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Understanding the effects of landscape heterogeneity on spatial genetic variation is a primary goal of landscape genetics. Ecological and geographic variables can contribute to genetic structure through geographic isolation, in which geographic barriers and distances restrict gene flow, and ecological isolation, in which gene flow among populations inhabiting different environments is limited by selection against dispersers moving between them. Although methods have been developed to study geographic isolation in detail, ecological isolation has received much less attention, partly because disentangling the effects of these mechanisms is inherently difficult. Here, I describe a novel approach for quantifying the effects of geographic and ecological isolation using multiple matrix regression with randomization. I explored the parameter space over which this method is effective using a series of individual-based simulations and found that it accurately describes the effects of geographic and ecological isolation over a wide range of conditions. I also applied this method to a set of real-world datasets to show that ecological isolation is an often overlooked but important contributor to patterns of spatial genetic variation and to demonstrate how this analysis can provide new insights into how landscapes contribute to the evolution of genetic variation in nature.

Background Studying population genetic structure and gene flow of plant populations and their influencing factors is of particular significance in the field of conservation biology, especially important for species such as rare and endangered plants. Tetraena mongolica Maxim. (TM), belongs to Zygophyllaceae family, a rare and endangered plant with narrow distribution. However, for the last decade, due to excessive logging, urban expansion, industrial and tourism development, habitat fragmentation and loss of natural habitats have become major threats to the population of endangered plants. Results In this study, genetic diversity, population genetic structure and gene flow of TM populations were evaluated by reduced representation sequencing technology, and a total of more than 133.45 GB high-quality clean reads and 38,097 high-quality SNPs were generated. Analysis based on multiple methods, we found that the existing TM populations have moderate levels of genetic diversity, and very low genetic differentiation as well as high levels of gene flow between populations. Population structure and principal coordinates analysis showed that 8 TM populations can be divided into two groups. The Mantel test detected no significant correlation between geographical distances and genetic distance for the whole sampling. Moreover, the migration model indicated that the gene flow is more of a north to south migration pattern in history. Conclusions This study demonstrates that the present genetic structure is mainly due to habitat fragmentation caused by urban sprawl, industrial development and coal mining. Our recommendation with respect to conservation management is that, all 8 populations should be preserved as a whole population, rather than just those in the core area of TM nature reserve. In particular, the populations near the edge of TM distribution in cities and industrial areas deserve our special protection.

Background Genetic diversity, genetic structure, and gene flow in plant populations and their influencing factors are important in conservation biology. Cypripedium macranthos is one of the few wild orchids with high ornamental value in northern China. However, over the past decade, excessive collection, trading, tourism development, habitat fragmentation, deceptive pollination, and seed germination difficulties have all caused a sharp decline in the number of C. macranthos individuals and its population. In order to propose a scientific and effective conservation strategy, the genetic diversity, genetic structure and gene flow of the current CM population are urgent scientific issues to be clarified. Results Here, 99 individuals of C. macranthos from north and northeast China were analyzed to evaluate the genetic diversity, gene flow among populations, and genetic structure by genotyping-by-sequencing. More than 68.44 Gb high-quality clean reads and 41,154 SNPs were obtained. Our data based on bioinformatics methods revealed that C. macranthos has lower genetic diversity, high levels of historical gene flow, and moderate-to-high genetic differentiation between populations. The gene migration model revealed that the direction of gene flow was mainly from northeast populations to north populations in China. The results of genetic structure analysis showed that 11  C. macranthos populations can be considered as two groups, and further divided into four subgroups. Moreover, the Mantel test detected no significant “Isolation by Distance” between populations. Conclusions Our study demonstrates that the present genetic diversity and genetic structure of C. macranthos populations were mainly caused by biological characteristics, human interference, habitat fragmentation, and restricted gene flow. Finally, constructive measures, which can provide a basis for the proposal of conservation strategies, have been suggested.

Animal pollinators directly affect plant gene flow by transferring pollen grains between individuals. Pollinators with restricted mobility are predicted to limit gene flow within and among populations, whereas pollinators that fly longer distances are likely to promote genetic cohesion. These predictions, however, remain poorly tested. We examined population genetic structure and fine-scale spatial genetic structure (FSGS) in six perennial understory angiosperms in Andean cloud forests of northwestern Ecuador. Species belong to three families (Gesneriaceae, Melastomataceae, and Rubiaceae), and within each family we paired one insect-pollinated with one hummingbird-pollinated species, predicting that insect-pollinated species have greater population differentiation (as quantified with the F ST statistic) and stronger FSGS (as quantified with the S P statistic) than hummingbird-pollinated species. We confirmed putative pollinators through a literature review and fieldwork, and inferred population genetic parameters with a genome-wide genotyping approach. In two of the three species pairs, insect-pollinated species had much greater (>2-fold) population-level genetic differentiation and correspondingly steeper declines in fine-scale genetic relatedness. In the Gesneriaceae pair, however, F ST and S P values were similar between species and to those of the other hummingbird-pollinated plants. In this pair, the insect pollinators are euglossine bees (as opposed to small bees and flies in the other pairs), which are thought to forage over large areas, and therefore may provide similar levels of gene flow as hummingbirds. Overall, our results shed light on how different animal pollination modes influence the spatial scale of plant gene flow, suggesting that small insects strongly decrease genetic cohesion.

