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Cowpea is a highly drought-adapted leguminous crop with great promise for improving agricultural sustainability and food security. Here, we report analyses derived from array-based genotyping of 2,021 accessions constituting a core subset of the worlds largest cowpea collection, held at the International Institute of Tropical Agriculture (IITA) in Ibadan, Nigeria. We used this dataset to examine genetic variation and population structure in worldwide cowpea. We confirm that the primary pattern of population structure is two geographically defined subpopulations originating in West and East Africa, respectively, and that population structure is associated with shifts in phenotypic distribution. Furthermore, we establish the cowpea core collection as a resource for genome-wide association studies by mapping the genetic basis of several phenotypes, with a focus on seed coat pigmentation patterning and color. We anticipate that the genotyped IITA Cowpea Core Collection will serve as a powerful tool for mapping complex traits, facilitating the acceleration of breeding programs to enhance the resilience of this crop in the face of rapid global climate change.

Desertification is a major threat to biodiversity in arid areas of the world, partly because many organisms in these regions already exist at or near the limits of their movement and physiology. Here, we used molecular data to investigate patterns of persistence and dispersal in an ecologically and economically important carpenter bee (Xylocopa grisescens Lepeletier) found throughout the semiarid Caatinga region of Brazil. We used a genome-wide approach (double digest restriction-site associated DNA, ddRAD) to gather genetic data from bees sampled from eight sites within a semiarid region subject to desertification in Northeastern Brazil. Across all populations, we observed a consistent heterozygosity and effective population size deficit along with low genetic differentiation. We did not find strong evidence of dispersal limitations caused by desertification in this study system despite data collection from sites up to 300 km distant. Thus, our data suggest that human-mediated changes in the Caatinga, such as habitat loss, have impacted the population genetic patterns of X. grisescens. However, these impacts have also been softened by the species' biological characteristics, such as its relatively high capacity for movement. This study provides insights into how habitat changes might impact the long-term survival of large solitary bees.

A potential application of single nucleotide polymorphisms (SNPs) in animal husbandry and production is identification of the animal breed. In this study, using chosen marker selection methods and genotypic data obtained with the use of Illumina Bovine SNP50 BeadChip for individuals belonging to ten cattle breeds, the reduced panels containing the most informative SNP markers were developed. The suitability of selected SNP panels for the effective and reliable assignment of the studied individuals to the breed of origin was checked by three allocation algorithms implemented in GeneClass 2. The studied breeds set included both Polish-native breeds under the genetic resources conservation programs and highly productive breeds with a global range. For all of the tested marker selection methods ("delta" and two FST-based variants), two separate methodological approaches of marker assortment were used and three marker panels were created with 96, 192, and 288 SNPs respectively, to determine the minimum number of markers required for effective differentiation of the studied breeds. Moreover, the usefulness of the most effective panels of markers to assess the population structure and genetic diversity of the analyzed breeds was examined. The conducted analyses showed the possibility of using SNP subsets from medium-density genotypic microarrays to distinguish breeds of cattle kept in Poland and to analyze their genetic structure. [ABSTRACT FROM AUTHOR]

Invasive species are one of the main threats to global biodiversity and, within marine ecosystems, tunicates feature some prominent examples. Styela plicata is an ascidian species inhabiting harbours in all temperate oceans and seas, thus being considered a thriving invasive species. However, this species' adaptive mechanisms, introduction history, and population structure have never been completely elucidated. Here, by genotyping 87 S. plicata individuals from 18 localities worldwide with 2b‐RADseq, we confirm the global presence of four chromosome inversions, demonstrate population structuring on this species, detect local adaptation signals, and infer historical demographic events. We show that North Carolina individuals constitute an unrelated population, Atlanto‐Mediterranean and Pacific localities form their own genetic clusters with substructuring, being the most evident the split between northern and southern Atlantic localities. The locality of South Carolina presents an intermediate genetic position between North Carolina and the other two groups pointing to a hybrid origin with recurrent gene flow. We generate and test demographic models, providing evidence of two independent introduction events to the Atlantic and Pacific, and an admixture that originated the population of South Carolina. Finally, we identify candidate loci for adaptation, with functions involved with cell processes, metabolism, development, and ion transport, among others. Overall, this study highlights the complex historical processes of S. plicata, which have led this species to its current distribution, population structure, and local adaptation footprint in oceans worldwide. [ABSTRACT FROM AUTHOR]

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 26 C. japonica f. japonica, 36 C. japonica f. dissecta (Y. Yabe) Hara and 4 C. 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 p, HO, HE and FIS 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 FST 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 GST, 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. [ABSTRACT FROM AUTHOR]

Introduction: Avocado (Persea americana) is a highly nutritious fruit gaining worldwide popularity. However, its cultivation is currently reliant on a limited number of cultivars with restricted genetic diversity. This study aims to investigate the genetic diversity and population structure of avocado germplasm and identify genetic loci associatedwith key fruit quality traits that influence customer preference. Methods: A diversity panel of 110 avocado accessions was analyzed using 4,706 high-quality single nucleotide polymorphisms (SNPs). Genetic diversity and population structure were analyzed using pairwise FST, AMOVA, admixture analysis, and phylogenetic analysis. Genome-wide association studies (GWAS) were conducted targeting nine fruit quality traits using two models: General Linear Model (GLM) with Principal Component Analysis (PCA) and Mixed Linear Model (MLM) with PCA and kinship (PCA + K). Results: The analysis revealed three distinct populations corresponding to the three avocado ecotypes: Guatemalan, West Indian, and Mexican. Phylogenetic analysis indicated a closer relationship between the Guatemalan and West Indian races compared to the Mexican race in our Florida germplasm collection. GWAS led to identification of 12 markers within 11 genomic regions significantly associated with fruit quality traits such as fruit color, shape, taste, and skin texture. These markers explained between 14.84% to 43.96% of the phenotypic variance, with an average of 24.63%. Annotation of these genomic regions unveiled candidate genes potentially responsible for controlling these traits. Discussion: The findings enhance our understanding of genetic diversity and population structure in avocado germplasm. The identified genetic loci provide valuable insights into the genetic basis of fruit quality traits, aiding breeding programs in developing improved avocado cultivars.Marker-assisted selection can accelerate the development of new varieties, promoting a more diverse and resilient avocado market. [ABSTRACT FROM AUTHOR]

Early in the SARS-CoV2 pandemic, in this journal, Hou et al. (BMC Med 18:216, 2020) interpreted public genotype data, run through functional prediction tools, as suggesting that members of particular human populations carry potentially COVID-risk-increasing variants in genes ACE2 and TMPRSS2 far more often than do members of other populations. Beyond resting on predictions rather than clinical outcomes, and focusing on variants too rare to typify population members even jointly, their claim mistook a well known artifact (that large samples reveal more of a population's variants than do small samples) as if showing real and congruent population differences for the two genes, rather than lopsided population sampling in their shared source data. We explain that artifact, and contrast it with empirical findings, now ample, that other loci shape personal COVID risks far more significantly than do ACE2 and TMPRSS2—and that variation in ACE2 and TMPRSS2 per se unlikely exacerbates any net population disparity in the effects of such more risk-informative loci. [ABSTRACT FROM AUTHOR]

Background: The tropical legume Mucuna pruriens (L.) DC. can meet three agricultural needs: low-cost protein, high-value medicines, and green manure or cover crops. But like other underutilized crops, it needs more modern breeding resources. Identifying marker-trait associations (MTAs) can facilitate marker-assisted breeding and crop improvement. Recent studies have demonstrated the feasibility of identifying MTAs using a small number of accessions (< 100). We have characterized a panel of 70 M. pruriens accessions across two consecutive years and performed association analysis for 16 phenotypic traits related to seed (seed length, seed width, seed thickness, seed yield per plant, hundred seed weight); pod (pod length, pod width, number of pods per cluster, number of pods per plant); inflorescence (inflorescence length, flower buds per inflorescence, flower length, pedicel length), and biochemical attributes (L-DOPA, total protein, total carbohydrate), using 66 genic-microsatellite markers following mixed linear model. Results: The results showed significant phenotypic (P < 0.05) and genetic diversity (Shannon's information index, I = 0.62) in our germplasm collection. Many tested traits were highly heritable (broad-sense heritability ranging from 42.86 to 99.93%). A total of 15 MTAs was detected at an adjusted significance level of P < 5.55 × 10− 3 for nine traits (seed length, seed thickness, seed width, hundred seed weight, seed yield per plant, inflorescence length, flower buds per inflorescence, flower length, and petiole length), contributed by 10 SSR markers (MPU_19, MPU_42, MPU_54, MPU_57, MPU_58, MPU_83, MPU_89, MPU_108, MPU_111, and MPU_122.) with phenotypic variance explained (PVE) ranging from 14.7 to 31.1%. Out of the ten trait-associated markers, the BLAST analysis revealed putative functions of seven markers, except MPU_57, MPU_58, and MPU_83. Conclusion: Fifteen MTAs identified for important traits with phenotypic variance explained > 10% from mixed linear model offer a solid resource base for improving this crop. This is the first report on association mapping in M. pruriens and our results are expected to assist with marker-assisted breeding and identifying candidate genes in this promising legume. [ABSTRACT FROM AUTHOR]

