino-derived breeds. To explain how the current Merino and Merino-derived breeds were obtained, we propose a scenario that includes several consecutive migrations of sheep populations that may serve as working hypotheses for subsequent studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-015-0139-z) contains supplementary material, which is available to authorized users.

Genetic diversity and structure in two protected Posidonia oceanica meadows

Posidonia oceanica meadows growing along the west Mediterranean coastline are under continuous anthropogenic pressure. The way meadow health correlates with genetic and genotypic diversity in P. oceanica, is still under debate. Here we report a microsatellite analysis of two P. oceanica meadows living in protected areas of the Ligurian (Monterosso al Mare, MPA of “Cinque Terre”) and central Tyrrhenian Sea (Santa Marinella, regional Site of Community Importance). Both meadows were recently classified as “disturbed”, according to shoot density and other phenological parameters. Between the two meadows, Santa Marinella showed higher genetic diversity, while clear genetic substructure was present in both sites, reflecting high spatial heterogeneity. The present study suggests that genetic diversity does not match unequivocally with shoot density and leaf morphology and that small scale intra-meadow heterogeneity is an important factor to consider for establishing the relation between genetic/genotypic variability and health of natural seagrass meadows.

Conservation genetics of Magnolia acuminata, an endangered species in Canada: Can genetic diversity be maintained in fragmented, peripheral populations?

The genetic diversity of peripheral populations is potentially important to the future adaptive capacity of species, although may be difficult to predict. A large number of species-at-risk in Canada are at the northern edge of their distribution, and many of these live in fragmented habitat. We used nuclear and chloroplast markers to assess patterns of genetic diversity and differentiation within and among populations of Canadian Magnolia acuminata (Cucumber tree), an endangered species in Canada that extends as far north as the fragmented Carolinian forest in southern Ontario. We also compared the genetic composition of Canadian M. acuminata to populations sampled throughout its central distribution in the USA. We found a high proportion of shared microsatellite alleles, plus a single cpDNA haplotype, distributed throughout the entire M. acuminata range. We also found that despite occupying fragmented habitat at their range periphery, Canadian populations showed little reduction in genetic diversity relative to the USA populations, and we attribute this to effective historical dispersal in a long-lived, polyploid species. However, a combination of private alleles, genetic substructuring, and lower levels of genetic diversity in seedlings compared to mature trees, suggests that current levels of gene flow are relatively low among Canadian populations. Therefore, despite high levels of genetic diversity in Canadian M. acuminata, managers should be aware that without intervention, populations will likely become increasingly isolated and experience a reduction in genetic diversity which in turn may threaten their long-term survival in Canada.

A new species of fish-eating rat, genus Neusticomys (Sigmodontinae), from Ecuador.

Inthis study, the genetic substructure and morphology of the species Neusticomysmonticolus was evaluated. A nuclear marker and mitochondrial maker were used to examine phylogeographic structure and to estimategenetic distances. Two statistical measurement analyses were applied to morphological data. These data recovered two morphologically distinct phylogeographic groups corresponding to populations on the eastern and western slopes of the Andes. Further, these eastern and western Andean slope populations of N. monticolus are 8.5 % divergent using sequence data from cytochrome-b (0.8 % divergent in the interphotoreceptor retinoid-binding protein gene). Populationscurrently assigned to N.monticolus constitutea species complex. The name N.monticolus is here restricted to western Andean slope populations. Populations on the eastern slope of the Andes are assigned to a new species, to which the authors assign the name Neusticomys vossi sp.nov.

