Patterns Of Genetic Variation Research Articles

Genetic diversity during selective sweeps in non-recombining populations.

Selective sweeps, resulting from the spread of beneficial, neutral, or deleterious mutations through a population, shape patterns of genetic variation at linked neutral sites. While many theoretical, computational, and statistical advances have been made in understanding the genomic signatures of selective sweeps in recombining populations, substantially less is understood in populations with little/no recombination. We present a mathematical framework based on diffusion theory for obtaining the site frequency spectrum (SFS) at linked neutral sites immediately post and during the fixation of moderately or strongly beneficial mutations. We find that when a single hard sweep occurs, the SFS decays as 1/ x for low derived allele frequencies ( x ), similar to the neutral SFS at equilibrium, whereas at higher derived allele frequencies, it follows a 1/ x 2 power law. These power laws are universal in the sense that they are independent of the dominance and inbreeding coefficient, and also characterize the SFS during the sweep. Additionally, we find that the derived allele frequency where the SFS shifts from the 1/ x to 1/ x 2 law, is inversely proportional to the selection strength: thus under strong selection, the SFS follows the 1/ x 2 dependence for most allele frequencies, resembling a rapidly expanding neutral population. When clonal interference is pervasive, the SFS immediately post-fixation becomes U-shaped and is better explained by the equilibrium SFS of selected sites. Our results will be important in developing statistical methods to infer the timing and strength of recent selective sweeps in asexual populations, genomic regions that lack recombination, and clonally propagating tumor populations.

The Range‐Wide Genetic Structure of a High‐Elevation Conifer Species, Subalpine Larch

ABSTRACTAimSubalpine larch is a long‐lived conifer with a restricted distribution at treeline in the mountains of western North America. Climate change is reducing the availability of this habitat and subalpine larch is unlikely to adapt to its changing environment due to its long generation time, relatively low levels of standing genetic variation and the high degree of habitat fragmentation across the species' range. This study seeks to elucidate the genetic structure of subalpine larch to inform future conservation and management efforts.LocationWestern North America.TaxonSubalpine larch (Larix lyallii Parl.).MethodsTissue was collected from high‐elevation populations across the entire species range. Restriction site associated DNA sequencing was used to generate single nucleotide polymorphism (SNP) data. Population genetic analyses identified genetic differentiation.ResultsClustering analyses performed using 751 neutral SNPs identified three genetically differentiated regions: the Cascade Range, the southern Rocky Mountains and the northern Rocky Mountains. AMOVA confirmed significant genetic differentiation among regions. A discriminant analysis of principal components and a dendrogram of Provesti's genetic distance both supported the hypothesis that genetically distinct lineages arose after dispersal from a single Pleistocene refugium. Significant isolation by distance (IBD) supported the key role of dispersal in shaping modern patterns of genetic variation in subalpine larch.Main ConclusionsPost‐Pleistocene dispersal resulted in genetic differentiation among groups of subalpine larch in the Cascade Range, the southern Rocky Mountains and the northern Rocky Mountains. These three regions should be prioritised for future management.

Genetic diversity and diversification patterns of puma (Puma concolor) populations in the southern end of the species distribution

The puma (Puma concolor Linnaeus, 1771) is the top predator with the widest distribution in America. Since the establishment of European settlers on the American continent, puma populations have experienced significant contractions and reductions in their original distribution. In Argentina, the management of the conflict between humans and pumas (direct persecution and habitat modification) focused on reduction or elimination methods, leading to a drastic contraction, even total eradication, of puma populations as seen in Patagonia and the eastern part of the country. Despite the lack of knowledge about puma population demographic trends, there are taxonomic issues that remain controversial and need to be resolved to implement appropriate management and conservation measures. Therefore, the aim of this study was to genetically characterize puma populations in the central-southern region of Argentina using two mitochondrial markers, evaluate their demographic history, compare our results at a macro-regional level, and discuss our findings in a conservation and management context. A total of 203 individuals were used, and a fragment of the control region and another of ND5 were sequenced. The genetic variability obtained was moderate. Substitution rates for each locus and the tMRCA were calculated from calibrated trees. In a concatenated tree, two main phylogenetic clades were identified (posterior probability = 1), although a reciprocal monophyly was not observed, with a divergence time of 228 thousand years and a 95% CI [117–363 thousand years]. When evaluating population structuring, three genetic clusters were found, one characteristic of the Patagonian region and the others in the central part of the country. Calculating the ФST values for pairs resulted in significant structuring between Patagonia and the rest of the populations, suggesting the arid diagonal as a possible barrier to gene flow. When evaluating the demographic history, neutrality tests would support a recent expansion in Patagonia. These findings are crucial in defining two distinct Management Units (MUs) in the southern part of puma distribution and providing valuable information for management and conservation measures for the species.

