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ABSTRACT Artificial breeding of mantis shrimp Oratosquilla oratoria, using the ecological breeding in earthen pond (EBEP) method, has been carrying out from 2019, and the produced larvae have always been used for supportive breeding programs in Bohai Bay. To assess the degree of fidelity of enhancement programs used an EBEP method to native genetic pools, genetic diversity at 10 microsatellite loci was analyzed in three hatchery offspring populations, their wild parent stocks, and their wild contemporaneous offspring. Significant decrease in the almost genetic diversity parameters and highly significant differences in shannon's information index (decreasing by 22.54%–40.97%) and allelic richness (33.80%–46.87%) were observed between in hatchery populations. This further created relatively more genetic differentiation between the hatchery and wild population, as the pairwise Fst values and genetic distances showed. The mean pairwise relatedness coefficients showed higher values within hatchery populations and lower values within wild populations. Hatchery populations contained the fewest full‐sib families and offspring were extremely distributed in 10–11 full‐sib groups in each hatchery population. The relatively small number of actual spawning females and large variance in parental contribution to the next generation possibly causes allele reduction in the hatchery population, which in turn leads to a decrease in allelic diversity and an increase in genetic similarities among individuals. Promoting synchrony of ovarian development in females, providing good conditions for incubation and larvae culture and balancing the contributions of parents will be important in future breeding propagation. [ABSTRACT FROM AUTHOR]

Eleven microsatellite markers previously developed from gooseberry sequences were tested on red and black currants. The results showed amplification of all microsatellite loci on black currant accessions, while on red currant accessions, there was no amplification at three loci (RucANS, RucDFR2-1, RucDFR1-3). Polymorphic loci were identified in both black and red currants. In the MTT-7 locus of the studied black currant genotypes, amplification of three fragments was observed, suggesting duplication of this locus. At the same time, in the MTT-7 locus of red currant, amplification typical of a monolocus microsatellite was observed. The RucHLH-1 and RucUFGT loci were tested on a hybrid red currant family (Belaya Potapenko × 1426-21-80). Using linkage mapping approach, the RucHLH-1 locus was mapped to the linkage group 4 of the red currant genome, and the RucUFGT locus (presumed), to the linkage group 1. The set of microsatellite loci for the genus Ribes is currently limited. This study shows that some of the SSR markers developed from gooseberry are amplified and reveal polymorphism on currants too, and can also be used to study both black and red currants. [ABSTRACT FROM AUTHOR]

Gene flow affects the genetic diversity and structure of tree species and can be influenced by stress related to changing climatic conditions. The study of tree species planted in locations outside their natural range, such as arboreta or botanical gardens, allows us to analyse the effect of severe fragmentation on patterns and distances of gene flow. Paternity analysis based on microsatellite marker genotyping was used to analyse how fragmentation affects gene flow among individuals of Quercus rubra L. distributed in a small isolated group of trees (15 trees) planted in the arboretum on the North Campus of the University of Göttingen. For paternity analysis, 365 seedlings from four seed parents were selected and genotyped using 16 microsatellites. The analysis revealed the majority of pollen (84.89%) originated from trees within the site and identified three large full-sib families consisting of 145, 63 and 51 full-sibs. The average pollen dispersal distance for the four seed parents ranged from 17.3 to 103.6 meters. We observed substantial genetic differentiation among effective pollen clouds of the four seed parents (G"ST = 0.407) as a result of cross pollination between neighboring trees. No self-fertilization was observed. Gene dispersal via pollen followed the expected distance-dependent pattern, and we observed a significant influx of external pollen (15.11%, ranging from 8.64 to 26.26% for individual seed parents) from a diverse set of donors (30). Long-distance pollen dispersal could explain the presence of significant genetic variation even in isolated natural Q. rubra populations. [ABSTRACT FROM AUTHOR]

Barramundi, or Asian seabass Lates calcarifer, is a commercially important food fish with a wide geographic distribution in the Indo-West Pacific region. Despite its economic significance, particularly in Taiwan, information on the sources of fertilized eggs, fry and stock management practices remains largely unavailable. To ensure sustainable exploitation and effective selective breeding programs, assessing the genetic diversity and population genetic structure of barramundi is crucial. This study investigated the genetic diversity and population genetic structure of three cultured populations (Chiayi A, Chiayi B, and Tainan) and one wild-caught population in Taiwan using mitochondrial DNA cytochrome b and eight microsatellite loci as genetic markers. The analysis of haplotype network revealed that all populations shared an ancestral haplotype, yet each population had its own unique haplotype. Notably, the wild and cultured populations showed the largest genetic distance. However, overall, the genetic distances among all populations were small and similar. This finding suggests potential gene exchange, possibly through broodstock exchange practices between farms. The valuable genetic information obtained from this study holds the potential to improve aquaculture programs through targeted breeding initiatives and inform the development of sustainable management policies for barramundi. [ABSTRACT FROM AUTHOR]

The population of the Northwest Pre-Caspian saiga (Saiga tatarica tatarica) numbered about 800 000 individuals in the middle of the last century. There was a dramatic decline at the end of the 20th century, and by 2015 the numbers of this saiga population reached about five thousand animals. The results of microsatellite loci and of mtDNA control region analysis obtained for museum saiga samples from the Northwest Pre-Caspian population, collected at the peak of their numbers in the 1950s, are presented. We compared these data with our previous results for the samples collected during the population depression in the years 1999–2016. There were no noticeable differences in the mtDNA control region diversity between the museum and modern saiga samples. The most vivid genetic consequence of the severe decline in population numbers was a significant increase of the inbreeding coefficient (Fis) calculated from the microsatellite loci. [ABSTRACT FROM AUTHOR]

Premise of research. Juniperus virginiana is the most widespread native conifer in the eastern United States. There are two disjoint varieties of J. virginiana , the eastern red cedar (var. virginiana) and the southern red cedar (var. silicicola). While the eastern red cedar occurs in the eastern United States, the southern red cedar primarily occurs along the coast marshes and swamps from North Carolina south to Florida and west to southeast Texas. Methodology. We studied the genetic variation and differentiation of the southern red cedar in Florida, Georgia, and North Carolina using eight microsatellite markers. Pivotal results. The genetic diversity of the southern red cedar was similar to that of other species of Juniperus. The mean number of alleles per locus was highest in the west coast region of Florida and the lowest in North Carolina. Analysis of molecular variance and Wright's F coefficients revealed significant differentiation among regions. Principal coordinate analysis and phylogenetic analysis revealed three distinct groups among the six regions. Mantel test showed significant correlations between geographic distance between regions and their genetic differentiation, suggesting that limited gene flow determines the genetic structure. In addition, a population tree suggested that coastal regions are central regions while North Carolina and inland Florida are marginal. Our findings also showed that a Bayesian model best describes the genetic structure of a southern red cedar with four clusters (K = 4). The model supports isolation by distance, but our results also indicate that environmental factors explain differences observed in inland regions. Conclusions. We found significant genetic diversity and differentiation among southern red cedar regions. Genetic differentiation can be explained, at least in part, by limitation in gene flow because of isolation by distance and isolation by environment. Our results support the predictions of the central-marginal model. [ABSTRACT FROM AUTHOR]

Population genetics is a valuable tool for assessing the impact of human‐altered landscapes on genetic connectivity in various species. However, when applied to insects, challenges arise due to potentially large effective population sizes (Ne), high dispersal capacities and the recency of anthropogenic impacts.This study assessed the population genetic structure of two pollinators across a human‐altered landscape in Luxembourg. Samples from the ashy mining bee (Andrena cineraria, N = 201) and the greater bee fly (Bombylius major, N = 637) were genotyped at 25 microsatellite loci, including a genotyping‐by‐amplicon‐sequencing approach for A. cineraria.Despite high statistical power of FST > 0.002 in B. major and FST > 0.0025 in A. cineraria, no deviations from genetic homogeneity were detected. For both species, there was no evidence for isolation‐by‐distance or genetic clustering. Genetic homogeneity was most likely the result of high levels of gene flow that compensate for the effects of genetic drift.Estimates of Ne ranged between several thousand to tens of thousands, although precision was low. Simulations highlighted that genetic lag times can substantially affect our ability to detect recent (<50 generations) population differentiation when Ne is very large. Lag times were shorter with data from 25,000 simulated di‐allelic loci, but only when sample sizes remained high.Insect genetic studies should consider lag times due to large Ne and ensure sample size and markers offer adequate power to reject the null hypothesis of no landscape effect on genetic connectivity. [ABSTRACT FROM AUTHOR]