This study aimed to identify and evaluate the genetic diversity of olive trees in Jordan, a country located in the eastern Mediterranean, where olive domestication originated. For this purpose, a total of 386 olive trees were analyzed, including 338 collected from two surveys (JOCC-1 and JOCC-2) across seven regions, and 48 selected accessions from the Olive Germplasm Bank of Jordan (JGBOC). These trees underwent comprehensive phenotypic and molecular characterization using different tools. Significant differences inmorphological traits were detected among tested regions using the Chi-square test. Principal components analysis revealed that fruit color change and growth habit as the most discriminating traits, segregating the trees into two groups, with the first group including the KANABISI cultivar and the second group including the KFARI BALADI cultivar. Utilizing Kompetitive Allele Specific PCR assay, two sets of informative SNPs were used for the genetic diversity analysis. Cladograms were constructed using the maximum likelihood method, revealing a consistent pattern where two clades containing identical genotypes were observed to cluster with the KFARI BALADI or KANABISI. In addition, the SNP data was used to perform a comparative analysis with the Worldwide Olive Germplasm Bank of Co'rdoba, which revealed 73 unreported olive genotypes from Jordan. Genetic structure analyses using Discriminant Analysis of Principal Components (DAPC) identified four clusters with distinctive patterns of relatedness among 149 unique accessions, including 52 olive accessions from various Mediterranean countries (IOCC-3). ADMIXTURE analysis revealed four genetic clusters, consistentwith the clustering observed inDAPC and cladogram analysis, indicating a high level of genetic admixture among Jordanian olive germplasm. In conclusion, the results show that olive trees in Jordan are highly diverse, providing valuable information for future conservation and management plans. [ABSTRACT FROM AUTHOR]

Simple Summary: Positive natural selection increases the frequency of beneficial genetic variations, promoting an organism's adaptability and survival in specific environments. In this study, we conducted whole-genome resequencing and population genetic structure analysis to investigate the genetic diversity of Zaobei cattle, local yellow cattle from China. By comparing Zaobei cattle with Simmental cattle, we identified several genomic regions exhibiting positive selection. Gene annotation of these regions revealed key traits of Zaobei cattle, such as heat tolerance, fertility, and superior meat quality. These findings not only help understand the characteristics of Zaobei cattle but also provide valuable genetic information for future breeding programs, thereby improving their production efficiency and economic value. This investigation provides a comprehensive analysis of genomic diversity and selection signatures in Zaobei beef cattle, an indigenous breed known for its adaptation to hot and humid climates and superior meat quality. Whole-genome resequencing was conducted on 23 Zaobei cattle, compared with 46 Simmental cattle to highlight genetic distinctions. Population structure analysis confirmed the genetic uniqueness of Zaobei cattle. Using methods such as DASDC v1.01, XPEHH, and θπ ratio, we identified 230, 232, and 221 genes through DASDC, including hard sweeps, soft sweeps, and linkage sweeps, respectively. Coincidentally, 109 genes were identified when using XPEHH and θπ ratio methods. Together, these analyses revealed eight positive selection genes (ARHGAP15, ZNF618, USH2A, PDZRN4, SPATA6, ROR2, KCNIP3, and VWA3B), which are linked to critical traits such as heat stress adaptation, fertility, and meat quality. Moreover, functional enrichment analyses showed pathways related to autophagy, immune response, energy metabolism, and muscle development. The comprehensive genomic insights gained from this study provide valuable knowledge for breeding programs aimed at enhancing the beneficial traits in Zaobei cattle. [ABSTRACT FROM AUTHOR]

Summary Understanding how life history shapes genetic diversity is a fundamental issue in evolutionary biology, with important consequences for conservation. However, we still have an incomplete picture of the impact of life history on genome‐wide patterns of diversity, especially in long‐lived semelparous plants. Puya raimondii is a high‐altitude semelparous species from the Andes that flowers at 40–100 years of age. We sequenced the whole genome and estimated the nucleotide diversity of 200 individuals sampled from nine populations. Coalescent‐based approaches were then used to infer past population dynamics. Finally, these results were compared with results obtained for the iteroparous species, Puya macrura. The nine populations of P. raimondii were highly divergent, highly inbred, and carried an exceptionally high genetic load. They are genetically depauperate, although, locally in the genome, balancing selection contributed to the maintenance of genetic polymorphism. While both P. raimondii and P. macrura went through a severe bottleneck during the Pleistocene, P. raimondii did not recover from it and continuously declined, while P. macrura managed to bounce back. Our results demonstrate the importance of life history, in particular generation time and reproductive strategy, in affecting population dynamics and genomic variation, and illustrate the genetic fragility of long‐lived semelparous plants. [ABSTRACT FROM AUTHOR]

A validated marker system is crucial to running an effective genomics-assisted breeding program. We used 36 Kompetitive Allele-Specific PCR (KASP) markers to genotype 376 clones from the biofortified cassava pipeline, and fingerprinted 93 of these clones with DArTseq markers to characterize breeding materials and evaluate their relationships. The discriminating ability of the 36-quality control (QC) KASP and 6602 DArTseq markers was assessed using 92 clones genotyped in both assays. In addition, trait-specific markers were used to determine the presence or absence of target genomic regions. Hierarchical clustering identified two major groups, and the clusters were consistent with the breeding program origins. There was moderate genetic differentiation and a low degree of variation between the identified groups. The general structure of the population was similar using both assays. Nevertheless, KASP markers had poor resolution when it came to differentiating the genotypes by seed sources and overestimated the prevalence of duplicates. The trait-linked markers did not achieve optimal performance as all markers displayed variable levels of false positive and/or false negative. These findings represent the initial step in the application of genomics-assisted breeding for the biofortified cassava pipeline, and will guide the use of genomic selection in the future. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Joint association analysis of multiple traits with multiple genetic variants can provide insight into genetic architecture and pleiotropy, improve trait prediction, and increase power for detecting association. Furthermore, some traits are naturally high-dimensional, e.g., images, networks, or longitudinally measured traits. Assessing significance for multitrait genetic association can be challenging, especially when the sample has population sub-structure and/or related individuals. Failure to adequately adjust for sample structure can lead to power loss and inflated type 1 error, and commonly used methods for assessing significance can work poorly with a large number of traits or be computationally slow. We developed JASPER, a fast, powerful, robust method for assessing significance of multitrait association with a set of genetic variants, in samples that have population sub-structure, admixture, and/or relatedness. In simulations, JASPER has higher power, better type 1 error control, and faster computation than existing methods, with the power and speed advantage of JASPER increasing with the number of traits. JASPER is potentially applicable to a wide range of association testing applications, including for multiple disease traits, expression traits, image-derived traits, and microbiome abundances. It allows for covariates, ascertainment, and rare variants and is robust to phenotype model misspecification. We apply JASPER to analyze gene expression in the Framingham Heart Study, where, compared to alternative approaches, JASPER finds more significant associations, including several that indicate pleiotropic effects, most of which replicate previous results, while others have not previously been reported. Our results demonstrate the promise of JASPER for powerful multitrait analysis in structured samples. We developed JASPER, a fast, robust method for multitrait association testing with a set of genetic variants. JASPER accommodates population structure and relatedness, while handling diverse trait types, making it a powerful tool for uncovering pleiotropic effects, as demonstrated in our analysis of gene expression traits in the Framingham cohort. [ABSTRACT FROM AUTHOR]