CattleAssigner: A framework for accurate assignment of individuals to cattle lineages and populations using minimum informative markers

Assigning individual animals to their respective breeds, populations or lineages has immense significance in the evolutionary analyses of global cattle populations besides detecting the underlying genetic variation that may likely have facilitated the adaptation of these breeds to diverse environmental conditions. It is also important in discovering the geographic patterns of genetic variation in cattle populations as well as tracing the geographical origin of breeds, food products, and diseases. Given this, the present study was undertaken to elucidate the minimum number of informative single nucleotide polymorphism (SNP) markers, originally generated using medium-density BovineSNP50 BeadChip across 1823 individuals represnting 73 populations, to assign individual animals to the corresponding lineage/group (African or European or Indicine or admixed) and respective populations within that lineage/group using two well-known supervised machine learning (ML) algorithms namely Random Forest (RF) and Extreme Gradient Boosting (XGBoost). Each of the two ML models were trained with the most informative SNP panels (with sizes of 48, 96, and 192) that were elucidated using two statistical methods i.e., principal component analysis (PCA) and Wright's fixation index (FST), and two ML methods (RF with Gini, and RF with MDA). Three panels with the topmost discriminant SNPs (at 192, 96, and 48 densities) were created for each of the marker preselection approaches. These panels were evaluated, based on their performance vis-à-vis animals’ assignment to respective lineage, population group or population. The results showed that XGBoost achieved the best accuracy of 95% with 192-SNP panel (selected via RF with MDA), followed by RF (93% accuracy) with 192-SNP panel (selected via RF with either Gini or MDA), for animal to lineage assignment. Similarly, RF trained with 48-SNP panel (selected via RF with Gini algorithm) achieved the best accuracy of 97% for assigning animals to African lineage, while it achieved the best accuracy of 89% for assigning animals to admixed populations using 96-SNP panel (selected via PCA). On the other hand, XGBoost achieved the best accuracy of 88% for assigning animals to European breeds using 192-SNP panel (selected via FST method). Furthermore, the results with both RF and XGBoost achieved a poor performance of assigning animals of Indicine lineage to the correct group as the best accuracy for such assignment was 66%, achieved using RF with 192-SNP panel (selected via FST method). In conclusion, the study reports the applicability of statistical and ML approaches for identification of discriminatory SNPs, useful the assignment of individuals to corresponding lineages and to respective populations within lineages besides revealing the efficiency of XGBoost and RF-based ML models in performing such assignments. Both the ML models achieved better performance as compared to statistical ones in assigning the animals to specific lineages while they faired comparably similar to each other for the assignment of individuals to respective populations within respective lineages or population groups.

Does rafting promote contemporary gene flow? Global and regional patterns of population genetic diversity and structure on the false limpet Siphonaria lateralis in the Southern Ocean

