Estimates Of Genetic Diversity Research Articles

Genetic Assessment of a Captive Population of Eurasian Stone-Curlew (Burhinus oedicnemus), Source for the Reinforcement of Wild Populations

Although ex situ conservation programs are increasingly valuable support tools for in situ conservation measures, success depends on these captive individuals to be genetically representative of the recipient population. The Eurasian stone-curlew (Burhinus oedicnemus) inhabit steppes that represent some of the most degraded and exploited habitats worldwide. A captive breeding program was implemented in Morocco as a pre-emptive effort for the conservation of the North African subspecies Burhinus oedicnemus saharae. However, the genetic origins of the founders of the captive flock were unknown. We applied a multi-locus approach to characterize the genetic ancestry of the current captive breeding flock by comparing it to wild populations from both Western and Eastern Morocco. Mitochondrial DNA and microsatellite markers were employed to assess levels of genetic diversity and relatedness within each sample, as well as potential genetic differentiation between wild and captive samples through PCA and admixture analyses. We recovered similar genetic diversity estimates, low levels of relatedness, and little differentiation between captive and wild samples. These results confirmed the Moroccan origin of the founders. We provide recommendations for the optimization of the Eurasian Stone Curlew conservation breeding program but also for future conservation breeding programs to ensure the effective conservation of genetic diversity and wild populations.

English

Coffee breeding programs aim at developing superior genotypes, which entail exploring the genetic variability existing in conilon/robusta coffee. This study aimed at examining the variability and estimate genetic param of physical and physiological nature in Coffea canephora seeds in order to provide bases for the selection of genotypes for superior seeds quality. Forty-three C. canephora genotypes were evaluated for 11 physical and physiological seed traits. Estimates of genetic param, environmental variance, phenotypic variance, genotypic variance, broad-sense heritability, variation index and Pearson's correlation were obtained. The Dissimilarity between genotypes was obtained by generalized Mahalanobis distance. The dendrogram was constructed using unweighted pair group method with arithmetic mean (UPGMA). C. canephora genotypes presented high germination potential and exhibited genetic diversity for all seed traits, with estimates of genetic variance greater than environmental variance. Heritability reached values above 96.0% and all genetic variation indices found were higher than unity. The UPGMA hierarchical method grouped the genotypes in three groups. The physical traits (circumference, area and roundness) were those that contributed the most to explaining the dissimilarity between genotypes. Genotypes Alecrim, AP, Bamburral, Z39 and Tardio C were the most divergent. The results revealed the presence of genetic variability between C. canephora genotypes and greater genetic than environmental influence on the characters of seeds, indicating that selection for the studied traits showed favorable conditions in terms of immediate gain.

Prioritizing Conservation Areas for the Hyacinth Macaw (Anodorhynchus hyacinthinus) in Brazil From Low-Coverage Genomic Data.

Estimates of current genetic diversity and population connectivity are especially important for endangered species that are subject to illegal harvesting and trafficking. Genetic monitoring can also ensure that management units are sustaining viable populations, while estimating genetic structure and population dynamics can influence genetic rescue efforts and reintroduction from captive breeding and confiscated animals. The Hyacinth Macaw (Anodorhynchus hyacinthinus) is a charismatic endangered species with a fragmented (allopatric) distribution. Using low coverage genomes, we aimed to investigate the dynamics across the remaining three large disjunct populations of Hyacinth Macaws in Brazil to inform conservation strategies. We obtained low coverage DNA data for 54 individuals from seven sampling sites. Our results showed that Hyacinth Macaws have four genetically structured clusters with relatively high levels of diversity. The Pantanal biome had two genetically distinct populations, with no obvious physical barriers that might explain this differentiation. We detected signs of gene flow between populations, with some geographical regions being more connected than others. Estimates of effective population size in the past million years of the species' evolutionary history showed a decline trend with the lowest Ne in all populations reached within the last few thousand years. Our findings suggest that populations from the Pantanal biome are key to connecting sites across its distribution, and maintaining the integrity of this habitat is important for protecting the species. Given the genetic structure found, we also highlight the need of conserving all wild populations to ensure the protection of the species' evolutionary potential.

Assessment of Genetic Variability in Groundnut (Arachis hypogaea L.)