Statistical and population genetics issues of two Hungarian datasets from the aspect of DNA evidence interpretation

When the DNA profile from a crime-scene matches that of a suspect, the weight of DNA evidence depends on the unbiased estimation of the match probability of the profiles. For this reason, it is required to establish and expand the databases that reflect the actual allele frequencies in the population applied. 21,473 complete DNA profiles from Databank samples were used to establish the allele frequency database to represent the population of Hungarian suspects. We used fifteen STR loci (PowerPlex ESI16) including five, new ESS loci. The aim was to calculate the statistical, forensic efficiency parameters for the Databank samples and compare the newly detected data to the earlier report. The population substructure caused by relatedness may influence the frequency of profiles estimated. As our Databank profiles were considered non-random samples, possible relationships between the suspects can be assumed. Therefore, population inbreeding effect was estimated using the FIS calculation. The overall inbreeding parameter was found to be 0.0106. Furthermore, we tested the impact of the two allele frequency datasets on 101 randomly chosen STR profiles, including full and partial profiles. The 95% confidence interval estimates for the profile frequencies (pM) resulted in a tighter range when we used the new dataset compared to the previously published ones. We found that the FIS had less effect on frequency values in the 21,473 samples than the application of minimum allele frequency. No genetic substructure was detected by STRUCTURE analysis. Due to the low level of inbreeding effect and the high number of samples, the new dataset provides unbiased and precise estimates of LR for statistical interpretation of forensic casework and allows us to use lower allele frequencies.

Interethnic variation of the MMP-9 microsatellite in Amerindian and Mexican Mestizo populations: considerations for genetic association studies.

We studied the interethnic variation of the MMP-9 microsatellite in the Mestizo and Amerindian populations using blood samples collected from 435 healthy unrelated individuals from the Central Valley of Mexico. DNA samples were genotyped using the -90 (CA)12-27 repeat near the MMP transcriptional start site using capillary electrophoresis. Our data were compared with those from African, Asian, and European populations (N = 729). Both Mestizo and Amerindian populations were in Hardy-Weinberg equilibrium (P ≥ 0.05). However, strong genetic heterogeneity was found within the Mestizo population (94%, P ≤ 0.0001), which exhibited the highest frequency of Amerindian, African, and European alleles. Likewise, Amerindians showed 6.7% variation among populations (P ≤ 0.0001), suggesting a genetic substructure potentially associated with linguistic affiliations. These findings were corroborated with principal component and population differentiation analyses, which showed relative proximity among the Mestizos and their historical parental populations: Asian (FST ≥ 0.05), European (FST ≥ 0.09), and African (FST ≥ 0.02). Nevertheless, important differences were found between Mestizo and Nahuas (P ≤ 0.0001), and between Mestizo and Me'Phaas (P ≤ 0.0001). These findings highlight the importance of determining local-specific patterns to establish the population variability of MMP-9 and other polymorphic markers. Validation of candidate markers is critical to identifying risk factors; however, this depends on knowledge of population genetic variation, which increases the possibility of finding true causative variants. We also show that dissimilar ethnic backgrounds might lead to spurious associations. Our study provides useful considerations for greater accuracy and robustness in future genetic association studies.

Human genetic diversity in the Japanese Archipelago: dual structure and beyond.

The Japanese Archipelago stretches approximately 3,000 kilometers from Hokkaido in the north to the Ryukyu Islands in the south, and has seen human activity since at least 30 thousand years ago (KYA). The Jomon period from 16 to 3 KYA is associated with cord-marked pottery and the people at that time, who were hunter-gatherers, occupied a range of locations across the Japanese Archipelago. The Yayoi period from 3 to 1.7 KYA saw the introduction of migrants from the Asian Continent who brought rice agriculture to the archipelago. The dual-structure model, which is based on craniofacial measurements, proposes that admixture between the Jomon and Yayoi people resulted in current-day Japanese. Subsequent genetic studies using uniparental and autosomal markers in current-day and ancient human samples are widely in support of the dual-structure model. These genetic data have also unveiled the uniqueness of the indigenous Ainu and Ryukyuan people while further demonstrating the genetic substructure within the Mainland Japanese.

Using heterozygosity-fitness correlations to study inbreeding depression in an isolated population of white-tailed deer founded by few individuals.

