Population Structure Research Articles

Genetic Diversity and Population Structure of the Japanese Serow (Capricornis crispus) in Gunma Prefecture Based on Mitochondrial DNA Control Region Sequences

Genetic Diversity and Population Structure of the Japanese Serow (Capricornis crispus) in Gunma Prefecture Based on Mitochondrial DNA Control Region Sequences

Study on the characteristics of genetic diversity and population structure of a rare and endangered species of Rhododendron nymphaeoides (Ericaceae) based on microsatellite markers

BackgroundRhododendron nymphaeoides is explicitly listed as an endangered species in the “the International Union for Conservation of Nature’s Red List (IUCN)”, “The Red List of Rhododendrons”, “Red List of China’s Higher Plants” and “Threatened Species List of China’s Higher Plants”. It is also listed as a provincial-level key protected wild plant in Sichuan, with few individuals in the wild and significant conservation value. The genetic diversity and population structure have never been described, making it difficult to plan conservation strategies for this plant.ResultsThis study utilized 15 pairs of microsatellite markers to examine the genetic diversity of 79 samples of R. nymphaeoides sourced from five different geographic populations. A total of 214 alleles were detected, with the average effective number of alleles (Ne) of 7.0324. The averages for the polymorphism information index (PIC) and expected heterozygosity (He) were 0.7832 and 0.8102, respectively, indicating that the R. nymphaeoides populations harbor a rich genetic information content, the genetic differentiation coefficients (FST) average was 1.2607. There was high genetic diversity among populations, with average observed heterozygosity (Ho) and expected heterozygosity (He) values of 0.6375 and 0.6663, respectively, suggesting a degree of inbreeding within populations. Mantel test results showed a significant positive correlation between geographic distance and genetic distance amongst populations (r = 0.8456, P = 0.0021), which conforms to the isolation-by-distance (IBD) model. Due to geographical barriers, there is also a high level of genetic differentiation among populations, with an average genetic differentiation coefficient (FST) of 0.2685. Analysis of molecular variance (AMOVA) indicated that the main source of molecular variance exists within populations (73%), rather than between populations (27%). There was higher historical gene flow (average = 1.0850) and lower contemporary gene flow (average = 1.2849), with seed and pollen dispersal being impeded. Under the Two-Phase Model (TPM) assumption, findings are consistent with the mutation-migration model, suggesting that there has been no genetic bottleneck. STRUCTURE analysis, principal coordinate analysis (PCoA), and UPGMA analysis all support the division of the five natural populations into three genetic clusters.ConclusionsThis is the first comprehensive analysis of the genetic diversity and population structure of the endangered plant R. nymphaeoides using microsatellite markers. The study results indicate that this endangered plant’s natural populations maintain a high level of genetic diversity. Due to geographical barriers, there is also a high level of genetic differentiation, with the primary source of genetic variation originating within populations. There is higher historical gene flow and lower contemporary gene flow, with seed and pollen dispersal being obstructed. The five populations can be divided into three evolutionary units, for which corresponding conservation management units should be established. These findings will benefit the conservation and development of the species and provide a theoretical basis for further studies on its evolution and biogeography.

PopGLen-A Snakemake pipeline for performing population genomic analyses using genotype likelihood-based methods.

PopGLen is a Snakemake workflow for performing population genomic analyses within a genotype-likelihood framework, integrating steps for raw sequence processing of both historical and modern DNA, quality control, multiple filtering schemes, and population genomic analysis. Currently, the population genomic analyses included allow for estimating linkage disequilibrium, kinship, genetic diversity, genetic differentiation, population structure, inbreeding, and allele frequencies. Through Snakemake, it is highly scalable, and all steps of the workflow are automated, with results compiled into an HTML report. PopGLen provides an efficient, customizable, and reproducible option for analyzing population genomic datasets across a wide variety of organisms. PopGLen is available under GPLv3 with code, documentation, and a tutorial at https://github.com/zjnolen/PopGLen. An example HTML report using the tutorial dataset is included in the supplementary material. Supplementary data are available at Bioinformatics online.