The present study was carried out with thirty advanced breeding lines of groundnut for estimation of genetic variability, heritability and genetic advance. Analysis of variance revealed highly significant differences among genotypes for all the studied characters indicating that there is substantial variability among the genotypes for these traits. High estimates of GCV and PCV was observed for pod yield per plant, kernel yield per plant, dry haulm yield per plant and number of mature pods per plant. High heritability coupled with high genetic advance as per cent of mean were recorded for number of mature pods per plant, pod yield per plant, kernel yield per plant, dry haulm yield per plant, number of immature pods per plant, plant height, harvest index and hundred kernel weight indicating the preponderance of additive gene action in expression of these traits and hence simple phenotypic selection would be effective for improvement of these characters.

Inclusion of imputed genotypes from non-genotyped dairy cattle in a Thai multibreed genomic-polygenic evaluation.

This study assessed the impact of incorporating imputed SNP information from non-genotyped animals on genomic-polygenic evaluations in a Thai multibreed dairy population under various levels of imputation accuracy. Data encompassed pedigree and phenotypic records for 305-day milk yield (MY), 305-day fat (Fat), and age at first calving (AFC) from 12,859 first-lactation cows, and genotypic records of various densities from 4,364 animals. A set of 64 animals genotyped with GeneSeek Genomic Profiler 80K and with four or more genotyped progenies was defined as target animals to simulate imputation scenarios for non-genotyped individuals. Actual and imputed genotypes were utilized to construct three SNP sets. All SNP Sets contained actual and imputed SNP markers from genotyped animals. SNP Set 1 contained no SNPs from target animals, whereas SNP Set 2 incorporated imputed SNPs from target animals, and SNP Set 3 added actual SNPs from target animals. Genomic-polygenic evaluations were conducted using a 3-trait single-step model that included contemporary group, calving age, and heterozygosity as fixed effects and animal additive genetic and residual as random effects. The imputation accuracy was similar across non-genotyped animals irrespective of the number of genotyped progenies (average: 40.55%; range: 34.68% to 53.82%). Estimates of additive genetic and environmental variances and covariances for MY and AFC varied across SNP sets. SNP Sets 1 and 2 had slightly higher additive genetic and lower environmental variances and covariances than SNP Set 3. Heritabilities and additive genetic, environmental, and phenotypic correlations between MY, Fat, and AFC were similar across all SNP Sets. Spearman rank correlations between genomic-polygenic EBVs from SNP Sets 2 and 3 were high for all traits (0.9990±0.0003). Utilization of phenotypic and pedigree data from imputed non-genotyped animals enhanced the efficiency and cost-effectiveness of the genetic improvement program in the Thai multibreed dairy cattle population.

Estimation of Genetic Variability for Yield and Its Component Traits in Chickpea (Cicer arietinum L.)

The present investigation was conducted with 12 chickpea genotypes, raised in randomized block design with three replications during the Rabi season 2023-2024 at at Organic Research Farm, Karguanji, Institute of Agricultural Sciences, Bundelkhand University, Jhansi (U.P.). The experiment was laid-out in randomized block design with three replications of the plant geometry was maintained at 30 cm x 10 cm. The present experimental material showed a wide range of phenotypic variation for number of seed per pod, number of primary branches per plant, biological yield per plant and seed yield per plant, number of secondary branches per plant, number of pods per plant and harvest index whereas, low phenotypic coefficient of variation was observed for plant height, 100-seed weight, days to 50 per cent flowering and days to maturity as revealed by high values of Coefficient of Range. The estimates of high heritability coupled with high genetic advance expressed as a per cent of mean were observed for biological yield per plant, seed yield per plant and number of pods per plant manifesting the preponderance of additive gene action on the expression of these traits. In the investigation, genotypes viz., RSG-44 and Aruna were superior not only for seed yield per plant but also related traits like 100-seed weight, biological yield per plant, number of pods per plant and number of primary branches per plant.