Objective: Min pigs are a unique genetic resource among local pig breeds in China. They have more excellent characteristics in cold and stress resistance, good meat quality, and a high reproductive rate. However, the genetic structure and driving factors remain unclear in the nucleus herd. In this study, the genetic diversity of Min pigs was studied to reveal the formation mechanism of its unique genetic structure. We hope to protect and develop the genetic resources of Min pigs. Methods: We analyzed different types of genes to identify the genetic structure and gene introgression pattern of Min pigs. The nuclear DNA dataset includes information on 21 microsatellite loci and 6 Y-chromosome genes, and the mitochondrial D-loop gene is selected to represent maternal lineages. The above genes are all from the nucleus herd of Min pigs. Results: The results of genetic structure identification and analysis of potential exogenous gene introgression patterns indicate that the nucleus herd of Min pigs maintains a high level of genetic diversity (polymorphism information content = 0.713, expected heterozygosity = 0.662, observed heterozygosity = 0.612). Compared with other Asian pig breeds, the formation of Min pig breeds is more special. Gene introgression from European pig breeds to Min pigs has occurred, which is characterized by complete introgression of paternal genes and incomplete introgression of maternal genes. Conclusion: Gene introgression caused by cross-breeding is not the main factor leading to the formation of the current genetic structure of Min pigs, but this process has increased the level of genetic diversity in the nucleus herd. Compared with the influence of gene introgression, our research suggest that artificial selection and environmental adaptive evolution make Min pigs form unique genetic characteristics. [ABSTRACT FROM AUTHOR]

During studies using molecular biological methods, 3000 cow blood samples of the Ayrshire, Holstein, and Jersey breeds from the herds of Krasnodar and Stavropol krais were genotyped by the loci BM1818, BM1824, BM2113, ETH10, ETH225, ETH3, INRA023, SPS115, TGLA126, TGLA122, TGLA227, TGLA53, CSN2 (rs43703011), and CSN3 (rs43703016). On average, the frequency of occurrence of homozygous genotypes for 12 microsatellite loci in Jersey cattle was 0.38; in Holstein and Ayrshire cattle, it was 0.30 and 0.27, respectively; the highest allelic diversity was found in Holstein cattle (9.0 ± 1.7 alleles per locus). It should be noted that there are significant differences in the genetic profile of Ayrshire cattle. For Ayrshire animals, the following allelic variants turned out to be typical (but rare in Jersey and Holstein cattle): 270 of the locus BM1818, 137 of the locus BM2113, 213 of the locus ETH10, 119 of the locus ETH3, 142 of the locus ETH225, 87 of the locus TGLA227, 166 of the locus TGLA53. In the studied subpopulation of Jersey cattle, the frequency of occurrence of the A2A2 genotype of the CSN2 locus (rs43703011) (beta casein) was 0.68, and in the Ayrshire and Holstein groups, it was only 0.25 and 0.31, respectively. The BB genotype of the CSN3 locus (rs43703016) (casein kappa) was found in the Jersey group of animals with a frequency of 0.76, and in Ayrshires and Holsteins, it was 0.04 and 0.15, respectively. The genotyped groups of Jersey, Ayrshire, and Holstein animals are significant in volume; we assume that the identified patterns are typical of cattle of these breeds in the south of Russia. We believe that the data obtained can be used in the future in practical work on classifying certain groups of livestock as typical Holstein, Ayrshire, or Jersey and when creating herds that produce milk of a certain type (for example, type A2 milk). [ABSTRACT FROM AUTHOR]

Although the European Roe Deer (Capreolus capreolus) is one of the most common and widespread ungulate species in Europe and inhabiting a variety of habitats, few studies have addressed its population structure at a large spatial scale using nuclear genetic data. The aims of our study were to: (i) investigate genetic diversity, level of admixture, and genetic structure across European Roe Deer populations; (ii) identify barriers to gene flow; and (iii) reveal factors that have impacted the observed pattern of population genetic structure. Using 12 microsatellite loci, we analyzed 920 European Roe Deer samples from 16 study sites from northern, southern, central, and eastern Europe. The highest genetic diversity was found in central and eastern sites, and lowest in the northern and southern sites. There were 2 main groups of genetically related populations in the study area—one inhabiting mainly Fennoscandia, and the second in the continental part of Europe. This second population was further divided into 3 to 5 spatially distributed genetic clusters. European Roe Deer belonging to the Siberian mitochondrial DNA clade, inhabiting large parts of eastern Europe, were not identified as a separate population in the analysis of microsatellite loci. No isolation by distance (IBD) was detected between roe deer from the fennoscandian and the continental study sites, but the Baltic Sea was inferred to be the main barrier to gene flow. Only weak IBD was revealed within the continental population. Three lower-level genetic barriers were detected in the western, southern, and eastern parts of the study area. The main factors inferred as shaping the observed genetic diversity and population structure of European Roe Deer were postglacial recolonization, admixture of different populations of the species originating from several Last Glacial Maximum refugial areas, and isolation of several study sites. [ABSTRACT FROM AUTHOR]

Forest fragmentation studies are now urgent due to increased rates of deforestation and forest fires worldwide. In South America, the bee-pollinated Cariniana estrellensis is one of the largest trees, and a paradigm for the health and sustainability of forest biomes. For a large-yet-fragmented population (four subpopulations) in the transition zone between Brazilian Savannah and Atlantic Forest, we carried out a study of pollen flow, mating system and spatial genetic structure using nine microsatellite loci. This revealed that the subpopulations are not reproductively isolated because of pollen flow from outside the study area (18.3%) and between subpopulations (16.1–31.3%). Pollen dispersal reached long distances (3.5 km), but mating occurred predominantly between larger-diameter trees located close to mother-trees. We found that C. estrellensis is self-compatible with reproduction mediated mainly by outcrossing (> 0.95), but matings were not random due to biparental inbreeding (tr: 0.048–0.124) and correlated-paternity (rp: 0.16–0.28), which was higher within (rpw: 0.524–0.95) than among fruits (rpa: 0.048–0.052). Inbreeding decreased from seedlings (0.088) to adults, indicating inbreeding depression between the seedling and adult stages. Subpopulations exhibited spatial genetic structure (50–200 m), revealing a pattern of genetic dispersion of isolation-by-distance. Seeds should be harvested from trees that are > 200 m apart for successful ex-situ conservation and populations should not be isolated by more than the maximum pollen-dispersion distance observed (3.5 km) for in-situ conservation. The findings are consistent with the maximum distance that bees can disperse pollen and thereby maintain genetic connectivity between populations and resilience to population fragmentation into forest remnants. [ABSTRACT FROM AUTHOR]

Background: The invasive brownrat (Rattus norvegicus) and the Oriental rats (Rattus tanezumi) are common commensal murid that are important hosts for rodent-borne diseases in southeast Asia. Understanding their population structure and genetic diversity is essential to uncover their invasion biology and distribution dynamics that are essential for controlling rodent-borne diseases. Methods: TA total of 103 R. norvegicus and 85 R. tanezumi were collected from 13 to 9 coastal areas of six provincial monitoring sentinel sites, respectivelyto assess patterns in their microsatellite loci and their mitochondrial coxl gene region. Results: Eleven sampled populations of R. norvegicus were divided into two major clusters by region. The observed heterozygosity values of all regional populations were smaller than expected genetic diversity heterozygosity values and deviated from Hardy-Weinberg equilibrium Nine sample populations of R. tanezumi were divided into three clusters; two that included sample from Hainan and Fujian provinces, and one that included samples from the other provinces and cities. The genetic diversity of R. tanezumi was highest in samples from Jiangsu and Guangdong provinces. Conclusion: The data in this paper confirm the two invasive rodent species from the southeastern coastal region of China may have relied on maritime transport to spread from the southern region of China to the Yangtze River basin. R. tanezumi may then hanve migrated unidirectionally, along the southeastern provinces of China towards the north, while R. norvegicus spread in a complex and multidirectional manner in Hainan, Fujian, Zhejiang and Jiangsu Provinces of the country. [ABSTRACT FROM AUTHOR]