Genetic characteristics of endemic Prunus tomentosa in China based on microsatellites

BackgroundPrunus tomentosa Thunb, a fruit tree native to China, is an important and excellent plant material. It exhibits high adaptability to almost all soil types and climatic conditions. The germplasm resources are found in the six geographical regions of China, covering a vast expanse, and comprise a variety of ecological types. However, little is known about genetic diversity and population structure, with its abundant genetic information. Nuclear simple sequence repeat markers, with biparentally inherited characteristics, is powerful for evaluating the genetic diversity of population. Therefore, this research assessed the genetic diversity and population structure of P. tomentosa by collecting extensive samples. The finding will contribute to not only proposing scientific conservation strategies of P. tomentosa but also developing the germplasm to breed novel cherry cultivar.ResultsA total of 822 germplasms from 40 populations were used for assessing. The indicators of genetic diversity showed high values, including observable heterozygosity (0.546), expected heterozygosity (0.819), Shannon’s information index (I = 1.951), polymorphism information content (0.799). The populations displaying the greatest diversity—Gan-XlM, Shaan-HM, and Gan-ZhC. In addition, extensive genetic differentiation was detected. The genetic differentiation coefficient (FST) values calculated from heterozygosity and analysis of molecular variance were greater than 0.15. Gene flow was relatively stable (number of migrants [Nm] = 1.065). Mantel test analysis showed that there was a significant correlation (R2 = 0.065, P < 0.05) between the genetic distance and the geographical distance of the populations. Integrated cluster, structure, and principal component analysis indicated that the 40 populations were clustered into a Northwest Group and a Northeast Group. However, the Chuan-Aba, Xin-TKS, and Xin-ALR populations were clearly differentiated.ConclusionsThe P. tomentosa populations showed high or moderate polymorphism. The genetic differentiation within each population was higher than that between populations. There was a significant correlation between the genetic distance and the geographical distance. Based on genetic diversity and population differentiation levers, the most diverse populations—Gan-XlM, Shaan-HS, and Gan-PL from Gansu and Shaanxi provinces, should first be protected and applied to the innovation of cherry germplasm, followed by significantly differentiated populations, including Chuan-Aba, Ning-HlM, and Gan-PL.

Re-evaluation of boundaries of Streptococcus mitis and Streptococcus oralis and demonstration of multiple later synonyms of Streptococcus mitis, Streptococcus oralis and Streptococcus thalassemiae: description of Streptococcus mitis subsp. carlssonii subsp. nov. and emended description of Streptococcus mitis.

The commensal species Streptococcus mitis and Streptococcus oralis are genetically diverse to a degree that challenges traditional definitions of species. This causes automatic identification based on DNA sequences or cellular extract profiles problematic. Based on an initial analysis of 266 genomes, we subjected a subset of 100 representative genomes to detailed phylogenetic, pairwise distance and gene pattern analyses. S. mitis and S. oralis constitute a continuum of clones that are genetically unique. To recognize most isolates as separate species is biologically and practically meaningless. We recommend bending the proposed similarity borders to accommodate the biological reality. Accordingly, we conclude that Streptococcus toyakuensis, Streptococcus chosunensis, Streptococcus gwangjuensis, Streptococcus humanilactis and Streptococcus hohhotensis are later heterotypic synonyms of S. mitis. Type strains of effectively but not validly published 'Streptococcus shenyangsis', 'Streptococcus symci' and 'Streptococcus vulneris' belong in S. mitis. Streptococcus parapneumoniae and Streptococcus nakanonensis are later synonyms of Streptococcus thalassemiae. Streptococcus downii is a later synonym of Streptococcus oralis subsp. dentisani, and the type of 'Streptococcus halitosis' belongs in Streptococcus oralis subsp. tigurinus. The genome sequence of the type of the recently proposed 'Streptococcus bouchesdurhonensis' is based on a mixed culture. Phylogenetic results and the pattern of presence/absence of accessory genes support the distinction of two subspecies of S. mitis, i.e. Sreptococcus mitis subsp. mitis subsp. nov. (type strain is NCTC 12261T) and Sreptococcus mitis subsp. carlssonii subsp. nov. (type strain is SK608=CCUG 55085T=LMG 33510T). The special population structure of the Streptococcus mitis-pneumoniae-pseudopneumoniae-thalassemiae complex renders automated classification of isolates based on average nucleotide identity or digital DNA-DNA hybridization values problematic. As an alternative, for initial taxonomic assignment, we present a whole-genome phylogeny-based method that enables phylogenetic comparison of new isolates in the context of a set of 117 well-characterized reference strains assigned to the Mitis/Sanguinis group.

