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Abstract Polyandry, the practice of females mating with multiple males, is a strategy found in many insect groups. Whether it increases the likelihood of receiving beneficial genes from male partners and other potential benefits for females is controversial. Strepsiptera are generally considered monandrous, but in a few species females have been observed copulating serially with multiple males. Here we show that the offspring of a single female can have multiple fathers in two Strepsiptera species: Stylops ovinae (Stylopidae) and Xenos vesparum (Xenidae). We studied female polyandry in natural populations of these two species by analysis of polymorphic microsatellite loci. Our results showed that several fathers can be involved in both species, in some cases up to four. Mating experiments with S. ovinae have shown that the first male to mates with a given female contributes to a higher percentage of the offspring than subsequent males. In X. vesparum, however, we found no significant correlation between mating duration and offspring contribution. The prolonged copulation observed in S. ovinae may have the advantage of reducing competition with sperm from other males. Our results show that monandry may not be the general pattern of reproduction in the insect order Strepsiptera.

Development of specialized beef cattle breeding contributes to increase in beef production, which directly affects the countrys food security. Currently, increasing productivity of animals is the major trend of cattle breeding development, which in turn requires improvement of breeding. The effectiveness of breeding work depends on the assessment of genetic value of breeding animals. To control authenticity of animal origin is a prerequisite for conducting breeding work. One of the main directions of cattle breeding in Kalmykia is breeding of Kalmyk cattle. The aim of the research was to study genetic diversity of Kalmyk cattle populations using microsatellite analysis. The study was conducted in the Regional Research and Production Center for Reproduction of Kalmyk State University. 60 Kalmyk cattle from Plodovitoe agricultural production company in Maloderbetovsky district were studied. PCR analysis was performed by 9 microsatellite loci: BM1824, BM 2113, INRA023, SPS 115, TGLA 122, TGLA 126, TGLA 227, ETH 10, ETH 225. It was found that the average number of alleles was 10.1, while the number of alleles per locus varied from 7 (BM 1824, SPS 115, ETH 10) to 18 (TGLA 122). The loci with the largest range of alleles were BM 2113 (12), INRA 023 (12), TGLA 122 (18) and TGLA 227 (12). The most informative loci were INRA 023, TGLA 122 and TGLA 227. The level of observed heterozygosity varied from 0.67 (ETH 10) to 0.83 (SPS 115, TGLA 227, ETH 225), and expected heterozygosity - from 0.86 (BM 1824, SPS 115, ETH 10) to 0.92 (BM 2113, INRA 023, TGLA 227). Analysis of fixation index data showed that 8 loci had negative index (BM 1824 (-0.22), BM 2113 (-0.26), INRA 023 (-0.26), SPS 115 (-0.18), TGLA 122 (-0.12), TGLA 126 (-0.10), ETH 10 (-0.28), ETH 225 (-0.04) and 1 locus (TGLA 227) had positive index (1.0). The results of the analysis of microsatellite loci showed that level of genetic diversity in the studied herd of Kalmyk cattle is high.

Abstract Background Tanzania is currently implementing therapeutic efficacy studies (TES) in areas of varying malaria transmission intensities as per the World Health Organization (WHO) recommendations. In TES, distinguishing reinfection from recrudescence is critical for the determination of anti-malarial efficacy. Recently, the WHO recommended genotyping polymorphic coding genes, merozoite surface proteins 1 and 2 (msp1 and msp2), and replacing the glutamate-rich protein (glurp) gene with one of the highly polymorphic microsatellites in Plasmodium falciparum to adjust the efficacy of antimalarials in TES. This study assessed the polymorphisms of six neutral microsatellite markers and their potential use in TES, which is routinely performed in Tanzania. Methods Plasmodium falciparum samples were obtained from four TES sentinel sites, Kibaha (Pwani), Mkuzi (Tanga), Mlimba (Morogoro) and Ujiji (Kigoma), between April and September 2016. Parasite genomic DNA was extracted from dried blood spots on filter papers using commercial kits. Genotyping was done using six microsatellites (Poly-α, PfPK2, TA1, C3M69, C2M34 and M2490) by capillary method, and the data were analysed to determine the extent of their polymorphisms and genetic diversity at the four sites. Results Overall, 83 (88.3%) of the 94 samples were successfully genotyped (with positive results for ≥ 50.0% of the markers), and > 50.0% of the samples (range = 47.6–59.1%) were polyclonal, with a mean multiplicity of infection (MOI) ranging from 1.68 to 1.88 among the four sites. There was high genetic diversity but limited variability among the four sites based on mean allelic richness (RS = 7.48, range = 7.27–8.03, for an adjusted minimum sample size of 18 per site) and mean expected heterozygosity (H e = 0.83, range = 0.80–0.85). Cluster analysis of haplotypes using STRUCTURE, principal component analysis, and pairwise genetic differentiation (F ST ) did not reveal population structure or clustering of parasites according to geographic origin. Of the six markers, Poly-α was the most polymorphic, followed by C2M34, TA1 and C3M69, while M2490 was the least polymorphic. Conclusion Microsatellite genotyping revealed high polyclonality and genetic diversity but no significant population structure. Poly-α, C2M34, TA1 and C3M69 were the most polymorphic markers, and Poly-α alone or with any of the other three markers could be adopted for use in TES in Tanzania.

Abstract Background Schistosomiasis is a water-based parasitic disease that affects humans, livestock and wild animals. While considerable resources are dedicated to the surveillance, disease mapping, control and elimination of human schistosomiasis, this is not the case for livestock schistosomiasis. Indeed, there are important data and knowledge gaps concerning the species present, population genetic diversity, infection prevalence, morbidity and economic impact. This study aimed to identify circulating schistosome species in cattle across Côte d’Ivoire and to investigate their population diversity and structuring. Methods Overall, 400 adult schistosomes were collected from slaughtered cattle at six sites across Côte d’Ivoire. Additionally, 114 miracidia were collected from live cattle at one site: Ferkessédougou, in the northern part of Côte d’Ivoire. DNA from all specimens was extracted and the cox1 and ITS1/2 regions amplified and analysed to confirm species. The genetic diversity and structuring of the schistosome populations were investigated using 12 microsatellite markers. Results All adult schistosomes and miracidia presented Schistosoma bovis mitochondrial cox1 profile. Nuclear ITS1/2 data were obtained from 101 adult schistosomes and four miracidia, all of which presented an S. bovis profile. Genetic diversity indices revealed a deficiency of heterozygotes and signals of inbreeding across all sites, while structure analyses displayed little geographic structuring and differentiation. Cattle in Côte d’Ivoire thus appear to be mono-species infected with S. bovis. Hybrids of Schistosoma haematobium × S. bovis have not been identified in this study. Cattle schistosomes appear to be panmictic across the country. Conclusions Our results contribute to a deeper understanding of schistosome populations in Ivorian cattle and emphasize a One Health approach of joint human and animal surveillance and prevention and control programmes for schistosomiasis. Graphical Abstract

Commercial panels of microsatellite (STR) loci are intended for DNA analysis of the domestic dog (Canis lupus familiaris) and, therefore, when genotyping the Grey wolf (Canis lupus lupus), most markers reveal significant deviations from the Hardy–Weinberg equilibrium and have a low informative value, which complicates their use in a forensic examination. The aim of this study was to select STR markers that equally effectively reflect population polymorphism in the wolf and the dog, and to create a universal panel for the identification of individuals in forensic science. Based on the study of polymorphisms of 34 STR loci, a CPlex panel of 15 autosomal loci and two sex loci was developed, which is equally suitable for identifying wolfs and dogs. Analysis of molecular variance (AMOVA) between samples revealed significant differentiation values (FST = 0.0828, p < 0.05), which allows the panel to be used for differentiating between wolf and dog samples. For the first time in the forensic examination of objects of animal origin in the Republic of Belarus, population subdivision coefficients (θ­-values) were calculated for each of the 15 STR loci of the test system being reported. It was shown that the values of the genotype frequency, when averaged over all studied animals without and with considering the θ­-value, differ by three orders of magnitude (3.39 · 10–17 and 4.71 · 10–14, respectively). The use of population subdivision coefficients will provide the researcher with the most relevant results of an expert identification study. The test system was validated in accordance with the protocol of the Scientific Working Group on DNA Analysis Methods. A computational tool was developed to automate the analysis of genetic data on the wolf and dog in the forensic examination; two guides were approved for practicing forensic experts. This methodology is being successfully used in expert practice in investigating cases of illegal hunting, animal abuse and other offenses in the Republic of Belarus.