Many cooperatively breeding species live in groups with complex structure—large group sizes, low and variable kin structure, and multiple breeding pairs. Since these mixed‐kin groups typically form because of immigration of unrelated individuals of both sexes in addition to limited offspring dispersal, differences in patterns of dispersal can generate variation in group structure, even within the same species or population. Here, we examine how environmentally mediated dispersal patterns influence variation in group structure in the plural breeding superb starling (Lamprotornis superbus), an avian cooperative breeder that inhabits a spatiotemporally variable savanna environment and forms mixed‐kin groups with variable group sizes and more than one breeding pair per group. Using 4068 genome‐wide polymorphic loci and fine‐scale, remotely sensed ecological data from 22 groups sampled across a nearly 200 km2 environmental gradient in central Kenya, we find evidence of not only frequent and long‐distance dispersal in both sexes (low isolation‐by‐distance and weak genetic structure), but also directional dispersal from small groups in lower quality habitat with low normalised difference vegetation index (NDVI) to large groups in higher quality habitat with high NDVI. Additionally, we find stronger genetic structure among groups in lower quality habitat, and higher genetic diversity and lower relatedness of groups in higher quality habitat. Previous work using long‐term data from groups in the same population has shown that groups with lower relatedness are larger and have more breeding pairs. Long‐distance, directional dispersal to maximise individual fitness can thus lead to smaller and simpler kin‐based social groups in lower quality habitat, but larger and more complex mixed‐kin groups in higher quality habitat. Such intraspecific, within‐population variation in group structure, including variation in kin structure of social groups, could have profound implications for the relative importance of the evolutionary mechanisms (i.e. direct vs. indirect fitness benefits) underlying the formation of cooperative societies. [ABSTRACT FROM AUTHOR]

Although repetitive DNA forms much of the human genome, its study is challenging due to limitations in assembly and alignment of repetitive short-reads. We have deployed k-Seek , software that detects tandem repeats embedded in single reads, on 2,504 human genomes from the 1,000 Genomes Project to quantify the variation and abundance of simple satellites (repeat units <20 bp). We find that the ancestral monomer of Human Satellite 3 makes up the largest portion of simple satellite content in humans (mean of ∼8 Mb). We discovered ∼50,000 rare tandem repeats that are not detected in the T2T-CHM13v2.0 assembly, including undescribed variants of telomericand pericentromeric repeats. We find broad homogeneity of the most abundant repeats across populations, except for AG-rich repeats which are more abundant in African individuals. We also find cliques of highly similar AG- and AT-rich satellites that are interspersed and form higher-order structures that covary in copy number across individuals, likely through concerted amplification via unequal exchange. Finally, we use pericentromeric polymorphisms to estimate centromeric genetic relatedness between individuals and find a strong predictive relationship between centromeric lineages and pericentromeric simple satellite abundances. In particular, ancestral monomers of Human Satellite 2 and Human Satellite 3 abundances correlate with clusters of centromeric ancestry on chromosome 16 and chromosome 9, with some clusters structured by population. These results provide new descriptions of the population dynamics that underlie the evolution of simple satellites in humans. [ABSTRACT FROM AUTHOR]

Species of the genus Eubranchus Forbes, 1838 (Mollusca: Gastropoda: Nudibranchia) are common faunistic elements of boreal benthic ecosystems, associated with hydroid communities. Recent studies have suggested that the widely distributed trans-Arctic E. rupium (Møller, 1842) constitutes a complex of at least three candidate species, but the detailed taxonomy of the complex remains unresolved. The purpose of the present paper is to conduct an integrative taxonomic study including molecular genetic methods (a phylogenetic analysis using COI , 16S rRNA and histone H3 with application of species delimitation methods) and morphological study (light and scanning electron microscopy) of E. rupium and closely related species. The specific aims of this study were to establish the species boundaries, morphological variability, and the phylogeographic structure within this group. The phylogeographic analysis included a TCS -based network analysis, an analysis of molecular variance (AMOVA), divergence time estimations, and ancestral area reconstructions. We demonstrate that specimens initially identified as E. rupium included three distinctive species: the nominal E. rupium with an amphiboreal range, the new species Eubranchus novik sp. nov. from the Sea of Japan, for which a taxonomic description is provided in this paper, and Eubranchus sp. from the northern Kuril Islands, which requires the collection and study of additional material for formal description. Our results confirm the amphiboreal distribution of E. rupium , as no geographic structure was found across Pacific, Arctic and Atlantic populations, and the results of the AMOVA analysis showed no differences between groups of samples from different geographic regions. The divergence of the ' Eubrancus rupium species complex' is estimated from the late Miocene or the Miocene–Pliocene boundary to the late Pliocene. It is hypothesised that the most probable ancestral region for the Eubranchus rupium species complex is the north-western Pacific, and the subsequent speciation likely occurred due to dispersal followed by allopatric speciation. ZooBank: Species of the genus Eubranchus Forbes, 1838 are common in boreal benthic ecosystems. Recent studies suggest the trans-Arctic Eubranchus rupium (Møller, 1842) is a species complex. This paper conducts an integrative taxonomic study of Eubranchus rupium and related species, confirming its amphiboreal distribution. The divergence of the species complex is estimated from the late Miocene or the Miocene–Pliocene boundary to the late Pliocene with the north-western Pacific as the probable ancestral region, followed by dispersal and allopatric speciation. (Image credit: Darya Grishina.) [ABSTRACT FROM AUTHOR]

Hymenocallis henryae is a rare, charismatic spider lily endemic to the Florida panhandle. Currently under review to determine if listing under the Endangered Species Act is warranted, this species has undescribed genetic diversity, information crucial to the listing process. We conducted field observations of 21 historic populations across the species' geographical range and performed genomic analyses of 279 individuals from 19 extant populations. Most populations had fewer than 40 individuals, while populations with >100 individuals were found exclusively on managed lands. Genetic diversity was uniformly low within populations (HE: 0.074–0.093), with low to moderate inbreeding coefficients (FIS: 0.068–0.431). Genetic differentiation was relatively low among most populations (FST: 0–0.098), although there was statistical support for isolation by distance. In addition, we found high genetic similarity and lack of population structure across the species range. Clonal propagation through fused bulbs is a common reproductive strategy. We confirmed current threats (habitat change, residential development, fire suppression) and identified several coastal populations threatened by sea level rise. It is recommended to continue with in situ protection and management as well as the establishment of ex situ living collections to preserve populations most at risk of extirpation from habitat loss and degradation. [ABSTRACT FROM AUTHOR]

This study combined population genetics and parentage analysis to obtain foundational data for the conservation of Magnolia kwangsiensis. M. kwangsiensis is a Class I tree species that occurs in two disjunct regions in a biodiversity hotspot in southwest China. We assessed the genetic diversity and structure of this species across its distribution range to support its conservation management. Genetic diversity and population structure of 529 individuals sampled from 14 populations were investigated using seven nuclear simple sequence repeat (nSSR) markers and three chloroplast DNA (cpDNA) fragments. Parentage analysis was used to evaluate the pollen and seed dispersal distances. The nSSR marker analysis revealed a high genetic diversity in M. kwangsiensis, with an average observed (Ho) and expected heterozygosities (He) of 0.726 and 0.687, respectively. The mean and maximum pollen and seed dispersal distances were 66.4 and 95.7 m and 535.4 and 553.8 m, respectively. Our data revealed two distinct genetic groups, consistent with the disjunct geographical distribution of the M. kwangsiensis populations. Both pollen and seed dispersal movements help maintain genetic connectivity among M. kwangsiensis populations, contributing to high levels of genetic diversity. Both genetically differentiated groups corresponding to the two disjunct regions should be recognized as separate conservation units. [ABSTRACT FROM AUTHOR]

Hemicentrotus pulcherrimus is an important commercial aquatic species. However, wild stocks have dramatically decreased in recent decades, and the gonads of H.pulcherrimus of different sexes showed significant differences in gonad index, gonad color, and flavour. Understanding the population genetic structure and sex-differentiation/determination mechanism can provide vital information for genetic conservation and improvement. In the present study, the SuperGBS method was used to identify genome-wide SNPs from a collection of 80 individuals consisting of four geographical populations covering the natural habitats of H. pulcherrimus in China seas. A total of 5785 high-quality SNPs were detected by using SuperGBS technology. The genetic diversity index showed that all populations had similar patterns with high Fis and low Ne, suggesting that it is necessary to carry out the conservation of H. pulcherrimus in China. Low genetic differentiation among the four geographical populations was detected by pairwise Fst, PCA, and admixture analysis. In addition, three sex-related SNPs located on three scaffolds were identified, suggesting a ZW-ZZ sex determination system in H. pulcherrimus. However, no sex-specific marker was identified in this study. Therefore, larger sample sizes and marker numbers need to be implemented to investigate the sex-associated markers and genes of H. pulcherrimus. In general, this study provides a molecular basis for population genetic structure and sex-differentiation/determination mechanism of H. pulcherrimus. [ABSTRACT FROM AUTHOR]