Discordant population structure inferred from male- and female-type mtDNAs from Macoma balthica, a bivalve species characterized by doubly uniparental inheritance of mitochondria

Discordant population structure inferred from male- and female-type mtDNAs from Macoma balthica, a bivalve species characterized by doubly uniparental inheritance of mitochondria

Conservation genetic evaluation of Juniperus communis sensu lato in Slovakia

This study explores the population structure, hybridization, and adaptation of Juniperus communis sensu lato in the context of its current habitat fragmentation, using inter-primer binding site markers and needle morphometry. Three native juniper taxa in Slovakia were analyzed: J. communis ssp. communis, J. communis ssp. nana, and their putative hybrid, J. communis nothovar. intermedia. The results reveal a moderate overall structure (ΦPT = 0.115, p = 0.001), indicating high gene flow within ssp. communis and low gene flow between ssp. communis and ssp. nana. However, after correcting for non-neutral loci, the inter-subspecies differentiation dropped significantly, suggesting adaptive divergence despite substantial gene flow. This conclusion was further supported using admixture regression of needle morphometry and ΦPT–QST comparison. We show that adaptive genetic differentiation may play a more significant role than phenotypic plasticity in these traits, a key consideration in preventing outbreeding depression in conservation management. Importantly, we also provide evidence for intermediate admixture and distinct selection pressures within two populations of nothovar. intermedia (Stolica, Kralova Studna), which may qualify their recognition as evolutionarily significant units (ESUs).

Effect of African swine fever on genetic diversity in Black Slavonian pig

African swine fever (ASF) is a highly contagious viral disease affecting domestic and wild pigs, leading to high mortality rates and significant economic losses. Local pig breeds, such as the Black Slavonian pig, are particularly vulnerable due to increased contact with wild boar. This study aimed to assess the genetic diversity parameters of Black Slavonian pigs in Eastern Croatia following a recent ASF outbreak using pedigree-based analyses. Pedigree data comprising 13,306 animals were analyzed, with a reference population of 1,658 individuals from 2018 onward. Genetic diversity parameters, including the average inbreeding coefficient, average relatedness, and effective population size, were estimated under two scenarios: one assuming no ASF-related culling and another excluding animals culled due to ASF. An optimal contribution selection procedure was applied to minimize relatedness within the population, and mating plans were developed for both scenarios to estimate future inbreeding and relatedness. The average inbreeding coefficient was 5.21% in the scenario without ASF-related culling and 4.27% in the scenario with ASF-related culling. Effective population size was 47.10 in the first scenario and 42.94 in the second, indicating a reduction in genetic diversity. Despite the slightly improved genetic diversity parameters in the ASF scenario, the reduced number of mating candidates increased the risk of inbreeding due to a higher likelihood of pairing related individuals. While genetic diversity remained relatively stable, the results suggest that ASF-related culling influenced population structure by removing highly related animals. However, the long-term impact on genetic variability requires further investigation. Future studies incorporating molecular genetic data would enhance the accuracy of relatedness estimation, as pedigree-based analyses may over- or underestimate genetic diversity due to shallow ancestry records.