Estimation of genetic variability, heritability and genetic advance of yield and related traits in F4 and F5 generations of okra (Abelmoschus esculentus [L.] Moench)

Estimation of genetic variability, heritability and genetic advance of yield and related traits in F4 and F5 generations of okra (Abelmoschus esculentus [L.] Moench)

Genetic Variability, Heritability, Genetic Advance, Path Coefficient Analysis, and Inter-Character Relationships in Colocynth (Citrullus colocynthis [L.] Schrad.) from Southeastern Villages of the Benin Republic

Genetic improvement of crops for important traits requires reliable estimates of genetic variability. heritability and genetic advance of intending parent materials to identify traits useful in planning an efficient breeding program through selection. Hence, the effectiveness of genetic improvement of a crop depends on the variability in the morpho-agronomic traits of individual genotypes. Understanding the variation that exists will allow the breeder to determine strategies to be adopted in his breeding program. The objectives of the present study were to estimate the magnitude of genetic variability and advance, heritability and inter-character relationships by simple correlations and path coefficient analysis in 40 local colocynth genotypes from Southeastern Benin. The experiment was carried out in a randomized complete block design with three replications in three locations for three years. 34 morpho-agronomic traits were observed in each genotype. Analysis of variance revealed that effects of genotype, genotype by year or location and genotype by year by location interactions were significant (p ≤ 0.01 or 0.05) for all the characters. Phenotypic coefficients of variation (PCV) values were relatively greater than genotypic coefficients of variation (GCV) for all traits. High magnitude of phenotypic and genotypic coefficients of variation as well as high heritability along with high genetic advance were recorded particularly for qualitative traits. All yield components, except time to emergence, time to tailspins, leaf limb width, fruit number per plant, fruit width, seed length, seed tegument percentage and stem pubescence texture, had significant and positive correlations with yield attributes represented by thousand-seed weight (TSW) and seed number per plant (SNP). Path coefficient analysis indicated that all the characters (except leaf pubescence texture, stem pubescence texture, fruit design produced by secondary skin color and male flower size) had positive direct effects on TSW and partly SNP. Results suggested that most of the 34 quantitative and qualitative traits studied could be effectively used as selection criteria in the breeding program of Citrullus colocynthis varieties with high yield.

VirID: Beyond Virus Discovery-An Integrated Platform for Comprehensive RNA Virus Characterization.

RNA viruses exhibit vast phylogenetic diversity and can significantly impact public health and agriculture. However, current bioinformatics tools for viral discovery from metagenomic data frequently generate false positive virus results, overestimate viral diversity, and misclassify virus sequences. Additionally, current tools often fail to determine virus-host associations, which hampers investigation of the potential threat posed by a newly detected virus. To address these issues we developed VirID, a software tool specifically designed for the discovery and characterization of RNA viruses from metagenomic data. The basis of VirID is a comprehensive RNA-dependent RNA polymerase database to enhance a workflow that includes RNA virus discovery, phylogenetic analysis, and phylogeny-based virus characterization. Benchmark tests on a simulated data set demonstrated that VirID had high accuracy in profiling viruses and estimating viral richness. In evaluations with real-world samples, VirID was able to identify RNA viruses of all types, but also provided accurate estimations of viral genetic diversity and virus classification, as well as comprehensive insights into virus associations with humans, animals, and plants. VirID therefore offers a robust tool for virus discovery and serves as a valuable resource in basic virological studies, pathogen surveillance, and early warning systems for infectious disease outbreaks.

Comparative assessment of genotyping-by-sequencing and whole-exome sequencing for estimating genetic diversity and geographic structure in small sample sizes: insights from wild jaguar populations.

Biologists currently have an assortment of high-throughput sequencing techniques allowing the study of population dynamics in increasing detail. The utility of genetic estimates depends on their ability to recover meaningful approximations while filtering out noise produced by artifacts. In this study, we empirically compared the congruence of two reduced representation approaches (genotyping-by-sequencing, GBS, and whole-exome sequencing, WES) in estimating genetic diversity and population structure using SNP markers typed in a small number of wild jaguar (Panthera onca) samples from South America. Due to its targeted nature, WES allowed for a more straightforward reconstruction of loci compared to GBS, facilitating the identification of true polymorphisms across individuals. We therefore used WES-derived metrics as a benchmark against which GBS-derived indicators were compared, adjusting parameters for locus assembly and SNP filtering in the latter. We observed significant variation in SNP call rates across samples in GBS datasets, leading to a recurrent miscalling of heterozygous sites. This issue was further amplified by small sample sizes, ultimately impacting the consistency of summary statistics between genotyping methods. Recognizing that the genetic markers obtained from GBS and WES are intrinsically different due to varying evolutionary pressures, particularly selection, we consider that our empirical comparison offers valuable insights and highlights critical considerations for estimating population genetic attributes using reduced representation datasets. Our results emphasize the critical need for careful evaluation of missing data and stringent filtering to achieve reliable estimates of genetic diversity and differentiation in elusive wildlife species.