In this study, 38 elite breeding pepper lines were genetically analyzed using SRAP markers and tested for resistance to PVY, TSWV, and PMMoV viruses using molecular markers. In the virus resistance tests, 1 line (37-H–D-6) from the Three-lobs population was found to be resistant to all 3 viruses tested. The 19 SRAP primer combinations used for genetic diversity yielded a total of 85 bands, 57 of which were polymorphic among pepper lines. While 2–8 bands per primer were obtained, the number of polymorphic bands ranged from 1 to 6. The average polymorphism rate of the primers was 66.44%. The PIC values ranged from 0.06 to 0.40 (with a mean of 0.18). In addition, the average gene diversity, effective allele number, and Shannon information index values of the primers were 0.21, 1.34, and 0.31, respectively. STRUCTURE analysis showed that the pepper lines were grouped into 4 clusters. PCoA and Q-matrix plots supported the cluster distribution. Some lines of the Sivri and Three-lobs pepper populations were observed as outliers in the plots. Kapia and Three-lobs were more similar to each other. This study showed that SRAP markers can be successfully used for genetic diversity of pepper breeding lines. [ABSTRACT FROM AUTHOR]

The population of common cuttlefish Sepia officinalis in the English Channel recently developed two life cycles: annual (spawning 1 y.o.) and biennial (spawning 2 y.o.) instead of the biennial strategy known before, associated with increasing environmental temperatures in recent decades because of climate changes. Both groups differ in the size of mature animals (110–196 mm mantle length vs. 140–262 mm) and the number of chambers in the cuttlebone (60–97 in annual vs. 93–152 in biennial). The annual group represented some 15%–20% of the population, and the proportion of early spawners increased during the reproductive period, from 3%–5% in February/March to 50%–70% in June/July. Among spawning cuttlefish males predominated as ~2:1. Such environmentally driven changes in historical ecology as exemplified by the cuttlefish might be a critical link in the adaptation of the cephalopod life cycles to changing ecosystems. [ABSTRACT FROM AUTHOR]

Identifying isolated populations is a key step towards enacting effective conservation management. European lobsters (Homarus gammarus) from Oosterschelde in the Netherlands are subject to fishery pressure and have previously been reported as genetically differentiated. They are also putatively of transplanted origin and have subsequently endured recent bottlenecking and environmental change. We assessed Oosterschelde lobsters to evaluate their demographic independence and appraise potential founder effects and evolutionary responses to isolation. Using restriction-site associated DNA sequencing, we genotyped 6185 single nucleotide polymorphisms across 188 individuals from 27 sites across the Atlantic range of H. gammarus to investigate population genetic diversity, structure, and potential adaptation. Our results show that Oosterschelde lobsters are genetically divergent from other stocks. We evidence extensive differentiation via both neutral and outlier loci, indicative of strong biophysical and demographic isolation, and detect signatures of reduced genetic diversity that may reflect weak founder effects or subsequent population contractions. Among outlier loci, we identify candidates for range-wide local adaptation via variants in genes of important biological functionality and link a private allele of Oosterschelde to a locus potentially conveying adaptive tolerance to environmental hypoxia. Given our findings, we advise proactive monitoring of Oosterschelde lobsters to explore whether existing management measures effectively conserve this discrete, self-recruiting population. [ABSTRACT FROM AUTHOR]

Context: With growing World population, the demand for higher-yield crops becomes more evident. The genetic diversity, which is crucial for breeding superior cultivars, can be shown by using molecular techniques such as start codon targeted (SCoT) markers. Aims: The motivation of this study was to unfold the genetic diversity of Turkish germplasm. Methods: Ninety-four pea samples (90 landraces, 3 pea breeding materials, and 1 registered variety), were assessed for their diversity by using SCoT markers. Key results: Eight SCoT markers produced a total of 84 scorable bands, of which 74 (88.1%) were polymorphic. There was an average of 9.25 polymorphic bands per primer. The range of diversity indices evaluated, such as polymorphism information content (0.13–0.38), effective numbers of alleles (1.22–1.69), Shannon's diversity index (0.21–0.54), and gene diversity (0.13–0.38), showed great genetic variation in the germplasm under this study. STRUCTURE algorithm suggested the presence of two populations. Polymorphism percentage was 87% and 74%, whereas fixation index was 0.21 and 0.01 for population A and population B respectively. According to analysis of molecular variance, most of the difference was found to lie within population (99%) rather than between populations (1%). In contrast, principal coordinates analysis suggested separation into three populations. Conclusions: The Nei's genetic distance of 94 Turkish pea samples revealed that Antalya_2 and Canakkale_2 are genetically the most diverse and can be utilised as parental lines for breeding purposes. Implications: The wide range of pea varieties found in the Turkish germplasm can serve as a valuable genetic resource for the overall pea breeding efforts. Ensuring universal food security is a crucial concern for all of humanity. Pea, as one of the most important legumes, faces many growing challenges in the light of changing climate, whereas growing superior cultivars is a key strategy to meet the ever-growing demands. Turkish pea germplasm encompasses a rich diversity that can be utilised in breeding programs, particularly among the more diverse samples, to generate cultivars adapted to new changing environments. This article belongs to the Collection Plant breeding- and genetics-based tools for food security under changing climate. [ABSTRACT FROM AUTHOR]

Peach (Prunus persica), a significant economic fruit tree in the Rosaceae family, is extensively cultivated in temperate and subtropical regions due to its abundant genetic diversity, robust adaptability, and high nutritional value. Originating from China over 4000 years ago, peaches were introduced to Persia through the Silk Road during the Han Dynasty and gradually spread to India, Greece, Rome, Egypt, Europe, and America. Currently grown in more than 80 countries worldwide, the expansion of peach cultivation in Egypt is mainly due to the development and utilization of peach varieties with low chilling requirements. These varieties exhibit unique phenotypic characteristics such as early maturity, reduced need for winter cold temperatures, low water requirements, and high economic value. In this study, a systematic analysis was conducted on the genetic characteristics and kinship relationships of peaches with low chilling requirements in Egypt. We conducted a comprehensive evolutionary and Identity-by-Descent (IBD) analysis on over 300 peach core germplasm resources, including Egyptian cultivars with low chilling requirements, to investigate their origin and genetic characteristics. The evolutionary analysis revealed that 'Bitter almond' is closely related to China's wild relative species Prunus tangutica Batal, while 'Early grand' shares one branch with Chinese ornamental peach cultivars, and 'Nemaguard' clusters with some ancient local varieties from China. The IBD analysis also indicated similar genetic backgrounds, suggesting a plausible origin from China. Similarly, the analysis suggested that 'Swelling' may have originated from the Czech Republic while 'Met ghamr' has connections to South Africa. 'Desert red', 'Early swelling', and 'Florida prince' are likely derived from Brazil. These findings provide valuable insights into the genetic characteristics of Egyptian peach cultivars. They offer a significant foundation for investigating the origin and spread of cultivated peaches worldwide and serve as a valuable genetic resource for breeding low chilling requirement cultivars, which is of considerable significance for the advancement of peach cultivation in Egypt. [ABSTRACT FROM AUTHOR]

To improve the quality and quantity of seaweed mariculture harvests, seedlings are frequently introduced from regions geographically apart from cultivation sites. The effects of such introduction have been insufficiently studied, despite increasing demands on seaweed cultivation as a measure against global warming. We here evaluated the degree of cryptic invasion occurring through mariculture using a brown algal species, Undaria pinnatifida. Cultivated materials used in the Seto Inland Sea, Japan, were introduced from northern Japan in the 1970s. Based on the clear genetic structure among Japanese Undaria populations, we compared mitochondrial haplotypes between wild populations and cultivated materials in the Seto Inland Sea. All cultivated materials analyzed had haplogroups native to northern Japan. Multiple haplogroups were observed in the wild populations, especially those in the eastern Seto Inland Sea, which is exceptional considering the reported genetic structure. Some northern Japan haplotypes were observed both in cultivated materials and wild individuals. A northern Japan haplogroup was predominant at several sites near Undaria-cultivation sites. These results strongly suggested that cryptic invasion through Undaria mariculture occurred here, although its ecological impact remains unclear. There is a clear risk of invasion by mariculture seedlings from other regions, even when native conspecific populations are present. [ABSTRACT FROM AUTHOR]