Opisthorchis felineus is a food-borne trematode which causes opisthorchiosis and affects mainly the liver and bile ducts of the liver with a possible risk of bile duct carcinogenesis resulting in cholangiocarcinoma. In Russia, O. felineus is mainly endemic in Western Siberia (Ob and Irtysh river basins) and occurs throughout the Volga, Kama, Don, and Dnepr river basins. The prevalence, intensity, and clinical significance of human infections and the incidence of cholangiocarcinoma vary geographically in endemic regions. Currently, there is substantial evidence on genetic variation of O. felineus, but information on the population genetic structure is so far very scarce. Because microsatellite DNA of this parasite is not available, we for the first time isolated sufficient microsatellite loci to examine the genetic diversity and population structure of O. felineus, using multiple nuclear loci approach. A total of ten highly polymorphic microsatellite loci from a constructed enriched genomic DNA library were characterized, using 29 samples representing huge O. felineus metapopulation extended in latitude over 5000 km from Middle Europe to Western Siberia. At least three populations can be discerned as result of analysis of the microsatellite loci genetic diversity. Based on the results for the first time, a hypothesis was put forward about the formation of a modern habitat of O. felineus. [ABSTRACT FROM AUTHOR]

The paper presents an extended (in comparison with previous studies) analysis of the population genetic structure of a migratory wide-range species with high abundance, the Eurasian crane, Grus grus L. Using seven highly polymorphic microsatellite loci, high and very similar values of genetic diversity parameters were obtained in samples of the western (G. g. grus) and eastern (G. g. lilfordi) subspecies. Coefficients of genetic differentiation between these subspecies (FST = 0.008, GST = 0.002) were also found to be low. According to AMOVA, 99% of genetic variation of G. grus is attributed to individual levels. Using the Bayesian clustering algorithm implemented in the STRUCTURE software, no clear population genetic structuring of the species was revealed. At the same time, visualization of spatial patternts of genetic variability in the Geneland software showed the presence of a cluster of "pure" subspecies of G. g. grus and G. g. lilfordi, surrounding a cluster of individuals from the zone of intergradation of these subspecies. This result, along with the observed very low F-statistics values, may indicate subtle genetic differences between the cranes from the studied area, possibly having a mutational nature. Lower allelic richness and lack of private alleles in the eastern subspecies G. g.lilfordi suggests its relative evolutionary youth and recent origin from the eastern marginal populations of the nominative western subspecies. [ABSTRACT FROM AUTHOR]

The Caucasian rock lizard species Darevskia portschinskii is one of the bisexual species participating in interspecific hybridisation as the paternal ancestor with the maternal ancestors D. mixta and D. raddei resulting in the successful formation of the parthenogenetic D. dahli and D. rostombekowi, respectively. Populations of D. portschinskii have been previously divided into two subspecies, D. p. portschinskii and D. p. nigrita according to their geographical distribution and the morphological data, but they have not been characterised genetically. Here, we used ten microsatellite markers to determine the genetic structure of the D. portschinskii populations. The utility of the developed microsatellite markers for investigating the genetic variability within and among populations with a heterogeneous spatial distribution was demonstrated. Our results showed that the intra- and interspecific differentiation of the studied populations were consistent with the morphological data on the subspecies status of the D. p. portschinskii and D. p. nigrita populations. A potential applicability of the developed microsatellite markers to study genetic diversity of Darevskia species and subspecies complexes is suggested. [ABSTRACT FROM AUTHOR]

Population genetic studies are crucial for evolutionary biologists because the population is the basic substrate on which evolution is forged. However little empirical evidence has been able to demonstrate the role that isolation and gene flow play in maintaining differentiation in populations at short geographic scales. Epidalea calamita exhibits a steep variation in body size and reproductive traits in southwestern Spain, associated with changes in the geological substrate. This implies a decrease of 70.9% of body mass and 28.5% in snout-vent length, on a microgeographic scale of only 60 km. Previous results from both metamorphic and juvenile common garden experiments showed that genetic differentiation may be a causal determinant of geographic variation in adult. This study tested whether neutral genetic differentiation can explain the geographical variation in the body size observed in E. calamita. It was addressed analyzing the level of genetic structuring and gene flow among populations along the cline, comparing the genetic diversity between and within populations, as well as between ecological environments. The study showed that the geographic variation in body size observed in E. calamita has evolved in absence of geographic isolation, with moderate gene flow connecting the populations. Thus, neutral genetic differentiation cannot explain the geographical variation observed. Future studies are needed on the interaction between the genetic component with the environmental factors and will be necessary to analyze the contribution of the maternal effects in the origin and evolution of the geographical variation in the body size observed in E. calamita from southern Spain. [ABSTRACT FROM AUTHOR]

This paper examines the size-age structure, growth and genetic polymorphism of the sterlet population of the Mologa River, Vologda Oblast, formed during reacclimatization measures. The introduction of sterlet into the Mologa River began in 2016, and since 2018 it has been found in research catches. In the channel medial sections of the river, the proportion of sterlet in total catches ranged from 31.4% to 49.3% in numbers and from 26.0% to 64.0% in biomass. In 2022, the catches included fish with a length of 22–51 cm and a weight of 64–958 g of five age groups. The size, weight and age composition of the emerging population is currently determined by the number of juvenile sterlet released in individual years. Mitochondrial DNA analysis revealed 23 different mtDNA haplotypes and low relative haplotype diversity. The level of observed nuclear DNA heterozygosity averaged 0.567 with a range from 0.149 to 0.871. Genetic heterogeneity of individuals in the emerging population of sterlet from the Mologa River is sufficient for the local population of a river.

AbstractThe Salmo trutta species complex includes threatened or intensively managed taxa. Domestic-Atlantic strains are widely farmed and massively introduced into the wild to support fisheries, although such practices seriously threaten native populations of Mediterranean brown trout through anthropogenic hybridization. Characterizing the distribution and genetic composition of wild populations across river catchments is crucial to identify conservation priorities and define appropriate management strategies. Here, we genotyped 586 brown trout at the diagnostic nuclear LDH-C1 gene and the mitochondrial D-loop fragment, to assess the conservation status of 33 sites in a protected area spanning river catchments from both the Adriatic and Tyrrhenian slopes in the northern Apennines (Italy). The results indicated a critical situation of widespread domestic-Atlantic introgression. Further analyses at 15 microsatellite loci on 159 individuals from 12 natural sites (along with 113 references from hatcheries) revealed similarity to hatchery stocks, higher genetic diversity and bottleneck signals in introgressed/exotic populations, consistently with relatively recent introductions of domestic-Atlantic individuals into wild sites. Conversely, the only native sites from a single river catchment on the Adriatic slope showed genetic distinctiveness, reduced diversity and demographic stability. We also found genetic evidence of a human-mediated introduction of allochthonous Mediterranean trout in a single wild site, as well as of a putative between-slopes translocation. We provide further insight into the occurrence and consequences of human manipulations on wild Mediterranean brown trout populations, contextually offering a reliable baseline for an ongoing conservation project aiming at preserving native populations of this endangered taxon.

Population genetic studies are crucial for evolutionary biologists because the population is the basic substrate on which evolution is forged. However little empirical evidence has been able to demonstrate the role that isolation and gene flow play in maintaining differentiation in populations at short geographic scales. Epidalea calamita exhibits a steep variation in body size and reproductive traits in southwestern Spain, associated with changes in the geological substrate. This implies a decrease of 70.9% of body mass and 28.5% in snout-vent length, on a micro-geographic scale of only 60 km. Previous results from both metamorphic and juvenile common garden experiments showed that genetic differentiation may be a causal determinant of geographic variation in adult. This study tested whether neutral genetic differentiation can explain the geographical variation in the body size observed in E. calamita. It was addressed analyzing the level of genetic structuring and gene flow among populations along the cline, comparing the genetic diversity between and within populations, as well as between ecological environments. The study showed that the geographic variation in body size observed in E. calamita has evolved in absence of geographic isolation, with moderate gene flow connecting the populations. Thus, neutral genetic differentiation cannot explain the geographical variation observed. Future studies are needed on the interaction between the genetic component with the environmental factors and will be necessary to analyze the contribution of the maternal effects in the origin and evolution of the geographical variation in the body size observed in E. calamita from southern Spain.

