Genetic Structure Research Articles

Distinct management units for the Critically Endangered angelshark (Squatina squatina) revealed in the Canary Islands

AbstractThe angelshark, Squatina squatina, is listed as Critically Endangered on the IUCN Red List of Threatened Species, and remaining populations are highly fragmented throughout its historical distribution. The Canary Islands archipelago in the North East Atlantic has been identified as a uniquely large stronghold for the species. In the present study, we compared the population genetic structure of S. squatina across different islands of the Canary Island archipelago using both microsatellite and single nucleotide polymorphism (SNP) markers. Both markers revealed significant differentiation of angelsharks between islands in the archipelago, with three main genetic units at: (1) Tenerife, (2) Gran Canaria and (3) the island group consisting of La Graciosa, Lanzarote and Fuerteventura. Our results imply a connectivity barrier between some adjacent islands, most likely driven by abyssal depths, and varying geological history and formation of each island and oceanographic patterns (i.e. seasonal coastal upwellings off the African coast). Therefore, we suggest that in the Canary Islands, S. squatina populations should be managed locally, with conservation and research priorities designed and implemented specifically for each of the three genetic units.

Genetic structure of wolf populations in North Eurasia: the effect of exclusion of closely related individuals from analysis

We describe the results of analysis of genetic structure and spatial autocorrelation in the populations of grey wolf (Canis lupus Linnaeus, 1758) on the territory of the Russian Federation and the Republic of Kazakhstan, based on 20 autosomal microsatellite markers. With the use of molecular markers, we uncovered hidden genealogical patterns reaching as far as 700–1600 km and having the most pronounced effect on distances up to 150 km. Our research has shown that identification and exclusion of closely related genotypes has limited effect on the results of analysis of intrapopulation genetic diversity. Meanwhile, such procedure is recommended for researching population structure, as it allows for streamlining some statistical approaches. Results of our work demonstrate integral effect of natal migration, working against the differentiation effect of philopatry. Finally, we also show that the exclusion of closely related individuals can lead to underestimation of values of genetic distances between populations.

Genetic Relationships and Population Structure among Nigerian Ethnic Groups (Ibibio, Igbo, Hausa, Tiv and Yoruba) Based on Nine DNA Loci

Abstract Context: Population-specific attributes typically determine the behavior of human genotypes and traits in individuals. Examining the genetic relationships between populations presents an opportunity to observe patterns of genetic changes over time. By comparing populations, it is possible to see factors that may have sparked the evolution of a trait or genotype as well as the genetic diversity of the populations. Genetic diversity in the groups in Nigeria is still largely undefined. This can be achieved with the use of genetic markers. Aims: To determine the genetic relationships between Igbo, Ibibio, Yoruba, Tiv, and Hausa ethnic groups using nine short tandem repeat DNA markers. Settings and Design: Observational studies of 250 consenting participants. Methods and Material: Individuals of Igbo, Yoruba, Hausa, Ibibio, and Tiv were randomly sampled from their ethnic homes in Nigeria at participating institutions. DNA was extracted from blood samples using commercial DNA kits, and tested for nine autosomal short tandem repeat loci alleles using PCR and electrophoresis. The allele types and sizes were read and recorded for each locus for every individual. Statistical Analysis Used: Allelic frequencies, population pairwise genetic distances (FST and RST, analysis of molecular variance (AMOVA), and principal component analysis (PCA) were calculated using GenAlEx v6.502. Results: The fixation index (FST) was between 0.001 and 0.500 in the five populations. The estimated variation was 99.98% within individuals and 0.10% among populations. Four heterogeneous clusters were observed with three axes accounting for 32.86% variation. Conclusions: The genetic relationships closely mirrored linguistic groupings showing that language may have shaped early interaction and ultimately gene transfer between these groups.