Rafting has been proposed as an effective mechanism for species without free-living pelagic larvae to achieve long-distance dispersal, theoretically preventing population differentiation over wide distributional ranges. Moreover, rafting has been advocated as a main dispersal mechanism for marine invertebrates with sub-Antarctic distributions, because of abundant buoyant kelps, driven by the Antarctic Circumpolar Current. Nonetheless, little attention has been given to the role of rafting to establish regular gene flow across the sub-Antarctic, and the geographic and temporal scales at which it occurs. Aiming to unravel these major questions about the extent of genetic connectivity across the Southern Ocean (SO), we studied the pulmonate limpet Siphonaria lateralis, a benthic species with encapsulated larvae, found on the rocky intertidal of sub-Antarctic islands and southern South America. Since S. lateralis is closely associated with D. antarctica, dispersal by rafting is plausible, as revealed by the absence of phylogeographic structure across the sub-Antarctic. We sampled 116 individuals from eight localities across the SO, and used 5,515 SNPs obtained through Genotyping-by-Sequencing, to determine contemporary genetic diversity, structure, and gene flow at two spatial scales; global, across the SO, and regional, within Kerguelen. Results identified substantial genetic structure, differentiating Patagonia, Falklands/Malvinas Islands, South Georgia and the Kerguelen archipelago, and low levels of contemporary gene flow. The most notable genetic differentiation was found between Patagonia/Falklands and South Georgia/Kerguelen. Structure was also significant between Patagonia and the Falkland/Malvinas Islands. Conversely, South Georgia and Kerguelen exhibited closer genetic affinity, and indications of recent but limited gene flow. Moreover, historical gene flow estimates between the four populations were low. At regional scale, noteworthy genetic structure persisted, and gene flow was insufficient to prevent genetic differentiation within Kerguelen. Consequently, rafting’s potential may be overestimated as a contemporary mechanism promoting gene flow across the SO, as these events may be sporadic, irregular, and unpredictable for marine invertebrates lacking a larval dispersal stage, since contemporary dispersal events don’t seem to facilitate high gene flow at both scales. Accordingly, other oceanographic factors or processes may hinder the establishment of species associated with macroalgae, and as consequence, contemporary genetic connectivity in the sub-Antarctic.

A Sister Species for the Blue Crab, Callinectes sapidus? A Tale Revealed by Mitochondrial DNA.

The Atlantic blue crab, Callinectes sapidus, is acknowledged as one of the worst invasive alien species in the Mediterranean, impacting biodiversity and human activities. Native to the western Atlantic, it has expanded to European coastal waters since the early 1900s. Despite its ecological and commercial importance, genetic research on this species is limited. Here we show a comprehensive investigation of the genetic variation and evolutionary history in Callinectes sapidus using 667 mitochondrial COI gene sequences. Our dataset encompasses 36 newly generated sequences from previously understudied Mediterranean sites and 631 from worldwide locations obtained from the GenBank public database. Our findings reveal two distinct, but closely related, genetic groups within the species' distribution range, suggesting the occurrence of a potential species complex. Furthermore, in the Mediterranean, low levels of genetic variability were observed except for substantial haplotypic differentiation in Turkish samples. This study depicts the global genetic diversity and evolutionary patterns of Callinectes sapidus, offering new insights into the taxonomic status of the species.

Mitonuclear and phenotypic discordance in an Atlantic Forest frog hybrid zone.

Discordance between mitochondrial and nuclear DNA is common among animals and can be the result of a number of evolutionary processes, including incomplete lineage sorting and introgression. Particularly relevant in contact zones, mitonuclear discordance is expected because the mitochondrial genome is haploid and primarily uniparentally inherited, whereas nuclear loci are evolving at slower rates. In addition, when closely related taxa come together in hybrid zones, the distribution of diagnostic phenotypic characters and their concordance with the mitochondrial or nuclear lineages can also inform on historical and ongoing dynamics within hybrid zones. Overall, genetic and phenotypic discordances provide evidence for evolutionary divergence and processes that maintain boundaries among sister species or lineages. In this study, we characterized patterns of genetic and phenotypic variation in a contact zone between Cycloramphus dubius and Cycloramphus boraceiensis, two sister species of frogs endemic to the Atlantic Coastal Forest of Brazil. We examined genomic-scale nuclear diversification across 19 populations, encompassing the two parental forms and a contact zone between them. We compared the distribution of genomic DNA variability with that of a mitochondrial locus (16S) and two morphological traits (dorsal tubercles and body size). Our results reveal multiple divergent lineages with ongoing admixture. We detected discordance in patterns of introgression across the three data types. Cycloramphus dubius males are significantly larger than C. boraceiensis males, and we posit that competition among males in the hybrid zone, coupled with mate choice by females, may be one mechanism leading to patterns of introgression observed between the species.

Climate change vulnerability and conservation strategies for tertiary relict tree species: Insights from landscape genomics ofTaxus cuspidata.