Short tandem repeats (STRs) are units of 1-6 bp that repeat in a tandem fashion in DNA. Along with single nucleotide polymorphisms and large structural variations, they are among the major genomic variants underlying genetic, and likely phenotypic, divergence. STRs experience mutation rates that are orders of magnitude higher than other well-studied genotypic variants. Frequent copy number changes result in a wide range of alleles, and provide unique opportunities for modulating complex phenotypes through variation in repeat length. While classical studies have identified key roles of individual STR loci, the advent of improved sequencing technology, high-quality genome assemblies for diverse species, and bioinformatics methods for genome-wide STR analysis now enable more systematic study of STR variation across wide evolutionary ranges. In this review, we explore mutation and selection processes that affect STR copy number evolution, and how these processes give rise to varying STR patterns both within and across species. Finally, we review recent examples of functional and adaptive changes linked to STRs.

Trophic polymorphism and temporal reproductive isolation are the drivers of sympatric differentiation in many fish taxa. We present a new case of ecologically based diversification of Arctic charr in a Transbaikalian mountain lake inhabited by reproductively isolated dwarf and normal forms. These forms differ in size, diets and morphology and breed, respectively, in April–May and in September–October representing a rare example of sympatric spring- and autumn-spawning charr pair. Microsatellite analysis reveals clear-cut genetic differences and low-level hybridization between them. Dwarf form charr are planktivorous and manifest uniform slow growth. Normal form charr, though genetically homogeneous, are highly heterogeneous in size-at-age. They are subdivided into omnivorous small-size and piscivorous large-size groups, which can be considered as incipient forms at an early divergence stage. As evidenced by back-calculated growth data, their size-at-age heterogeneity results from highly variable individual growth patterns, which include different combinations of slow and fast growth periods presumably associated with spawning and non-spawning years. Growth acceleration in late ontogeny may result in the transformation of some normal charr from the smaller into the larger group during their lifetime. [ABSTRACT FROM AUTHOR]

Small pelagic fish play an important role in marine trophic webs and human food security. Among those, Sardinella aurita represents an extremely valuable resource in West Africa, where it is assumed to conform a transboundary stock. During the last decade, quantitative stock assessment has not been possible in NW African waters due to the limitation of the indices used; however, a critical biomass decline has been observed, and the stock is considered overexploited. In order to delineate the population structure of the species in West Africa, twelve microsatellites were developed ad hoc and genotyped on some 1300 individuals collected from Morocco to Angola. The significant differentiation detected between the northernmost samples (Morocco to Guinea) and the southernmost ones (Liberia to Angola) was due to one candidate locus to positive selection. The signal of this locus resided uniquely in the frequency of allele SauMS002_131, which displayed a remarkable latitudinal cline. Allele frequency, starting around 47%–63% in Moroccan-Guinean waters and dropping to 0% off Gabon and southwards, accounts for the North–South declining trend and can be used as a meaningful tool to assist population structure outline for this species in West Africa for management purposes in order to ensure sustainable regionally shared fisheries. [ABSTRACT FROM AUTHOR]

Geckos exhibit derived karyotypes without a clear distinction between macrochromosomes and microchromosomes and intriguing diversity in sex determination mechanisms. We conducted cytogenetic analyses in six species from the genera Nephrurus , Phyllurus , and Saltuarius of the gecko family Carphodactylidae. We confirmed the presence of a female heterogametic system with markedly differentiated and heteromorphic sex chromosomes in all examined species, typically with the W chromosome notably larger than the Z chromosome. One species, Nephrurus cinctus , possesses unusual multiple Z1Z1Z2Z2/Z1Z2W sex chromosomes. The morphology of the sex chromosomes, along with repetitive DNA content, suggests that the differentiation or emergence of sex chromosomes occurred independently in the genus Phyllurus. Furthermore, our study unveils a case of spontaneous triploidy in a fully grown individual of Saltuarius cornutus (3n = 57) and explores its implications for reproduction in carphodactylid geckos. We revealed that most carphodactylids retain the putative ancestral gekkotan karyotype of 2n = 38, characterized by predominantly acrocentric chromosomes that gradually decrease in size. If present, biarmed chromosomes emerge through pericentric inversions, maintaining the chromosome (and centromere) numbers. However, Phyllurus platurus is a notable exception, with a karyotype of 2n = 22 chromosomes. Its eight pairs of biarmed chromosomes were probably formed by Robertsonian fusions of acrocentric chromosomes. The family underscores a remarkable instance of evolutionary stability in chromosome numbers, followed by a profound transformation through parallel interchromosomal rearrangements. Our study highlights the need to continue generating cytogenetic data in order to test long-standing ideas about reproductive biology and the evolution of genome and sex determination. [ABSTRACT FROM AUTHOR]

Multiple factors can facilitate invasion success, with the absence of natural enemies, such as predators and parasites, recognised as conferring a significant advantage on invasive over native species. Pumpkinseed Lepomis gibbosus (Centrarchidae) represents one of the most successful freshwater fish invaders in Europe. Previous research has highlighted genetic differences between pumpkinseed populations in Türkiye and those in other European regions, attributed to rapid adaptation to new environmental conditions. This study aimed to investigate whether these highly adapted pumpkinseed populations in Türkiye benefit from a potential release from parasites, as proposed by the enemy-release hypothesis. Genetic characterisation of pumpkinseed populations from both European and Asian parts of Türkiye revealed that they share the same cytochrome c oxidase I haplotype as European populations. Microsatellite analysis indicated low genetic diversity, with STRUCTURE analysis confirming the clustering of all Turkish populations, suggesting a common source. Consistent with the low genetic diversity indicative of a small founding population, we observed a limited number of co-introduced parasite species, including the myxozoan Myxobolus dechtiari, the monogenean Onchocleidus dispar, and the digenean Posthodiplostomum centrarchi. Parasite infection by local parasites acquired in Türkiye was rare. Parasite diversity, species richness, and equitability were low, with only nine parasite taxa identified in all four pumpkinseed populations. The most diverse parasite community was found in Değirmenköy Reservoir, located in the European part of Türkiye, where seven parasite taxa were identified. While our study did not uncover genetically distinct pumpkinseed populations in Türkiye, the fish demonstrated resilience against most local parasite species, potentially providing them with an advantage over native species, aligning with the enemy-release hypothesis. [ABSTRACT FROM AUTHOR]

The present research aimed to characterize the genetic diversity and relationships among extant Arabian horse sire lines in Bulgaria, using 15 equine microsatellite markers. The evaluation included 537 Arabian horses representing nine sire lines (SAKLAWI I, LATIF, SEANDERICH, IBRAHIM, SHABAB, DJEBEL MOUSA, KUHAILAN AFAS, BAIRACTAR, and SARHAN). The obtained results indicated that within these lines, the mean number of alleles ranged from 4.15 in SARHAN to 5.54 in SAKLAWI I and LATIF. The mean expected heterozygosity (He) ranged from 0.54 in the SEANDERICH line to 0.67 in SAKLAWI I. The inbreeding coefficient for the entire Arabian populations was rather low: FIS = −0.109, fluctuating from −0.204 in SHABAB to −0.041 in SAKLAWI I. The mean genetic differentiation, FST, was 0.096, demonstrating that nearly 90% of the total genetic variation was due to genetic differentiation within each population. STRUCTURE analysis indicated a genetic similarity between SHABAB and LATIF, between IBRAHIM and KUHAILAN AFAS, as well as between SAKLAWI I, SEANDERICH, and BAIRACTAR. This study of the genetic diversity of Arabian sire lines in Bulgaria can assist in developing a national strategy for the exclusion of non-purebred animals from breeding programs in order to preserve the genetic profile of the original Arabian lines. [ABSTRACT FROM AUTHOR]