The Caucasian rock lizard species Darevskia portschinskii is one of the bisexual species participating in interspecific hybridisation as the paternal ancestor with the maternal ancestors D. mixta and D. raddei resulting in the successful formation of the parthenogenetic D. dahli and D. rostombekowi, respectively. Populations of D. portschinskii have been previously divided into two subspecies, D. p. portschinskii and D. p. nigrita according to their geographical distribution and the morphological data, but they have not been characterised genetically. Here, we used ten microsatellite markers to determine the genetic structure of the D. portschinskii populations. The utility of the developed microsatellite markers for investigating the genetic variability within and among populations with a heterogeneous spatial distribution was demonstrated. Our results showed that the intra- and interspecific differentiation of the studied populations were consistent with the morphological data on the subspecies status of the D. p. portschinskii and D. p. nigrita populations. A potential applicability of the developed microsatellite markers to study genetic diversity of Darevskia species and subspecies complexes is suggested.

The Sebastes inermis complex includes three sympatric species (Sebastes cheni, viz Sebastes inermis, and Sebastes ventricosus) with clear ecomorphological differences, albeit incomplete reproductive isolation. The presence of putative morphological hybrids (PMH) with plausibly higher fitness than the parent species indicates the need to confirm whether hybridization occurs within the complex. In this sense, we assessed the dynamics of genetic divergence and hybridization within the species complex using a panel of 10 microsatellite loci, and sequences of the mitochondrial control region (D-loop) and the intron-free rhodopsin (RH1) gene. The analyses revealed the presence of three distinct genetic clusters, large genetic distances using D-loop sequences, and distinctive mutations within the RH1 gene. These results are consistent with the descriptions of the three species. Two microsatellite loci had signatures of divergent selection, indicating that they are linked to genomic regions that are crucial for speciation. Furthermore, nonsynonymous mutations within the RH1 gene detected in S. cheni and "Kumano" (a PMH) suggest dissimilar adaptations related to visual perception in dim-light environments. The presence of individuals with admixed ancestry between two species confirmed hybridization. The presence of nonsynonymous mutations within the RH1 gene and the admixed ancestry of the "Kumano" morphotype highlight the potential role of hybridization in generating novelties within the species complex. We discuss possible outcomes of hybridization within the species complex, considering hybrid fitness and assortative mating. Overall, our findings indicate that the genetic divergence of each species is maintained in the presence of hybridization, as expected in a scenario of speciation-with-gene-flow. [ABSTRACT FROM AUTHOR]

Genetic methods based on the study of the variability of mitochondrial (COI) and nuclear (microsatellites) DNA were used to study the processes of morphogenesis in the genus Eleginus. The revealed level of genetic difference characterizes the Pacific saffron cod (Eleginus gracilis) and navaga (Eleginus nawaga) as independent species that diverged in a relatively recent period at the boundary of the Pliocene and Pleistocene. The White Sea populations of navaga by microsatellite markers differed from the Navaga inhabiting the basins of the Kara and the Barents seas. At the same time, it is assumed that the Kara-Barents Sea region could have acted as a "glacial refugium," which ensured the postglacial settlement of navaga, including in the "watered" White Sea depression. Phylogenetic analysis based on diversity of COI haplotypes reveals demand of possible reorganization in the order Gadiformes, including Eleginus in an independent subfamily—sister in relation to the subfamilies Gadinae, Lotinae, and Merlucciinae. The prospects of improving genetic methodological approaches in the framework of the development of research on Saffron cod are noted. [ABSTRACT FROM AUTHOR]

Microsatellite markers, also known as short tandem repeats (STRs), are important for marker-assisted selection to detect genetic polymorphism, and they are uniformly distributed in eukaryotic genomes. To analyze the relationship between microsatellite loci and lactation traits of Holstein cows in Xinjiang, 175 lactating cows with similar birth dates, the same parity, and similar calving dates were selected, and 10 STR loci closely linked to quantitative trait loci were used to analyze the correlation between each STR locus and four lactation traits (daily milk yield, milk fat percentage, milk protein percentage, and lactose percentage). All loci showed different degrees of genetic polymorphism. The average values of observed alleles, effective alleles, expected heterozygosity, observed heterozygosity, and polymorphic information content of the 10 STR loci were 10, 3.11, 0.62, 0.64, and 0.58, respectively. Chi-square and G-square tests showed that all populations of loci were in accordance with the Hardy–Weinberg equilibrium. Analysis of the correlation between STR locus genotype and lactation performance in the whole lactation period showed three loci (namely, BM143, BM415, and BP7) with no significant correlation with all lactation traits, two loci (BM302 and UWCA9) related to milk yield, three loci (BM103, BM302, and BM6425) related to milk fat percentage, two loci (BM302 and BM6425) related to milk protein percentage, and three loci (BM1443, BM302, and BMS1943) related to lactose percentage. The microsatellite loci selected in this study showed rich polymorphism in the experimental dairy cow population and were related to the lactation traits, which can be used for the evaluation of genetic resources and early breeding and improvement of Holstein dairy cows in Xinjiang. [ABSTRACT FROM AUTHOR]

The work was performed in order to study the morphological and agriculturally important traits and molecular genetic allelic polymorphism of the cultivated varieties and wild forms of soybean using microsatellite DNA with the aim of identification and certification of their genotypes. Unique DNA profiles of the studied soybean cultivars and wild forms were obtained by PCR analysis using six microsatellite loci (Satt1, Satt2, Satt5, Satt9, Sourgr1, and Soyhsp176). Twenty-four alleles have been identified, with the number of alleles per locus ranging from two to ten. For each locus, Polymorphism Information Content (PIC) varied from 0.28 to 0.86 and the average was 0.62; the effective number of alleles varied from 1.38 to 6.92 and the average was 3.30. Cultivated soybean varieties differed by from 1 to 4 loci. The dendrogram constructed for the studied soybean genotypes by the unweighted pair group method with arithmetic mean (UPGMA) with the aid of the POPGENE v. 1.32 software revealed two large clusters. Cluster I included the cultivated soybean varieties, while cluster II included wild soybean forms, which overall pointed to the significant genetic differences between these two groups. The highest morphological differences were revealed between the Topaz and Dauriya varieties, both in the phenotype (pubescence coloration and density and seed and eye color and shape) and in all agriculturally important traits (vegetation period—95 and 112 days; yield—26.8 and 30.9 hundred kg/ha; plant height—64 and 81 cm; lower bean attachment height—13 and 16 cm; weight of 1000 seeds—174.7 and 185.4 g; protein content—40.3 and 38.2%; oil content—19.2 and 19.8%, respectively). For the first time, molecular genetic passports of nine soybean cultivars bred in the All-Russia Soybean Research Institute for their genotype identification have been obtained based on the findings of this study. [ABSTRACT FROM AUTHOR]

Bulb mites are an economically significant pest of subterranean parts of plants and a versatile laboratory animal. However, the genetic structure of their populations remains unknown. To fill this gap in our knowledge of their biology, we set up a field experiment in which we allowed mites to colonize onion bulbs, and then determined the genetic structure of colonisers based on a panel of microsatellite loci. We found moderate but significant population structure among sites separated by ca. 20 m (FST range 0.03–0.21), with 7% of genetic variance distributed among sites. Allelic richness within some bulbs was nearly as high as that in the total population, suggesting that colonisation of bulbs was not associated with strong population bottlenecks. The significant genetic structure we observed over small spatial scales seems to reflect limited dispersal of mites in soil. [ABSTRACT FROM AUTHOR]

Simple Summary: The Raja miraletus species complex exhibits high levels of morphological and ecological stasis along with the antipodean distribution in the Eastern Atlantic and Indian Oceans. We investigated genetic variability and differentiation between taxa and geographical populations by integrating mitochondrial and nuclear DNA markers. The extraordinary occurrence of at least five different sibling taxa in the Northeastern Atlantic Ocean and Mediterranean Sea is documented, supporting cryptic speciation and stabilising selection. Despite a high species diversity, skates (Rajiformes) exhibit remarkably conservative morphology and ecology. Limited trait variations occur within and between species, and cryptic species have been reported among sister and non-sister taxa, suggesting that species complexes may be subject to stabilising selection. Three sibling species are currently recognised in the Raja miraletus complex: (i) R. miraletus occurring along the Portuguese and Mediterranean coasts, (ii) R. parva in the Central-Eastern Atlantic off West Africa and (iii) R. ocellifera in the Western Indian Ocean off South Africa. In the present study, the genetic variation at mitochondrial and nuclear markers was estimated in the species complex by analysing 323 individuals sampled across most of its geographical distribution area to test the hypothesis that restricted gene flow and genetic divergence within species reflect known climate and bio-oceanographic discontinuities. Our results support previous morphological studies and confirm the known taxonomic boundaries of the three recognised species. In addition, we identified multiple weakly differentiated clades in the Northeastern Atlantic Ocean and Mediterranean, at least two additional cryptic taxa off Senegal and Angola, a pronounced differentiation of ancient South African clades. The hidden genetic structure presented here may represent a valuable support to species' conservation action plans. [ABSTRACT FROM AUTHOR]