Late blight caused by Phytophthora infestans is an economically important disease of potato and tomato worldwide. In Canada, an increase in late blight incidence and severity coincided with changes in genetic composition of P. infestans . We monitored late blight incidence on tomato and potato in Pacific western and eastern Canada between 2019 and 2022, identified genotypes of P . infestans , and examined their population genetic diversity. We identified four major existing genotypes US11, US17, US8, and US23 as well as 25 new genotypes. The US11 genotype was dominant in Pacific western Canada, accounting for 59% of the total population. We discovered the US17 genotype for the first time in Canada. We revealed a higher incidence of late blight and quite diverse genotypes of P . infestans in Pacific western Canada than in eastern Canada. We found high genetic diversity of P. infestans population from Pacific western Canada, as evidenced by the high number of multilocus genotypes, high values of genetic diversity indices, and emergence of 25 new genotypes. Considering the number of disease incidence, the detection of diverse known genotypes, the emergence of novel genotypes, and the high number of isolates resistant to metalaxyl-m (95%) from Pacific western Canada, the region could play a role in establishing sexual recombination and diverse populations, which could ultimately pose challenges for late blight management. Therefore, continuous monitoring of P. infestans populations in Pacific western region and across Canada is warranted. Key points • Genotypes of P. infestans in Pacific western were quite diverse than in eastern Canada. • We discovered US17 genotype for the first time in Canada and identified 26 novel genotypes. • Approximately 95% of P. infestans isolates were resistant to metalaxyl-m.

Background Y chromosome genetic markers, with strict paternal inheritance and lack of recombination, are particularly valuable tools for tracing male lineages. They complement autosomal analyses in forensic applications and anthropological inference by increasing resolution for patrilineal structure. Methods We genotyped 382 unrelated male individuals from two Tibeto-Burman-speaking populations in Guizhou (Tujia, n  = 220; Bai, n  = 162) using the Goldeneye DNA Identification System Y Plus kit comprising 44 Y-markers. We calculated haplotype-level forensic indices and assessed inter-population structure via Rst-based multidimensional scaling (MDS) and a neighbor-joining (NJ) tree, based on genetic distances with 47 reference groups. Y-chromosomal haplogroups were predicted from Y-STR profiles to characterize paternal lineages. Results In the Tujia population, 338 alleles and 219 haplotypes were detected, with allelic frequencies ranging from 0.0045 to 0.9364. The haplotype diversity (HD), haplotype match probability (HMP), and discrimination capacity (DC) were 0.9999, 0.0046, and 0.9955, respectively. In the Bai population, 309 alleles and 141 haplotypes were detected, with allelic frequencies ranging from 0.0062 to 0.9691, with HD = 0.9979, HMP = 0.0083, and DC = 0.8704. Population genetic analysis revealed that the Guizhou Tujia and Bai groups share closer genetic affinity with Southern Han than with Northern Han and cluster with Tibeto-Burman-speaking groups, including the Sichuan and Guizhou Yi populations. Similarly, the Y-STR haplogroup prediction results revealed a multilayered paternal structure dominated by haplogroup O2a2, accompanied by contributions from indigenous East Asian lineages and minor inputs from West Eurasia and other regions. Conclusions Our study provides valuable Y-STR data and forensic parameters for Tibeto-Burman-speaking ethnic groups in China, as well as population genetics evidence in patrilineal history. The Tujia and Bai of Guizhou exhibit a complex paternal genetic structure, offering insights into the demographic dynamics of Southwest China. The 43 Y-marker system exhibits high polymorphism and strong discriminatory power, supporting its utility as a powerful supplementary tool for forensic investigations, particularly for male lineage inference and suspect screening.