Influence of variance component estimates on genomic predictions for growth and reproductive-related traits in Nellore cattle.

This study aimed to estimate variance components (VCs) for growth and reproductive traits in Nellore cattle using two relationship matrices (pedigree relationship A matrix and pedigree plus genomic relationship H matrix), and records collected before and after genomic selection (GS) implementation. The study also evaluated how genomic breeding values (GEBV) are affected by variance components and discarding old records. The analysed traits were weight at 120 days (W120), weight and scrotal circumference at 450 days (W450 and SC450, respectively). Three datasets were used to estimate VCs, including all phenotypic information (All) or records for animals born before or after GS implementation (Before or After datasets, respectively). Both relationship matrices were considered for VC estimation, the A matrix was used in all three datasets and VC from each combination were named as A_Before, A_After, and A_All). The H was used in two datasets: H_All and H_After. Different VCs were used for GEBV prediction through ssGBLUP. This step used two possible Datasets, using all available phenotypic data (Dataset 1) or just records collected since GS implementation (Dataset 2). Validation was conducted using accuracy, bias and dispersion according to the LR method and prediction accuracy from corrected phenotypes. The heritability of all traits increased from A_Before to A_After, while estimates for A_All were intermediary. In the previous order, the estimates were 0.16, 0.17, and 0.15 for W120; 0.31, 0.39, and 0.35 for W450; 0.35, 0.47, and 0.41 for SC. For W450 and SC, using the H matrix reduced the heritability (0.33 and 0.32 for W450; 0.41 and 0.38 for SC for H_After and H_All, respectively). For W120, Dataset1 and VCs from A_After showed the highest accuracy for direct and maternal GEBV (0.953 and 0.868). For W450, Dataset 1 and VC from H_After allowed the highest accuracy (0.854) but use Dataset 2 and same VC source yield similar value (0.846). For SC, Dataset 2 with VC from H_After showed the highest accuracy (0.925). To use Dataset 2 does not cause important changes in bias or dispersion with respect to Dataset 1. The VC and genetic parameters changed for W120, W450, and SC450, using records before or after the GS implementation. For W450 and SC450, genetic variance and heritability estimates increased with the use of GS. For W120, genomic predictions were more accurate using A for VC estimation. Accuracy gains were observed for W450 and SC450 using H in VC estimation and/or discarding records before GS. It is possible to discard phenotypic records before GS implementation without generating bias or dispersion in the GEBV of young candidates.

Identification and mapping of sex-linked markers in giant abalone (Haliotis gigantea Gmelin)

Giant abalone (Haliotis gigantea Gmelin) is an economically important species within Haliotis genus, yet the genetic basis of sex in this species is still poorly understood. Therefore, we screened and mapped sex-linked SNPs and InDels, and subsequently developed a PCR-based method for genetic sex identification in giant abalone. Based on whole-genome sequencing reads, we obtained a total 6,159,941 high-quality SNPs and 2,623,263 high-quality InDels. Among them, 1,737 SNPs and 179 InDels were detected as sexually dimorphic, assuming a male heterogametic sex determination system. The majority of these variants, 99.1 % for SNPs and 99.4 % for InDels, were clustered on Chr.4 (0.02 Mb to 23.22 Mb). Furthermore, the estimation of genetic divergence between the sexes using FST showed that the genomic windows with the top 1 % FST values were concentrated on Chr.4 (0.5 Mb to 19.0 Mb) and Chr.5 (20.0 Mb to 35.0 Mb). Based on the sexually dimorphic variants on Chr.4, three PCR-based markers were successfully developed to determine the genetic sex of giant abalone. PCR validation using a tested panel of 67 females and 67 males from a cultivated population demonstrated compliance rates for these three markers ranging from 97.7 % to 99.3 %. These results suggest that the sex determination system is male heterogametic in giant abalone. Thus, this study provides valuable insights and tools for further research on the mechanisms of sex determination and differentiation, as well as for monitoring sex ratios in wild and cultivated populations in giant abalone.