The Salmo trutta species complex includes threatened or intensively managed taxa. Domestic-Atlantic strains are widely farmed and massively introduced into the wild to support fisheries, although such practices seriously threaten native populations of Mediterranean brown trout through anthropogenic hybridization. Characterizing the distribution and genetic composition of wild populations across river catchments is crucial to identify conservation priorities and define appropriate management strategies. Here, we genotyped 586 brown trout at the diagnostic nuclear LDH-C1 gene and the mitochondrial D-loop fragment, to assess the conservation status of 33 sites in a protected area spanning river catchments from both the Adriatic and Tyrrhenian slopes in the northern Apennines (Italy). The results indicated a critical situation of widespread domestic-Atlantic introgression. Further analyses at 15 microsatellite loci on 159 individuals from 12 natural sites (along with 113 references from hatcheries) revealed similarity to hatchery stocks, higher genetic diversity and bottleneck signals in introgressed/exotic populations, consistently with relatively recent introductions of domestic-Atlantic individuals into wild sites. Conversely, the only native sites from a single river catchment on the Adriatic slope showed genetic distinctiveness, reduced diversity and demographic stability. We also found genetic evidence of a human-mediated introduction of allochthonous Mediterranean trout in a single wild site, as well as of a putative between-slopes translocation. We provide further insight into the occurrence and consequences of human manipulations on wild Mediterranean brown trout populations, contextually offering a reliable baseline for an ongoing conservation project aiming at preserving native populations of this endangered taxon. [ABSTRACT FROM AUTHOR]

Background: The Manapany day gecko (Phelsuma inexpectata) is endemic to the south of Reunion Island. Threatened by habitat fragmentation and loss, human activities and invasive species, P. inexpectata is considered as critically endangered. Conservation measures are required but data on the species are missing, notably on its genetic diversity and population structure for which no specific markers are available to date. Here, we aimed to develop molecular markers to allow genetic studies of P. inexpectata. Methods and results: We developed and characterized 20 polymorphic microsatellite markers based on 23 P. inexpectata individuals sampled from 10 sites. Then, the markers were tested on a total of 101 individuals, 30 from a natural site and 71 from an anthropized site. The mean values of Na, Ho and He were 2.3 (± 0.2), 0.353 (± 0.053) and 0.345 (± 0.046) in the natural site and 2.8 (± 0.3), 0.345 (± 0.051) and 0.338 (± 0.048) in the anthropized site, respectively. Based on the combined loci, the probability of identity (PID) for unrelated specimens were 2.7 × 10–7 and 2.6 × 10–7 in the natural and anthropized site, respectively. Conclusions: This work provides the first set of microsatellite markers for P. inexpectata, constituting a valuable tool to conduct classical genetic studies on the species, such as estimating genetic diversity, population structure and kinship relationships among individuals. Such studies will provide relevant information on P. inexpectata and will therefore be helpful in the implementation of conservation measures for this threatened species. [ABSTRACT FROM AUTHOR]

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Abstract Background Important information on movement pathways and introduction routes of invasive parasites can be obtained by comparing the genetic makeup of an invader with its spatial genetic structure in other distribution areas. Sometimes, the population genetic structure of the host might be more informative than that of the parasite itself, and it is important to collect tissue samples of both host and parasite. However, host tissue samples are frequently not available for analysis. We aimed to test whether it is possible to generate reliable microsatellite profiles of host individuals by amplifying DNA extracted from a nematode parasite, using the raccoon (Procyon lotor) and the raccoon roundworm (Baylisascaris procyonis) as a test case. Methods Between 2020 and 2021, we collected tissue as well as a single roundworm each from 12 raccoons from central Germany. Both the raccoon and the roundworm DNA extracts were genotyped using 17 raccoon-specific microsatellite loci. For each roundworm DNA extract, we performed at least eight amplification reactions per microsatellite locus. Results We extracted amplifiable raccoon DNA from all 12 roundworms. We obtained at least two amplification products for 186 of the 204 possible genotypes. Altogether 1077 of the 1106 genotypes (97.4%) matched the host-DNA derived reference genotypes and thus did not contain genotyping errors. Nine of the 12 roundworm-derived genetic profiles matched the reference profiles from the raccoon hosts, with one additional genetic profile containing genotyping errors at a single locus. The remaining two genetic profiles were deemed unsuitable for downstream analysis because of genotyping errors and/or a high proportion of missing data. Conclusions We showed that reliable microsatellite-based genetic profiles of host individuals can be obtained by amplifying DNA extracted from a parasitic nematode. Specifically, the approach can be applied to reconstruct invasion pathways of roundworms when samples of the raccoon hosts are lacking. Further research should assess whether this method can be replicated in smaller species of parasitic nematodes and other phyla of parasites more generally. Graphical Abstract

Background: Important information on movement pathways and introduction routes of invasive parasites can be obtained by comparing the genetic makeup of an invader with its spatial genetic structure in other distribution areas. Sometimes, the population genetic structure of the host might be more informative than that of the parasite itself, and it is important to collect tissue samples of both host and parasite. However, host tissue samples are frequently not available for analysis. We aimed to test whether it is possible to generate reliable microsatellite profiles of host individuals by amplifying DNA extracted from a nematode parasite, using the raccoon (Procyon lotor) and the raccoon roundworm (Baylisascaris procyonis) as a test case. Methods: Between 2020 and 2021, we collected tissue as well as a single roundworm each from 12 raccoons from central Germany. Both the raccoon and the roundworm DNA extracts were genotyped using 17 raccoon-specific microsatellite loci. For each roundworm DNA extract, we performed at least eight amplification reactions per microsatellite locus. Results: We extracted amplifiable raccoon DNA from all 12 roundworms. We obtained at least two amplification products for 186 of the 204 possible genotypes. Altogether 1077 of the 1106 genotypes (97.4%) matched the host-DNA derived reference genotypes and thus did not contain genotyping errors. Nine of the 12 roundworm-derived genetic profiles matched the reference profiles from the raccoon hosts, with one additional genetic profile containing genotyping errors at a single locus. The remaining two genetic profiles were deemed unsuitable for downstream analysis because of genotyping errors and/or a high proportion of missing data. Conclusions: We showed that reliable microsatellite-based genetic profiles of host individuals can be obtained by amplifying DNA extracted from a parasitic nematode. Specifically, the approach can be applied to reconstruct invasion pathways of roundworms when samples of the raccoon hosts are lacking. Further research should assess whether this method can be replicated in smaller species of parasitic nematodes and other phyla of parasites more generally. [ABSTRACT FROM AUTHOR]

The mud flounder Paralichthys orbignyanus (Pleuronectiformes, Paralichthyidae) inhabits shallow waters of low salinities and mud bottoms in the temperate marine coastal regions of the Bonaerensean Ecoregion of the Argentinean Biogeographic Province in the south‐western Atlantic Ocean. Specimens of P. orbignyanus were collected from Lagoa dos Patos (LDP) (southern Brazil), Mar Chiquita (MCH) and Marisol (MAR) both located in Buenos Aires (Argentina), and San Antonio Oeste (SAO) in the San Matías Gulf, Rio Negro (Argentina). A fragment of the mitochondrial DNA of the Control Region and seven microsatellite loci were characterized. In the Control Region, P. orbignyanus showed high variability, low nucleotide diversity, mild population expansion and a coalescence time of 35,000 years before the present. Flounders provided evidence of a genetic structure between the sampling sites LDP, MCH, MAR vs. SAO. On the other hand, P. orbignyanus displayed a lower to moderate contemporary genetic structure among all samples except between LDP and MCH. With no evidence of isolation by distance, this analysis supports a model of limited gene flow that is likely to be associated with a consistent larvae retention in all sampling sites. In addition, the present connectivity is ascribed to a lower migration process from SAO in the San Matías Gulf congruent with the prevailing littoral drift. [ABSTRACT FROM AUTHOR]