Microsatellite markers (MS) have been widely used for parentage verification in most of the livestock species over the past decades mainly due to their high polymorphic information content. In the genomic era, the spread of genotype information as single‐nucleotide polymorphism (SNP) has raised the question to effectively use SNPs also for parentage testing. Despite the clear advantages of SNP panels in terms of cost, accuracy, and automation, the transition from MS to SNP markers for parentage verification is still very slow and, so far, only routinely applied in cattle. A major difficulty during this transition period is the need of SNP data for parents and offspring, which in most cases is not yet feasible due to the genotyping cost. To overcome the unavailability of same genotyping platform during the transition period, in this study we aimed to assess the feasibility of a MS imputation pipeline from SNPs in four native sheep dairy breeds: Comisana (N = 331), Massese (N = 210), Delle Langhe (N = 59) and Sarda (N = 1003). Those sheep were genotyped for 11 MS and with the Ovine SNP50 Bead Chip. Prior to imputation, a quality control (QC) was performed, and SNPs located within a window of 2 Mb from each MS were selected. The core of the developed pipeline was made up of three steps: (a) storing of both MS and SNP data in a Variant Call Format file, (b) masking MS information in a random sample of individuals (10%), (c) imputing masked MS based on non‐missing individuals (90%) using an imputation program. The feasability of the proposed methodology was assessed also among different training − testing split ratio, population size, number of flanking SNPs as well as within and among breeds. The accuracy of the MS imputation was assessed based on the genotype concordance as well as at parentage verification level in a subset of animals in which assigned parents' MS were available. A total of 8 MS passed the QC, and 505 SNPs were located within the ±2 Mb window from each MS, with an average of 63 SNPs per MS. The results were encouraging since when excluding the worst imputed MS (OARAE129), and regardless on the analyses performed (within and across breeds) for all breeds, we achieved an overall concordance rate over 94%. In addition, on average, the imputed offspring MS resulted in equivalent parentage outcome in 94% of the cases when compared to verification using original MS, highlighting both the feasibility and the eventual practical advantage of using this imputation pipeline. [ABSTRACT FROM AUTHOR]

Trees and shrubs belonging to the genus Juniperus L. are pivotal species in arid and semiarid ecosystems in the Northern Hemisphere. However, unfavourable phenomena are observed in their populations due to global warming. We aimed to investigate the soil requirements, genetic diversity and population history of Juniperus sabina L. from Europe, Georgia, and Kyrgyzstan. Genetic resources were evaluated in 16 populations using nuclear microsatellites, while past demographic events were described based on the chloroplast DNA haplotypes. Seven chemical parameters in 36 soil samples from the European range of J. sabina were compared. In the studied area, three distinct phylogenetic lineages corresponding to different varieties of J. sabina, namely var. sabina, var. balkanensis, and the Asian variety, were revealed. Unimodal mismatch distributions and significantly negative Tajima's D and Fu's Fs parameters indicated that the sabina and balkanensis varieties underwent a population expansion. Microsatellite variation was moderate, potentially influenced by inbreeding, clonal propagation, and limited gene flow between populations. Bayesian clustering revealed five genetic groups. Compared to var. sabina, the balkanensis variety occupies areas with significantly higher potassium content in the soil, which probably mitigates the adverse effects of drought in its localities. [ABSTRACT FROM AUTHOR]

Introduction: Quaternary glaciations, in particular the last glacial maximum (LGM), have shaped the contemporary distribution of many species. In Europe, survival of temperate species during range contractions was mainly associated with refugia in Mediterranean peninsulas, allowing south to north recolonization. Additionally, the Ponto-Caspian refugium provided an east to west migration route. Methods: Here, we investigated genetic diversity and structure of the dispersal-restricted Primula vulgaris Huds., a temperate herb of supposed Caucasian origin, using 12 highly polymorphic nuclear microsatellite loci to trace the colonization of this species in three European regions. We studied 38 populations, namely an eastern mountainous region (Caucasus), a central region (Carpathian Mountains and Dinaric Alps) and a western lowland region (North European Plain). The role of an eastern refugium of the species was tested by performing Approximate Bayesian computation analyses to elucidate its demographic and phylogeographic history, detecting bottleneck and expansion events, and estimating effective (ancestral and current) population sizes and time of divergence. Results and discussion: We found the eastern and central regions featuring the highest allelic richness and genetic differentiation being strong between and within regions. Stepwise-like mutation processes (RST > FST), together with isolation-by-distance patterns, contributed to genetic differentiation. Demographic event models showed that P. vulgaris experienced bottlenecks as well as expansions across its range during the Quaternary glacial cycles, with the last expansion about 6,000, 4,000, and 2,000 generations ago for eastern, central, and western populations, respectively. The best supported origin model pointed to the Caucasus population being closest to an ancestral situation, and from where central and western populations diverged subsequently. Divergence time of the Caucasus populations from an ancestral lineage referred to the Upper Pleistocene (Middle Weichselian). Divergence of Carpathian populations, including a Lower Danube valley corridor, was estimated during and across the LGM (Late Weichselian), confirming central populations as potential secondary cryptic refugium. Western populations recently diverged during the Holocene, most probably in the Atlanticum phase (7,000-3,900 years ago). Within regions, genetic structure was also shaped by latitude, longitude, or altitudinal migration, and for western lowlands, by recent bottleneck and genetic drift processes. [ABSTRACT FROM AUTHOR]

The black‐footed cat (Felis nigripes) is endemic to the arid regions of southern Africa. One of the world's smallest wild felids, the species occurs at low densities and is secretive and elusive, which makes ecological studies difficult. Genetic data could provide key information such as estimates on population size, sex ratios, and genetic diversity. In this study, we test if microsatellite loci can be successfully amplified from scat samples that could be noninvasively collected from the field. Using 21 blood and scat samples collected from the same individuals, we statistically tested whether nine microsatellites previously designed for use in domestic cats can be used to identify individual black‐footed cats. Genotypes recovered from blood and scat samples were compared to assess loss of heterozygosity, allele dropout, and false alleles resulting from DNA degradation or PCR inhibitors present in scat samples. The microsatellite markers were also used to identify individuals from scats collected in the field that were not linked to any blood samples. All nine microsatellites used in this study were amplified successfully and were polymorphic. Microsatellite loci were found to have sufficient discriminatory power to distinguish individuals and identify clones. In conclusion, these molecular markers can be used to monitor populations of wild black‐footed cats noninvasively. The genetic data will be able to contribute important information that may be used to guide future conservation initiatives. [ABSTRACT FROM AUTHOR]

Understanding the forces that shape population genetic structure is fundamental both for understanding evolutionary trajectories and for conservation. Many factors can influence the geographic distribution of genetic variation, and the extent to which local populations differ can be especially difficult to predict in highly mobile organisms. For example, many species of seabirds are essentially panmictic, but some show strong structure. Pigeon Guillemots (Cepphus columba; Charadriiformes: Alcidae) breed in small colonies scattered along the North Pacific coastline and feed in shallow nearshore waters year‐round. Given their distribution, gene flow is potentially lower and population genetic structure is stronger than in most other high‐latitude Northern Hemisphere seabirds. We screened variation in the mitochondrial control region, four microsatellite loci, and two nuclear introns in 202 Pigeon Guillemots representing three of five subspecies. Mitochondrial sequences and nuclear loci both showed significant population differences, although structure was weaker for the nuclear loci. Genetic differentiation was correlated with geographic distance between sampling locations for both the mitochondrial and nuclear loci. Mitochondrial gene trees and demographic modeling both provided strong evidence for two refugial populations during the Pleistocene glaciations: one in the Aleutian Islands and one farther east and south. We conclude that historical fragmentation combined with a stepping‐stone model of gene flow led to the relatively strong population differentiation in Pigeon Guillemots compared to other high‐latitude Northern Hemisphere seabird species. Our study adds to growing evidence that Pleistocene glaciation events affected population genetic structure not only in terrestrial species but also in coastal marine animals. [ABSTRACT FROM AUTHOR]

