Abstract This study introduces a new species, Boechera sierraensis , recently discovered in the Sierra Nevada of California. Previous research has shown that this taxon possesses exceptional tolerance to environmental stressors, including heat, drought, and high light intensity, which make it a valuable research subject in the face of accelerating climate change. However, species delimitation within the genus Boechera is notoriously difficult due to extensive morphological convergence and complex evolutionary dynamics. While polyploidy has often been cited as a major driver of speciation in the genus, repeated interspecific hybridization coupled with rampant apomictic reproduction also plays major roles in the process. These factors contribute to blurred species boundaries and underscore the need for careful taxonomic evaluation. We conducted cytogenetic, pollen, microsatellite DNA, and morphological analyses to investigate the ploidy, genetic makeup, and evolutionary origin of this Sierran endemic originally identified as Arabis lemmonii var. depauperata . Specimens were compared to 5014 samples from the Boechera Microsatellite Website. Chromosome spreads were prepared and 15 microsatellite loci studied. Morphological and geographical data were analyzed in light of the microsatellite results. Our analyses revealed these plants to be apomictic triploids containing three divergent subgenomes derived from B. lemmonii , B. paupercula , and B. retrofracta . The presence of this trihybrid species has since been confirmed at multiple locations in the Sierra Nevada, and morphological analyses allow separation from closely related taxa. The identification key and description provided here will hopefully facilitate further research into the broader ecological and evolutionary significance of Boechera sierraensis and related species.

The invasive white‐footed ant Technomyrmex difficilis has emerged as a rising pest in several regions, yet its invasion dynamics remain underexplored. This species outcompetes native ants and causes agricultural losses by tending pest insects, including aphids and mealybugs. This study provides the first integrated analysis of the species’ behavioral, chemical, and genetic variation across Texas and Florida populations. Observations suggest that the recently discovered Texas population of white‐footed ants originated from Florida. Microsatellite and mitochondrial DNA analyses revealed low genetic diversity in both populations, with a shared haplotype consistent with the Texas population originating from Florida. STRUCTURE analysis further supported genetic clustering between the two regions. Despite similar within‐colony coefficients of relatedness for workers, the populations differed in reproductive strategy: Florida colonies showed signs of inbreeding and high inter‐colony aggression, whereas Texas colonies exhibited potential localized outbreeding, low aggression, and more uniform cuticular hydrocarbon profiles. Aggression was positively correlated with chemical divergence but not with genetic differentiation. This study establishes a foundational understanding and highlights the importance of integrating multiple types of data to understand the invasion biology of Technomyrmex difficilis.

ABSTRACTThe Asian elephant (Elephas maximus), a crucial flagship and umbrella species in forest ecosystems, possesses significant conservation value. However, it has been categorized as endangered due to several factors, including land use change, human disturbance, and climate change. To evaluate the genetic diversity of Chinese Asian elephant populations and provide a scientific basis for the establishment of the Asian Elephant National Park, microsatellite and mitochondrial DNA analyses were conducted on seven populations distributed across Yunnan Province, China. A total of 121 unique genotypes and five mitochondrial DNA (mtDNA) haplotypes were identified. The results revealed that all populations exhibited varying degrees of inbreeding, with the Mengla population showing the highest inbreeding levels. Significant genetic differentiation was observed between the Mengla and other populations. Interestingly, the Yexianggu population exhibits relatively high genetic diversity despite having undergone a population bottleneck and exhibited significant heterozygote excess. Nevertheless, the overall genetic diversity of Chinese Asian elephants remains relatively low compared to that of populations in other countries. To ensure the long‐term viability of the Nangunhe population, it is imperative to facilitate gene flow between this and other populations. Finally, based on geographic subdivision analysis, we propose that the seven Asian elephant populations should be considered as three conservation management units, namely unit 1 (Nangunhe), unit 2 (Mengla), and unit 3 (Yexianggu, Mengman, Puwen, Kongge, and Menga). This study provides a solid reference for the scientific conservation of the Asian elephant in the future.