Genetic and Haplotype Diversity of Clarias gariepinus (Burchell 1822) Based on Cytochrome c Oxidase I (COI) Gene

The evaluation of mitochondrial DNA and genetic analysis is helpful for economically significant species. Clarias gariepinus is a critical species in aquaculture. This study investigates the genetic diversity and population differentiation of C. gariepinus from 19 countries using 164 sequences of the mitochondrial DNA’s Cytochrome c oxidase I (COI) gene. The haplotype analysis revealed a total of 17 haplotypes, with a nucleotide diversity (π) of 0.012 and a haplotype diversity (Hd) of 0.87. The results of an AMOVA and fixation index indicated significant genetic variation and structure among the populations. Additionally, neutrality tests and mismatch distribution analysis supported the hypothesis of under-purifying selection in C. gariepinus. The findings suggested that the population did not experience expansion. In conclusion, the genetic analysis highlighted substantial variation among C. gariepinus populations from different locations, providing valuable insights for the global management of this species.

Assessment of conservation status of Ferula huber‐morathii: association with population genetic structure and regional climate

Ferula huber‐morathii is an endemic and medicinally important plant. This species is distributed in eight Turkish localities, including three newly identified ones. Its extent of occurrence and area of occupancy is determined to be 3963 km2 and 32 km2 respectively. All localities are characterized by East Mediterranean and sub‐Mediterranean precipitation regimes; however, temperatures increase excessively and precipitation decreases during the flowering period of the species. The population sizes are quite small, and the number of reproducing individuals in some populations is below ten. Analyses of ISSR markers showed the percentage of polymorphic loci to be 94% at the species level and 56% at the population level. The level of genetic differentiation (measured by GST) was 0.37 and the estimated level of gene flow among populations (NM) was 0.84. The percentage of variance occurring within and among populations, determined by AMOVA, was 75% and 25%, respectively. STRUCTURE analysis revealed two genetic clusters of individuals with a geographic structure, similar to that found in UPGMA and an ordination analysis. Some populations turned out to have both low numbers of individuals and low genetic diversity. Since many of the populations are subject to anthropogenic disturbance, the species should remain in the EN category. At the same time, it is suggested that a new in‐situ conservation area should be created around nearby dams, situated in the same climate area as the currently known populations.

Genetic overlap between inflammatory bowel disease and iridocyclitis: insights from a genome-wide association study in a European population.

Inflammatory bowel disease (IBD) is occasionally associated with ophthalmic diseases, including iridocyclitis (IC). The co-occurrence of IBD and IC has been increasingly observed, possibly due to shared genetic structures. A three-part analysis was executed utilizing genome-wide association study (GWAS) data on IBD and IC. First, the overall genetic correlation between the two traits was observed using linkage disequilibrium score regression (LDSC). Subsequent to this, a local genetic correlation analysis was conducted utilizing the heritability estimation from summary statistics (HESS) methodology. Finally, the conditional/conjunctional false discovery rate (cond/conjFDR) statistical framework was utilized to ascertain the degree of genetic overlap between the two traits. Positive overall correlations were observed among IBD, ulcerative colitis (UC), and IC, encompassing both acute/subacute and chronic IC presentations. While a significant correlation was identified between Crohn's disease (CD) and IC, it was not evident for acute/subacute or chronic IC (P > 0.05). Notably, IBD (encompassing CD and UC) demonstrated local genetic correlations with IC and acute/subacute IC, with pronounced enrichment notably on chromosomes 1 and 6, though such correlations were not observed with chronic IC. The conjFDR analysis confirmed the genetic overlap between the two diseases. The shared genes overlapping between IBD (encompassing CD and UC) and IC were IL23R, GPR35, and ERAP1. For acute/subacute IC and chronic IC, there were six overlapping genes (GPR35, RPL23AP12, IL23R, SNAPC4, ERAP1, and INAVA) and one overlapping gene (INAVA), respectively. This study confirms the existence of a shared genetic structure between IBD and IC, providing a biological basis for their comorbidity. Additionally, this finding has significant implications for preventing and treating these two diseases.

Characterization of Y chromosome diversity in newfoundland and labrador: evidence for a structured founding population.