Hybridization in antelope species has been widely reported in South African national parks and provincial reserves as well as on private land due to anthropogenic effects. In a closed management setting, hybridization may occur due to the crossbreeding of closely related species with unequal sex ratios, resulting in either sterile or fertile offspring. In this study, we used molecular techniques to evaluate the risk of anthropogenic hybridization between blesbok (Damaliscus pygargus phillipsi) and red hartebeest (Alcelaphus buselaphus caama) in an isolated group that purposely included the two species with unequal sex ratios (one red hartebeest male and 19 male and female blesbok). Genetic analysis based on microsatellites confirmed the presence of seven hybrid individuals. Mitochondrial analysis verified that hybridization occurred between blesbok females and the red hartebeest male. STRUCTURE and NEWHYBRIDS classified the hybrids as F1. It is suspected that the hybrid individuals were sterile as the males had undeveloped testes and only F1 hybrids were detected. Thus, the risk of hybridization between these two species may be limited in the wild. In captive settings, genetic monitoring should be included in management plans for blesbok and red hartebeest to ensure that the long‐term consequences of wasted reproductive effort are limited. [ABSTRACT FROM AUTHOR]

Most of Switzerland is inhabited by the nominotypical subspecies of the barred grass snake (Natrix helvetica helvetica), which is characterized by mitochondrial DNA lineage E. Only in the northeast of the country, the common grass snake (N. natrix) occurs and hybridizes with N. h. helvetica in a narrow contact zone. However, we discovered that in southern and western Switzerland barred grass snakes representing another mtDNA lineage (lineage C) are widely distributed. Lineage C is typical for Alpine populations of the southern subspecies N. h. sicula. Our microsatellite analyses of the Swiss samples revealed differences between the two subspecies and also a substructure with two clusters in each subspecies. Furthermore, we discovered a contact and hybrid zone of N. h. helvetica and N. h. sicula along the northern shore of Lake Geneva and also confirm that interbreeding with alien common grass snakes (N. n. moreotica, mtDNA lineage 7) occurs there. This finding is of concern for nature conservation and measures should be taken to prevent further genetic pollution. Using morphometrics, we found no differences between the two subspecies of N. helvetica, while N. natrix was slightly distinct from N. helvetica. [ABSTRACT FROM AUTHOR]

Chromosomal patterns are valuable tools in evolutionary approaches. Despite the remarkable expansion of fish cytogenetic data, they are still highly deficient concerning deep oceanic species, including the Gempylidae snake mackerels. The snake mackerels are important commercial species composed by meso- and bento-pelagic predators with very limited information available about their lifestyle and genetics patterns. This study presents the first chromosomal data of two circumglobal species of this family, Ruvettus pretiosus and Promethichthys prometheus, from the São Pedro and São Paulo Archipelago. Conventional analyses, chromosomal staining with base-specific fluorochromes, and fluorescence in situ hybridization (FISH) for mapping of repetitive DNA classes were used. Both species have 2n = 48 chromosomes, but they highly differ regarding the karyotype formula (FN = 50 and FN = 84). The 18S rDNA/Ag-NOR and the 5S rDNA sites have a syntenic bi-telomeric array in R. pretiosus, but an independent distribution in P. prometheus. The transposable elements are dispersed, while the microsatellites are also clustered in the centromeric and terminal regions of some chromosomes. It is noteworthy that despite the 2n conservation, a marked macro and microstructural diversifications, mainly mediated by pericentric inversions, differentiates the karyotypes of the species, pointing to a particular chromosomal trajectory of the gempylids among marine fish. [ABSTRACT FROM AUTHOR]

In order to ensure the long-term sustainability of the conservation process of Norwegian plum germplasm, as well as to enhance the possibility of its utilization, a central plum heritage cultivar collection was established in 2020. In this study, 40 plum accessions maintained at the Ullensvang plum heritage cultivar collection were genetically characterized using a set of nine microsatellite markers recently approved by the ECPGR Prunus working group. The obtained molecular data were used to investigate the genetic identity, diversity, and structure among the analyzed accessions. No redundancies were detected among the plum accessions, which is in stark contrast to the previous molecular study on plum samples collected through an on-farm inventory of Southern Norway. Furthermore, the obtained data indicate that the Ullensvang collection contains a significant genetic diversity of Norwegian plum germplasm, previously held in decentralized sites. With that in mind, this collection can certainly be considered for the role of the National Clonal Plum Germplasm Repository. The nine microsatellite markers, recommended by ECPGR, revealed a genetic structure not entirely tied to previously proposed pomological groups, possibly indicating a history of hybridization among members of the various groups. [ABSTRACT FROM AUTHOR]

Elucidating the effects of domesticated organisms escaping into the natural environment represents a topic of importance in both evolutionary and conservation biology. However, when excluding the abundant data on salmonids, there is a lack of knowledge on this topic for marine fish aquaculture, which continues to expand globally. In order to bridge this empirical gap, we investigated a suspected escape of sexually mature domesticated Atlantic cod from a commercial marine fish farm in northern Norway. This involved genotyping samples of fish from cages on the farm, putatively identified escapees and wild cod captured in the region and samples of recently spawned eggs collected in the sea. Genetic analyses confirmed a farmed ancestry of the suspected escapees, and significantly, 27% of the sampled cod eggs. Furthermore, statistical analyses revealed a strong reduction in genetic variation in all samples of the farmed cod, including low effective population size and high degree of siblingship. These results thus document the escape of sexually mature adult cod and the release of fertilized domesticated cod eggs into the natural environment. Although it is possible that some of the mature escapees spawned post‐escape, the fact that only a single egg of potential hybrid farmed × wild origin was identified, together with the high number of mature cod in the farm, points to within cage spawning as the primary source of these eggs. This suggestion is supported by oceanic particle‐drift modelling, verifying that transport of eggs between the farm and the egg sampling locations was plausible. This study represents a rare documentation of interaction between domesticated and wild populations for a marine fish, pointing towards potential impacts on the local wild population. [ABSTRACT FROM AUTHOR]

To understand the success of invasive alien species, it is necessary to evaluate the site-specific eco-evolutionary challenges they face in their new environments. We explored whether the rearrangement of genetic diversity is linked to the invasiveness of Prosopis juliflora by (i) comparing different stages of invasion (founding vs invasive populations) in two invaded areas (Afar Region, Ethiopia and Baringo County, Kenya) to evaluate whether different stages are dominated by different genetic attributes (e.g., characteristic genotypes or levels of genetic diversity) and by (ii) evaluating if landscape features affected dispersal between invasive populations in the two invaded areas. We hypothesised that different invasion stages would have unique genetic characteristics due to either site-specific demographic and/or dispersal dynamics. We also compared the genetic characteristics at an 'invasive–non-invasive congener' level by studying the non-invasive P. pallida, introduced to Baringo County, and assessed whether it hybridises with P. juliflora. In the Afar Region, the establishment and spread of P. juliflora were characterised by extensive gene flow that homogenised genetic diversity across all populations. In contrast, in Baringo County, invasive populations had lower genetic diversity than founders, and genetic differentiation was lower between invasive populations than between invasive and founder populations. In both invaded areas, we found no evidence that dispersal was hampered by geographic distance, bioclimatic conditions, or distance to roads, rivers and villages, at least at the spatial scales of our study; indicating frequent long-distance dispersal. Allelic richness was higher in P. juliflora than P. pallida founders and hybrids were mainly planted trees probably resulting from the sympatric cultivation of the two species following their introduction. Thus, management actions on Prosopis invasion in eastern Africa should consider site-specific dynamics occurring during the invasion. [ABSTRACT FROM AUTHOR]