Estimation of Additive and Dominance Genetic Variances for Growth and Multiple Stress at Different Ages in Pacific White Shrimp Litopenaeus vannamei

AbstractThis study aimed to estimate the additive and dominance genetic variance in growth and multiple‐stress tolerance traits in 7‐week‐old and 15‐week‐old Pacific white shrimp Litopenaeus vannamei. Four different animal models were studied by including all or different subsets of the following effects: additive genetic effects (A), additive genetic and common environmental effects (A + C), additive genetic and dominance effects (A + D), and additive, common environmental, and dominance effects (A + D + C). Variance components were estimated using the average information restricted maximum likelihood method. In general, estimates of additive genetic variance were inflated under the simple model (A) and decreased remarkably under the more complex models (A + C, A + D, and A + D + C). The genetic parameters of two‐stage (7‐week and 15‐week shrimp) growth and multiple‐stress tolerance traits were more suitable for estimation using the A + C model. The additive effects (0.311–0.754) of seven traits in 7‐week shrimp were greater than the dominance effects (4.950 × 10−7 to 0.201), whereas the additive effects of the same seven traits in adult shrimp ranged from 7.712 × 10−8 to 0.468 and the dominance effects ranged from 0.074 to 0.577. Except for survival time, carapace length, and carapace width, the additive effects of the other traits were smaller than the corresponding dominance effects. Thus, better genetic improvement of 7‐week and 15‐week shrimp growth and multiple‐stress tolerance can be obtained with selective breeding than with crossbreeding and better genetic improvement of 7‐week shrimp growth traits can be obtained with crossbreeding than with selective breeding. Our study further enriches the database for enhancing growth and stress resistance in Pacific white shrimp and provides reference information for growth improvement and multiple‐stress resistance breeding.

Prediction of resistance, virulence, and host-by-pathogen interactions using dual-genome prediction models

Key messageIntegrating disease screening data and genomic data for host and pathogen populations into prediction models provides breeders and pathologists with a unified framework to develop disease resistance.Developing disease resistance in crops typically consists of exposing breeding populations to a virulent strain of the pathogen that is causing disease. While including a diverse set of pathogens in the experiments would be desirable for developing broad and durable disease resistance, it is logistically complex and uncommon, and limits our capacity to implement dual (host-by-pathogen)-genome prediction models. Data from an alternative disease screening system that challenges a diverse sweet corn population with a diverse set of pathogen isolates are provided to demonstrate the changes in genetic parameter estimates that result from using genomic data to provide connectivity across sparsely tested experimental treatments. An inflation in genetic variance estimates was observed when among isolate relatedness estimates were included in prediction models, which was moderated when host-by-pathogen interaction effects were incorporated into models. The complete model that included genomic similarity matrices for host, pathogen, and interaction effects indicated that the proportion of phenotypic variation in lesion size that is attributable to host, pathogen, and interaction effects was similar. Estimates of the stability of lesion size predictions for host varieties inoculated with different isolates and the stability of isolates used to inoculate different hosts were also similar. In this pathosystem, genetic parameter estimates indicate that host, pathogen, and host-by-pathogen interaction predictions may be used to identify crop varieties that are resistant to specific virulence mechanisms and to guide the deployment of these sources of resistance into pathogen populations where they will be more effective.

Genetic diversity and connectivity of the invasive gastropod, Callinina georgiana (Caenogastropoda: Viviparidae) across a fragmented riverscape: A mitonuclear perspective