A heterozygosity–fitness correlations (HFCs) may reflect inbreeding depression, but the extent to which they do so is debated. HFCs are particularly likely to occur after demographic disturbances such as population bottleneck or admixture. We here study HFC in an introduced and isolated ungulate population of white-tailed deer Odocoileus virginianus in Finland founded in 1934 by four individuals. A total of 422 ≥ 1-year-old white-tailed deer were collected in the 2012 hunting season in southern Finland and genotyped for 14 microsatellite loci. We find significant identity disequilibrium as estimated by g2. Heterozygosity was positively associated with size- and age-corrected body mass, but not with jaw size or (in males) antler score. Because of the relatively high identity disequilibrium, heterozygosity of the marker panel explained 51% of variation in inbreeding. Inbreeding explained approximately 4% of the variation in body mass and is thus a minor, although significant source of variation in body mass in this population. The study of HFC is attractive for game- and conservation-oriented wildlife management because it presents an affordable and readily used approach for genetic monitoring that allowing identification of fitness costs associated with genetic substructuring in what may seem like a homogeneous population.

Population genetics for 23 Y-STR loci in Tibetan in China and confirmation of DYS448 null allele

Tibetan is one of 56 ethnic groups in China, where a level of genetic sub-structure might be expected. Although a global analysis of Y-chromosomal haplotype diversity for 23 STR loci and Y-STR databases with PPY23 kit were created with collaborative effort, there was a lack of data for Tibetan population. In this study we evaluated 248 unrelated male individuals of Chinese Tibetan living in the Tibet Autonomous Region to explore the underlying genetic structure of Tibetan populations. These samples were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) by using PPY23 kit. A total of 224 different haplotypes were found. Haplotype diversity was 0.9990. Both Rst pairwise analyses and multidimensional scaling plot showed the genetic structure of Tibetan population was significantly different from some of Chinese ethnic groups and neighboring populations. There were few interesting null features at DYS448 observed by PPY23 that deserved some comment. It revealed that PPY23 marker set provided substantially stronger discriminatory power in Tibetan population.

Assessment of Genetic Diversity and Population Structure in a Global Reference Collection of 531 Accessions of Carthamus tinctorius L. (Safflower) Using AFLP Markers

Carthamus tinctorius L. (safflower) is an important oilseed crop that is cultivated in several countries. The present study investigates the genetic diversity and population structure of 531 safflower accessions from 43 countries representing all safflower growing regions of the world. Diversity analysis was performed using ten informative EcoRI/MseI amplified fragment length polymorphism primer pairs that were identified by screening 150 primer combinations. The selected primer pairs generated 381 fragments of which 157 were polymorphic among the analyzed accessions. The genetic diversity indices obtained for the entire collection (I = 0.4536, H = 0.2955) indicated high levels of molecular variability. The distance-based, neighbor-joining method classified the accessions into six clusters with internal subgroupings that were in consonance with 19 clusters obtained using Bayesian model-based BAPS analysis. Clusters obtained through STRUCTURE analysis (at K = 4) could not be correlated with their geographically diverse origins, while BAPS analysis (at K = 19) revealed geographical delineation with low admixture levels among most of the studied accessions. Accessions from Far East and Egypt clustered in distinct groups, indicating conserved nature of their gene pools. The Near East and Iran–Afghanistan regions were collectively found to harbor maximum diversity in accordance with earlier reports. Accessions from the Indian subcontinent showed substantial diversity that was previously undetected. The American accessions showed low molecular variability in contrast to earlier studies. Genetic sub-structuring within gene pools and inter-relationships between accessions belonging to different regional pools was also observed. To the best of our knowledge, this is the first comprehensive study of existing genetic variability in a large collection of safflower germplasm with a global distribution, which provides a more accurate representation of genetic structuring in the crop. This information will facilitate selection of elite genotypes for broadening the genetic base of various breeding programs in safflower.