The aim of the study was to assess the effectiveness of a microsatellite DNA analysis to genetically identify dog breeds and crossbreeds, using reference populations of purebred individuals and Bayesian clustering methods. The study was conducted based on 21 microsatellite markers (STR) that are recommended by the International Society for Animal Genetics (ISAG) for routine canine pedigree verification. The genetic diversity and population structure were assessed for 4 selected breeds: Golden Retriever, Bernese Mountain Dog, Poodle and Chinese Crested Dog. These reference populations were then used to analyse two case studies involving breed verification. Key genetic parameters were calculated, including the observed (HO) and expected heterozygosity (HE), degree of inbreeding (FIS) and the polymorphism information content (PIC). The probability of exclusion was estimated in cases of knowing the genotype of one of the parents (CPE1) and both parents (CPE2). A relatively high level of genetic diversity among the studied breeds, constituting reference populations, was found to be above 50% for HO and PIC, with no inbreeding. The probability of CPE1 and CPE2 was obtained at the level of 99% and 99.99%, respectively, which allowed the use of these markers for a parentage analysis. Bayesian clustering (STRUCTURE) and a Principal Coordinates Analysis (PCoA) were applied to assess the genetic structure and to identify the admixture in genotypes of the crossbred individuals. In both cases, the analyses successfully confirmed the breed’s pedigree or detected mixed ancestry, which was further supported by the parentage testing. The results confirm that the applied STR marker panel is suitable for breed identification and the detection of hybrid ancestries in dogs. While further research is needed to validate the method across a wider range of breeds, the study provides a valuable foundation for the development of DNA‐based tests to support breed verification and the assessment of breed compositions in designer and hybrid dogs.

Somatic cell nuclear transfer (SCNT) allows the multiplication of elite livestock and conservation of endangered species. However, restrictions on cow slaughter limit the access to oocytes for SCNT applications in Indian cattle breeds. To overcome this limitation, we utilized transvaginal ovum pick-up (OPU) method to collect oocytes, which were then used for the production of cloned embryos via the handmade cloning (HMC) technique. A total of 98 Sahiwal oocytes were collected, leading to the successful reconstruction of 24 SCNT Gir embryos. Out of these, five developed into blastocysts, which were transferred into five recipient cows. Two pregnancies were confirmed, but one was lost due to hydro-allantois condition. The other pregnancy continued to term, and a healthy Gir female calf weighing 32kg was born. Microsatellite DNA analysis confirmed the genetic identity of the cloned calf to its donor. Postnatally, the calf was monitored for serum cytokine parameters, telomere length, and reproductive potentials. Cytokine profiling revealed variations between the cloned calf and naturally conceived counterparts; however, the born cloned calf did not exhibit any pathological conditions and has high telomere length compared to age-matched counterparts, and surviving well. Furthermore, to assess cloned cow utility in reproductive biotechnologies, we produced blastocyst stage embryos (35%) through OPU-IVF method and established one pregnancy from five transfers (20%). In conclusion, this study reports the first successful SCNT of Indian cattle breed and demonstrates the feasibility of the cloned cow for the production of OPU-IVF embryos.

Background: Microsatellite DNA sequencing has emerged as an important method for determining genetic variety and parentage in domesticated species, including popular dog breeds. The role of microsatellite markers helps in understanding the genetic landscape of dog breeds in India, where the growing popularity of particular breeds has generated worries about inbreeding and loss of genetic variety. Methods: For the parentage testing in canine microsatellite length, polymorphism markers were used to check the efficacy of the markers. In the current study 5 fluorescently labeled 12 SSR markers were used to check the use of the markers in popular owned-dog breeds (Labrador, German Shepherd, Pug, Mudhol Hound, Tibetan Mastiff, Gaddi dog, Beagle, Belgian Malinois, Pointer, and Cane Corso). The number of alleles, heterozygosity, polymorphism information content and probability of exclusion were determined for all the markers to check the effectiveness of the markers. Result: The analysis utilized a panel of microsatellite markers to evaluate genetic variation among several breeds including Punjab, Haryana, Himachal Pradesh and Karnataka. The mean number of alleles per locus ranged from 5 to 29 and the effective number ranged from 3.6 to 15.2. The expected heterozygosity was greater than 0.73. The population inbreeding coefficient (FIS) demonstrated that there was no inbreeding in the breeds studied. The polymorphism information content and the probability of the exclusion values were greater than 0.65. The combined probability of exclusion for all the breeds was (2.82E-12) 0.99999995. The findings revealed that the 12 particular microsatellite markers chosen for paternity testing demonstrated substantial exclusion probability for determining parentage.