Population genetic structure and historical demography of Saccostrea echinata in the Northern South China sea and Beibu Gulf

Marine invertebrates, such as oysters, were once thought to form large, panmictic populations with little genetic differentiation due to their high reproductive capacity and dual life stages. However, recent studies have shown significant genetic structuring and moderate gene flow across populations, influenced by factors like ocean currents, historical climate events, and environmental changes. The black-lip oyster (Saccostrea echinata), with its extensive dispersal potential, is ideal for population genetics studies. In current study, mitochondrial DNA (COI gene) was utilized to investigate the population structure, genetic diversity, and demographic history of S. echinata in the northern South China Sea (NSCS) and Beibu Gulf. Results revealed high genetic diversity with 82 haplotypes from 190 specimens, a star-shaped haplotype network, and significant genetic differentiation, with most variation occurring within populations. Genetic analysis identified three distinct genetic groups across the sampled regions. Historical demographic analysis indicated population expansion approximately 44–155 Kya after the Last Glacial Maximum. Genetic structure was shaped by historical climatic events causing isolation and secondary contact, as well as contemporary ocean currents influencing gene flow. The study highlights the complex interplay of genetic diversity, population structure, and historical dynamics in S. echinata, with implications for conservation and aquaculture in the Asia-Pacific region.

Genomic insights into Mediterranean pepper diversity using ddRADSeq.

This work investigated the genetic diversity and population structure of 99 pepper lines (Capsicum annuum L.), acclimated to Mediterranean climate conditions, using double-digest restriction site-associated DNA sequencing (ddRADSeq). The aims were to understand the genetic relationships among these lines, correlate genetic clusters with botanical classifications, and provide insights into pepper domestication in the region. Obtained were 318.76 million raw sequence reads overall, averaging 3.21 million reads per sample. A total of 8475 high-quality SNPs were identified and used to assess genetic diversity and population structure. Chromosome NC_061113.1 displayed the highest amount and Chromosome NC_061118.1 the fewest of these SNPs, which were not equally spaced around the genome. Heterozygosity measures and a negative inbreeding coefficient point to the great genetic diversity seen, therefore highlighting the genetic health of the population. Different genetic clusters found by phylogenetic study and STRUCTURE analysis can be used in breeding programs to mix desired features from many genetic backgrounds. This work showed how well ddRADSeq generates high-quality SNPs for genomic research on peppers, therefore offering useful molecular tools for genomic selection and marker-assisted selection. The analysis identified significant genetic diversity and distinct genetic clusters which are valuable for breeding programs focused on crop improvement. These findings enhance our understanding of pepper domestication and provide valuable genetic resources for breeding programs aimed at improving pepper varieties.

Impact of barriers on Cyrno‐Sardinian endemisms: A comparative study of population genetics and phylogeography within taxa of Centranthus sect. Nervosae (Caprifoliaceae)

Abstract This study explores the impact of geographic barriers on the distribution and survival of Mediterranean endemic species, focusing on Centranthus sect. Nervosae, a tetraploid species complex found in Corsica and Sardinia. The aim is to analyse how these barriers influence genetic diversity, population structure, and phylogeographic pattern, thereby impacting conservation strategies and future resilience of the selected study species. Genotyping involved biparental markers (16 nuclear microsatellites for the population genetic survey) and Sanger sequencing of uniparental markers (six plastid sequences for the phylogeographic survey). Screening of microsatellites revealed a diploidisation process, and haplotype fixation in plastid sequence was observed across all populations. Results from both survey methods clearly indicate that isolation and barriers have significantly impacted the genetic structure of populations, subjecting them to genetic drift, bottlenecks and related evolutionary phenomena. Over time, these factors have resulted in the observed low haplotypic variability and nuclear microsatellite diversity. Reduced genetic variability, combined with factors such as inbreeding and genetic drift, highlight the vulnerability of these populations to extinction. Consequently, this multi‐approach survey has contributed to defining conservation strategies, stressing the need to preserve genetic diversity and mitigate the impacts of human activities and environmental changes on endemic plant communities in island‐like environments. The study emphasises the importance of integrating multiple marker types to deepen our understanding of conservation genetics and evolutionary history, thereby contributing to the assessment, and planning of potential safeguarding strategies for such endemic species.