• This is the first report on morphological, phytochemical, and genetic diversity assessment along with ENM for Allium stracheyi Baker in Uttarakhand, western Himalaya. • The species have important ethnomedical value such as being used as an appetizer, cardioactive, carminative, expectorant, cordial, and stomach troubles. • Correlation studies revealed a strong positive relationship among studied parameters. • Population structure and UPGMA analysis separated the 103 accessions into two sub-populations (ΔK=2). • Population attributes and ecological niche modeling (ENM) displayed suitable habitats for conservation strategies. Allium stracheyi Baker (Himalayan Allium spice) is an economically important herbaceous plant commonly known for its unique flavor and therapeutic potential. The species is distributed from 2000 to 4000 m above sea level in the western Himalayan region. A. stracheyi is used as an appetizer, cardioactive, carminative, expectorant, cordial, in curing stomach troubles, and in treating constipation. However, systematic information on the diversity and distribution of A. stracheyi species is not available to date. In this study, 14 populations of A. stracheyi gathered from Uttarakhand were subjected to morphological, phytochemical, genetic diversity assessment and mapping potential habitat areas through ecological niche modelling tools. Considerable differences (p < 0.05) were recorded in plant height, fresh weight, dry weight, leaf diameter, and stem diameter of species. Maximum total phenols (3.93 mg GAE/g) and flavonoids (6.17 mg QE/g) content were observed in the Kailashpur population, while total tannin content (1.84 mg TAE/g) was higher in the Malari population. The HPLC analysis enabled the identification of five phenolic constituents, namely, gallic acid, catechin, naringin, salicylic acid, and p-coumaric acid, and recorded high variations among the populations. A total of 53 clear and reproducible fragments were recorded using 15 inter-simple sequence repeats (ISSRs) markers. The highest (He = 0.338; Pp = 90.57 %) genetic diversity was recorded in the Kailashpur population, and the lowest (He = 0.185; Pp = 47.17 %) in the Niti population. UPGMA and a Bayesian-based population structure analysis unanimously grouped A. stracheyi populations into two sub-populations (ΔK = 2). It is observed that A. stracheyi possesses high antioxidant activity and genetic diversity. The study also identified and predicted Niti, Mana, and Jawar valley of Uttarakhand as highest suitability areas under the current climate scenario. These findings can be helpful in planning effective conservation strategies and breeding programs for A. stracheyi. [Display omitted] [ABSTRACT FROM AUTHOR]

• Miombo trees were larger in the high rainfall region compared with low rainfall areas. regions. • Size class distributions exhibited distinct patterns, with relative frequency varying among diameter classes. • The univariate analysis confirmed aggregation at small spatial scales across sites. • Nearest neighbour analysis confirmed the existence of competition at all sites. Our study investigates the intricate ecological mechanisms shaping miombo woodlands across a rainfall gradient in Zimbabwe. We comprehensively analysed vegetation structure, tree morphology, and spatial patterning across three distinct ecological regions characterized by varying mean annual precipitation (MAP). Results reveal that taller and larger trees are prevalent in the more humid site, while higher tree density is observed in the drier site. The spatial analysis highlights a significant aggregation of adult miombo species across all sites, with juveniles exhibiting a propensity to cluster around adult trees. These findings underscore the pivotal role of ecological gradients, such as precipitation, in shaping miombo woodland structure. However, the absence of clear spatial patterns across the rainfall gradient suggests that precipitation may have less influence on the spatial distribution of miombo trees. Understanding these complex ecological dynamics is essential for developing targeted conservation and management strategies that align with the unique attributes of miombo woodlands, critical ecosystems within the African landscape particularly vulnerable to global climate change. [ABSTRACT FROM AUTHOR]

Myotis septentrionalis (Northern Long-eared Bat) has recently suffered a >90% decline in population size in North America due to white-nose syndrome (WNS). We assessed genetic diversity, population structure, current effective population size, and demographic history of M. septentrionalis distributed across the United States to determine baseline levels pre-WNS. We analyzed RADseq data from 81 individuals from Kentucky, Louisiana, Michigan, Minnesota, North Carolina, Oklahoma, and Wisconsin. Additionally, we examined population genetic structure using discriminant analysis of principal components, fastStructure, and STRUCTURE. We then estimated effective population size and demographic history using fastsimcoal2. Similar levels of genetic diversity were found across all samples. We found no population genetic structure in the varied analyses from these contemporary samples. The best model for demographic history estimated a rapid population expansion followed by a slower expansion approximately 340,000 years ago. The vagility of M. septentrionalis , along with male dispersal and random mating, may provide a buffer against serious bottleneck effects stemming from rapid population declines due to WNS. This research provides a baseline for tracking and monitoring the influence of WNS on genetic diversity such as potential reduced diversity or increased population structuring in the future. [ABSTRACT FROM AUTHOR]

Summary: Scots pine is the foundation species of diverse forested ecosystems across Eurasia and displays remarkable ecological breadth, occurring in environments ranging from temperate rainforests to arid tundra margins. Such expansive distributions can be favored by various demographic and adaptive processes and the interactions between them.To understand the impact of neutral and selective forces on genetic structure in Scots pine, we conducted range‐wide population genetic analyses on 2321 trees from 202 populations using genotyping‐by‐sequencing, reconstructed the recent demography of the species and examined signals of genetic adaptation.We found a high and uniform genetic diversity across the entire range (global FST 0.048), no increased genetic load in expanding populations and minor impact of the last glacial maximum on historical population sizes. Genetic‐environmental associations identified only a handful of single‐nucleotide polymorphisms significantly linked to environmental gradients.The results suggest that extensive gene flow is predominantly responsible for the observed genetic patterns in Scots pine. The apparent missing signal of genetic adaptation is likely attributed to the intricate genetic architecture controlling adaptation to multi‐dimensional environments. The panmixia metapopulation of Scots pine offers a good study system for further exploration into how genetic adaptation and plasticity evolve under gene flow and changing environment. See also the Commentary on this article by Duffy, 243: 830–832. [ABSTRACT FROM AUTHOR]

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Jamun plant displays enormous diversity throughout Pakistan, which necessitates its screening, evaluation, and validation to document elite genotypes having better traits for the benefit of the fruit industry and farmers. Surveys were made in natural Jamun habitats across Punjab, Pakistan, and genotypes were marked based on visual diversity of trees and fruits. In total, 60 Jamun genotypes were selected for characterization based on phenotypic and genetic markers. Phenotypic characters related to trees, leaf, and flower along with fruit qualitative traits were assessed in situ. Results revealed significant diversity with high (>25%) coefficient of variance values and the first two components of correspondence analysis exhibited 41.71% variation among genotypes. A strong association was observed among traits like upright tree and round fruit shape (0.74), bluish-colored fruit and pinkish pulp (0.85), and elliptic-shaped fruit with low fruit waxiness (−0.72). Leaves of phenotypically characterized plants were brought to Wheat Biotechnology Lab., University of Agriculture, Faisalabad, Pakistan, where Jamun genotypes were investigated genetically using Random Amplified Polymorphic DNA (RAPD) and Inter Simple Sequence Repeat (ISSR) markers. A total of 132 bands were scored, of which 108 were polymorphic, corresponding to almost 81% polymorphism among collected genotypes. High polymorphism information content values were observed against RAPD (0.389) and ISSR (0.457) markers. Genotypes were compared in relation to genetic markers, which exhibited that almost 86% of genetic variability was attributed to differences among accessions, while 14% of variation was due to differences between collections of different areas. Findings of this study confirmed wide phenotypic and genetic distinctness of Jamun in Pakistan that can aid breeders for marker-assisted selection and germplasm enhancement for future crop improvement programs. [ABSTRACT FROM AUTHOR]

Nypa fruticans, commonly known as the Nipa palm, belongs to the true mangrove plants of the Arecaceae family. In China, it is naturally distributed only on Hainan Island and designated as a second-class National Key Protected Wild Plants List. Field research and indoor simulation experiments were systematically employed to study the resource status of N. fruticans and the adaptation of seed germination to environmental factors. The results showed that: (1) Four natural populations of N. fruticans, approximately 9319 trees within a total area of 3.96 hm2, were distributed in Haikou, Wenchang, Qionghai, and Wanning on Hainan Island. Only the Wanning population was developed in small patches, while other populations were scattered sporadically. (2) A total of 23 mangrove species belonged to 19 genera in 13 families, which were recorded in all study sites, of which 18 were true mangroves and 5 were semi-mangrove species. The vertical structures of 4 N. fruticans communities exhibited the consistent pattern, characterized by distinct layers including the tree, shrub, and herb layers. However, notable differences in species composition and dominant species were observed among the layers of each community. (3) The population dynamics of N. fruticans in Haikou, Qionghai, and Wanning were declining, while the population in Wenchang was growing. (4) Seed germination of N. fruticans was not resistant to strong light and required some shade treatment with an optimal light intensity of 60%. The suitable salinity range for seed germination was 0‰ to 10‰. With the increase of salinity, the germination rate and seedling rate showed an increasing and then decreasing trend with maximum values of 63.3% and 50.0% at 5‰, which showed the sensitivity of seed germination to salinity, with low salinity promoting germination whereas high salinity inhibiting germination. Around 8 h/d of flooding time was most suitable for the seed germination, and 10 h/d was a critical flooding time. This study provides a theoretical basis for population recovery, resource utilization, and other further research of N. fruticans. [ABSTRACT FROM AUTHOR]