The most accurate and fastest tool in solving issues of genetic identification of animals, regardless of their physiological condition and age, are microsatellites (STR - Short Tandem Repeats), which are markers and have a number of features. Information on the genetic diversity of the cattle population by microsatellite markers can be used not only to study the genetic structure, but also to confirm the origin of offspring by parents. In the studied group of Jersey and Holstein cattle, the average number of microsatellite alleles per locus was 7.5-7.6. The average number of effective alleles of the studied loci in the Jersey breed was 3.2 and in the Holstein breed 3.7. The highest levels of observed and expected heterozygosity in the Jersey breed (0.767 and 0.882) were found at the Eth10 locus, and the lowest (0.581 and 0.559) at the Bm1824 locus. The average level of observed and expected heterozygosity was approximately 0.672 and 0.702. In the Holstein breed, the highest values of observed and expected heterozygosity were found at the Tgla122 locus (0.839 and 0.893), and the lowest 0.466 and 0.472 at the Sps115 locus. The average level of observed and expected heterozygosity was 0.694 and 0.693. The Wright fixation index was -0.047 for the Jersey breed and 0.049 for the Holstein breed. It should also be noted that the results of microsatellite DNA analysis must be taken into account and applied to develop plans for selection and breeding work, assess the genetic structure of breeds, and maintain the level of heterozygosity in herds.

Bighead carp (Hypophthalmichthys nobilis) has an essential role in freshwater fisheries worldwide, especially in China, yet its germplasm resources in the upstream Yangtze River have been scarcely studied. We used nine polymorphic microsatellite markers to assess genetic diversity and differentiation in seven bighead carp populations from the upper-middle Yangtze River. In five populations from the upstream and two populations from the midstream of the Yangtze River, a total of 101 alleles were detected, with the mean value of alleles per population varying from 5.3 to 8.4. Moderate genetic diversity of seven populations was detected with the values of Ho, He and PIC ranging from 0.598 to 0.683, 0.647 to 0.703 and 0.591 to 0.639, respectively. Weak population differentiations (Fst = 0.0000–0.0478) were observed, which indicated that bighead carp populations up and down the Three Gorges Dam (TGD) could be regarded as a group. Structure and clustering analysis consistently supported that the bighead carp samples examined in this study were clustered as one group, except a population from Dongting Lake (DTL), the second largest lake of China, in the midstream of the Yangtze River. This study provided evidence of moderate genetic diversity and weak differentiation among bighead carp populations from upstream and midstream regions of the Yangtze River, suggesting that the TGD has not yet had a significant influence on population genetic structure. These results are valuable for conservation genetics and sustainable utilization of bighead carp resources in the Yangtze River.

Molecular genetic analyses are effective in revealing the origin, kinship, and genetic diversity of zoo animals. In this study, we carried out the genetic characterization of captive founder individuals of the South American fur seal (Arctocephalus australis) in Japanese zoos and aquariums based on analyses of mitochondrial sequences and nuclear microsatellite loci. In mitochondrial DNA analysis, the haplotype diversity and nucleotide diversity of the overall population were 0.8949 and 0.0119, respectively. Microsatellite DNA analysis revealed that the observed heterozygosity within the overall population was 0.722. In addition, we did not detect genetic bottlenecks. The results from two kinds of DNA analyses indicated that the genetic diversity in this captive population was equivalent to that previously reported in wild populations. The detected mitochondrial haplotypes were the same as or phylogenetically close to those previously reported in wild populations in southern Brazil, Uruguay, Argentina, and southern Chile but diverged from those previously reported in a wild population in Peru. Genetic clustering analyses using microsatellite genotypes revealed that no clear genetic structures in this captive population.