MEDICAL SITES OF IMPERIAL RUSSIA AS ELEMENTS OF MODERNISATION OF THE ZEMSTVO MEDICAL SYSTEM IN THE EARLY 20TH CENTURY

The article examines the medical districts of Imperial Russia as a significant element of the modernisation of the zemstvo medical system at the turn of the 20th century. In the context of social and economic changes that occurred at this time, the authors analyse how the creation of medical districts influenced the availability of medical care in rural areas, as well as the quality of services provided. The modernisation of zemstvo medicine is associated with innovations in the organisation of healthcare, the introduction of new medical technologies and education of specialists, which provided a more systematic approach to the treatment and prevention of diseases. Medical districts served as an important connecting unit between the population and government structures, forming a new medical infrastructure. In addition, the article emphasises the role of medical districts in solving pressing social problems, such as high infant mortality and the spread of infectious diseases, which demonstrates the need for active government participation in the healthcare sector. This period became the basis for subsequent reforms in Soviet medicine and had a significant influence on the formation of modern principles of medical care.

Genetic Diversity and Population Structural Analysis of Areca catechu Revealed by Single-Nucleotide Polymorphism Markers

The areca nut (Areca catechu L.) is a prominent tropical and subtropical crop of economic importance renowned for its significant medicinal value. It is recognized as one of the most prominent components of the four traditional Southern Chinese medicines. However, the lack of comprehensive genetic diversity data and reliable molecular markers has posed challenges in assessing and improving the areca nut germplasm for breeding programs. This study analyzed 196 areca nut materials, employing 40,173 high-quality single-nucleotide polymorphisms (SNPs) to evaluate the genetic relationships among the samples. Population structure analysis identified three distinct groups based on the optimal K-value, with the principal component analysis (PCA) results consistent with the results of population structure division. A phylogenetic tree constructed using the neighbor-joining method revealed clear separations among the samples based on their geographic origins. The nucleotide diversity (π) values ranged from 2.46 × 10−5 to 5.71 × 10−5, indicating limited genetic diversity within the areca nut population. The pairwise population differentiation index (Fst) revealed moderate genetic differentiation among the groups. The discovery of these SNPs will be helpful for areca nut conservation and utilization. The results of this study indicate the limited genetic diversity within areca nut germplasm resources, providing insights for management and breeding.

Genetic Diversity and Population Structure of Largefin Longbarbel Catfish (Hemibagrus macropterus) Inferred by mtDNA and Microsatellite DNA Markers

The largefin longbarbel catfish (Hemibagrus macropterus), a freshwater species endemic to China with fundamental economic importance, requires investigation into its genetic structure for effective management. In this study, we employed mitochondrial cytochrome b (Cytb) gene sequences and 14 microsatellite loci to elucidate the genetic structure of 195 individuals across eight distinct populations. The Cytb analysis revealed a haplotype number (H) of 31, haplotype diversity (Hd) of 0.853, and nucleotide diversity (π) of 0.0127. Population neutrality tests indicated that Tajima’s D (−0.59467) and Fu and Li’s D* (0.56621) were not statistically significant, and the mismatch distribution exhibited a multimodal pattern. Microsatellite analysis revealed that the mean number of alleles (Na), observed heterozygosity (Ho), and polymorphic information content (PIC) across all loci were 18.500, 0.761, and 0.808, respectively. The UPGMA phylogram constructed based on genetic distance identified two distinct clusters, with paired Fst values ranging from 0.108 to 0.138. These results suggest that the largefin longbarbel catfish is in a state of dynamic equilibrium with high genetic diversity. Furthermore, there was significant genetic differentiation between the YB population and the other seven populations, indicating that the population in the upper reaches of the Yangtze River should be managed as a distinct unit.

Popfinder: A Highly Effective Artificial Neural Network Package for Genetic Population Assignment.