Limited gene flow and high genetic diversity in the threatened Betic midwife toad (Alytes dickhilleni): evolutionary and conservation implications

Habitat fragmentation may involve a loss of genetic diversity and increments the vulnerability to species persistence. It could be a particular issue when coupled with other negative factors as the predicted climatic changes and the emergence of infectious diseases. In Southern Iberian Peninsula several endemic amphibian species have confined and fragmented distributions, including the Betic midwife toad Alytes dickhilleni. Herein, we present the first range-wide assessment of genetic diversity and structure in this species, using mitochondrial and microsatellite data. A mitochondrial fragment of the ND4 gene was amplified for 65 individuals and a set of 20 microsatellite loci, specifically developed for this species, was genotyped for 490 individuals from several sampling sites distributed across the species entire range. While both markers revealed high genetic diversity, only for microsatellites a marked genetic substructure was apparent. Our results evidence low levels of gene flow, suggesting the persistence of the species in fragmented habitats for several generations and a very limited connectivity between most of mountain ranges. The high diversity within A. dickhilleni populations could help to respond to the emergence of new diseases and to the predicted effects of climatic changes in Southeastern Iberian Peninsula. We hypothesize that the lack of gene flow is due to the absence of available breeding habitats and recommend that future management efforts of A. dickhilleni include the creation and maintenance of aquatic breeding habitats in a way that most of genetic diversity is preserved.

The influence of environmental variability of a coastal lagoon ecosystem on genetic diversity and structure of white seabream [Diplodus sargus (Linnaeus 1758)] populations

AbstractAs coastal lagoons serve as nursery areas for some marine and estuarine fish, selective pressures of these brackish or hypersaline lagoons may influence the genetic structure of species and populations. We examined spatial and temporal genetic patterns at eight microsatellite loci in white seabream [Diplodus sargus (Linnaeus 1758)] recruits from the Mar Menor (Southeast Spain) and compared these loci with those in coastal populations from the open sea, observing a high degree of genetic diversity and spatio‐temporal genetic stability. However, the results suggest the presence of subpopulations or genetic substructures in the Mar Menor D. sargus population that could be interpreted as a homogeneous mixture of individuals from three differentiated subpopulations in the Mediterranean and evidence of the Wahlund effect. It also suggests that D. sargus adults return to their original spawning habitat, thus conserving the genetic differences among the respective populations over time. Overall, this study demonstrates the importance of the Mar Menor coastal lagoon as a nursery area for the conservation of genetic diversity of D. sargus populations.

Ethnolinguistic structuring of sorghum genetic diversity in Africa and the role of local seed systems.

Sorghum is a drought-tolerant crop with a vital role in the livelihoods of millions of people in marginal areas. We examined genetic structure in this diverse crop in Africa. On the continent-wide scale, we identified three major sorghum populations (Central, Southern, and Northern) that are associated with the distribution of ethnolinguistic groups on the continent. The codistribution of the Central sorghum population and the Nilo-Saharan language family supports a proposed hypothesis about a close and causal relationship between the distribution of sorghum and languages in the region between the Chari and the Nile rivers. The Southern sorghum population is associated with the Bantu languages of the Niger-Congo language family, in agreement with the farming-language codispersal hypothesis as it has been related to the Bantu expansion. The Northern sorghum population is distributed across early Niger-Congo and Afro-Asiatic language family areas with dry agroclimatic conditions. At a finer geographic scale, the genetic substructure within the Central sorghum population is associated with language-group expansions within the Nilo-Saharan language family. A case study of the seed system of the Pari people, a Western-Nilotic ethnolinguistic group, provides a window into the social and cultural factors involved in generating and maintaining the continent-wide diversity patterns. The age-grade system, a cultural institution important for the expansive success of this ethnolinguistic group in the past, plays a central role in the management of sorghum landraces and continues to underpin the resilience of their traditional seed system.