Differentiating Separate Primary Lung Adenocarcinomas From Intrapulmonary Metastases With Emphasis on Pathological and Molecular Considerations: Recommendations From the International Association for the Study of Lung Cancer Pathology Committee

The results of a comparative study of the genetic structure, parameters of intraspecific genetic diversity, and spatial differentiation of 35 populations of Picea abies–P. obovata–P. koraiensis species complex, located within the areas of distribution of “pure” species and in the contact zones of their ranges were presented. P. abies populations from Eastern Europe (Belarus, Poland); spruce populations from the European part of Russia, the Urals, and the West Siberian Plain, located in the zone of P. abies and P. obovata introgressive hybridization; P. obovata populations from various parts of the extensive range of this species in Siberia and Mongolia; and P. koraiensis populations from the Russian Far East and Northeast China were analyzed. The study of genetic variability and differentiation of populations was based on the analysis of variability of three microsatellite loci: Pt63718, Pt71936, and Pt26081, developed on the basis of Pinus thunbergii Parl chloroplast genome. The use of these DNA markers made it possible to obtain data indicating a fairly high degree of P. koraiensis genetic divergence from two other spruce species included in the complex, P. abies and P. obovata. Korean spruce growing in the Far East differs significantly from the populations of these species in the number and composition of haplotypes, the level of genetic diversity, and population structure, which gives us reason to consider it as a separate species.

Abstract The genetic identity and conservation status of lake ecotype of brown trout (Salmo trutta) populations in Slovenia’s Alpine lakes Bled and Bohinj have been subjected to changes due to historical stocking practices. We aimed to evaluate the genetic differentiation and origins of these populations to advise for correct conservation strategies. Using microsatellite and mitochondrial DNA analysis on 365 trout specimens, we explored the genetic diversity and structure of these populations, comparing them with potential originators. Results revealed distinct genetic profiles between Bled and Bohinj lake trout, with Bohinj lake trout closely aligned with the native Danubian lineage and Bled lake trout showing a hybrid composition, significantly influenced by hatchery-introduced Atlantic lineage strains. The genetic distinction between these populations underscores the complexity of their conservation, showcasing the impact of human-mediated introductions on natural populations. The urgent need for conservation measures to preserve the Bohinj population’s native genetic pool is highlighted, underlining the must to prevent the transfer of individuals from Lake Bled or elsewhere and to reconsider stocking practises in order to prevent further genetic dilution of these iconic European lake dwellers.

This study traced the maternal lineage of the domestic swine populations using mitochondrial DNA control region markers and genetic diversity using microsatellite markers in Uttarakhand, an Indian state situated at the foothills of the world's youngest (geo-dynamically sensitive) mountain system, "the Himalayas". Analysis of 68 maternally unrelated individuals revealed 20 haplotypes. The maternal signature of the Pacific, Southeast Asian, European, and ubiquitously distributed Chinese haplotypes was present in Uttarakhand's domestic pig population. The D3 haplotype reported in wild pigs from North India was also identified in 47 domestic samples. A unique gene pool, UKD (Uttarakhand Domestic), as another lineage specific to this region has been proposed. Genotypes were analyzed, using 13 sets of microsatellite markers. The observed (Ho) and expected (He) heterozygosities were 0.83 ± 0.02 and 0.84 ± 0.01, respectively. The average polymorphic information content value of 0.83 ± 0.01 indicated the high informativeness of the marker. The overall mean FIS value for all the microsatellite markers was low (F = 0.04, P < 0.01). Seven loci deviated from Hardy-Weinberg equilibrium (HWE) at a significant level (p < 0.05). Two clusters were identified, indicating overlapping populations. These results suggested that though belonging to different maternal lineages, the traditional management practices in Uttarakhand have allowed for genetic mixing and the sharing of genetic material among pig populations. It could contribute to increased genetic diversity but might also result in the loss of distinct genetic characteristics or breed purity of the local breeds if not carefully managed.