Genetic diversity analysis provides the scientific basis for the preservation, evaluation, and utilization of the germplasm resources of tree species. We explored the genetic diversity and structure of Populus tomentosa elite trees in North China using 13 nuclear microsatellite markers. We compared nine groups of accessions including 20 originating from Beijing (BJ), 122 from Hebei (HB), 20 from Shandong (SD), 113 from Henan (HN), 270 from Shanxi (SX), 54 from Shaanxi (SAX), 8 from Gansu (GS), 10 from Anhui (AH), and 6 from Jiangsu (JS). All of the studied primer pairs were polymorphic and generated 125 alleles. Analyses of molecular variance revealed that 79%, 14%, and 8% of the total variation was due to variations within the individual, among individuals, and among populations, respectively. Based on principal coordinate and STRUCTURE cluster analyses, individuals distributed in the southern region (HN, SAX, AH, and JS) were roughly classified into one group, while those distributed in the northeastern region (BJ, HB, and SD) and northwestern regions (SX) were separately divided into one group each. Moreover, the northwestern region included two-thirds of the SX trees, and the remainder were in the northeast region. By analyzing genetic diversity and structure within populations, individuals with different genetic backgrounds were screened for constituent training populations (TRS), including broad allelic variation for related traits. This ensures that the genomic prediction model can accurately capture genetic effects and provide reliable predictions across a broad spectrum of genetic backgrounds. Therefore, our results will benefit genome breeding technology. [ABSTRACT FROM AUTHOR]

Waxy maize is mainly cultivated in South Korea for the production of food and snacks, and colored maize with increased anthocyanin content is used in the production of functional foods and medicinal products. Association mapping analysis (AMA) is supported as the preferred method for identifying genetic markers associated with complex traits. Our study aimed to identify molecular markers associated with two anthocyanin content and six seed coat color traits in near-isogenic lines (NILs) of colored waxy maize assessed through AMA. We performed AMA for 285 SSR loci and two anthocyanin content and six seed coat color traits in 10 NILs of colored waxy maize. In the analysis of population structure and cluster formation, the two parental lines (HW3, HW9) of "Mibaek 2ho" variety waxy maize and the 10 NILs were clearly divided into two groups, with each group containing one of the two parental inbred lines. In the AMA, 62 SSR markers were associated with two seed anthocyanin content and six seed coat color traits in the 10 NILs. All the anthocyanin content and seed coat color traits were associated with SSR markers, ranging from 2 to 12 SSR markers per characteristic. The 12 SSR markers were together associated with both of the two anthocyanin content (kuromanin and peonidin) traits. Our current results demonstrate the effectiveness of SSR analysis for the examination of genetic diversity, relationships, and population structure and AMA in 10 NILs of colored waxy maize and the two parental lines of the "Mibaek 2ho" variety waxy maize. [ABSTRACT FROM AUTHOR]

A key goal of coral restoration is to re-establish self-sustaining coral populations and ensure resilience to future stressors, which requires that genetic diversity is maximised. However, coral genetic and genotypic (clonal) diversity is variable across reef sites via success of sexual recruitment, and cryptic species diversity can complicate breeding efforts. Assessing genotypic and genetic diversity of colonies to be used in restoration is therefore critical to avoid founder, inbreeding or outbreeding effects. Considering recent efforts to upscale coral propagation on the Great Barrier Reef (GBR), we examined species, population and clonal structure of a commonly out-planted tabular Acropora species—Acropora hyacinthus (Dana, 1864). A total of 189 colonies were sampled from six reef systems throughout the northern-central GBR and genotyped using an Acropora-specific Affymetrix microarray, which resulted in 1387 variant sites that passed quality control. Cryptic species were readily resolved and all sampled A. hyacinthus colonies represented unique genotypes within sites at three reefs. At reefs that contained multi-ramet genets (clonal genotypes), the mean and maximum between-ramet distances were 0.68 and 1.99 m, respectively. Therefore, sampling colonies > 2 m apart increases the likelihood these colonies represent distinct genets. Such a sampling design therefore maximises genotypic diversity when sourcing colonies for propagation and out-planting. Based on these variant sites, we found no between-reef genetic divergence based on locality. Furthermore, through unintentional sampling of non-target tabular Acroporid species, we show how this genotyping method may be used for resolving taxonomic uncertainty as well as population dynamics. [ABSTRACT FROM AUTHOR]

Understanding how bovine tuberculosis (TB) is maintained in wildlife reservoirs is critical for the management of this disease impacting cattle in many countries. For the primary wildlife reservoir of the disease in New Zealand, the brushtail possum (Trichosurus vulpecula), transmission of this contagious bacterial disease among possums is often assumed to be linked to home range overlap. Identifying drivers of possum home range, and home range overlap between individuals, is thus important for informing wildlife reservoir TB management in New Zealand. We monitored four sub-populations of free-living possums in New Zealand native forests during 10 consecutive months using live trapping, to give the first direct insight into how the frequency and area of overlaps alters with density, sex and age. A total of 832 individuals were captured (average 9.3, range from 1 to 40 captures per animal with a median value of 7) and 35,820 home range overlaps were recorded. Both the number and area of overlaps were significantly associated with age class, with 66.6% of overlaps occurring between adults, 30% between adults and juveniles, and only 3.4% between juveniles. Overall, adult males showed significantly higher numbers of overlaps than expected, while adult and juvenile females showed significantly lower numbers of overlaps than expected and no differences were observed in juvenile males. In addition, males exhibited more and larger overlaps than females. The number and size of overlaps per individual decreased with increasing local population density. Understanding shared areas of activity among individuals can provide insights into the interactions occurring and potential pathways for diseases transmitted by contact such as TB. These results can inform to develop effective strategies for the control of diseases carried and dispersed by possums. [ABSTRACT FROM AUTHOR]

Main conclusion: The pilot-scale genome-wide association study in the US proso millet identified twenty marker–trait associations for five morpho-agronomic traits identifying genomic regions for future studies (e.g. molecular breeding and map-based cloning). Proso millet (Panicum miliaceum L.) is an ancient grain recognized for its excellent water-use efficiency and short growing season. It is an indispensable part of the winter wheat-based dryland cropping system in the High Plains of the USA. Its grains are endowed with high nutritional and health-promoting properties, making it increasingly popular in the global market for healthy grains. There is a dearth of genomic resources in proso millet for developing molecular tools to complement conventional breeding for developing high-yielding varieties. Genome-wide association study (GWAS) is a widely used method to dissect the genetics of complex traits. In this pilot study of the first-ever GWAS in the US proso millet, 71 globally diverse genotypes of 109 the US proso millet core collection were evaluated for five major morpho-agronomic traits at two locations in western Nebraska, and GWAS was conducted to identify single nucleotide polymorphisms (SNPs) associated with these traits. Analysis of variance showed that there was a significant difference among the genotypes, and all five traits were also found to be highly correlated with each other. Sequence reads from genotyping-by-sequencing (GBS) were used to identify 11,147 high-quality bi-allelic SNPs. Population structure analysis with those SNPs showed stratification within the core collection. The GWAS identified twenty marker–trait associations (MTAs) for the five traits. Twenty-nine putative candidate genes associated with the five traits were also identified. These genomic regions can be used to develop genetic markers for marker-assisted selection in proso millet breeding. [ABSTRACT FROM AUTHOR]

Wheat is one of the most important staple food crops in Ethiopia and elsewhere in the world. Knowledge of its genetic diversity provides breeders a chance to develop new, improved cultivars with desirable traits. In this research the genetic diversity and population structure of 180 bread wheat germplasms representing eight populations was analyzed using 10 Inter simple sequence repeat (ISSR) markers used. Based on diversity indices all the ISSR markers were polymorphic and highly informative. High within-populations genetic diversity with a mean allele values of 1.47, effective alleles of 1.33, Shannon's Information index of 0.29, Nei's gene diversity of 0.19, and percent polymorphic loci of 80.5% were obtained in this research. Among the populations, those from the International Septoria Observation Nursery (ISEPTON) showed relatively, the highest observed number of alleles (1.47), effective number of alleles (1.33), Shannon's Information index (0.4) and Nei's gene diversity (0.19). Thus, the ISEPTON lines could be a good source of useful alleles to be used in wheat improvement programs. Analysis of molecular variance revealed that 95% of the total genetic variation resides within populations, while the remaining 5% is accounted to among populations. Clustering using unweighted pair group method with arithmetic mean, principal coordinate analysis and population structure analysis did not group the wheat populations into genetically distinct clusters following their breeding objectives. In the present research adequate polymorphism and reproducible fingerprint profiles were explored from of the genetic structure analysis in the wheat germplasms. The information obtained could thus be useful in future bread wheat breeding programs as well it its sustainable use. [ABSTRACT FROM AUTHOR]