The population of Newfoundland and Labrador (NL) is largely derived from settlers who migrated primarily from England and Ireland in the 1700s-1800s. Previously described as an isolated founder population, based on historical and demographic studies, data on the genetic ancestry of this population remains fragmentary. Here we describe the largest investigation of patrilineal ancestry in NL. To determine the paternal genetic structure of the population, 1,110 Y chromosomes from an NL-based cohort were analyzed using 5,761 Y-specific SNPs. We identified 160 distinct terminal haplogroups, the majority of which (71.4%) belong to the R1b haplogroup. When compared with global reference populations, the NL population haplogroup composition and frequencies primarily resemble those observed in English and Irish ancestral source populations. There is also evidence of genetic contributions from Basque, French, Portuguese, and Spanish fishermen and early settlers who frequented NL. Interestingly, the observed population structure shows geographical and religious clustering that can be associated with the settlement of the ancestral source populations from predominantly Protestant, England, and Catholic, Ireland respectively. For example, the R1b-M222 haplogroup, seen in people of Irish descent, is found clustered in the Irish-settled Southeast region of NL. The clustering and expansion of Y haplogroups in conjunction with the geographical and religious clusters illustrate that limited subsequent in-migration, geographic isolation, and societal factors have contributed to the genetic substructure of the NL population and its designation as a founder population.

Population structure of Desmophyllum pertusum found along the United States eastern continental margin

ObjectiveThe connectivity and genetic structuring of populations throughout a region influence a species’ resilience and probability of recovery from anthropogenic impacts. By gaining a comprehensive understanding of population connectivity, more effective management can be prioritized. To assess the connectivity and population genetic structure of a common cold-water coral species, Desmophyllum pertusum (Lophelia pertusa), we performed Restriction-site Associated DNA Sequencing (RADseq) on individuals from nine sites ranging from submarine canyons off New England to the southeastern coast of the United States (SEUS) and the Gulf of Mexico (GOM). Fifty-seven individuals and 3,180 single-nucleotide polymorphisms (SNPs) were used to assess genetic differentiation.ResultsHigh connectivity exists among populations along the SEUS, yet these populations were differentiated from those to the north off New England and in Norfolk Canyon along the North Atlantic coast of the United States, as well as those in the GOM. Interestingly, Norfolk Canyon, located just north of North Carolina, and GOM populations exhibited low levels of genetic differentiation, corroborating previous microsatellite analyses and signifying gene flow between these populations. Increasing sample sizes from existing populations and including additional sampling sites over a larger geographic range would help define potential source populations and reveal fine-scale connectivity patterns among D. pertusum populations.

Genome-Wide Identification and Characterization Thaumatin-like Protein (TLP) Genes in Wild Olive (Olea europaea var. sylvestris)

The wild olive tree (Olea europaea var. sylvestris) is the ancestor of all olive varieties, displaying remarkable adaptability to diverse climatic conditions and soil types. This iconic tree of the Mediterranean Basin stands out for its ability to withstand environmental stresses, such as water scarcity and temperature variations, playing a crucial role in the ecology, economy, and culture of the region. In this study, 42 TLP genes were characterized in the wild olive tree, distributed across 14 chromosomes and nine scaffolds. In silico analysis revealed the presence of domains associated with antifungal activity in some sequences, indicating their potential role in pathogen resistance. The structural diversity of OeTLP genes was explored through multiple alignments, conserved motifs and phenetic analysis. Correlation was observed between phenetic diversity, genetic structure, and motif patterns, suggesting different functions among OeTLP groups. Additionally, the distribution of exons and introns in the pheneticc tree provided further insights into the evolution of these genes. Comparative modeling of OeTLPs unveiled three-dimensional models with good structural quality and distinctive surface charge characteristics. This study provides a comprehensive understanding of the physicochemical, structural, and phenetic features of TLP genes in Wild Olive, contributing to knowledge about this species' response to environmental stresses and pathogens.

Polymorphic insertions of DcSto miniature inverted-repeat transposable elements reveal genetic diversity structure within the cultivated carrot.

