Spatial principal component analysis points at global genetic structure in the Western Mediterranean

Multi-dimensional landscape ecological risk assessment and its drivers in coastal areas

The eastern coastal areas of Japan are threatened by multiple ecological risks due to frequent natural disasters, climate changes, human activities, etc. Identification spatio-temporal variations and driving mechanisms of landscape ecological risk could be used as significant basis for policymakers. In this study, taking the eastern coastal areas of Japan affected by the 2011 Great East Japan Earthquake and Tsunami Disaster as the study area, the "Nature-Landscape Pattern-Human Society" (NA-LP-HS) multi-dimensional ecological risk assessment framework was established to analyze the spatio-temporal patterns, and identity driving factors using spatial cluster analysis and spatial principal component analysis (SPCA) based on ArcGIS from 2009 to 2021. The findings revealed the distinct geographic patterns in landscape ecological risk, with a noticeable decline from the southwest to the northeast. During the period from 2009 to 2015, the driving factors leading to a sharp risk increase were natural disasters and vegetation coverage. These high-risk areas were concentrated in Sendai Bay and its surroundings. From 2015 to 2021, ecological instability was primarily attributed to a reduction in vegetation coverage, the occurrence of natural disasters, and heightened rainfall erosion. These high-risk areas were mainly clustered within the Tokyo-centered urban agglomeration. Spatial clustering of ecological risks was obvious across all time periods. The key factors contributing to the clustering of high ecological landscape risks focused on the "landscape pattern" criterion, specifically including vegetation coverage, land use land cover. This study demonstrated the ability of multi-dimensional ecological risk assessment to identify high-risk areas and driving factors, and these results could provide a visual analysis and decision-making basis for sustainable development of coastal areas.

Dinucleotide (CA)n tandem repeats on the human X-chromosome and the history of the Mediterranean populations

BACKGROUND

Tandem repeats (STRs) are genomic markers of particular interest in forensic and population genetics. Most of the population data currently available correspond to the variation of STRs of forensic panels, which barely include dinucleotide tandem repeats.

AIMS

The aim of the study is to test the usefulness of a battery of dinucleotide STRs on the X chromosome for population and forensic studies.

SUBJECTS AND METHODS

A total of 672 individuals from 12 Mediterranean populations and two external references were analysed for 15 X-STR following the instructions of the commercial company and using control DNA from the CEPH centre whose sequences are published in GenBank. Genotypic results were analysed using standard population genetics methods including estimates of linkage disequilibrium, population structure and gene flow. Common forensic efficiency parameters were calculated.

RESULTS

The analysed X-STRs show high values of genetic diversity, comparable to other STRs of more common use. No significant associations between markers were found. A slight population structure was detected between the two shores of the Mediterranean. The X-STRs studied here present a similar degree of variability to that of other X-STRs used in forensics.

CONCLUSION

Tandem-repeated dinucleotides are a good tool for evidencing population differences here. Forensic parameters indicate that the dinucleotide X-STRs are suitable for forensic use.

A survey of sub-Saharan gene flow into the Mediterranean at risk loci for coronary artery disease

This study tries to find detectable signals of gene flow of Sub-Saharan origin into the Mediterranean in four genomic regions previously associated with coronary artery disease. A total of 366 single-nucleotide polymorphisms were genotyped in 772 individuals from 10 Mediterranean countries. Population structure analyses were performed, in which a noticeable Sub-Saharan component was found in the studied samples. The overall percentage of this Sub-Saharan component presents differences between the two Mediterranean coasts. D-statistics suggest possible Sub-Saharan introgression into one of the studied genomic regions (10q11). We also found differences in linkage disequilibrium patterns between the two Mediterranean coasts, possibly attributable to differential Sub-Saharan admixture. Our results confirm the potentially important role of human demographic history when performing epidemiological studies.

Population variation of LIN28B in the Mediterranean: Novel markers for microgeographic discrimination

OBJECTIVES

The aim of this study is to determine whether the LIN28B gene is differentially distributed in the Mediterranean region through the analysis of the allele distribution of three single nucleotide polymorphisms (SNPs), namely rs7759938, rs314277, and rs221639, in 24 populations. These SNPs have been recently related to the age at menarche, pubertal height growth, peripubertal body mass index, levels of prenatal testosterone exposure, and cancer survival.

METHODS

A total of 1,197 DNA samples were genotyped. The allele frequencies were used to determine the relationship between populations, with data from the 1000 Genomes Project being used for external comparisons. The genotype distributions and the population structure between populations and groups of populations were determined.

RESULTS

The population results indicate a significant degree of variation (F_ST  = 0.043, P < 0.0001). Allele frequencies show significant differences among populations. A hierarchical variance analysis is consistent with a primary differentiation between populations on the North and South coasts of the Mediterranean. This difference is especially evident in the unexpected distribution of the SNP rs221639, which shows one of the highest F_ST (11.5%, P < 0.0001) values described in the Mediterranean region thus far.

CONCLUSION

The population differentiation and the structuring of the genetic variance, in agreement with previous studies, indicate that the SNPs in question are good tools for the study of human populations, even at a microgeographic level. Am. J. Hum. Biol. 28:905-912, 2016. © 2016Wiley Periodicals, Inc.

Potential Signals of Natural Selection in the Top Risk Loci for Coronary Artery Disease: 9p21 and 10q11

BACKGROUND

Coronary artery disease (CAD) is a complex disease and the leading cause of death in the world. Populations of different ancestry do not always share the same risk markers. Natural selective processes may be the cause of some of the population differences detected for specific risk mutations.

OBJECTIVE

In this study, 384 single nucleotide polymorphisms (SNPs) located in four genomic regions associated with CAD (1p13, 1q41, 9p21 and 10q11) are analysed in a set of 19 populations from Europe, Middle East and North Africa and also in Asian and African samples from the 1000 Genomes Project. The aim of this survey is to explore for the first time whether the genetic variability in these genomic regions is better explained by demography or by natural selection.

RESULTS

The results indicate significant differences in the structure of genetic variation and in the LD patterns among populations that probably explain the population disparities found in markers of susceptibility to CAD.

CONCLUSIONS

The results are consistent with potential signature of positive selection in the 9p21 region and of balancing selection in the 9p21 and 10q11. Specifically, in Europe three CAD risk markers in the 9p21 region (rs9632884, rs1537371 and rs1333042) show consistent signals of positive selection. The results of this study are consistent with a potential selective role of CAD in the configuration of genetic diversity in current human populations.

Immunoglobulin genes in Andalusia (Spain). Genetic diversity in the Mediterranean space

Andalusia is the most densely populated region of Spain since ancient times, and has a rich history of contacts across the Mediterranean. Earlier studies have underlined the relatively high frequency of the Sub-Saharan GM 1,17 5* haplotype in western Andalusia (Huelva province, n=252) and neighbouring Atlantic regions. Here, we provide novel data on GM/KM markers in eastern Andalusians (n=195) from Granada province, where African GM*1,17 5* frequency is relatively high (0.044). The most frequent GM haplotypes in Andalusia parallel the most common in Europe. Altogether, these data allow us to gain insight into the genetic diversity of southern Iberia. Additionally, we assess population structure by comparing our Iberian samples with 41 Mediterranean populations. GM haplotype variation across the Mediterranean reflects intense and complex interactions between North Africans and South Europeans along human history, highlighting that African influence over the Iberian Peninsula does not follow an isotropic pattern.