The unprecedented habitat fragmentation or loss has threatened the existence of many species. Therefore, it is essential to understand whether and how these species can pace with the environmental changes. Recent advantages in landscape genomics enabled us to identify molecular signatures of adaptation and predict how populations will respond to changing environments, providing new insights into the conservation of species. Here, we investigated the pattern of neutral and putative adaptive genetic variation and its response to changing environments in a tertiary relict tree species, Taxus cuspidata Sieb. et Zucc, which is distributed in northeast China and adjacent regions. We investigated the pattern of genetic diversity and differentiation using restriction site-associated DNA sequencing (RAD-seq) and seven nuclear microsatellites (nSSRs) datasets. We further explored the endangered mechanism, predicted its vulnerability in the future, and provided guidelines for the conservation and management of this species. RAD-seq identified 16,087 single nucleotide polymorphisms (SNPs) in natural populations. Both the SNPs and nSSRs datasets showed high levels of genetic diversity and low genetic differentiation in T. cuspidata. Outlier detection by F ST outlier analysis and genotype-environment associations (GEAs) revealed 598 outlier SNPs as putative adaptive SNPs. Linear redundancy analysis (RDA) and nonlinear gradient forest (GF) showed that the contribution of climate to genetic variation was greater than that of geography, and precipitation played an important role in putative adaptive genetic variation. Furthermore, the genetic offset and risk of non-adaptedness (RONA) suggested that the species at the northeast edge may be more vulnerable in the future. These results suggest that although the species has maintained high current genetic diversity in the face of recent habitat loss and fragmentation, future climate change is likely to threaten the survival of the species. Temperature (Bio03) and precipitation (Prec05) variables can be potentially used as predictors of response of T. cuspidata under future climate. Together, this study provides a theoretical framework for conservation and management strategies for wildlife species in the context of future climate change.

Genetic structure and climate niche differentiation among populations of Leopardus geoffroyi.

Geoffroy's cat (Leopardus geoffroyi) is a small-sized felid native to South America. Given the species' distribution covering a wide variety of habitats, and the presence of high levels of anthropization in part of its range, it is possible that genetically differentiated groups exist and that they occupy different climatic niches. We assessed patterns of contemporary genetic diversity and structure in the species across most of its range, characterizing each inferred genetic group based on ecological niche models. We genotyped 11 microsatellites for 142 samples covering most of Geoffroy's cat distribution, and investigated patterns of genetic structure and diversity, applying spatial and nonspatial Bayesian clustering methods and a spatial principal component analysis. We created ecological niche models for each genetic cluster, evaluating whether these clusters occupy different climatic spaces and display differences in the suitability of different values of the climatic variables analyzed. We identified two genetic clusters, one in the north-northeast and the other in the south-southwest of the species' distribution. These clusters showed moderate FST values between them and differences in dispersal/genetic diversity. We found isolation-by-distance patterns globally and within each cluster. We observed lower expected heterozygosity compared with other studies and a north-south gradient in allelic richness. The southern cluster showed lower genetic variability and a more restricted climatic niche suggesting that this group is more vulnerable to the effects of the current context of climate change. Individuals from the southern genetic cluster are under different pressures, likely a product of the particularly dry habitat they occupy. Climatic variables associated with habitat suitability suggest the southern cluster has affinity for the arid and semiarid conditions present in its distribution. Conservation measures should consider the genetic structure observed and differences in climatic spaces to maintain the evolutionary potential of the species.

Codon Usage Analysis Reveals Distinct Evolutionary Patterns and Host Adaptation Strategies in Duck Hepatitis Virus 1 (DHV-1) Phylogroups.

Duck hepatitis virus 1 (DHV-1) is a major threat to the global poultry industry, causing significant economic losses due to high mortality rates in young ducklings. To better understand the evolution and host adaptation strategies of DHV-1, we conducted a comprehensive codon usage analysis of DHV-1 genomes. Our phylogenetic analysis revealed three well-supported DHV-1 phylogroups (Ia, Ib, and II) with distinct genetic diversity patterns. Comparative analyses of the codon usage bias and dinucleotide abundance uncovered a strong preference for A/U-ended codons and a biased pattern of dinucleotide usage in the DHV-1 genome, with CG dinucleotides being extremely underrepresented. Effective number of codons (ENC) analysis indicated a low codon usage bias in the DHV-1 ORF sequences, suggesting adaptation to host codon usage preferences. PR2 bias, ENC plot, and neutrality analyses revealed that both mutation pressure and natural selection influence the codon usage patterns of DHV-1. Notably, the three DHV-1 phylogroups exhibited distinct evolutionary trends, with phylogroups Ia and Ib showing evidence of neutral evolution accompanied by selective pressure, while the phylogroup II evolution was primarily driven by random genetic drift. Comparative analysis of the codon usage indices (CAI, RCDI, and SiD) among the phylogroups highlighted significant differences between subgroups Ia and Ib, suggesting distinct evolutionary pressures or adaptations influencing their codon usage. These findings contribute to our understanding of DHV-1 evolution and host adaptation, with potential implications for the development of effective control measures and vaccines.