Miniature inverted-repeat transposable elements (MITEs) are a potent source of polymorphisms in plant genomes. A genotyping system, named DcS-ILP, based on polymorphic insertions of Stowaway MITEs (DcStos) localized in introns and identified in the reference genome DH1, has been developed for carrot. Here, we report an extension of the DcS-ILP genotyping system by incorporation of non-reference insertions identified in resequenced genomes representing the eastern gene pool. We genotyped 52 carrot accessions representing the eastern and western carrot gene pools with 92 markers developed previously (western DcS-ILP panel) together with 84 newly developed markers (eastern DcS-ILP panel). Overall, the DcS-ILP markers revealed a highly structured genetic diversity separating the eastern and the western carrot accessions at K = 2 and differentiating Indian breeding lines from the eastern accessions at K = 3. The eastern DcS-ILP panel proved to be more robust with respect to the eastern carrot gene pool, while it provided little information on the western accessions, as many of the DcSto insertions present in the eastern gene pool were absent in the western gene pool. As the western carrot accessions represent improved cultivars, DcSto insertional polymorphisms allowed detection of a selection-driven bottleneck at the improvement stage. Selection in the course of the improvement stage generally operated on standing variation, as the subset of DcSto insertions present in the western carrot likely originated from transposition events preceding the separation of both gene pools. However, occasional frequency shifts in the opposite direction were also revealed, possibly indicating selection for favorable variants associated with DcSto insertions.

Larval Transport Pathways for Lutjanus peru and Lutjanus argentiventris in the Northwestern Mexico and Tropical Eastern Pacific

Understanding how ocean currents influence larval dispersal and measuring its magnitude is critical for conservation and sustainable exploitation, especially in the Tropical Eastern Pacific (TEP), where the larval transport of rocky reef fish remains untested. For this reason, a lagrangian simulation model was implemented to estimate larval transport pathways in Northwestern Mexico and TEP. Particle trajectories were simulated with data from the Hybrid Ocean Coordinate Model, focusing on three simulation scenarios: (1) using the occurrence records of Lutjanus peru and L. argentiventris as release sites; (2) considering a continuous distribution along the study area, and (3) taking the reproduction seasonality into account in both species. It was found that the continuous distribution scenario largely explained the genetic structure previously found in both species (genetic brakes between central and southern Mexico and Central America), confirming that the ocean currents play a significant role as predictors of genetic differentiation and gene flow in Northwestern Mexico and the TEP. Due to the oceanography of the area, the southern localities supply larvae from the northern localities; therefore, disturbances in any southern localities could affect the surrounding areas and have impacts that spread beyond their political boundaries.

Genetic Diversity and Forensic Utility of X-STR Loci in Punjabi and Kashmiri Populations: Insights into Population Structure and Ancestry

Background: X-chromosomal short tandem repeats (X-STRs) are crucial in forensic applications, particularly in complex kinship cases, and play an important role in population genetics. However, there is limited data on X-STR variation in Pakistani populations, especially among ethnic groups like Kashmiri and Punjabi. Methodology: This study investigates the forensic and genetic properties of 12 X-STRs from the Investigator Argus X-12 Kit (QIAGEN, Hilden, Germany) in 125 families (75 Kashmiri, 50 Punjabi) from Azad Jammu and Kashmir and Punjab, Pakistan. Results: In both populations, a total of 222 alleles were identified across the 12 X-STR loci (Punjabi 171 alleles, Kashmiri 161 alleles), with allele frequencies ranging from 0.0056 to 0.3033. DXS10148 was the most polymorphic locus with 28 alleles, while DXS7132 was the least polymorphic with 9 alleles. Most loci were in linkage equilibrium, except for the DXS10135/DXS10148 pair in males, with no loci exhibiting significant linkage disequilibrium in females. The combined power of discrimination was 0.999 999 9977 for Kashmiri males, 0.999 999 999 999 9746 for Kashmiri females, and 0.999 999 999 999 9781 for Punjabi females. In Kashmiri males, 34, 31, 28, and 32 haplotypes were observed across the four linkage groups (LG1, LG2, LG3, and LG4), though these groups did not form stable haplotypes, as indicated by Linkage Equilibrium within and significant Linkage Disequilibrium between groups. Conclusions: Genetic structure analysis using Principal Component Analysis and STRUCTURE revealed distinct clustering patterns for the Kashmiri and Punjabi populations, indicating unique genetic backgrounds and ancestry influences, particularly distinguishing them from East Asian populations. This study provides a comprehensive analysis of X-STR variation in Punjabi and Kashmiri populations, offering valuable insights for forensic and population genetic studies.