The aim of the investigations is to reveal polymorphic microsatellite markers in order to study genetical diversity of sugar beet. Seedlings of sugar beet MS-lines and multi- and monogerm pollinators have been the material for the investigation. In experiments, 11 polymorphic Unigenes-markers and eight SSR-primers have been used to test starting materials. It has been determined that the length range of the obtained DNA-fragments is from 80 to 3000 bp. Most of the primers have provided stable amplification of DNA polymorphic fragments. The greatest level of polymorphism information content (PIC) has been determined for the loci identified using the following primers: Unigene 27 833 (PIC = 0.89), Unigene 2305 (PIC = 0.84), Unigene 17 623 (PIC = 0.84), Unigene 16 898 (PIC = 0.84), Unigene 24 552 (PIC = 0.64), Unigene 7492 (PIC = 0.82), FD1002 (PIC = 0.72), and Sb15 (PIC = 0.74). This enables clear differentiation of sugar beet breeding material. These loci have been related to various metabolic processes and play a large role in protective mechanisms of beet plants. The used primers make it possible to amplify up to 13 polymorphic bands per genotype. In Unigene 27 833, an SSR-locus, 13 PCR-products of 100–2800 bp in length have been identified. In total, 162 DNA-amplicons have been revealed. The value of polymorphism information content (PIC) is 0.89. It follows from the presented data that all nuclear microsatellite loci of the studied sugar beet samples included in the analysis show genetical variability, which allows for recommending them for use to identify genotypes of the crop. Based on the alleles revealed, the template of the investigated sugar beet samples' genetic affinity has been calculated, clusters have been constructed, and genetical distance (Euclidean) has been calculated. Genetical passports have been made according to the PAST algorithm. The greatest determined genetical distance (D) is 5.83 between an MS-form and the tetraploid pollinator developed by Lgovskaya Breeding Experimental Station. To produce sugar beet heterosis hybrids, parent pairs have been suggested taking into account distantly-related of initial forms. [ABSTRACT FROM AUTHOR]

The identification of discrete intraspecific units, such as genetically informed management units (MUs), is important to effectively develop and implement conservation strategies for protected species. Harbour seals (Phoca vitulina) occurring in Irish waters are currently viewed as a single nationwide panmictic population (and hence MU), although this assumption is not based on any knowledge of population structure because of the lack of available genetic data.Thus, the present study used mitochondrial control region sequences and between nine and 11 microsatellite loci from harbour seals from Ireland and Northern Ireland (up to n = 123) and adjacent UK/European waters (up to n = 289) to provide insights into the genetic population structure and diversity of harbour seals in the areas studied.Within the island of Ireland, genetic analyses revealed the presence of three genetically distinct local populations, characterized by high genetic diversity, hereby defined as: East Ireland (EI), North‐west & Northern Ireland (NWNI), and South‐west Ireland (SWI).Using previously published and newly generated data, a subsequent wider scale analysis revealed that the EI and SWI local populations were genetically distinct from neighbouring UK/European areas, whereas seals from the NWNI area could not be distinguished from a previously identified Northern UK metapopulation. Migration rate estimates showed that NWNI receives migrants from North‐west Scotland, with NWNI acting as a genetic source for both SWI and EI.The present study provides the most comprehensive genetic assessment of harbour seals in European waters to date, with findings indicating that conservation strategies for harbour seals in Irish waters should be amended to accommodate at least three genetically distinct local populations/MUs. The use of approaches considering both ecological and genetic parameters is recommended for future assessments and delineation of units of ecological relevance for conservation management purposes. [ABSTRACT FROM AUTHOR]

Sex‐biased dispersal is common in many animals, with male‐biased dispersal often found in studies of mammals and reptiles, including interpretations of spatial genetic structure, ostensibly as a result of male–male competition and a lack of male parental care. Few studies of sex‐biased dispersal have been conducted in turtles, but a handful of studies, in saltwater turtles and in terrestrial turtles, have detected male‐biased dispersal as expected. We tested for sex‐biased dispersal in the endangered freshwater turtle, the spotted turtle (Clemmys guttata) by investigating fine‐scale genetic spatial structure of males and females. We found significant spatial genetic structure in both sexes, but the patterns mimicked each other. Both males and females typically had higher than expected relatedness at distances <25 km, and in many distance classes greater than 25 km, less than expected relatedness. Similar patterns were apparent whether we used only loci in Hardy–Weinberg equilibrium (n = 7) or also included loci with potential null alleles (n = 5). We conclude that, contrary to expectations, sex‐biased dispersal is not occurring in this species, possibly related to the reverse sexual dimorphism in this species, with females having brighter colors. We did, however, detect significant spatial genetic structure in males and females, separate and combined, showing philopatry within a genetic patch size of <25 km in C. guttata, which is concerning for an endangered species whose populations are often separated by distances greater than the genetic patch size. [ABSTRACT FROM AUTHOR]

Genetic structure and phylogeographic patterns of natural populations are of great importance in assessing the conservation status of species. These population properties can be estimated using molecular markers of either mitochondrial DNA (mtDNA) or nuclear DNA (nDNA) to understand the historical, ecological and dispersal patterns that influence genetic exchange within and between populations. Basilinna xantusii is a sexually dimorphic hummingbird endemic to the Baja California Peninsula (BCP). It comprises three ancestral mitochondrial lineages linked to vicariant events, late Pleistocene climate changes and the geographical distribution of oases. This study aimed to determine and understand the current population genetic structure of this hummingbird. The genotypes of 16 microsatellite loci from 100 individuals collected across the geographical range of this species were compared with mtDNA sequences previously published. Cluster analyses identified five populations, two with almost no genetic admixture in the northern part of the BCP and three others with varying levels of admixed ancestry across the BCP. In San José de Magdalena, at the northernmost end of the range of Xantus's Hummingbird, 40% of individuals collected belong to one genetic cluster and the remaining 60% to another, both genetic clusters showing very little admixed ancestry. We hypothesize that, despite being in sympatry, these individuals do not interbreed, unlike the other populations where individuals showed ancestry coefficients of the other genetic groups. The philopatric behaviour of males and the long‐range dispersal capacity of females probably determine the observed genetic differentiation pattern. The mito‐nuclear discordance detected could be due to the molecular markers used and to female‐biased dispersal. Gene flow is asymmetric in this species, being greater from north to south than vice versa, which is probably related to differences in the seasonality of precipitation across the BCP and to urbanization of the oases. [ABSTRACT FROM AUTHOR]

Simple Summary: The oriental honey bee, Apis cerana, is an important pollinator of crops and natural phytocoenosis in Asia. Natural barriers in the form of forests, mountains, rivers and seas have created the prerequisites for the formation of subspecies and ecotypes of the A. cerana. We analyzed the genetic structure of A. cerana samples from the Russian Far East, Vietnam and South Korea. High haplotype diversity was found in all samples of A. cerana based on analysis of the tRNAIeu-COII locus sequences. The found polymorphisms can be used as genetic markers to differentiate subspecies of A. cerana. In this article, we present the results of the genetic analysis of Apis cerana samples from the Russian Far East, South Korea and Vietnam. An analysis of the polymorphism of seven microsatellite loci and an assessment of the haplotype diversity of the mtDNA tRNAleu-COII locus were performed. A fragment of about 431 bp in tRNAleu-COII was sequenced. The analysis showed the presence of 14 haplotypes, while the predominant haplotype was Japan1. Microsatellite data revealed two differentiated clusters. The first cluster contained tropical climate A. cerana samples from Vietnam, and the second cluster combined temperate climate A. cerana samples from the Russian Far East and South Korea. [ABSTRACT FROM AUTHOR]

Simple Summary: The California condor is a critically endangered representative of New World vultures maintained under restoration and reintroduction programs. Within a California condor genome research project, we made a preliminary step toward a genetic linage map for this iconic bird species. The respective linkage data were generated using a panel of 121 condors. The condors were genotyped for 123 polymorphic microsatellite markers. The condor genotyping and mapping results are a useful addition to the previously obtained physical and cytogenetic maps and can be further utilized in condor genome sequence assembly. The development of a linkage map is an important component for promoting genetic and genomic studies in California condors, an endangered New World vulture species. Using a set of designed anonymous microsatellite markers, we genotyped a reference condor population involving 121 individuals. After marker validation and genotype filtering, the genetic linkage analysis was performed using 123 microsatellite loci. This resulted in the identification of 15 linkage groups/subgroups that formed a first-generation condor genetic map, while no markers linked to a lethal chondrodystrophy mutation were found. A panel of polymorphic markers that is instrumental in molecular parentage diagnostics and other genetic studies in the California condor was selected. Further condor conservation genomics research will be focused on updating the linkage map and integrating it with cytogenetic and BAC-based physical maps and ultimately with the genome sequence assembly. [ABSTRACT FROM AUTHOR]