Patterns of genetic diversity, gene flow and genetic structure of three Peninsular Indian elephant populations indicate population connectivity

Patterns of genetic diversity, gene flow and genetic structure of three Peninsular Indian elephant populations indicate population connectivity

Mitochondrial DNA of the Arabian Camel Camelus dromedarius.

The Camelidae family, ranging from southwest Asia to north Africa, South America, and Australia, includes key domesticated species adapted to diverse environments. Among these, the Arabian camel (Camelus dromedarius) is vital to the cultural and economic landscape of the Arabian Peninsula. This review explores the mitochondrial DNA of the dromedary camel, focusing on the D-loop region to understand its genetic diversity, maternal inheritance, and evolutionary history. We aim to investigate the unique characteristics of Arabian camel mtDNA, analyze the D-loop for genetic diversity and maternal lineage patterns, and explore the implications of mitochondrial genomic studies for camel domestication and adaptation. Key findings on mtDNA structure and variation highlight significant genetic differences and adaptive traits. The D-loop, essential for mtDNA replication and transcription, reveals extensive polymorphisms and haplotypes, providing insights into dromedary camel domestication and breeding history. Comparative analyses with other camelid species reveal unique genetic signatures in the Arabian camel, reflecting its evolutionary and adaptive pathways. Finally, this review integrates recent advancements in mitochondrial genomics, demonstrating camel genetic diversity and potential applications in conservation and breeding programs. Through comprehensive mitochondrial genome analysis, we aim to enhance the understanding of Camelidae genetics and contribute to the preservation and improvement of these vital animals.

Using Historical Habitat Shifts Driven by Climate Change and Present Genetic Diversity Patterns to Predict Evolvable Potentials of Taxus wallichiana Zucc. in Future

Using Historical Habitat Shifts Driven by Climate Change and Present Genetic Diversity Patterns to Predict Evolvable Potentials of Taxus wallichiana Zucc. in Future

Mid-pass whole-genome sequencing in a Malagasy cohort uncovers body composition associations

The majority of human genomic research studies have been conducted in European-ancestry cohorts, reducing the likelihood of detecting potentially novel and globally impactful findings. Here, we present mid-pass whole-genome sequencing data and a genome-wide association study in a cohort of 264 self-reported Malagasy individuals from three locations on the island of Madagascar. We describe genetic variation in this Malagasy cohort, providing insight into the shared and unique patterns of genetic variation across the island. We observe phenotypic variation by location and find high rates of hypertension, particularly in the Southern Highlands sampling site, as well as elevated self-reported malaria prevalence in the West Coast site relative to other sites. After filtering to a subset of 214minimally related individuals, we find a number of genetic associations with body composition traits, including many variants that are only observed in African populations or populations with admixed African ancestry from the 1000 Genomes Project. This study highlights the importance of including diverse populations in genomic research for the potential to gain novel insights, even with small cohort sizes. This project was conducted in partnership and consultation with local stakeholders in Madagascar and serves as an example of genomic research that prioritizes community engagement and potentially impacts our understanding of human health and disease.

Unveiling population structure and selection signatures of riverine and genetically improved rohu, Labeo rohita using genome wide SNPs.

Captive breeding, along with artificial selection can significantly impact population structure by influencing allele frequencies and driving populations towards specific adaptation. Selective sweeps are powerful forces in shaping genetic variation within populations and can drive rapid spread of beneficial alleles while simultaneously reducing genetic diversity in localized regions of the genome. The present work was undertaken to assess the genetic structure and consequences of artificial selection in 10th generation of genetically improved rohu by comparing with wild populations. The present study used 11,022 high-quality genome wide SNPs to compare the population genetic structure and signatures of selection between Jayanti rohu population and its wild counterpart. Outlier analysis revealed presence of 14 adaptive SNPs, out of which 5 were classified to be under decisive selection pressure. Notably, Jayanti rohu (JR) displayed 297 private alleles exclusive to its population. Chromosomes 7 and 16 emerged as potential hotspots containing a majority of the identified SNPs. Structure and principal component analysis revealed two distinct clusters, effectively distinguishing the JR and wild rohu populations. Phylogenetic analysis indicated a separate cluster of JR population distant from wild groups. The results of present study shall help in elucidating patterns of genetic variation and characterizing selection signatures associated with captive bred and natural populations of rohu. The genomic resources generated through this work shall be helpful in improving the traceability of selectively bred germplasm for developing future strategies of genetic management.