Sturgeons (Family: Acipenseridae) are among the most endangered taxa worldwide. Significant resources have been invested into the conservation of global sturgeon populations, including the development of commercial aquaculture programs. These programs are intended to improve conservation outcomes by reducing the harvest of wild populations while still meeting commercial demand for sturgeon products. However, there is growing concern that commercial aquaculture programs may contribute to wild population declines through continued, illegal harvest and the escape and/or release of captive individuals into wild environments. These concerns may be particularly acute in the country of Georgia which, despite its small territory and altered landscape, is a globally significant hotspot for sturgeon diversity. In order to understand the potential threat of captive culture on wild sturgeon populations in Georgia, we used mitochondrial DNA sequencing and microsatellite analyses to identify the species and origin of sturgeons encountered in commercial settings. Microsatellite analyses showed significant differentiation between wild and commercial Russian sturgeon populations and highlighted the potential for wild-caught individuals to be present in coastal markets in Georgia. The analyses of mitochondrial haplotypes also suggested that commercial markets may contain sturgeon species that are not native to the region. Overall, our results suggest that wild sturgeon populations may still be exploited to support captive aquaculture programs and commercial sales.

For the parentage testing in canine microsatellite length polymorphism markers were used to check the efficacy of the markers. In the current study 5’ fluorescently labeled 12 SSR markers were used to check the use of the markers in popular owned-dog breeds (Labrador, German Shepherd, Pug, Mudhol Hound, Tibetan Mastiff, Gaddi dog, Beagle, Belgian Malinois, Pointer, and Cane Corso) maintained of India (not necessarily indigenous breeds). The number of alleles, heterozygosity, polymorphism information content, and probability of exclusion were determined for all the markers to check the effectiveness of the markers. The mean number of alleles per locus ranged from 5 to 29 and the effective number of alleles ranged from 3.6 to 15.2. The expected heterozygosity was greater than 0.73. The population inbreeding coefficient (FIS) demonstrated that there was no inbreeding in the breeds studied, as the samples were collected from owners and dog breeders belonging to various states, including Punjab, Haryana, Himachal Pradesh, and Karnataka. The polymorphism information content and the probability of the exclusion values were greater than 0.65. the combined probability of exclusion for all the breeds was (2.82E-12) 0.99999995. The results indicated that the selected 12 markers are effective enough to determine the parentage of the dogs.

Abstract Bull trout (Salvelinus confluentus) research has historically focused on highly impacted systems or occurred in a reactionary manner following overharvest. Here, we used telemetry and multi‐state capture–recapture modelling to inform management decision‐making for this highly migratory, conservation‐listed species in British Columbia's upper Fraser River watershed (UFW). Our work reduced critical information gaps surrounding the seasonal migration patterns, distribution, and survival rates of fluvial bull trout within the region. By using results of an existing microsatellite DNA analysis, we were able to assign each tagged individual to one of five spawning populations. This assignment allowed us to investigate potential differences in migratory behaviour and seasonal habitat use among the different spawning populations. We identified that the majority of tagged UFW fluvial bull trout made repeated, long‐distance migrations (&gt;300 km one direction) to appropriate spawning, overwintering and foraging habitats. The five populations did not vary in their seasonal transition probabilities at the spatial scale investigated, suggesting key habitats are important to multiple populations. We also detected post‐spawning migration and distribution patterns that suggest UFW bull trout exploit seasonal resource pulses during salmon smolt outmigration. Our results highlight the importance of protecting, restoring and maintaining a diverse assemblage of complex habitats and the natural connections between them (e.g. between tributary spawning habitats and larger rivers) at a spatial scale that supports migratory bull trout life histories. This work provides valuable information for prioritizing conservation actions and identifying restoration opportunities both in the UFW and across the species' range.