Abstract Aquatic invasive species are a significant threat to global freshwater biodiversity. This study focuses on the banded mystery snail, Callinina georgiana, an invasive species in the Adirondack region of northern New York—an important section of the New York Great Lakes Basin. This project aims to explore the genetic connectivity of C. georgiana within its invasive range using a combination of mitochondrial and nuclear markers. Sampling was conducted in the Raquette River and adjacent waterways, with a total of 229 snails collected from 16 distinct populations distributed across eight different waterbodies. Also included were two populations from the species' native range in the southern U.S.A. DNA was extracted, and a 710‐bp fragment of the mitochondrial DNA marker cytochrome c oxidase 1 and a 351‐bp fragment of nuclear marker histone‐3 were amplified. Population genetic analyses including haplotype patterning, AMOVA and genetic diversity estimates, neutrality tests and tests for isolation by distance were performed to assess connectivity patterns. Results showed moderate to high levels of genetic admixture within the snail's invasive range as indicated by the lack of geographic patterning of haplotypes and low to moderate levels of genetic differentiation across multiple sites. Demographic analyses combined with high numbers of private haplotypes indicate historic population expansion. Interestingly, a case of mitonuclear discordance was detected for native and invasive populations as evident by incongruent haplotype patterns for the cytochrome c oxidase 1 and histone‐3 markers. Callinina georgiana exhibits a high level of genetic connectivity in its invasive range. The presence of dams does not significantly affect apparent gene flow, indicating that anthropogenic activities, such as boat traffic might be key in dispersing the snails across this fragmented freshwater system. This study offers new insights into the dispersal and genetic structure of an invasive freshwater snail. It highlights the importance of considering anthropogenic factors when confronting complex patterns of genetic diversity. The findings are significant for biodiversity conservation and provide a basis for developing strategies to manage and contain the spread of aquatic invasive species such as C. georgiana, especially in regions with high human activity.

Multi-season-based estimation of genetic diversity, correlation and path analysis in spearmint (Mentha spicata L.) half-sib populations

Spearmint (Mentha spicata L.) is popular for its medicinal benefits and industrial uses, in this study forty-three half-sib progenies were evaluated over three seasons at CSIR-CIMAP, Research Centre Pantnagar to study genetic variability, correlation, path coefficient analysis and Mahalanobis D2 diversity by using five morphological and two biochemical traits. These forty-three half-sib populations were derived from nine commercially existing spearmint varieties through an intra-population improvement method. Results of correlation and path coefficient studies indicated the paramount importance of certain key traits in the selection process. Notably, traits such as herb yield per plot (kg), plant height (cm) and oil content (%) emerged as pivotal, exhibiting positive correlations, high heritability and moderate to high genetic advance. These attributes, therefore need primacy in the selection of superior lines. Furthermore, genotypes OPSP-106, OPSP-92, OPSP-47, OPSP-35 and OPSP-76 showed significant genetic divergence. These accessions hold promise as parent candidates for hybridization experiments aimed at finding transgressive segregants in later generations. Additionally, this study highlighted the presence of specific oil components, such as carvone and limonene, offering insights into potential avenues for targeted breeding efforts. This study provides a holistic view of the genetic makeup of Mentha spicata genotypes, enabling informed decisions in breeding programs. By prioritizing traits and maximizing genetic diversity, the results of this investigation will contribute to the development of improved spearmint varieties with enhanced morphological and biochemical characters, thus advancing the medicinal and industrial applications of spearmint.

Low genetic differentiation despite high habitat fragmentation in an endemic and endangered species of Iridaceae from South America: implications for conservation

Abstract To conserve threatened species effectively, it is crucial to map the genetic variation of the remaining populations. Thus, using 15 microsatellites markers, from which 10 were specially developed for this study, we investigated genetic structure and gene flow patterns of Herbertia zebrina Deble, a critically endangered species endemic from grasslands of southern Brazil. We also investigated the degree of habitat fragmentation and the impacts on levels of genetic diversity, mating system and pollinators of the species. STRUCTURE and discriminant analysis of principal components identified the existence of three genetic clusters. Populations were not isolated by distance, and genetic differentiation among populations was low (7.0%). Migration rates were also low, but no evidence of genetic bottlenecks was found. However, effective population-scaled mutation rates (Θ) were < 1, suggesting that populations could be experiencing genetic drift, but the reason remains unknown. The results indicate that measurements of habitat fragmentation were not significantly correlated with genetic diversity estimates, which tend to increase with fragment size. H. zebrina was identified as an outcrossing species and specialized pollinators, such as Chalepogenus goeldianus and Lanthanomelissa betinae were rarely observed. Our findings suggest that genetic differentiation across multiple populations within the entire geographic distribution of H. zebrina is very low and populations may struggle to adapt to the current environmental and pollination changes. However, habitat fragmentation is still too recent to detect significant impacts on the levels of genetic variation. Thus, conservation plans are necessary to avoid further declines of this species.

Influence of dams on sauger population structure and hybridization with introduced walleye.