Genetic spatialization in Montana cattle breed.

Brazil is among the world's top beef producers and exporters, and the Montana breed of livestock has gained popularity due to its exceptional meat quality and ability to adapt to the tropical climate. This differentiates it from other breeds, such as the Zebu and Taurine. A methodology that mapped sixteen farms across five Brazilian states was adopted to investigate the link between SNP genetic data and animal collection location. The data was georeferenced using the Geographic Information System and the ArcGIS 10.3 software, considering a geographic coordinate system and the WGS 84 datum. The Alleles in Space (AIS) software was used to study the relationship between the SNP genetic data and the animal collection location. Various analyses were conducted, including the Mantel correlation, genetic barrier identification, and spatial autocorrelation. The results suggest that there is a correlation between genetic and geographical distances, supporting the idea that geographical distance can affect genetic diversity. This information is vital to understand the genetic structure of populations concerning geographical space and is crucial for optimizing Brazilian agricultural production.

Analysis of genetic structure and identification of important genes associated with muscle growth in Fujian Muscovy duck

Fujian Muscovy duck is a well-known meat waterfowl in Fujian Province due to its high meat production, superior breeding potential, and strong resistance. To fully explore the genetic characteristics of these advantages, Fujian black Muscovy duck and white Muscovy duck were used for whole-genome re-sequencing and transcriptome analyses. Population structure analysis showed significant differentiation between the two feather strains. Runs of homozygosity analysis indicated a stronger artificial influence on the black-feathered strain, with ROH island genes notably enriched in muscle tissue-related terms and pathways. Selective sweep and transcriptome analysis revealed a significant enrichment of genes linked to muscle tissue and muscle fiber-related terms and pathways. Key candidate genes identified, such as MEF2C, MYOZ2, and METTL21C, are believed to play crucial roles in meat production in Fujian Muscovy duck. This study offers a new perspective on improving meat production in Fujian Muscovy duck, which can benefit breeding strategies and production management.

Genetic Diversity and Association Analysis of Traits Related to Water-Use Efficiency and Nitrogen-Use Efficiency of Populus deltoides Based on SSR Markers.

Populus deltoides is one of the primary tree species for bioenergy production in temperate regions. In arid/semi-arid northern China, the scarcity of water and nitrogen significantly limits the productivity of poplar plantations. The identification of relevant molecular markers can promote the breeding of resource-efficient varieties. In this study, 188 genotypes of P. deltoides from six provenances served as experimental material. Genetic differentiation analysis, analysis of molecular variance (AMOVA), principal coordinate analysis (PCoA), unweighted pair group method with arithmetic mean (UPGMA) clustering, and genetic structure analysis were performed using selected simple sequence repeat (SSR) markers. Based on these analyses, the association analysis of water-use efficiency (WUE) and nitrogen-use efficiency (NUE) were conducted using general linear model (GLM) and mixed linear model (MLM) approaches. The results showed that 15 pairs of SSR primers successfully amplified across all 188 individuals, with an average of 7.33 alleles (Na) observed per primer pair. The polymorphism information content (PIC) ranged from 0.060 to 0.897, with an average of 0.544, indicating high genetic diversity in the selected markers. The average inbreeding coefficient intra-population (Fis), inbreeding coefficient inter-population (Fit), and inter-population genetic fraction coefficient (Fst) values were 0.005, 0.135, and 0.132, respectively, indicating high heterozygosity, substantial inbreeding within populations, and moderate genetic differentiation, with an average gene flow (Nm) of 1.964, suggesting substantial gene flow between populations. Additionally, molecular variance was primarily within individuals (84.12%). Genetic structure analysis revealed four subgroups, with some degree of genetic admixture among the provenances. In the GLM model, 11 markers were significantly associated with five traits (p < 0.05), with an average contribution rate of 15.82%. Notably, SSR132 and SSR143 were significantly associated with multiple traits (p < 0.05). The MLM model identified two markers (SSR47 and SSR85) significantly associated with ground diameter (p < 0.05) and one marker (SSR80) significantly associated with NUE (p < 0.05). This study identifies loci associated with WUE and NUE, laying a foundation for future genetic improvement and marker-assisted breeding strategies in poplar.