The Pallas's cat (Otocolobus manul) is one of the most understudied taxa in the Felidae family. The species is currently assessed as being of "Least Concern" in the IUCN Red List, but this assessment is based on incomplete data. Additional ecological and genetic information is necessary for the long-term in situ and ex situ conservation of this species. We identified 29 microsatellite loci with sufficient diversity to enable studies into the individual identification, population structure, and phylogeography of Pallas's cats. These microsatellites were genotyped on six wild Pallas's cats from the Tibet Autonomous Region and Mongolia and ten cats from a United States zoo-managed population that originated in Russia and Mongolia. Additionally, we examined diversity in a 91 bp segment of the mitochondrial 12S ribosomal RNA (MT-RNR1) locus and a hypoxia-related gene, endothelial PAS domain protein 1 (EPAS1). Based on the microsatellite and MT-RNR1 loci, we established that the Pallas's cat displays moderate genetic diversity. Intriguingly, we found that the Pallas's cats had one unique nonsynonymous substitution in EPAS1 not present in snow leopards (Panthera uncia) or domestic cats (Felis catus). The analysis of the zoo-managed population indicated reduced genetic diversity compared to wild individuals. The genetic information from this study is a valuable resource for future research into and the conservation of the Pallas's cat. [ABSTRACT FROM AUTHOR]

Effective management of migrating fish stocks requires an understanding of population structure and each stock's contribution to the fishery. Water bodies spanning across national borders pose a particular challenge. We investigated the genetic structure of 13 adfluvial brown trout populations from natal rivers and conducted a genetic mixed‐stock analysis of brown trout from the cross‐border Lake Pyaozero Basin in eastern Fennoscandia, using 16 microsatellite loci. Our analysis revealed a clear genetic structure of three distinct geographic groups, consisting of river‐specific populations. The Western and Southern groups, which included 11 rivers, contributed over 90% to the mixed stock in the lacustrine rearing area. This mixed stock of several river‐specific subpopulations renders poorly managed fishing in the area a significant threat to the entire native adfluvial brown trout population complex. [ABSTRACT FROM AUTHOR]

Leaf samples of 226 cultivated olive trees were collected from traditionally managed olive orchards and genotyped with eleven consensual SSR markers. The proportion of shared allele distance was used for the estimation of distances between olive genotypes. Cluster analyses were performed using a Fitch–Margoliash least-squares algorithm. The number of different genetic subgroups of olive genotypes (K) was investigated using STRUCTURE analysis. The standardization of allele lengths was performed to enable the comparison SSR profiles of Croatian olive genotypes with olive profiles obtained with the same SSR primers in OleaDB and WOGB databases. Overall, 73 SSR profiles of known Croatian varieties and 53 profiles of unknown olive genotypes were differentiated. Synonyms were detected in 18 varieties, and we found intra-varietal differences in 15 varieties. Three genetic subgroups of olive genotypes were determined. Following allele length standardization achieved using nine referral samples, the genetic profiles of 126 cultivated olive genotypes were compared to OleaDB and WOGB databases, out of which 92 genotypes were found to be unique to Croatian olive germplasm. The results revealed the wide genetic diversity of olive germplasm beyond the known, registered varieties. The FAZ_oliveDB database containing the profiles of 126 Croatian olive genotypes was created and made available for public use. [ABSTRACT FROM AUTHOR]

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Genetic diversity is essential to evolution and a recognized target of conservation. When threats are high and populations are small, in-situ gene conservation needs to be reinforced with an ex-situ approach, where a genetically representative sample of the target taxon is safeguarded in a favorable environment. The fragmented habitat of Pinus nigra subsp. salzmannii (Dunal) Franco 1943 (Salzmann's pine) is threatened by wildfires. In France, gene flow from massive plantations of other subspecies of black pines threatens its genetic diversity. Here, using individual tree genotypic data at thirteen microsatellite loci, we identified differentiated lineages for in-situ gene conservation. Discriminating between autochthonous and hybrid trees, we proposed a method for the creation of an ex-situ core collection. We confirmed that Salzmann's pine is an original genetic lineage within the western European and Mediterranean black pine subspecies. We identified five genetic groups in France that can serve as the basis for in-situ gene conservation. Maximizing overall genetic diversity while maintaining among population diversity, we identified 80 native and non-hybridized trees that can form the basis of a representative ex-situ core collection. Our cost-effective methods combining in-situ and ex-situ conservation can be easily applied to many forest tree species. [ABSTRACT FROM AUTHOR]

The southeastern United States is a hotspot of biodiversity, but aquatic habitats are fragmented by anthropogenic activities such as hydrologic alteration. Small-stream-inhabiting fish can suffer population declines, loss of genetic diversity, and migration impediment from riverine impoundment. The Trispot Darter (Etheostoma trisella) is a small, freshwater fish endemic to the southeastern United States. E. trisella was previously believed to be extinct and has now been listed as threatened under the U.S. Endangered Species Act, due to destruction of its limited habitat and a restricted range. We used mitochondrial DNA (NADH dehydrogenase subunit 2 gene), seven microsatellite loci, and 9732 single nucleotide polymorphisms (SNPs) to evaluate population structure and diversity in E. trisella. Mitochondrial data provided evidence of historical connectivity between populations, with haplotype sharing across populations and weak support for population structure. Microsatellite and SNP data, however, indicate that populations have more recently become isolated. Furthermore, we detect three distinct management units (i.e., genetic groups) which reflect isolated geographic localities (i.e., Little Canoe Creek, Ballplay Creek, and a system including the Conasauga and Coosawattee rivers). We also detected a recent bottleneck event in the Ballplay Creek population as well as a low effective population size. Tests of isolation by distance further suggest that populations are structured by riverine isolation rather than geographic distance. A better understanding about the distribution, abundance, and habitat occupancy of all E. trisella populations will be important for informing future decisions for conservation of the species. [ABSTRACT FROM AUTHOR]

Risk factors that make rare plant taxa particularly susceptible to population declines include a self-incompatible breeding system combined with small population size, small range, and isolated populations separated by unsuitable habitat. Phlox pilosa ssp. sangamonensis is an endangered, self-incompatible, and narrowly endemic taxon with isolated population fragments in east-central Illinois. Here we combined a field and genetic study of Phlox pilosa ssp. sangamonensis as a study of its taxonomic status and conservation, especially because some of its remaining populations are small (< 30 flowering individuals). First, we used six polymorphic nuclear microsatellite loci developed for P. pilosa ssp. pilosa to characterize the genetics of 212 individuals in all 10 known populations of P. pilosa ssp. sangamonensis. We tested the taxon's genetic differentiation from congeners in east-central Illinois: two populations of Phlox pilosa ssp. fulgida, two populations of Phlox pilosa ssp. pilosa, and three populations of Phlox divaricata ssp. laphamii. We also quantified reproduction in each population. We surveyed fruit set for three years and tested correlations with flowering population size and distance to other flowering individuals. For one year, we collected data on seed set from successfully formed capsules. Phlox pilosa ssp. sangamonensis was genetically distinct from, and had putatively lower genetic variation, than Phlox divaricata ssp. laphamii, Phlox pilosa ssp. fulgida, and Phlox pilosa ssp. pilosa. Overall genetic diversity in P. pilosa ssp. sangamonensis appeared low, especially in small populations. Fruit set was positively associated with P. pilosa ssp. sangamonensis population size, with larger population (> 100 flowering individuals) fruit set being more than twice as high compared to smaller (< 30 flowering individuals) ones. Across populations, individuals with a greater distance to flowering neighbors also showed reduced fruit set, although the relationship was not as strong as for population size. In the year we studied seed set, we also found a positive association between population size and seed set, with approximately 30% more seeds per capsule being produced in the larger populations relative to small ones. Our data suggest that P. pilosa ssp. sangamonensis is a genetically distinct taxon from nearby Phlox taxa, and its smaller populations could be at risk of further decline, possibly due to mate or pollen limitation, and/or low genetic diversity. Management for this endangered taxon should facilitate recruitment in small (< 100 flowering individuals) populations and maintain habitat quality for the large populations. [ABSTRACT FROM AUTHOR]