Extremes of snow and temperature affect patterns of genetic diversity and differentiation in the alpine butterfly Parnassius smintheus.

Weather is an important short-term, local driver of population size and dispersal, which in turn contribute to patterns of genetic diversity and differentiation within species. Climate change is leading to greater weather variability and more frequent extreme weather events. While the effects of long-term and broad-scale mean climate conditions on genetic variation are well studied, our understanding of the effects of weather variability and extreme conditions on genetic variation is less developed. We assessed the influence of temperature and snow depth on genetic diversity and differentiation of populations of the alpine butterfly, Parnassius smintheus. We examined the relationships between a suite of variables, including those representing extreme conditions, and population-level genetic diversity and differentiation across 1453 single nucleotide polymorphisms, using both linear and gravity models. We additionally examined effects of land cover variables known to influence dispersal and gene flow in this species. We found that extreme low temperature events and the lowest recorded mean snow depth were significant predictors of genetic diversity. Extreme low temperature events, mean snow depth and land cover resistance were significant predictors of genetic differentiation. These results are congruent with known effects of early winter weather on population size and habitat connectivity on dispersal in P. smintheus. Our results demonstrate the potential for changes in the frequency or magnitude of extreme weather events to alter patterns of genetic diversity and differentiation.

Recurrent selection shapes the genomic landscape of differentiation between a pair of host-specialized haplodiploids that diverged with gene flow.

Understanding the genetics of adaptation and speciation is critical for a complete picture of how biodiversity is generated and maintained. Heterogeneous genomic differentiation between diverging taxa is commonly documented, with genomic regions of high differentiation interpreted as resulting from differential gene flow, linked selection and reduced recombination rates. Disentangling the roles of each of these non-exclusive processes in shaping genome-wide patterns of divergence is challenging but will enhance our knowledge of the repeatability of genomic landscapes across taxa. Here, we combine whole-genome resequencing and genome feature data to investigate the processes shaping the genomic landscape of differentiation for a sister-species pair of haplodiploid pine sawflies, Neodiprion lecontei and Neodiprion pinetum. We find genome-wide correlations between genome features and summary statistics are consistent with pervasive linked selection, with patterns of diversity and divergence more consistently predicted by exon density and recombination rate than the neutral mutation rate (approximated by dS). We also find that both global and local patterns of FST, dXY and π provide strong support for recurrent selection as the primary selective process shaping variation across pine sawfly genomes, with some contribution from balancing selection and lineage-specific linked selection. Because inheritance patterns for haplodiploid genomes are analogous to those of sex chromosomes, we hypothesize that haplodiploids may be especially prone to recurrent selection, even if gene flow occurred throughout divergence. Overall, our study helps fill an important taxonomic gap in the genomic landscape literature and contributes to our understanding of the processes that shape genome-wide patterns of genetic variation.

Genetic diversity, population structure, and phylogenetic relationships of a widespread East Asia herb, Cryptotaenia japonica Hassk. (Apiaceae) based on genomic SNP data generated by dd-RAD sequencing.