As a renowned tea with a historical significance in China, Gushan semi-rock tea originated from the Gushan Mountain in Fujian, China. This study describes the genetic diversity, population structure, and distribution characteristics of 76 tea samples collected from Gushan Mountain and neighboring regions, using single nucleotide polymorphism (SNP) markers. The results show that the average information index (I) is 0.490, the average observed heterozygosity (Ho) is 0.384, the average expected heterozygosity (He) is 0.329, and the average fixation index (F) is − 0.132. The genetic variation mainly comes from intraregional variation, which accounts for 82% of the total variation. Furthermore, there is a closer connection between tea plants in Southern, Northern, and Eastern Fujian. The frequency of genetic exchange between tea plants in the Gushan semi-rock tea and those in Southern, Northern, and Eastern Fujian is relatively low, showing obvious uniqueness. The findings of this study help fill the gap in tea genome research in the Gushan semi-rock tea and provide valuable information on the genetic diversity of tea resources in Gushan area. The results can be utilized in future genomics, phylogeny, and breeding programs aimed at developing new tea cultivars. [ABSTRACT FROM AUTHOR]

Genetic diversity and population structure analysis is vital for germplam conservation and efficient utilization. A set of 188 tetraploid wheat (Triticum turgidum spp) genotypes, including 166 landraces and 22 improved cultivars, were genotyped using high density genotyping by sequencing by diversity arrays technology sequencing. We investigated the genetic diversity and population structure for the study panel as well as the landraces, separately based on 10,349 DArTSeq markers distributed across A and B genomes. The whole tetraploid wheat study panel was clustered into two populations: pop1 and pop2 comprising 150 landraces and three released cultivars and 19 released cultivars and 12 landraces, respectively. Further population structure analysis of the tetraploid wheat landraces revealed two subgroups of the landraces. Population structure based on the analysis of molecular variance (AMOVA) revealed significant (P < 0.001) variation between populations and within populations for both the study panels and the landraces. Total variation within population (88%, 97%) was higher than total variation between populations (12%, 3%) for both study panel and the landraces. The AMOVA result was also verified by the population structure analysis based on genetic differentiation (Fst), which was reported to be little (Fst = 0.028) and moderate (Fst = 0.117) for the landraces and the study panel, respectively, thereby implying no significant differentiation among populations. The lower genetic differentiation led to more gene flow in the study panel (Nm = 1.891) and in the landraces (Nm = 8,612) which is an indication of more gene exchange preventing genetic differentiation among populations implying a low level of diversity among subpopulations, that was confirmed by the AMOVA result. The genetic indices of the study panel revealed that pop2 (I = 0.523, Ne = 1.612, He = 0.353, uHe = 0.359) was more diverse than pop1 (I = 0.415, Ne = 1.423, He = 0.263, uHe = 0.264), which comprised of 98.04% landraces along with 1.96% released cultivars. Likewise, pop2 (I = 0.432, Ne = 1.442, He = 0.276, uHe = 0.277) of the landraces was more diverse than Pop1 (I = 1.380, Ne = 1.380, He = 0.234, uHe = 0.236). Furthermore, principal component analysis (PCA) of the tetraploid wheat study panel grouped the released cultivars together and the landraces separately. However, PCA of the landraces did not show clear groupings. The first two components together explained 77% (PC1 = 65%, PC2 = 12%) and 68% (PC1 = 48%, PC2 = 20%) of the total variation in the tetraploid wheat study panel and landraces, respectively. The total number of different alleles in pop1 (4762, 4624) and pop2 (4708, 4760) were revealed in the study panel and the landraces, respectively. 127 genotypes were reported to have one or more private alleles at 755 loci, an indication of key adaptive genes at these loci to be exploited in breeding program. In conclusion, high genetic diversity was detected in Ethiopian tetraploid wheat germplasm, which could be utilized for future wheat breeding program. Furthermore, the higher genetic variation observed within populations than between populations reveal that more attention should be given to individual accessions within populations to explore the existing genetic diversity. [ABSTRACT FROM AUTHOR]

Cinnamomum cassia (L.) J.Presl, a tropical aromatic evergreen tree belonging to the Lauraceae family, is commonly used in traditional Chinese medicine. It is also a traditional spice used worldwide. However, little is currently known about the extent of the genetic variability and population structure of C. cassia. In this study, 71 individuals were collected from seven populations across two geographical provinces in China. Nine morphological features, three chemical components, and single nucleotide polymorphism (SNP) markers were used in an integrated study of C. cassia germplasm variations. Remarkable genetic variation exists in both phenotypic and chemical compositions, and certain traits, such as leaf length, leaf width, volatile oil content, and geographic distribution, are correlated with each other. One-year-old C. cassia seedling leaf length, leaf width, elevation, and volatile oil content were found to be the main contributors to diversity, according to principal component analysis (PCA). Three major groupings were identified by cluster analysis based on the phenotypic and volatile oil data. This was in line with the findings of related research using 1,387,213 SNP markers; crucially, they all demonstrated a substantial link with geographic origin. However, there was little similarity between the results of the two clusters. Analysis of molecular variance (AMOVA) revealed that the genetic diversity of C. Cassia populations was low, primarily among individuals within populations, accounting for 95.87% of the total. Shannon's information index (I) varied from 0.418 to 0.513, with a mean of 0.478 (Na=1.860, Ne =1.584, Ho =0.481, He =0.325, and PPB =86.04%). Genetic differentiation across populations was not significant because natural adaptation or extensive exchange of seeds among farmers between environments, thus maintaining the relationship. Following a population structure analysis using the ADMIXTURE software, 71 accessions were found to be clustered into three groups, with 38% of them being of the pure type, a finding that was further supported by PCA. Future breeding strategies and our understanding of the evolutionary relationships within the C. cassia population would benefit greatly from a thorough investigation of phenotypic, chemical, and molecular markers. [ABSTRACT FROM AUTHOR]

Many studies suggest that aside from environmental variables, such as topography and climate, species‐specific ecological traits are relevant to explain the geographic distribution of intraspecific genetic lineages. Here, we investigated whether and to what extent incorporating such traits systematically improves the accuracy of random forest models in predicting genetic differentiation among pairs of localities. We leveraged available ecological datasets for birds and tested the inclusion of two categories of ecological traits: dispersal‐related traits (i.e. morphology and foraging ecology) and demographic traits (such as species survival rate and generation length). We estimated genetic differentiation from published mitochondrial DNA sequences for 28 species of birds (1578 total genetic samples, 391 localities) in the Atlantic Forest of South America. Aside from the aforementioned ecological traits, we included geographic, topographic and climatic distances between localities as environmental predictors. We then created models using all available data to evaluate model uncertainty both across space and across the different categories of predictors. Finally, we investigated model uncertainty in predicting genetic differentiation individually for each species (a common challenge in conservation biology). Our results show that while environmental conditions are the most important predictors of genetic differentiation, model accuracy largely increases with the addition of ecological traits. Additionally, the inclusion of dispersal traits improves model accuracy to a larger extent than the inclusion of demographic traits. Similar results are observed in models for individual species, although model accuracy is highly variable. We conclude that ecological traits improve predictive models of genetic differentiation, refining our ability to predict phylogeographic patterns from existing data. Additionally, demographic traits may not be as informative as previously hypothesized. Finally, prediction of genetic differentiation for species with conservation concerns may require further careful assessment of the environmental and ecological variation within the species range. [ABSTRACT FROM AUTHOR]

Introduction: Mango is a vital horticultural fruit crop, and breeding is an essential strategy to enhance ongoing sustainability. Knowledge regarding population structure and genetic diversity in mango germplasm is essential for crop improvement. Methods: A set of 284 mango accessions from different regions of the world were subjected to high-throughput sequencing and specific-locus amplified fragment (SLAF) library construction to generate genomic single-nucleotide polymorphism (SNP). Results: After filtering, raw data containing 539.61 M reads were obtained. A total of 505,300 SLAFs were detected, of which, 205,299 were polymorphic. Finally, 29,136 SNPs were employed to dissect the population structure, genetic relationships, and genetic diversity. The 284 mango accessions were divided into two major groups: one group consisted mainly of mango accessions from Australia, the United States, Cuba, India, Caribbean, Israel, Pakistan, Guinea, Burma, China, and Sri Lanka, which belonged to the Indian type (P1); the other group contained mango accessions from the Philippines, Thailand, Indonesia, Vietnam, Cambodia, Malaysia, and Singapore, which belonged to Southeast Asian type (P2). Genetic diversity, principal component analysis (PCA), and population structure analyses revealed distinct accession clusters. Current results indicated that the proposed hybridization occurred widely between P1 and P2. Discussion: Most of the accessions (80.99%) were of mixed ancestry, perhaps including multiple hybridization events and regional selection, which merits further investigation. [ABSTRACT FROM AUTHOR]