Asian house rat Rattus tanezumi, a common commensal rat in southern China, was first discovered in Shanxi Province, northern China, in the early 1990s. Its rapid expansion threatens to reduce the diversity of native species and poses a serious threat to local biodiversity. In this study, samples were collected from fourteen different locations using onenight trapping method, and eight populations of Rattus tanezumi were captured. Seventy-six samples were successfully genotyped at 12 microsatellite loci and 70 mitochondrial DNA (mtDNA) cytochrome c oxidase subunit I gene sequences were amplified and sequenced. The analysis of genetic diversity and population structure about R. tanezumi significantly reveal evolutionary forces and non-random mating within populations in Shanxi, which could be concluded as a bottleneck or selective sweep. The genetic and geographical distances were uncorrelated, suggesting that geographic distance had no (or a weak) effect on genetic distance. Furthermore, we found four new haplotypes that are most similar to a nonrandom subset of those in their native range in southern China. The haplotypes could be more common in Shanxi due to a genetic bottleneck or natural selection. Further evidence is needed to reveal the mechanisms of genetic exchange and molecular evolution underlying these patterns. Our results provide fundamental insights into the potential introduction routes and the relevant features of successful invasions. [ABSTRACT FROM AUTHOR]

Abstract Background PRDM9 is a key regulator of meiotic recombination in most metazoans, responsible for reshuffling parental genomes. During meiosis, the PRDM9 protein recognizes and binds specific target motifs via its array of C2H2 zinc-fingers encoded by a rapidly evolving minisatellite. The gene coding for PRDM9 is the only speciation gene identified in vertebrates to date and shows high variation, particularly in the DNA-recognizing positions of the zinc-finger array, within and between species. Across all vertebrate genomes studied for PRDM9 evolution, only one genome lacks variability between repeat types – that of the North Pacific minke whale. This study aims to understand the evolution and diversity of Prdm9 in minke whales, which display the most unusual genome reference allele of Prdm9 so far discovered in mammals. Results Minke whales possess all the features characteristic of PRDM9-directed recombination, including complete KRAB, SSXRD and SET domains and a rapidly evolving array of C2H2-type-Zincfingers (ZnF) with evidence of rapid evolution, particularly at DNA-recognizing positions that evolve under positive diversifying selection. Seventeen novel PRDM9 variants were identified within the Antarctic minke whale species, plus a single distinct PRDM9 variant in Common minke whales – shared across North Atlantic and North Pacific minke whale subspecies boundaries. Conclusion The PRDM9 ZnF array evolves rapidly, in minke whales, with at least one DNA-recognizing position under positive selection. Extensive PRDM9 diversity is observed, particularly in the Antarctic in minke whales. Common minke whales shared a specific Prdm9 allele across subspecies boundaries, suggesting incomplete speciation by the mechanisms associated with PRDM9 hybrid sterility.

The results of studies of the genetic structure of the Central European wild boar (Sus scrofa scrofa) population and four breeds of domestic pigs (Duroc, Yorkshire, Large White and Landrace) bred in the Central Black Earth region of Russia are presented in this work. Based on 12 microsatellite loci, a significant ( p

Abstract Background Anopheles arabiensis is a member of Anopheles gambiae complex and the main malaria vector in Sudan. There is insufficient population genetics data available on An. arabiensis for an understanding of vector population structure and genetics, which are important for the malaria vector control programmes in this country. The objective of this investigation is to study the population structure, gene flow and isolation by distance among An. arabiensis populations for developing control strategies. Methods Mosquitoes were collected from six sites located in three different states in Sudan, Khartoum, Kassala and Sennar, using pyrethrum spray catch of indoor resting mosquitoes. Anopheline mosquitoes were identified morphologically and based on species specific nucleotide sequences in the ribosomal DNA intergenic spacers (IGS). Seven published An. gambiae microsatellite loci primers were used to amplify the DNA of An. arabiensis samples. Results PCR confirmed that An. arabiensis was the main malaria vector found in the six localities. Of the seven microsatellite loci utilized, six were found to be highly polymorphic across populations, with high allelic richness and heterozygosity with the remaining one being monomorphic. Deviation from Hardy–Weinberg expectations were found in 21 out of 42 tests in the six populations due to heterozygote deficiency. Bayesian clustering analysis revealed two gene pools, grouping samples into two population clusters; one includes four and the other includes two populations. The clusters were not grouped according to the three states but were instead an admixture. The genetic distances between pairs of populations ranged from 0.06 to 0.24. Significant FST was observed between all pairwise analyses of An. arabiensis populations. The Kassala state population indicated high genetic differentiation (FST ranged from 0.17 to 0.24) from other populations, including one which is also located in the same state. High gene flow (Nm = 1.6–8.2) was detected among populations within respective clusters but limited between clusters particularly with respect to Kassala state. There was evidence of a bottleneck event in one of the populations (Al Haj Yousif site). No isolation by distance pattern was detected among populations. Conclusions This study revealed low levels of population differentiation with high gene flow among the An. arabiensis populations investigated in Sudan, with the exception of Kassala state.

Aedes albopictus is an indigenous primary vector of dengue and Zika viruses in China. Understanding the population spatial genetic structure, migration, and gene flow of vector species is critical to effectively preventing and controlling vector-borne diseases. The genetic variation and population structure of Ae. albopictus populations collected from 22 cities along the Yangtze River Basin were investigated with nine microsatellite loci and the mitochondrial CoxI gene. The polymorphic information content (PIC) values ranged from 0.534 to 0.871. The observed number of alleles (Na) values ranged from 5.455 to 11.455, and the effective number of alleles (Ne) values ranged from 3.106 to 4.041. The Shannon Index (I) ranged from 1.209 to 1.639. The observed heterozygosity (Ho) values ranged from 0.487 to 0.545. The FIS value ranged from 0.047 to 0.212. All Ae. albopictus populations were adequately allocated to three clades with significant genetic differences. Haplotype 2 is the most primitive molecular type and forms 26 other haplotypes after one or more site mutations. The rapid expansion of high-speed rail, aircraft routes and highways along the Yangtze River Basin have accelerated the dispersal and communication of mosquitoes, which appears to have contributed to inhibited population differentiation and promoted genetic diversity among Ae. albopictus populations. [ABSTRACT FROM AUTHOR]

Habitat loss and fragmentation can lead to smaller and more isolated populations and reduce genetic diversity and evolutionary potential. Conservation programs can benefit from including monitoring of genetic factors in fragmented populations to help inform restoration and management. We assessed genetic diversity and structure among four major populations of the Cactus Wren (Campylorhynchus brunneicapillus) in San Diego County in 2011–2012 and again in 2017–2019, using 22 microsatellite loci. We found a significant decline in heterozygosity in one population (San Pasqual) and a decline in allelic richness and effective population size in another (Sweetwater). Genetic diversity in the remaining two populations was not significantly different over time. Local diversity declined despite evidence of dispersal among some populations. Approximately 12% of genetically determined family groups (parents, offspring, siblings) included one or more members sampled in different territories with distances ranging from 0.2 to 10 km. All but one inferred dispersal events occurred within the same genetic population. Population structure remained relatively stable, although genetic differentiation tended to increase in the later sampling period. Simulations suggest that at currently estimated effective sizes, populations of Cactus Wrens will continue to lose genetic diversity for many generations, even if gene flow among them is enhanced. However, the rate of loss of heterozygosity could be reduced with increased gene flow. Habitat restoration may help bolster local population sizes and allelic richness over the long term, whereas translocation efforts from source populations outside of San Diego may be needed to restore genetic diversity in the short term. [ABSTRACT FROM AUTHOR]