Serotonin transporter gene 5-HTTLPR VNTR allele frequency distribution in Africa and Eurasia

Background. VNTR-polymorphism at 5 HTTLPR regulatory region of human serotonin transporter gene SLC6A4, which is associated with some psychiatric diseases and personality traits, is presented by two alleles, S and L, affecting the gene transcription level. A correlation between the S allele frequency in populations of European and Asian origin and a Hofstede’s individualism-collectivism index was revealed and a hypothesis of culture-gene coevolution was suggested (Chiao, Blizinsky, 2010). Methods. As another reason for the correlation we examined underlying population genetic substructure, which may affect genetic association level. Results. We have experimentally established the 5 HTTLPR genotypes for 2144 individuals to calculate S and L allele frequencies in 21 populations of Eurasia and Africa. In contrast to Eurasia populations, we have found low S allele frequencies in all four African populations studied, although the collectivism index in the populations was high. The total set of Eurasian and African populations analysis does not confirm the correlation (R= 0.263, p=0.146). We have applied principal component (PC) analysis to check a correlation between S allele frequency distribution and a frequency distribution for alleles which are supposed to be neutral. PC analysis for 68 alleles of five CODIS STR loci revealed correlation between PC2 and S allele frequency (R= 0.820, p0.0001). The correlation means that S allele frequency distribution corresponds to general genetic variability distribution in the human populations studied. The correlation between the Hofestede’s index and frequency of four out of 68 STR alleles is even higher than the correlation with S allele frequency in the same populations. Conclusion. Our findings do not support the hypothesis on culture-gene coevolution of “individualism-collectivism” and the S allele frequency of serotonin transporter gene.

Distribution of anticoagulant rodenticide resistance in Rattus norvegicus in the Netherlands according to Vkorc1 mutations.

BACKGROUNDRodenticide resistance to anticoagulants in Rattus norvegicus will lead to increased difficulties in combating these pest animals. Here, the authors present the results of a survey in the Netherlands where tissue samples and droppings were tested using a newly developed TaqMan PCR test for genotypic variation at codon 139 in the Vkorc1 gene associated with anticoagulant rodenticide resistance. Test results are linked to results of a questionnaire that was conducted among pest controllers.RESULTSGenetic mutations at codon 139 of the Vkorc1 gene in R. norvegicus can be encountered in many parts of the Netherlands. In 34/61 rat tails, a genotype was found that is linked to anticoagulant rodenticide resistance (56%). In droppings, 42/169 samples (25%) showed a resistance-mediating genotype. In addition, indications of a clear genetic substructure in the Netherlands were found. In some regions, only resistance-mediating genotypes were found, corroborating results from the questionnaire in which pest controllers indicated they suspected resistance to anticoagulant rodenticides.CONCLUSIONThis is the first study to demonstrate the presence of multiple genetic mutations at codon 139 of the Vkorc1 gene in R. norvegicus in the Netherlands. As rodenticides should keep their efficacy because they are a last resort in rodent management, more studies are urgently needed that link specific genetic mutations to the efficacy of active substances. © 2014 Society of Chemical Industry

The peopling of Greenland: further insights from the analysis of genetic diversity using autosomal and X-chromosomal markers.

The peopling of Greenland has a complex history shaped by population migrations, isolation and genetic drift. The Greenlanders present a genetic heritage with components of European and Inuit groups; previous studies using uniparentally inherited markers in Greenlanders have reported evidence of a sex-biased, admixed genetic background. This work further explores the genetics of the Greenlanders by analysing autosomal and X-chromosomal data to obtain deeper insights into the factors that shaped the genetic diversity in Greenlanders. Fourteen Greenlandic subsamples from multiple geographical settlements were compared to assess the level of genetic substructure in the Greenlandic population. The results showed low levels of genetic diversity in all sets of the genetic markers studied, together with an increased number of X-chromosomal loci in linkage disequilibrium in relation to the Danish population. In the broader context of worldwide populations, Greenlanders are remarkably different from most populations, but they are genetically closer to some Inuit groups from Alaska. Admixture analyses identified an Inuit component in the Greenlandic population of approximately 80%. The sub-populations of Ammassalik and Nanortalik are the least diverse, presenting the lowest levels of European admixture. Isolation-by-distance analyses showed that only 16% of the genetic substructure of Greenlanders is most likely to be explained by geographic barriers. We suggest that genetic drift and a differentiated settlement history around the island explain most of the genetic substructure of the population in Greenland.

Population substructure in Cache County, Utah: the Cache County study.