A comprehensive map of copy number variations in dromedary camels based on whole genome sequence data

Copy number variants (CNVs) are structural variants within the eukaryotic genome that vary among individuals of a species. These variants have been associated with different phenotypic traits, making them a valuable consideration as markers for designing breeding programmes. In this study, whole genome sequence data of 60 dromedary camel samples originating from the Arabian Peninsula were analyzed to construct a comprehensive dromedary CNV map. Utilizing four CNV callers employing read-depth, split-read and paired-end mapping approaches, a total of 37,519 CNV events (17,847 deletions and 19,672 duplications) were called on the dromedary autosomes. These CNV events were merged into 2,557 regions, categorized as 1,322 losses, 122 gains, and 1,113 “mixed regions” comprising both types. The cumulative size of the CNV regions amounted to 22.5 Mb, covering roughly 1.16% of the dromedary autosomes. Approximately 32% of the defined CNV regions (comprising 60% losses, 18% gains, and 0.27% mixed regions) were found in ≥ 90% of the dromedary samples, classifying them as prevalent regions. Genes with biological functions related to the different adaptive physiologies of dromedary camels, such as fertility, heat stress, musculoskeletal development, and fat metabolism, were overlapping with or in close proximity to ~ 68% of the defined CNV regions, demonstrating their potential role in dromedaries’ physiology. This study presents the first comprehensive CNV map of dromedary camels and builds on the present knowledge in understanding the genetic structure of this species.

Chinese Populations of Magnaporthe oryzae Serving as a Source of Human-Mediated Gene Flow to Asian Countries: A Population Genomic Analysis

Magnaporthe oryzae, a filamentous heterothallic ascomycete fungus that serves as the causative agent of rice blast disease, is globally distributed in rice-growing regions. Populations shaped by environmental factors and human intervention play important roles in the formation of genetic structure. In this study, population structures and spatiotemporal dynamics were investigated based on large-scale whole genomic sequences of rice-infecting M. oryzae around the world. By analyzing these genetic structures, we identified divergent clades that crossed geographic boundaries. While we observed associations between the isolates and their geographic origins, we also found that there were frequent migration events occurring across Asia in main rice cultivation regions. Within Asia, China was the migration origin, facilitating gene flows to Japan and South Korea. Since the 1970s, the genetic diversity of M. oryzae populations in China has also shown a steadily increasing trend, continuing through to the 2020s. Additionally, our analysis of the evolutionary history of Asian M. oryzae populations provided insights into the population expansion that has taken place in recent decades. Overall, our findings indicate that human-mediated gene flows played a pivotal role in shaping the genetic structure of M. oryzae.

Using eDNA to Supplement Population Genetic Analyses for Cryptic Marine Species: Identifying Population Boundaries for Alaska Harbour Porpoises.