Indian Mahogany (Toona ciliata, Family: Meliaceae) is a fast-growing and multi-purpose timber species. The species is well adapted to sub-tropical climates and generally grows in moisture-prone areas. It is frequently naturalized throughout the western sub-Himalayan tract, valleys of the outer Himalayas, and Eastern and Western Ghats and also cultivated on a fairly large scale in the plains of India, but no information about SSR-based genetic diversity and population structuring of T. ciliata in the Indian context has been available till now. Notably, population genetic analysis of T. ciliata is important for its long-term conservation, management, and genetic improvement programs. Thus, the present study was conducted to characterize natural populations of T. ciliata using simple sequence repeat (SSR) markers. In total, 444 individuals collected from 15 distant geographical locations in the western Himalayas were analyzed with 10 SSR loci. A total of 71 alleles were generated, with a mean of seven alleles, which ranged from 4 to 12 alleles for individual marker loci. Overall, a low level of genetic diversity (mean He = 0.315, range = 0.251–0.366) and high genetic differentiation (FST = 0.338) were recorded for the analyzed populations. Genetic clustering and STRUCTURE analysis revealed a strong genetic structure where most analyzed populations were grouped into two major clusters, indicating the existence of two gene pools. Further, the partitioning of genetic variance was significant (p ≤ 0.001) which revealed 34% of genetic variance among the populations. The Mantel test was used to estimate the genetic distance in relation to horizontal and altitudinal geographical distance, but a non-significant correlation was obtained. The results indicated that genetic distance between populations is not influenced by horizontal and altitudinal geographical distance. Overall, the study on population genetic analysis of T. ciliata will be of paramount importance to the researchers, foresters, and policymakers for guiding future conservation decisions. [ABSTRACT FROM AUTHOR]

Premise of the study: Coula edulis Baill (Coulaceae) is a common tree species in the Guineo-Congolian forests producing an edible fruit known as African walnut, which is an important food and income resource for rural populations. However, the species suffers from a deficit of natural regeneration. We developed here nuclear microsatellite markers for C. edulis to be able to study the genetic structure of its natural populations and gene flow. Methods and results: A genomic library was obtained using the Illumina platform, and 21 polymorphic microsatellite loci were developed. The polymorphic microsatellites displayed eight to 22 alleles per locus (average: 14.2), with a mean expected heterozygosity ranging from 0.33 to 0.72 in five populations from Central and West Africa. Conclusions: The high polymorphism of the nuclear microsatellite markers developed makes them useful to investigate gene flow and the organization of genetic diversity in C. edulis, and to assess whether particular genetic resources require conservation efforts. [ABSTRACT FROM AUTHOR]

Background: Tanzania is currently implementing therapeutic efficacy studies (TES) in areas of varying malaria transmission intensities as per the World Health Organization (WHO) recommendations. In TES, distinguishing reinfection from recrudescence is critical for the determination of anti-malarial efficacy. Recently, the WHO recommended genotyping polymorphic coding genes, merozoite surface proteins 1 and 2 (msp1 and msp2), and replacing the glutamate-rich protein (glurp) gene with one of the highly polymorphic microsatellites in Plasmodium falciparum to adjust the efficacy of antimalarials in TES. This study assessed the polymorphisms of six neutral microsatellite markers and their potential use in TES, which is routinely performed in Tanzania. Methods: Plasmodium falciparum samples were obtained from four TES sentinel sites, Kibaha (Pwani), Mkuzi (Tanga), Mlimba (Morogoro) and Ujiji (Kigoma), between April and September 2016. Parasite genomic DNA was extracted from dried blood spots on filter papers using commercial kits. Genotyping was done using six microsatellites (Poly-α, PfPK2, TA1, C3M69, C2M34 and M2490) by capillary method, and the data were analysed to determine the extent of their polymorphisms and genetic diversity at the four sites. Results: Overall, 83 (88.3%) of the 94 samples were successfully genotyped (with positive results for ≥ 50.0% of the markers), and > 50.0% of the samples (range = 47.6–59.1%) were polyclonal, with a mean multiplicity of infection (MOI) ranging from 1.68 to 1.88 among the four sites. There was high genetic diversity but limited variability among the four sites based on mean allelic richness (RS = 7.48, range = 7.27–8.03, for an adjusted minimum sample size of 18 per site) and mean expected heterozygosity (He = 0.83, range = 0.80–0.85). Cluster analysis of haplotypes using STRUCTURE, principal component analysis, and pairwise genetic differentiation (FST) did not reveal population structure or clustering of parasites according to geographic origin. Of the six markers, Poly-α was the most polymorphic, followed by C2M34, TA1 and C3M69, while M2490 was the least polymorphic. Conclusion: Microsatellite genotyping revealed high polyclonality and genetic diversity but no significant population structure. Poly-α, C2M34, TA1 and C3M69 were the most polymorphic markers, and Poly-α alone or with any of the other three markers could be adopted for use in TES in Tanzania. [ABSTRACT FROM AUTHOR]

Background: Schistosomiasis is a water-based parasitic disease that affects humans, livestock and wild animals. While considerable resources are dedicated to the surveillance, disease mapping, control and elimination of human schistosomiasis, this is not the case for livestock schistosomiasis. Indeed, there are important data and knowledge gaps concerning the species present, population genetic diversity, infection prevalence, morbidity and economic impact. This study aimed to identify circulating schistosome species in cattle across Côte d'Ivoire and to investigate their population diversity and structuring. Methods: Overall, 400 adult schistosomes were collected from slaughtered cattle at six sites across Côte d'Ivoire. Additionally, 114 miracidia were collected from live cattle at one site: Ferkessédougou, in the northern part of Côte d'Ivoire. DNA from all specimens was extracted and the cox1 and ITS1/2 regions amplified and analysed to confirm species. The genetic diversity and structuring of the schistosome populations were investigated using 12 microsatellite markers. Results: All adult schistosomes and miracidia presented Schistosoma bovis mitochondrial cox1 profile. Nuclear ITS1/2 data were obtained from 101 adult schistosomes and four miracidia, all of which presented an S. bovis profile. Genetic diversity indices revealed a deficiency of heterozygotes and signals of inbreeding across all sites, while structure analyses displayed little geographic structuring and differentiation. Cattle in Côte d'Ivoire thus appear to be mono-species infected with S. bovis. Hybrids of Schistosoma haematobium × S. bovis have not been identified in this study. Cattle schistosomes appear to be panmictic across the country. Conclusions: Our results contribute to a deeper understanding of schistosome populations in Ivorian cattle and emphasize a One Health approach of joint human and animal surveillance and prevention and control programmes for schistosomiasis. [ABSTRACT FROM AUTHOR]

Anthropogenic pressures on nature have been causing population declines for centuries. Intensified persecution of apex predators, like the golden eagle, resulted in population bottlenecks during the 19th and 20th centuries. To study population genetics and demographic history of the golden eagle throughout its distribution, we collected museum samples from previously underrepresented regions, such as Russia and Central Asia. We used 12 microsatellite loci and a fragment of the mitochondrial DNA control region to re‐evaluate phylogeography of Eurasian golden eagles and study the impacts of the population bottleneck. Our results revealed a north–south genetic gradient, expressed by the difference between Mediterranean and Holarctic lineages, as well as genetically distinct Northern Europe and Central Asia and Caucasus regions. Furthermore, Northern Europe exhibited the lowest, whereas Central Asia and Caucasus had the highest genetic diversity. Although golden eagles maintained relatively high genetic diversity, we detected genetic signatures of the recent bottleneck, including reduced genetic diversity and a decline in the effective female population size around the year 1975. Our study improves the knowledge of the genetic composition of Eurasian golden eagles and highlights the importance of understanding their historical population dynamics in the face of ongoing and future conservation efforts. [ABSTRACT FROM AUTHOR]