Dams have negatively affected freshwater biodiversity throughout the world. These negative effects tend to be exacerbated for aquatic taxa with migratory life histories, and for taxa whose habitat is fundamentally altered by the formation of large reservoirs. Sauger (Sander candadensis; Percidae), large-bodied migratory fishes native to North America, have seen population declines over much of the species' range, and dams are often implicated for their role in blocking access to spawning habitat and otherwise negatively affecting river habitat. Furthermore, hybridization appears to be more frequent between sauger and walleye in the reservoirs formed by large dams. In this study, we examine the role of dams in altering sauger population connectivity and facilitating hybridization with introduced walleye in Wyoming's Wind River and Bighorn River systems. We collected genomic data from individuals sampled over a large spatial scale and replicated sampling throughout the spawning season, with the intent to capture potential variation in hybridization prevalence or genomic divergence between sauger with different life histories. The timing of sampling was not related to hybridization prevalence or population divergence, suggesting limited genetic differences between sauger spawning in different time and places. Overall, there was limited hybridization detected, however, hybridization was most prevalent in Boysen Reservoir (a large impounded section of the Wind River). Dams in the lower Wind River and upper Bighorn River were associated with population divergence between sauger upstream and downstream of the dams, and demographic models suggest that this divergence has occurred in concordance with the construction of the dam. Sauger upstream of the dams exhibited substantially lower estimates of genetic diversity, which implies that disrupted connectivity between Wind River and Bighorn River sauger populations may already be causing negative demographic effects. This research points towards the importance of considering the evolutionary consequences of dams on fish populations in addition to the threats they pose to population persistence.

Pervasive conservation of intron number and other genetic elements revealed by a chromosome-level genomic assembly of the hyper-polymorphic nematode Caenorhabditis brenneri.

With within-species genetic diversity estimates that span the gambit of that seen across the entirety of animals, the Caenorhabditis genus of nematodes holds unique potential to provide insights into how population size and reproductive strategies influence gene and genome organization and evolution. Our study focuses on Caenorhabditis brenneri, currently known as one of the most genetically diverse nematodes within its genus and metazoan phyla. Here, we present a high-quality gapless genome assembly and annotation for C. brenneri, revealing a common nematode chromosome arrangement characterized by gene-dense central regions and repeat rich peripheral parts. Comparison of C. brenneri with other nematodes from the 'Elegans' group revealed conserved macrosynteny but a lack of microsynteny, characterized by frequent rearrangements and low correlation iof orthogroup sizes, indicative of high rates of gene turnover. We also assessed genome organization within corresponding syntenic blocks in selfing and outcrossing species, affirming that selfing species predominantly experience loss of both genes and intergenic DNA. Comparison of gene structures revealed strikingly small number of shared introns across species, yet consistent distributions of intron number and length, regardless of population size or reproductive mode, suggesting that their evolutionary dynamics are primarily reflective of functional constraints. Our study provides valuable insights into genome evolution and expands the nematode genome resources with the highly genetically diverse C. brenneri, facilitating research into various aspects of nematode biology and evolutionary processes.

Diversity and Genetic Structure of a Natural Population of Mauritia flexuosa L. f. in APA-Pandeiros, Using Microsatellite Markers

Genetic diversity is essential to ensure that species maintain high adaptive evolutionary potential to resist environmental stochasticity. Thus, this research aimed to estimate the genetic diversity and structure of a natural population of Mauritia flexuosa and its stages, using five microsatellite primers. DNA was extracted from leaves collected from individuals of the three classes (G1-adult, G2-juvenile and G3-regenerant). Genetic diversity estimates indicated an average of 7.8 alleles/locus and lower observed heterozygosity (Ho) than expected heterozygosity (He) in the population (0.272-0.395 and 0.275-0.401, respectively). The Shannon Index (I) indicated moderate genotypic diversity and richness in the analyzed population, and exclusive alleles were found at the different stages. Also found were a lower population index (FST = 0.019) and a higher individual fixation index (FIS = 0.169). Classes G1 and G2 exhibited greater genetic similarity to each other than to G3, which had more distant genetic characteristics. These results revealed lower genetic diversity among regenerating (G3) individuals and greater genetic diversity among adults (G1). Immediate strategies for in situ and ex situ genetic conservation of M. flexuosa are essential to preserve its genetic variability and assist future programs for the improvement.