The ability to assign biological samples to source populations with high accuracy and precision based on genetic variation is important for numerous applications from ecological studies through wildlife conservation to epidemiology. However, population assignment when genetic differentiation is low is challenging, and methods to address this problem are lacking. The application of artificial neural networks to population assignment using genomic data is highly promising. Here we present popfinder: a new, easy-to-use Python-based artificial neural network pipeline for genetic population assignment. We tested popfinder both with simulated genetic data from populations connected by varying levels of gene flow and with reduced-representation sequence data for three species of seabirds with weak to no population genetic structure. Popfinder was able to assign individuals to their source populations with high accuracy, precision and recall in most cases, including both simulated and empirical data sets, except in the empirical data set with the weakest population structure, where the comparator programs also performed poorly. Compared to other available software, popfinder was slower on the simulated data sets due to hyperparameter tuning and the fact that it does not reduce the dimensionality of the data set; however, all programs ran in seconds on empirical data sets. Additionally, popfinder provides a perturbation ranking method to help develop optimised SNP panels for genetic population assignment and is designed to be user-friendly. Finally, we caution users of all assignment programs to watch both for leakage of data during model training, which can lead to overfitting and inflation of performance metrics, and for unequal detection probabilities.

Genome-wide association study for resistance to Macrophomina phaseolina in maize (Zea mays L.)

Maize (Zea mays L.) is a frequently used food source in human and animal nutrition. Macrophomina phaseolina is a fungal pathogen causing charcoal rot disease in many plants, especially maize. This pathogen causes high yield losses in maize. The development of resistant maize genotypes is of great importance in controlling this disease. In this study, the population structure of 120 different maize genotypes with varying levels of disease resistance was determined and genome-wide association studies were performed. Each genotype was subjected to the pathogen under controlled conditions and their phenotypic responses to the disease were analyzed. Afterwards, single nucleotide polymorphisms were determined by DArT-seq sequencing. After filtering the SNP data, 37,470 clean SNPs were obtained. The population structure was analyzed with STRUCTURE software, and it was determined that the population was divided into two subgroups. The relationship between phenotypic and genotypic data was analyzed using the MLM (Q + K) model in TASSEL software. As a result, seven SNPs markers located on four different chromosomes were associated with disease resistance. The related markers can be used in the future for the development of maize varieties resistant to M. phaseolina by marker-assisted selection.

Genomic Baselines for Muskellunge in West Virginia: Implications for Stocking and Conservation

Muskellunge (Esox masquinongy) are a recreationally and ecologically important apex predator found throughout North America. In West Virginia, the genetic structuring and diversity of native muskellunge is poorly understood. The supplementary stocking of non-native muskellunge has further complicated the issue, as the introgression of non-native alleles and prevalence of non-native muskellunge post stocking remains unclear as well. Using ddRAD sequencing, several datasets were generated to investigate the population structure and genomic diversity of muskellunge in West Virginia. Populations stocked with New York-strain muskellunge exhibited significant introgression, with genetic composition diverging from unstocked native West Virginia populations. However, one population showed greater genetic similarity to native and unstocked populations despite New York-strain prevalence, suggesting resilience against genetic alteration. Fixed SNPs between the New York and West Virginia strains were identified that can be used for broodstock screening and the enhancement of native populations. A genetically distinct population was identified in the Little Kanawha River system, with this population having the highest levels of genomic diversity among native populations as well as a high number of private alleles. However, elevated inbreeding coefficients highlight potential conservation concerns for this unique population. This study establishes a genomic baseline for muskellunge in West Virginia and underscores the importance of preserving native genomic diversity while balancing the demands of recreational fishing programs.