Previous studies of Loggerhead Shrikes (Laniidae: Lanius ludovicianus) in North America have indicated considerable intraspecific genetic and phenotypic differentiation, but the congruence between genetic and phenotypic differentiation remains obscure. We examined phenotypic differences in beak shape and bite force among geographic groupings across a 950 km range, from the lower Imperial Valley to the upper Central Valley of California, USA. We integrated these analyses with a population genetic analysis of six microsatellite markers to test for correspondence between phenotypic and genetic differences among geographic groups. We found significant phenotypic differentiation despite a lack of significant genetic differentiation among groups. Pairwise beak shape and bite force distances nevertheless were correlated with genetic (FST) distances among geographic groups. Furthermore, the phenotypic and genetic distance matrices were correlated with pairwise geographic distances. Takentogether, these results suggest that phenotypic differences might be influenced by neutral processes, inbreeding (as indicated by high heterozygosity deficiencies we observed), local adaptation, and/or phenotypic plasticity. [ABSTRACT FROM AUTHOR]

During the last 40 years, the volumes of African pangolins feeding the illegal wildlife trade have dramatically increased. We conducted a conservation genetics survey of the most traded African species, the white bellied pangolin (WBP; Phataginus tricuspis), across three West African countries including Guinea, Côte d'Ivoire, and Ghana. Our study combining mitochondrial DNA sequencing and microsatellite genotyping is the first to reveal a wide pattern of admixture between two of the six mitochondrial lineages as previously delimited within WBP. We found a signature of isolation by distance but a lack of population genetic structuring, supporting the idea that WBP may have underestimated dispersal abilities. Levels of genetic diversity were low in West African lineages (WAfr and Gha) compared to Central Africa, reinforcing the picture of genetic pauperization shared by West African WBP. We observed a 85%–98% decline in the effective population size of WBP occurring c. 3200 to 400 ya, with current numbers (520–590) at the lower end of the conservative thresholds for minimum viable population size. The microsatellite markers were powerful enough to differentiate between individuals and identify replicated samples, confirming the utility of this approach in tracing the pangolin trade. Genetic diversity estimates confirmed that Yopougon, the main bushmeat market from Abidjan (Côte d'Ivoire), was fed by a large trade network as confirmed by vendors reporting 10 different sources situated 62–459 km away from the market. We conclude that WBP distributed in the Upper Guinean Block should be considered a single management unit of high conservation concern, as impacted by genetic diversity erosion, drastic decline in effective population size, and wide range sourcing for feeding urban bushmeat markets. Given the genetic admixture pattern detected within WBP from West Africa, we advocate for a multi‐locus strategy to trace the international trade of the species. [ABSTRACT FROM AUTHOR]

Bontebok (Damaliscus pygargus pygargus) and blesbok (D. p. phillipsi) are classified as separate sub‐species. The blesbok has a widespread distribution throughout South Africa and is listed as least concern by the International Union for Conservation of Nature (IUCN) Red List of Threatened Species. Bontebok on the other hand is endemic within the Cape Floristic Region of the Western Cape in South Africa and has been listed as near‐threatened species on the IUCN Red List of Threatened Species. Bontebok populations experienced a severe bottleneck and were brought back from the brink of extinction in the 1830s. Currently, the subspecies is threatened by hybridisation with blesbok resulting in fertile offspring. To date, molecular investigations using neutral markers have determined that genetic diversity in pure South African bontebok was significantly lower than in pure blesbok. Here, we investigated genetic diversity in bontebok, blesbok and hybrid individuals using microsatellites and an adaptive marker (toll‐like receptor two (TLR2)). The study of single nucleotide polymorphisms (SNPs) revealed five mutations in TLR2 in different individuals and subspecies of D. pygargus. This included three non‐synonymous and two synonymous mutations. The three amino acid substitution mutations were predicted to have no effect on protein function. Two of the five mutations, one of which resulted in an amino acid substitution, were not present in bontebok. The other three mutations were present to varying frequencies in the three groups. We confirm low adaptive and neutral diversity in bontebok. These mutations provide insights into the genetic diversity and relationships among the two sub‐species of D. pygargus and may have implications for their conservation and management. [ABSTRACT FROM AUTHOR]

Assessing the genetic diversity and gene flow among populations in combination with ecological data provides valuable insight into the spatial use and genetic structure of wildlife. Anthropic impact generates landscape changes that threaten species by favouring their isolation in small patches and limiting their connectivity. However, in some cases, it can increase genetic exchange among wild populations. Here, we used a set of 16 microsatellites to study the genetic diversity, population genetic structure, and historical and current gene flow of coypu (Myocastor coypus) populations, a semi-aquatic rodent that inhabits watercourses of the highly anthropized agroecosystems of the Pampas region. Our results showed moderate to high levels of genetic diversity and revealed the existence of genetic structure among populations. Bayesian analysis showed different patterns of genetic structure among and within sampling sites. Also, the patterns of historical gene flow differed from that seen today. These results, together with previous studies, suggest that anthropic pressure, habitat fragmentation and ephemeral landscapes in a highly modified ecosystem could alter the dispersal patterns of coypus in their native range, which would otherwise be different in an environment with low anthropic impact. The results provide new information that could be used in effective conservation programmes. [ABSTRACT FROM AUTHOR]

Background: Peanut is a widely cultivated food crop of the legume family and is a major source of vegetable oil and protein in the global agricultural economy. However, the productivity of peanuts is severely affected by abiotic stress, particularly drought. Therefore, it is necessary to identify genes related to abiotic stress tolerance and analyze genetic diversity by SSR markers related to drought tolerance in peanut varieties. Methods: PCR amplification was used for the isolation of the DREB2C gene. The DREB2C gene sequence was analyzed using bioinformatic tools to identify functional domains, 3D modeling structures and other important characteristics. RT-qPCR was performed to evaluate the expression level of the DREB2C gene in the different tissues of peanut cultivars. A phylogenetic tree was constructed based on SSR markers linked to drought tolerance to assess the genetic diversity among peanut cultivars. Result: The present study identified the DREB2C gene in peanut cultivar L14. The gene encodes a polypeptide chain of 492 amino acids lacking transmembrane domains and signal peptides and with a conserved domain (AP2/ERF) and DNA binding site. The 3D protein structure was predicted with high confidence using various tools. The gene expression was investigated in different tissues and at different growth and developmental stages, as well as in various cultivars. Based on SSR markers linked to drought tolerance, the study revealed that peanut cultivars in Vietnam exhibit a medium level of diversity. It may be suggested that crossbreeding between different groups may increase variability among crops, allowing the generation of dominant varieties with improved drought tolerance. [ABSTRACT FROM AUTHOR]

With aim to improve characterization and eventually, utilisation of garlic collection from the Institute of Field and Vegetable Crops in Serbia, the genetic diversity of 52 accessions was estimated based on microsatellite markers, agronomic, biochemical and phenotypic traits (UPOV descriptor). The Shannon index H′ with a value of 0.47–0.95 indicated a high level of diversity for the greatest number of examined traits according to the UPOV descriptor. Based on agronomic and biochemical traits, groups of genotypes with the highest potential for yield and bioactive properties improvement were singled out. Molecular evaluation indicated the presence of duplicates in the collection and necessity of further research with additional number of DNA markers. The obtained results are important from the aspects of breeding and development of new varieties with improved yield and functional value as well as more economical conservation of genetic resources. Since diversity of plant genetic resources constantly decreases, the obtained results have long-term significance because preserved and genetically variable collections represent a valuable source of desirable genes for future human needs. [ABSTRACT FROM AUTHOR]