BackgroundPopulation stratification is a key concern for genetic association analyses. In addition, extreme homogeneity of ethnic origins of a population can make it difficult to interpret how genetic associations in that population may translate into other populations. Here we have evaluated the genetic substructure of samples from the Cache County study relative to the HapMap Reference populations and data from the Alzheimer's Disease Neuroimaging Initiative (ADNI).ResultsOur findings show that the Cache County study is similar in ethnic diversity to the self-reported "Whites" in the ADNI sample and less homogenous than the HapMap CEU population.ConclusionsWe conclude that the Cache County study is genetically representative of the general European American population in the USA and is an appropriate population for conducting broadly applicable genetic studies.

Genome-wide single-generation signatures of local selection in the panmictic European eel.

Next-generation sequencing and the collection of genome-wide data allow identifying adaptive variation and footprints of directional selection. Using a large SNP data set from 259 RAD-sequenced European eel individuals (glass eels) from eight locations between 34 and 64(o) N, we examined the patterns of genome-wide genetic diversity across locations. We tested for local selection by searching for increased population differentiation using F(ST) -based outlier tests and by testing for significant associations between allele frequencies and environmental variables. The overall low genetic differentiation found (F(ST) = 0.0007) indicates that most of the genome is homogenized by gene flow, providing further evidence for genomic panmixia in the European eel. The lack of genetic substructuring was consistent at both nuclear and mitochondrial SNPs. Using an extensive number of diagnostic SNPs, results showed a low occurrence of hybrids between European and American eel, mainly limited to Iceland (5.9%), although individuals with signatures of introgression several generations back in time were found in mainland Europe. Despite panmixia, a small set of SNPs showed high genetic differentiation consistent with single-generation signatures of spatially varying selection acting on glass eels. After screening 50 354 SNPs, a total of 754 potentially locally selected SNPs were identified. Candidate genes for local selection constituted a wide array of functions, including calcium signalling, neuroactive ligand-receptor interaction and circadian rhythm. Remarkably, one of the candidate genes identified is PERIOD, possibly related to differences in local photoperiod associated with the >30° difference in latitude between locations. Genes under selection were spread across the genome, and there were no large regions of increased differentiation as expected when selection occurs within just a single generation due to panmixia. This supports the conclusion that most of the genome is homogenized by gene flow that removes any effects of diversifying selection from each new generation.

An ancient Mediterranean melting pot: investigating the uniparental genetic structure and population history of sicily and southern Italy.

Due to their strategic geographic location between three different continents, Sicily and Southern Italy have long represented a major Mediterranean crossroad where different peoples and cultures came together over time. However, its multi-layered history of migration pathways and cultural exchanges, has made the reconstruction of its genetic history and population structure extremely controversial and widely debated. To address this debate, we surveyed the genetic variability of 326 accurately selected individuals from 8 different provinces of Sicily and Southern Italy, through a comprehensive evaluation of both Y-chromosome and mtDNA genomes. The main goal was to investigate the structuring of maternal and paternal genetic pools within Sicily and Southern Italy, and to examine their degrees of interaction with other Mediterranean populations. Our findings show high levels of within-population variability, coupled with the lack of significant genetic sub-structures both within Sicily, as well as between Sicily and Southern Italy. When Sicilian and Southern Italian populations were contextualized within the Euro-Mediterranean genetic space, we observed different historical dynamics for maternal and paternal inheritances. Y-chromosome results highlight a significant genetic differentiation between the North-Western and South-Eastern part of the Mediterranean, the Italian Peninsula occupying an intermediate position therein. In particular, Sicily and Southern Italy reveal a shared paternal genetic background with the Balkan Peninsula and the time estimates of main Y-chromosome lineages signal paternal genetic traces of Neolithic and post-Neolithic migration events. On the contrary, despite showing some correspondence with its paternal counterpart, mtDNA reveals a substantially homogeneous genetic landscape, which may reflect older population events or different demographic dynamics between males and females. Overall, both uniparental genetic structures and TMRCA estimates confirm the role of Sicily and Southern Italy as an ancient Mediterranean melting pot for genes and cultures.