Single-nucleotide polymorphisms (SNPs) represent the most prevalent form of genomic polymorphism and are extensively used in population genetics research. Using dd-RAD sequencing, a high-throughput sequencing method, we investigated the genome-level diversity, population structure, and phylogenetic relationships among three morphological forms of the widely distributed taxon Cryptotaenia japonica Hassk., which is native to East Asia. Our study aimed to assess the species status of C. japonica according to its genetic structure and genetic diversity patterns among 66 naturally distributed populations, comprising 26C. japonica f. japonica, 36C. japonica f. dissecta (Y. Yabe) Hara and 4C. japonica f. pinnatisecta S. L. Liou accessions. Based on genomic SNP data generated by dd-RAD sequencing, we conducted genetic diversity, principal component, neighbor-joining (NJ) phylogenetic, admixture clustering, and population differentiation analyses. The findings revealed the following: (1) 5,39,946 unlinked, high-quality SNPs, with mean π, H O, H E and F IS values of 0.062, 0.066, 0.043 and -0.014, respectively, were generated; (2) population divergence was unaffected by isolation through distance; (3) six main distinct regions corresponding to geographic locations and exhibiting various levels of genetic diversity were identified; (4) pairwise F ST analysis showed significant (P < 0.05) population differentiation in 0%-14% of populations among the six regions after sequential Bonferroni correction; and (5) three migration events (historical gene flow) indicated east‒west directionality. Moreover, contemporary gene flow analysis using Jost's D, Nei's G ST, and Nm values highlighted the middle latitude area of East Asia as a significant contributor to genetic structuring in C. japonica. Overall, our study elucidates the relatively low genetic differentiation and population structure of C. japonica across East Asia, further enhancing our understanding of plant lineage diversification in the Sino-Japanese Floristic Region.

Analysis of the Genetic Variation and Geographic Distribution Patterns of Xanthomonas citri pv. citri Strains in Citrus Production in Burkina Faso.

It is essential to have a thorough knowledge of the genetic variation among different strains of Xanthomonas citri pv. citri, which is responsible for causing citrus bacterial canker. This understanding is important for studying disease characteristics, population structure, and evolution and ultimately for developing sustainable methods of control. A total of 48 strains obtained from citrus production areas in Burkina Faso in 2012, 2020, and 2021 were subjected to Polymerase Chain reaction (PCR) tests using specific primers. The aim was to examine the distribution of type 3 effectors and determine the geographical origins of the strains. The examination of the distribution of type 3 non-transcription-activator-like effectors (TALEs) revealed a broader range of strains obtained in 2020 and 2021 than in 2012. However, all the strains possessed a shared set of three genes, specifically, XopE2, XopN, and AvrBs2. Furthermore, all examined effectors were observed in the Bobo-Dioulasso region. Regarding the characterization of TALEs, two profiles containing two to three TALEs were discovered. Profile 1, consisting of two TALEs, was found in 37 X. citri pv. citri strains, whereas Profile 2, comprising three TALEs, was detected in 11 strains. Among the three TALEs (A, B, and C) that were identified, TALEs B and C were present in all the strains. The correlation matrix indicated a positive association between the type 3 effector content of strains and the duration of their isolation. Principal component analysis revealed a limited organization of the strains under investigation. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Phenotypic diversity and population structure of Pecan (Carya illinoinensis) collections reveals geographic patterns

Pecan (Carya illinoinensis) is an economically important nut crop known for its genetic diversity and adaptability to various climates. Understanding the growth variability, phenological traits, and population structure of pecan populations is crucial for breeding programs and conservation. In this study, plant growth and phenological traits were evaluated over three consecutive seasons (2015–2017) for 550 genotypes from 26 provenances. Significant variations in plant height, stem diameter, and budbreak were observed among provenances, with Southern provenances exhibiting faster growth and earlier budbreak compared to Northern provenances. Population structure analysis using SNP markers revealed eight distinct subpopulations, reflecting genetic differentiation among provenances. Notably, Southern Mexico collections formed two separate clusters, while Western collections, such as 'Allen 3', 'Allen 4', and 'Riverside', were distinguished from others. 'Burkett' and 'Apache' were grouped together due to their shared maternal parentage. Principal component analysis and phylogenetic tree analysis further supported subpopulation differentiation. Genetic differentiation among the 26 populations was evident, with six clusters highly in agreement with the subpopulations identified by STRUCTURE and fastSTRUCTURE. Principal components analysis (PCA) revealed distinct groups, corresponding to subpopulations identified by genetic analysis. Discriminant analysis of PCA (DAPC) based on provenance origin further supported the genetic structure, with clear separation of provenances into distinct clusters. These findings provide valuable insights into the genetic diversity and growth patterns of pecan populations. Understanding the genetic basis of phenological traits and population structure is essential for selecting superior cultivars adapted to diverse environments. The identified subpopulations can guide breeding efforts to develop resilient rootstocks and contribute to the sustainable management of pecan genetic resources. Overall, this study enhances our understanding of pecan genetic diversity and informs conservation and breeding strategies for the long-term viability of pecan cultivation.