Within the whitefly Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) complex, two cryptic species, namely Middle East-Asia Minor 1 (MEAM1) and Mediterranean (MED), are important invasive pests affecting global agriculture and horticulture. They were introduced into China sequentially in the mid-1990s and around 2003, respectively. Subsequently, the latter invader MED has outcompeted the earlier invader MEAM1, becoming the dominant population in the field. Although extensive studies have explored the underlying mechanisms driving this shift, the contribution of population genetics remains notably underexplored. In this study, we analyzed the genetic diversity and structure of 22 MED and 8 MEAM1 populations from various regions of China using mitochondrial DNA sequencing and microsatellite genotyping. Our results indicate low and moderate levels of genetic differentiation among geographically separate populations of MED and MEAM1, respectively. Median-joining network analysis of mtCOI gene haplotypes revealed no clear geographic structuring for either, with common haplotypes observed across provinces, although MED had more haplotypes. Comparative analyses revealed that MED presented greater genetic diversity than MEAM1 on the basis of two markers. Furthermore, analysis of molecular variance supported these findings, suggesting that while some genetic variation exists between populations, a significant amount is also present within populations. These findings reveal the population genetics of the two invasive cryptic species of the B. tabaci complex in China and suggest that the disparities in genetic diversity drive the displacement of their populations in the field. This work also provides valuable information on the genetic factors influencing the population dynamics and dominance of these invasive whitefly species. [ABSTRACT FROM AUTHOR]

Analyzing the genetic diversity and selection characteristics of sheep (Ovis aries) holds significant value in understanding their environmental adaptability, enhancing breeding efficiency, and achieving effective conservation and rational utilization of genetic resources. In this study, we utilized Illumina Ovine SNP 50 K BeadChip data from four indigenous sheep breeds from the southern margin of the Taklamakan Desert (Duolang sheep: n = 36, Hetian sheep: n = 74, Kunlun sheep: n = 27, Qira black sheep: n = 178) and three foreign meat sheep breeds (Poll Dorset sheep: n = 105, Suffolk sheep: n = 153, Texel sheep: n = 150) to investigate the population structure, genetic diversity, and genomic signals of positive selection within the indigenous sheep. According to the Principal component analysis (PCA), the Neighbor-Joining tree (NJ tree), and Admixture, we revealed distinct clustering patterns of these seven sheep breeds based on their geographical distribution. Then used Cross Population Extended Haplotype Homozygosity (XP-EHH), Fixation Index (FST), and Integrated Haplotype Score (iHS), we identified a collective set of 32 overlapping genes under positive selection across four indigenous sheep breeds. These genes are associated with wool follicle development and wool traits, desert environmental adaptability, disease resistance, reproduction, and high-altitude adaptability. This study reveals the population structure and genomic selection characteristics in the extreme desert environments of native sheep breeds from the southern edge of the Taklimakan Desert, providing new insights into the conservation and sustainable use of indigenous sheep genetic resources in extreme environments. Additionally, these findings offer valuable genetic resources for sheep and other mammals to adapt to global climate change. [ABSTRACT FROM AUTHOR]

India's rich diversity encompasses individuals from varied geographical, cultural, and ethnic backgrounds. In the field of population genetics, comprehending the genetic diversity across distinct populations plays a crucial role. This study presents significant findings from genetic data obtained from the Sikkimese population of India. Autosomal markers were crucial for evaluating forensic parameters, with a combined paternity index of 1 × 109. Notably, Penta E emerged as a distinguishing marker for individual identification in the Sikkim population. Fst genetic distance values revealed insights into genetic isolation among different groups, enhancing our understanding of population dynamics in the central Himalayan region. The NJ-based phylogenetic tree highlighted close genetic relationships, of the Sikkim population with the Nepalese population surrounding neighbouring Himalayan populations providing glimpses into common ancestry. In summary, this study contributes valuable data to population genetics and underscores the importance of genetic variation in comprehending population dynamics and forensic applications. [ABSTRACT FROM AUTHOR]

The intensely rich flora of lowland tropical rain forests includes rare species that represent a significant portion of the overall diversity. In the Pasoh Forest Reserve, Malaysia, Timonius is represented by two sympatric species: T. wallichianus, and a new species described and illustrated here. The new species T. pasohensis is rare and so far known only from this reserve. The population characteristics of the new species and the commoner and more widespread T. wallichianus were compared in the 50-ha plot. The distribution of both species overlapped in several habitat types. The torus translation test indicated that T. pasohensis is positively associated with swamps and slopes, whereas T. wallichianus prefers alluvium. However, other factors such as competition, fecundity, susceptibility to droughts, and herbivory, may also be important in influencing the distribution of the two species. They have a similar population structure but are distinctly different in other aspects. From 1986 to 2015, the abundance of T. pasohensis has greatly declined to less than half its original population, and saplings and trees < 10 cm diameter at breast height appear to be the most affected. In contrast, the population size of T. wallichianus has remained relatively stable during the same period, possibly owing to the abundance of suitable habitat type and higher seed set. [ABSTRACT FROM AUTHOR]

The European sprat is a small plankton-feeding clupeid present in the northeastern Atlantic Ocean, in the Mediterranean Sea, and in the brackish Baltic Sea and Black Sea. This species is the target of a major fishery and, therefore, an accurate characterization of its genetic population structure is crucial to delineate proper stock assessments that aid ensuring the fishery's sustainability. Here, we present (i) a draft genome assembly, (ii) pooled whole genome sequencing of 19 population samples covering most of the species' distribution range, and (iii) the design and test of a single nucleotide polymorphism (SNP)-chip resource and use this to validate the population structure inferred from pooled sequencing. These approaches revealed, using the populations sampled here, three major groups of European sprat: Oceanic, Coastal, and Brackish with limited differentiation within groups even over wide geographical stretches. Genetic structure is largely driven by six large putative inversions that differentiate Oceanic and Brackish sprats, while Coastal populations display intermediate frequencies of haplotypes at each locus. Interestingly, populations from the Baltic and the Black Seas share similar frequencies of haplotypes at these putative inversions despite their distant geographic location. The closely related clupeids European sprat and Atlantic herring both show genetic adaptation to the brackish Baltic Sea, providing an opportunity to explore the extent of genetic parallelism. This analysis revealed limited parallelism because out of 125 independent loci detected in the Atlantic herring, three showed sharp signals of selection that overlapped between the two species and contained single genes such as PRLRA , which encodes the receptor for prolactin, a freshwater-adapting hormone in euryhaline species, and THRB , a receptor for thyroid hormones, important both for metabolic regulation and the development of red cone photoreceptors. [ABSTRACT FROM AUTHOR]

Examining patterns of genetic diversity are crucial for conservation planning on endangered species, while inferring the underlying process of recent anthropogenic habitat modifications in the context potential long‐term demographic changes remains challenging. The globally endangered scaly‐sided merganser (SSME), Mergus squamatus, is endemic to a narrow range in Northeast Asia, and its population has recently been contracted into two main breeding areas. Although low genetic diversity has been suggested in the Russian population, the genetic status and demographic history of these individuals have not been fully elucidated. We therefore examined the genetic diversity and structure of the breeding populations of the SSME and investigated the relative importance of historical and recent demographic changes to the present‐day pattern of genetic diversity. Using 10 nuclear microsatellite (SSR) markers and mitochondrial DNA (mtDNA) control region sequences, we found limited female‐inherited genetic diversity and a high level of nuclear genetic diversity. In addition, analysis of both markers consistently revealed significant but weak divergence between the breeding populations. Inconsistent demographic history parameters calculated from mtDNA and bottleneck analysis results based on SSR suggested a stable historical effective population size. By applying approximate Bayesian computation, it was estimated that populations started to genetically diverge from each other due to recent fragmentation events caused by anthropogenic effects rather than isolation during Last Glacial Maximum (LGM) and post‐LGM recolonization. These results suggest that limited historical population size and shallow evolutionary history may be potential factors contributing to the contemporary genetic diversity pattern of breeding SSME populations. Conservation efforts should focus on protecting the current breeding habitats from further destruction, with priority given to both the Russian and Chinese population, as well as restoring the connected suitable breeding grounds. [ABSTRACT FROM AUTHOR]