Background Researching the genetic structure, genetic diversity, and the identification of reproduction-related genes in local goat populations is essential for developing effective conservation strategies and enhancing breeding efficiency. Results This study detected a total of 22,117,964 single nucleotide polymorphism sites and 5,563,682 insertion/deletion polymorphism sites across 136 samples from seven varieties. Population structure analysis divided the seven goat breeds into three primary genetic clades: Bor constituted an independent cluster; DZ and JC shared a common clade; while QB, MG, CZ, and YS formed a third distinct genetic group. Phylogenetic analysis indicated that indigenous meat goat breeds in Southwest China shared close genetic relationships and exhibited inbreeding. Gene flow results further confirmed the existence of genetic exchange among these southwestern meat goat populations. Genetic diversity analysis indicated that these local southwestern meat goat breeds possessed higher genetic diversity compared to Bor, suggesting potential heterozygote selection advantages. Genomics selection scans detected signatures of positive selection in genes regulating ovarian steroid biosynthesis ( 3BHSD , LOC102181972 , PPP3CA ), ovum development ( EREG , MLH1 ), and meiotic division in oocytes ( CDK2 ). Conclusions These discoveries have significant implications for enhancing thegenetic diversity of these local breeds, facilitating conservation efforts, and improving the adaptability of goats in Southwest China. Additionally, this research provides a foundation for investigating genomic characteristics in other important local goat breeds.

1. Spatially explicit Bayesian clustering techniques offer a powerful tool for ecology and wildlife management, as genetic divisions can be correlated with landscape features. We used these methods to analyse the genetic structure of a population of European wild boar Sus scrofa with the aim of identifying effective barriers for disease management units. However, it has been suggested that the methods could produce biased results when faced with deviations from random mating not caused by genetic discontinuities, such as isolation by distance (IBD). 2. We analysed a data set consisting of 697 wild boar multilocus genotypes using spatially explicit ( baps, geneland) and non-explicit ( structure) Bayesian methods. We also simulated and analysed data sets characterized by different degrees of IBD, with and without genetic discontinuities. 3. When analysing the empirical data set, different programs did not converge on the same clustering solution and some clusters were difficult to explain biologically. Results from the simulated data showed that IBD, also present in the empirical data set, could cause the Bayesian methods to overestimate genetic structure. Simulated barriers were identified correctly, but the programs superimposed further clusters at higher IBD levels . 4. It was not possible to ascertain with confidence whether the clustering solutions offered by the various programs were an accurate reflection of population genetic structure in our empirical data set or were artefacts created by the underlying IBD pattern. 5. Synthesis and applications: We show that Bayesian clustering methods can overestimate genetic structure when analysing an individual-based data set characterized by isolation by distance. This bias could lead to the erroneous delimitation of management or conservation units. Investigators should be critical and suspicious of clusters that cannot be explained biologically. Data sets should be tested for isolation by distance and conclusions should not be based on the output from just one method.

Using genealogy to study the demographic history of a population makes it possible to overcome the models and assumptions often used in population genetics. The Quebec founder population is one of the few populations in the world having access to the complete genealogy of the last 400 years. The goal of this study is to follow the evolution of the Quebec population structure over time from the beginning of European colonization until the present day. To do so, we calculated the kinship coefficients of all ancestors’ pairs in the ascending genealogy of 665 subjects from eight regional and ethnocultural groups per 25-year period. We show that the Quebec population structure appeared progressively in the St. Lawrence valley as early as 1750 with the distinction of the Saguenay and Gaspesian groups. At that time, the ancestors of two groups, the Sagueneans and the Acadians from the Gaspé Peninsula, experienced a marked increase in kinship and inbreeding levels which have shaped the structure and led to the contemporary population structure. Interestingly, this structure arose before the colonization of the Saguenay region and at the very beginning of the Gaspé Peninsula settlement. The resulting regional founder effects in these groups led to differences in the present-day identity-by-descent sharing, the Gaspé and North Shore groups sharing more large segments and the Sagueneans more short segments. This is also reflected by the distribution of the number of most recent common ancestors at different generations and their genetic contribution to the studied subjects.

The genetic structure of sheep reflects their domestication and subsequent formation into discrete breeds. Understanding genetic structure is essential for achieving genetic improvement through genome-wide association studies, genomic selection and the dissection of quantitative traits. After identifying the first genome-wide set of SNP for sheep, we report on levels of genetic variability both within and between a diverse sample of ovine populations. Then, using cluster analysis and the partitioning of genetic variation, we demonstrate sheep are characterised by weak phylogeographic structure, overlapping genetic similarity and generally low differentiation which is consistent with their short evolutionary history. The degree of population substructure was, however, sufficient to cluster individuals based on geographic origin and known breed history. Specifically, African and Asian populations clustered separately from breeds of European origin sampled from Australia, New Zealand, Europe and North America. Furthermore, we demonstrate the presence of stratification within some, but not all, ovine breeds. The results emphasize that careful documentation of genetic structure will be an essential prerequisite when mapping the genetic basis of complex traits. Furthermore, the identification of a subset of SNP able to assign individuals into broad groupings demonstrates even a small panel of markers may be suitable for applications such as traceability.