Isolation by distance and biogeographical boundaries define patterns of population genetic structure for harbour porpoise along the Pacific coast from California to British Columbia. Until recently, inadequate sample sizes in many regions constrained efforts to characterise population genetic structure throughout the coastal waters of Alaska. Here, tissue samples from beachcast strandings and fisheries bycatch were supplemented with targeted environmental DNA (eDNA) samples in key regions of Alaska coastal and inland waters. Using a geographically explicit, hierarchical approach, we examined the genetic structure of Alaska harbour porpoises, using both mitochondrial DNA (mtDNA) sequence data and multilocus SNP genotypes. Despite a lack of evidence of genetic differentiation from nuclear SNP loci, patterns of relatedness and genetic differentiation from mtDNA suggest natal philopatry at multiple geographic scales, with limited gene flow among sites possibly mediated by male dispersal. A priori clustering of sampled areas at an intermediate scale (eastern and western Bering Sea, Gulf of Alaska and Southeast Alaska) best explained the genetic variance (12.37%) among regions. In addition, mtDNA differentiation between the Gulf of Alaska and eastern Bering Sea, and among regions within the Gulf of Alaska, indicated significant genetic structuring of harbour porpoise populations in Southeast Alaska. The targeted collection of eDNA samples from strata within Southeast Alaska was key for elevating the statistical power of our mtDNA dataset, and findings indicate limited dispersal between neighbouring strata within coastal and inland waters. These results provide evidence supporting a population boundary within the currently recognised Southeast Alaska Stock. Together, these findings will prove useful for ongoing management efforts to reduce fisheries conflict and conserve genetic diversity in this iconic coastal species.

Genetic Diversity in the Orenburg Goat Breed Revealed by Single-Nucleotide Polymorphism (SNP) Analysis: Initial Steps in Saving a Threatened Population

Background/Objectives: Orenburg goats are renowned for their soft down that acts as a substrate for warm clothing, particularly shawls that have an international reputation. As with many local livestock breeds, however, the Orenburg is presently at risk of extinction, an issue that can be addressed by assessing population genetic diversity and, thereafter, encouraging as much outbreeding as possible. Using single-nucleotide polymorphism (SNP)-based data, therefore, we analyzed the genetic diversity and population structure of modern Orenburg goats using samples collected from an expedition to Orenburg Oblast in 2024. Methods: We applied the Goat SNP50 BeadChip (Illumina, San Diego, CA, USA) for the genotyping of Orenburg goats from modern and archived populations. SNP genotypes of three Orenburg populations sampled in 2017 and 2019, Altai Mountain, Altai White, and Soviet Mohair breeds, were added to the dataset. Results: Principal component analysis and network and admixture analyses demonstrated that the genetic background inherent to the archived group of Orenburg goats was maintained in all modern populations. Values of genetic diversity indicators in modern populations were compatible with those obtained in comparison groups. Runs of homozygosity (ROH) were found in all the Orenburg goat populations (with a mean ROH length of 72.6–108.9 Mb and mean ROH number of 28–36). Genomic inbreeding based on ROH was low in all the Orenburg populations (FROH = 0.03–0.045). Conclusions: We showed that the ancestral background is retained in present-day Orenburg goats sampled in 2024. We provide the genetic basis through which certain breeder animals may be selected and bred traditionally or ex situ through a conservation program of gamete preservation.

A genetic assessment of natural barriers for isolating a proposed Greenback Cutthroat Trout reintroduction area

AbstractObjectiveNative inland trout conservation efforts rely on physical barriers to exclude nonnative salmonids from target habitats. We used genetic techniques to evaluate a series of natural waterfalls for their potential to serve as barriers to prevent nonnative salmonids from entering a proposed reintroduction area for federally threatened Greenback Cutthroat Trout Oncorhynchus virginalis stomias.MethodsGenetic samples were collected from nonnative Brook Trout Salvelinus fontinalis at 11 sampling reaches above and below natural waterfalls (height: ~1–3 m under base flow conditions) along a 33‐km segment of Colorado's upper Cache la Poudre River near the outflow of the proposed reintroduction area. To evaluate whether upstream movement of Brook Trout is restricted by any of these waterfalls, we characterized longitudinal trends in genetic diversity along the river corridor and examined patterns of genetic differentiation and population structure in relation to waterfall locations using a panel of microsatellites.ResultWe found no evidence that the waterfalls served as complete movement barriers for nonnative Brook Trout based on genetic clustering analyses, estimates of population differentiation, and longitudinal genetic patterns. Our multilocus assessment did not identify alleles restricted to downstream reaches, and the river segment was genetically homogenized.ConclusionOur evaluation suggests that the existing waterfalls do not fully prevent upstream movement by nonnative Brook Trout, and thus barrier modification would be needed to establish an isolated Greenback Cutthroat Trout population in the proposed wilderness area.