In 1989, a skin of a small spotted cat, from the Galeras Volcano in southern Colombia (Nariño Department), was donated to the Instituto Alexander von Humboldt (identification, ID 5857) at Villa de Leyva (Boyacá Department, Colombia). Although originally classified as Leopardus tigrinus, its distinctiveness merits a new taxonomic designation. The skin is distinct from all known L. tigrinus holotypes as well as from other Leopardus species. Analysis of the complete mitochondrial genomes from 44 felid specimens (including 18 L. tigrinus and all the current known species of the genus Leopardus), the mtND5 gene from 84 felid specimens (including 30 L. tigrinus and all the species of the genus Leopardus), and six nuclear DNA microsatellites (113 felid specimens of all the current known species of the genus Leopardus) indicate that this specimen does not belong to any previously recognized Leopardus taxon. The mtND5 gene suggests this new lineage (the Nariño cat as we name it) is a sister taxon of Leopardus colocola. The mitogenomic and nuclear DNA microsatellite analyses suggest that this new lineage is the sister taxon to a clade formed by Central American and trans-Andean L. tigrinus + (Leopardus geoffroyi + Leopardus guigna). The temporal split between the ancestor of this new possible species and the most recent ancestor within Leopardus was dated to 1.2-1.9 million years ago. We consider that this new unique lineage is a new species, and we propose the scientific name Leopardus narinensis.

Establishment of invasive aquatic species is increasing globally due to factors related to globalization and accelerated trade between regions. Such invasions and subsequent establishment generally cause ecosystem disturbance with occasional local and/or regional socioeconomic impacts. The paiche (tentatively identified as Arapaima gigas), one of the largest fish in the Amazon, was introduced into Bolivia via Peru in the 1960s and has generated significant changes in Amazonian fisheries. In recent years, it has been proposed that the genus Arapaima is composed of different species distributed along the Amazon Basin. The present study evaluated the genetic variability of the paiche in the Bolivian Amazon Basin (sub-basins of the Orthon, Madre de Dios and Beni rivers) using nuclear (nDNA- microsatellites) and mitochondrial (mtDNA NADH and CO1) genetic markers to determine species identity and population structure. Microsatellite DNA analysis suggested that the three populations corresponding to geographic sub-basins are genetically distinct. The genetic distance between populations was not significantly related to the geographic distance between collection sites. We suggest that the founder population in Bolivia was composed of a limited number of individuals that subsequently dispersed in search of environmental conditions similar as those habitats from which they were extracted. Planning for the sustainable use of the species by fisheries should consider the existence of different populations in the Bolivian sub- basins. Recruitment seems to depend on exchanges between nearby surrounding aquatic habitats rather than between sub-basins.

Indonesia is an archipelagic country with a high level of population diversity such as religion, ethnicity, culture and also genetic diversity. Environmental factors also have an impact on the genetic variation and diversity of the population, including high mobility and migration triggering the tendency for inter-ethnic marriages to occur. This environmental factor is one of the reasons for research based on DNA analysis on ethnicity in Indonesia for the purpose of forensic identification. One of the DNA analyzes for forensic identification is the microsatellite DNA analysis method with a high sensitivity level.&#x0D;

As a contribution to improving management of the Japanese wild boar (Sus scrofa leucomystax), which has recently expanded its range and is having some negative effects on the ecosystem, we conducted a landscape genetic study using individual-based genetic analysis and multiple landscape elements to elucidate its dispersal patterns in the early stage of its expansion. Microsatellite DNA analysis of Japanese wild boars in the Hokuriku region of Japan revealed the existence of two ancestral genetic clusters, that they had migrated via different pathways, and that they were inadequately admixed. We also inferred the most suitable habitats for Japanese wild boar using MaxEnt and concluded that lower elevation and snowfall may favor the occurrence of wild boar individuals. Landscape genetic analysis indicated regional differences in Japanese wild boar dispersal patterns, according to the spatial heterogeneity of genetic features and landscape elements. On the western side of the study area, where individuals with a high frequency of one of two ancestral clusters were more abundant, significant effects of isolation by distance and resistance due to the above two landscape factors were detected, suggesting unidirectional dispersion influenced by the alpine landscape. In contrast, on the eastern side, there was indication of resistance to dispersal of individuals predominantly possessing another ancestral cluster, suggesting the influence of irregularly arranged suitable habitats due to the complexity of the mountainous terrain. Based on our findings, we conclude that Japanese wild boar dispersal patterns may be influenced by landscape elements, such as alpine mountains.