Geckos of clade III of the Tarentola mauritanica species complex are widespread throughout southern Europe and northern Africa. We investigated the genetic variability of the Italian populations by performing a widespread sampling throughout the mainland and the two main islands of Sicily and Sardinia. We analysed 199 newly generated sequences of the mitochondrial 16S rRNA gene and 269 nuclear genotypes inferred from nine microsatellite loci from 307 individuals. We found 13 new mitochondrial haplotypes in Italy, whereas previous findings reported a single haplotype widespread throughout the country and in the rest of Europe, which currently make Italy the centre of genetic diversity of this taxon. There was no evidence of mitochondrial DNA structuring with geographic correlation. At the population genetic level, our multilocus approach based on nuclear markers returned a shallow genetic structure. Nonetheless, we disclosed the presence of at least four distinct genetic clusters (namely the Adriatic, two Tyrrhenian and the Calabrian clusters). Our findings do not support the two hypotheses proposed to explain the low level of mitochondrial polymorphism in this taxon, namely the genetic hitch‐hiking due to selective sweep and the historical human‐mediated colonization hypotheses. Based on the fossil record, the presence in Italy of this taxon since the Pleistocene Epoch is plausible. Given the discordance in genetic structure between mitochondrial and nuclear DNA, the exact role of the Italian Peninsula in shaping the observed patterns of genetic diversity during the Pleistocenic climatic oscillations needs further investigation. [ABSTRACT FROM AUTHOR]

Aim: As climate change accelerates, assessing how climate shapes gene flow and neutral and adaptive genetic differentiation on landscapes is increasingly important. Aardvarks (Orycteropus afer) are ecologically important in sub‐Saharan Africa but are sensitive to human pressures and increasing aridity. We used individual, population and landscape genetic approaches to infer the influence of landscape, climate and potential adaptive differences on gene flow. Location: We surveyed 8 protected and 4 privately owned areas in South Africa, 2 protected areas in Eswatini and one location in Kenya during 2016–2018. Methods: We developed microsatellite markers and methods for DNA extraction from faeces, collected and genotyped faecal samples from focal areas and estimated genetic structure. We inferred space use from individual redetections, tested for close relatives and estimated genetic neighbourhood distance. We applied individual‐based landscape genetic analyses at multiple scales to test hypotheses about genetic differentiation by landscape resistance and potential adaptive differences. Results: We developed 19 variable microsatellite loci and collected 253 faecal samples from 13 focal areas. We genotyped 104 samples successfully at ≥8 loci as needed for individual identification. The genetic structure suggested 3 regional divisions in South Africa. We detected individuals at locations ≤7.3 km distant and closely related individuals at ≤44 km; genetic neighbourhood distance was <55 km. Lower precipitation increased landscape resistance and strongly predicted genetic differentiation at most spatial scales. Temperature differences at sampling sites also influenced structure, suggesting climate‐associated adaptive differences. Main Conclusions: The genetic structure of aardvarks is strongly shaped by climate, with arid areas limiting gene flow and reflects apparent isolation by adaptation associated with temperature. Dispersal distances likely are <55 km. The markers we developed will facilitate studies of space use, dispersal, population density or survival. Aridification will increase fragmentation and we recommend monitoring aardvark presence as an indicator of ecosystem change associated with aridification. [ABSTRACT FROM AUTHOR]

The big-scale sand smelt (Atherina boyeri) is an Atlanto-Mediterranean amphidromous fish species found within the Black Sea. Here, we assess differences in the parasite fauna of big-scale sand smelt populations from their natural range in the northwestern Black Sea and from their expansion range in the Lower and Middle River Dnipro. In addition, we undertook a microsatellite analysis to assess the genetic similarity of fish from the different locations. We found that the parasite community of fish in their natural range was wider than that from their expansion range. While the Gulf of Odesa was most distant from all other localities by parasite community composition and the Dnipro Reservoir was characterised by an absence of parasites (newest and most distant expansion locality), only fish from the Danube Delta showed a significant genetic difference. Our results suggest that the parasite community of big-scale sand smelt is primarily influenced by environmental factors, such as habitat type, water salinity and/or prey composition. Both microsatellite analysis and parasite community species composition (e.g. the presence of the marine Telosentis exiguus in the Kakhovka Reservoir and freshwater Raphidascaris sp. in the Gulf of Odesa) confirmed that populations in the River Dnipro reservoirs had, at some time, been connected with native marine populations, thus also confirming the species’ amphidromous nature. [ABSTRACT FROM AUTHOR]

Comparative genotyping of a population of zeboid cattle (Bos taurus × Bos indicus) and eight populations of B. taurus breeds, including six domestic breeds (the Kholmogory, Yaroslavl, Red Gorbatov, Kostroma, Tagil, and Gray Ukrainian) and two transboundary European breeds (Holstein and Brown Swiss), has been conducted using 14 STR markers (BM1824, BM2113, CSRM60, CSSM66, ETH3, ETH10, ETH225, ILSTS006, INRA023, SPS115, TGLA53, TGLA122, TGLA126, and TGLA227). A total of 562 individuals were examined. On the basis of the results of the STR analysis, it was found that all population samples of B. taurus were characterized by an average allelic richness AR = 4.87–6.7 and a fairly high level of genetic variability HE = 0.69–0.76 with a slight predominance of random matings FIS = –0.1–0.0. In zeboid cattle, the corresponding indicators were AR = 5.96, HE = 0.72, and FIS = –0.0278. At the same time, differences in the genetic structure of the B. taurus breeds under consideration were largely determined by population demographic fluctuations, and the genetic and the phenotypic heterogeneity detected in the population of zeboid cattle were determined by a decrease in the effect of artificial selection. [ABSTRACT FROM AUTHOR]

The Black Skimmer (Rynchops niger) is a charismatic representative of coastal-nesting waterbird communities in North America and freshwater riverine and coastal systems in South America. Skimmers are at high risk of decline due to threats including habitat loss, human activity, and climate change throughout the annual cycle. To understand range-wide population connectivity, eight microsatellite loci were used to reveal genetic differentiation between North American Pacific and Atlantic Coasts, including the Gulf of Mexico, and very strong differentiation between the North American sites and a site in Peru, South America. A reduced dataset, incorporating previously published data from South America, documented strong inter-continental differentiation and moderate differentiation among sites within South America in a pattern inconsistent with current subspecies designations, and suggesting a more complex pattern of dispersal. We recommend combined use of telemetry and genomic tools to assist in future delineation of skimmer subspecies ranges and non-breeding habitat use in South America. Because genetic diversity was relatively low in North America and higher in South America, genetics could determine whether skimmers in South America represent the ancestral population now expanding along the Atlantic and Pacific Coasts of North America. Detailed knowledge of seasonal movement and non-breeding habitat use that can be obtained by telemetry and population-wide molecular analyses will be essential to informing effective management across the Americas. [ABSTRACT FROM AUTHOR]

Most male date palms available for pollinating different female cultivars have mainly originated from seed propagation resulting in many different local males that represent a source of genetic diversity. Favourable fruit production is related to the quality of pollen and its compatibility with a certain female variety. Therefore, the genetic characterisation of the male progenitors should be the first step to establish a selection programme to produce superior males through different procedures. In this study, the genetic diversity and population structure of 72 male date palm accessions were investigated using 15 microsatellite loci. The highest mean number of alleles per locus was obtained for Tozeur group. Bayesian model-based clustering analysis indicated the presence of two differentiated endemic male date palm genetic clusters, continental and insular, with the presence of introduced accessions originating from the Middle East. The diversity analysis in the insular region of Tunisia, which had never been performed before, revealed that this germplasm enclosed valuable endemic resources supporting the hypothesis of the presence of wild material. These findings are crucial for identifying interesting genotypes that can be integrated into international coordinated actions of Phoenix dactylifera L. breeding programmes and the protection and conservation of valuable resources. [ABSTRACT FROM AUTHOR]