Determining population structure from k-mer frequencies

Background Understanding population structure within species provides information on connections among different populations and how they evolve over time. This knowledge is important for studies ranging from evolutionary biology to large-scale variant-trait association studies. Current approaches to determining population structure include model-based approaches, statistical approaches, and distance-based ancestry inference approaches. Methods In this work, we identify population structure from DNA sequence data using an alignment-free approach. We use the frequencies of short DNA substrings from across the genome (k-mers) with principal component analysis (PCA). K-mer frequencies can be viewed as a summary statistic of a genome and have the advantage of being easily derived from a genome by counting the number of times a k-mer occurred in a sequence. In contrast, most population structure work employing PCA uses multi-locus genotype data (SNPs, microsatellites, or haplotypes). No genetic assumptions must be met to generate k-mers, whereas current population structure approaches often depend on several genetic assumptions and can require careful selection of ancestry informative markers to identify populations. We compare our k-mer based approach to population structure estimated using SNPs with both empirical and simulated data. Results In this work, we show that PCA is able to determine population structure just from the frequency of k-mers found in the genome. The application of PCA and a clustering algorithm to k-mer profiles of genomes provides an easy approach to detecting the number and composition of populations (clusters) present in the dataset. Using simulations, we show that results are at least comparable to population structure estimates using SNPs. When using human genomes from populations identified by the 1000 Genomes Project, the results are better than population structure estimates using SNPs from the same samples, and comparable to those found by a model-based approach using genetic markers from larger numbers of samples. Conclusions This study shows that PCA, together with the clustering algorithm, is able to detect population structure from k-mer frequencies and can separate samples of admixed and non-admixed origin. Using k-mer frequencies to determine population structure has the potential to avoid some challenges of existing methods and may even improve on estimates from small samples.

Population panmixia of the pelagic shrimp Lucensosergia lucens between Japanese and Taiwanese waters in the western North Pacific

The pelagic shrimp Lucensosergia lucens is a commercially important species in Japan and Taiwan; however, a recent significant decline in L. lucens catch has been reported in Suruga Bay, Japan. In the present study, multiple molecular approaches were used to understand the population structure of L. lucens in Japanese and Taiwanese waters. Our analysis of mitochondrial cytochrome c oxidase subunit I and control region obtained by Sanger sequencing showed no evidence of different population structures, contrary to the previous study based on the control region. Genome-wide single-nucleotide polymorphism (SNP) analysis using multiplexed inter-simple sequence repeats genotyping by sequencing revealed panmixia in Japanese and Taiwanese populations. The contemporary migration rates estimated from the SNP data suggest that the Kuroshio Current plays a key role in L. lucens transportation from Taiwan to Japan. Additionally, mitogenome sequences obtained by genome skimming showed no region-specific genetic lineages in Japan or Taiwan. The results obtained by multiple molecular approaches suggested that L. lucens is widely distributed with a dispersal capacity in the Kuroshio and adjacent regions in the western North Pacific. Because apparent panmixia of L. lucens was observed in Japanese and Taiwanese waters, international cooperation is needed for the sustainable fishing of this shrimp.

The Canadian collaborative project on genetic susceptibility to multiple sclerosis cohort population structure and disease etiology

BackgroundPrevious genetic and epidemiological studies have examined subpopulations from the Canadian Collaborative Project on Genetic Susceptibility to Multiple Sclerosis (CCPGSMS) patient cohort, but an encompassing analysis of the study population has not yet been carried out.ObjectiveThis retrospective study examines patterns of multiple sclerosis (MS) prevalence in 13,663 cohort members, including 4,821 persons with MS or suspected MS and 8,842 family members.MethodsWe grouped participants into epidemiologic subgroups based on age of MS onset, clinical stage at diagnosis, symptom type at disease onset, sex, proband status, disability as measured by the EDSS, and ancestry based on reported ethnicity.ResultsWe observed a 2.7:1 MS prevalence ratio of women to men, though disease severity was greater for male patients. Variation in the age of disease onset between patients was only slightly associated with sex and strongly associated with disease type. Specific types of clinical symptoms at disease onset were associated with the prognosis. Regional residence did not correlate with disease onset, type, or severity.ConclusionPopulation trends, as presented here, are not explained by environmental factors alone, highlighting the need for a comprehensive genetic analysis to understand disease variance across families.