Studies that rely on noninvasive collection of DNA for birds often use feces or feathers. Some birds, such as vultures, regurgitate undigested matter in the form of pellets that are commonly found under roost sites. Our research demonstrates that regurgitated pellets are a viable, noninvasive source of DNA for molecular ecology studies of vultures. Our objectives were to amplify 5 microsatellite loci designed for distinguishing Turkey Vultures (Cathartes aura) and Black Vultures (Coragyps atratus) in a single, multiplexed PCR, and to determine how long the target nuclear DNA persists after a vulture pellet is regurgitated and exposed to the environment. We collected pellets from captive Black Vultures and placed them in an outdoor aviary for a maximum estimated total of 12, 24, 36, or 48 h. We swabbed pellet surfaces for extraction and amplified vulture DNA using the panel of markers. All amplified alleles fell within predicted ranges of Black Vultures for all 5 loci, supporting the use of this microsatellite panel for vulture species identification. Overall amplification success for samples collected 0–12 h after regurgitation was 82.3%. Pellets collected 12–24 h, 24–36 h, and 36–48 h after regurgitation had only 18%, 10.2%, and 4.5% amplification success, respectively, which may have been due to a rain event. Our approach will be useful for noninvasive genetic sampling targeting nuclear DNA. These results should encourage noninvasive genetic sampling studies of other species that regurgitate pellets, such as raptors, water birds, or shorebirds. Estudios que dependen de colecta no invasiva de ADN de aves muchas veces utilizan heces o plumas. Algunas aves, como los zopilotes, regurgitan materia sin digerir en forma de egagrópilas que se encuentran comúnmente bajo los dormideros. Nuestra investigación muestra que las egagrópilas regurgitadas son una fuente de ADN viable y no invasiva para estudios de ecología molecular de zopilotes. Nuestros objetivos fueron amplificar 5 loci microsatelitales diseñados para distinguir aura gallipavo (Cathartes aura) y zopilote negro (Coragyps atratus) en un solo PCR múltiple así como determinar cuánto tiempo persiste el ADN nuclear blanco después de que una egagrópila de zopilote es regurgitada y expuesta al ambiente. Colectamos egagrópilas de zopilotes negros en cautiverio y las colocamos en un aviario al aire libre durante un tiempo máximo estimado de 12, 24, 36 y 48 h. Realizamos un frotis de la superficie de las egagrópilas para una extracción y amplificación del ADN de los zopilotes usando el panel de marcadores. Todos los alelos amplificados cayeron en los rangos predichos para los zopilotes negros para todos los 5 loci, lo que apoya el uso de este panel de microsatélites para identificación de especies de zopilotes. El éxito general de amplificación de muestras colectadas de muestras colectadas 0-12 h después de regurgitadas fue de 82.3%. Las egagrópilas colectadas 12–24 h, 24–36 h y de 36–48 h tuvieron solamente 12%, 10.2% y 4.5% de éxito de amplificación, respectivamente, lo que podría ser debido a un evento de lluvia. Nuestro enfoque será útil para muestreos genéticos no invasivos dirigidos a ADN nuclear. Estos resultados deberían fomentar los estudios de muestreo genético no invasivo en otras especies que regurgiten egagrópilas, como rapaces, aves acuáticas y aves playeras. Palabras clave: ADN no invasivo, ADN nuclear, éxito de amplificación, loci microsatelitales, PCR mútiple. [ABSTRACT FROM AUTHOR]

Differentiation among populations, sometimes despite ongoing gene exchange, is a key step in speciation. Therefore, comparison of intra‐ and interspecific differentiation patterns is of great significance to understanding speciation. The genus Quercus is an interesting system to test speciation models in the presence of gene flow, due to its weak interspecific reproductive barriers. The aim of the present study was to characterize the degree and pattern of morphological and genetic differentiation among different morphotypes in the white oak Quercus laeta, some corresponding to the previously described species Quercus centralis, Q. laeta, Quercus prinopsis, and Quercus transmontana, as well as geographically structured variation within Q. transmontana not described previously. Our goal was to evaluate if some of these can be considered distinct specific entities or are rather part of a continuum of variation. Nine microsatellite loci and two intergenic regions of chloroplast DNA were analyzed. Morphological differences were evaluated using geometric morphometrics. Chloroplast DNA showed low differentiation, suggesting introgression or sharing of ancestral haplotypes among the Q. laeta morphotypes. Nuclear microsatellites indicated differentiation into two distinct main genetic groups, which were congruent with morphological differentiation. In conclusion, nuclear markers and morphological variations suggest the existence of at least two different entities within Q. laeta. [ABSTRACT FROM AUTHOR]

Among the main measures adopted to reduce anthropogenic impacts on elasmobranch communities, understanding the ecology of deep-sea sharks is of paramount importance, especially for potentially vulnerable species highly represented in the bycatch composition of commercial fisheries such as the blackmouth catshark Galeus melastomus. In the present work, we unravelled the first indication of population genetic structure of G. melastomus by using a novel and effective panel of nuclear, and polymorphic DNA markers and compared our results with previous findings supporting high genetic connectivity at large spatial scales. Given the lack of species-specific nuclear markers, a total of 129 microsatellite loci (Simple Sequence Repeats, SSRs) were cross-amplified on blackmouth catshark specimens collected in eight geographically distant areas in the Mediterranean Sea and North-eastern Atlantic Ocean. A total of 13 SSRs were finally selected for genotyping, based on which the species exhibited signs of weak, but tangible genetic structure. The clearcut evidence of genetic differentiation of G. melastomus from Scottish waters from the rest of the population samples was defined, indicating that the species is genetically structured in the Mediterranean Sea and adjacent North-eastern Atlantic. Both individual and frequency-based analyses identified a genetic unit formed by the individuals collected in the Tyrrhenian Sea and the Strait of Sicily, distinguished from the rest of the Mediterranean and Portuguese samples. In addition, Bayesian analyses resolved a certain degree of separation of the easternmost Aegean sample and the admixed nature of the other Mediterranean and the Portuguese samples. Here, our results supported the hypothesis that the interaction between the ecology and biology of the species and abiotic drivers such as water circulations, temperature and bathymetry may affect the dispersion of G. melastomus, adding new information to the current knowledge of the connectivity of this deep-water species and providing powerful tools for estimating its response to anthropogenic impacts.

Abstract Habitat loss and fragmentation can lead to smaller and more isolated populations and reduce genetic diversity and evolutionary potential. Conservation programs can benefit from including monitoring of genetic factors in fragmented populations to help inform restoration and management. We assessed genetic diversity and structure among four major populations of the Cactus Wren (Campylorhynchus brunneicapillus) in San Diego County in 2011–2012 and again in 2017–2019, using 22 microsatellite loci. We found a significant decline in heterozygosity in one population (San Pasqual) and a decline in allelic richness and effective population size in another (Sweetwater). Genetic diversity in the remaining two populations was not significantly different over time. Local diversity declined despite evidence of dispersal among some populations. Approximately 12% of genetically determined family groups (parents, offspring, siblings) included one or more members sampled in different territories with distances ranging from 0.2 to 10 km. All but one inferred dispersal events occurred within the same genetic population. Population structure remained relatively stable, although genetic differentiation tended to increase in the later sampling period. Simulations suggest that at currently estimated effective sizes, populations of Cactus Wrens will continue to lose genetic diversity for many generations, even if gene flow among them is enhanced. However, the rate of loss of heterozygosity could be reduced with increased gene flow. Habitat restoration may help bolster local population sizes and allelic richness over the long term, whereas translocation efforts from source populations outside of San Diego may be needed to restore genetic diversity in the short term.

Despite a high species diversity, skates (Rajiformes) exhibit remarkably conservative morphology and ecology. Limited trait variations occur within and between species, and cryptic species have been reported among sister and non-sister taxa, suggesting that species complexes may be subject to stabilising selection. Three sibling species are currently recognised in the Raja miraletus complex: (i) R. miraletus occurring along the Portuguese and Mediterranean coasts, (ii) R. parva in the Central-Eastern Atlantic off West Africa and (iii) R. ocellifera in the Western Indian Ocean off South Africa. In the present study, the genetic variation at mitochondrial and nuclear markers was estimated in the species complex by analysing 323 individuals sampled across most of its geographical distribution area to test the hypothesis that restricted gene flow and genetic divergence within species reflect known climate and bio-oceanographic discontinuities. Our results support previous morphological studies and confirm the known taxonomic boundaries of the three recognised species. In addition, we identified multiple weakly differentiated clades in the Northeastern Atlantic Ocean and Mediterranean, at least two additional cryptic taxa off Senegal and Angola, a pronounced differentiation of ancient South African clades. The hidden genetic structure presented here may represent a valuable support to species’ conservation action plans.