Intrapopulation Genetic Diversity Research Articles

Genetic Variability of the Laxmann’s Shrew (<i>Sorex caecutiens</i> Laxmann, 1788) of the Kolyma River Basin and Chukotka

Nucleotide sequence polymorphism and haplotypic diversity of the cytochrome b gene were studied in samples of the Laxmann’s Shrew Sorex caecutiens koreni from the populations of the Kolyma River basin and Chukotka. 56 cytb-haplotypes differing among themselves by 87 mutations in 84 sites were found. The cytb-haplotypes of individuals of the subspecies S. c. koreni and S. c. macropygmaeus were shown to belong to the same maternal mtDNA lineage, their monophyletic origin from the same ancestral haplotype Scb1, and the presence of identical cytb-haplotypes in both subspecies. The mutual isolation of the shrew populations in the upper basin of the Kolyma River and Chukotka is shown. The proportion of intrapopulation genetic variability is 95.74%, intergroup variability is 5.74%, and intragroup variability is –1.48%, which reflects a very high level of intrapopulation variability of cytb haplotypes in the studied groups of S. c. koreni, their monophyletic origin, and the genetic unity of the Chukchi samples. The values of molecular diversity indices testify to the stability of populations that have a high value of effective abundance for a long time.

Repeated migration, interbreeding and bottlenecking shaped the phylogeography of the selfing grass Brachypodium stacei.

Brachypodium stacei is the most ancestral lineage in the genus Brachypodium, a model system for grass functional genomics. B. stacei shows striking and sometimes contradictory biological and evolutionary features, including a high selfing rate yet extensive admixture, an ancient Miocene origin yet with recent evolutionary radiation, and adaptation to different dry climate conditions in its narrow distribution range. Therefore, it constitutes an ideal system to study these life history traits. We studied the phylogeography of 17 native circum-Mediterranean B. stacei populations (39 individuals) using genome-wide RADseq SNP data and complete plastome sequences. Nuclear SNP data revealed the existence of six distinct genetic clusters, low levels of intra-population genetic diversity and high selfing rates, albeit with signatures of admixture. Coalescence-based dating analysis detected a recent split between crown lineages in the Late Quaternary. Plastome sequences showed incongruent evolutionary relationships with those recovered by the nuclear data, suggesting interbreeding and chloroplast capture events between genetically distant populations. Demographic and population dispersal coalescent models identified an ancestral origin of B. stacei in the western-central Mediterranean islands, followed by an early colonization of the Canary Islands and two independent colonization events of the eastern Mediterranean region through long-distance dispersal and bottleneck events as the most likely evolutionary history. Climate niche data identified three arid niches of B. stacei in the southern Mediterranean region. Our findings indicate that the phylogeography of B. stacei populations was shaped by recent radiations, frequent extinctions, long-distance dispersal events, occasional interbreeding, and adaptation to local climates.

Genetic Diversity and Phylogeography of the Relict Tree Fern Culcita macrocarpa: Influence of Clonality and Breeding System on Genetic Variation.

The tree fern Culcita macrocarpa, a threatened Iberian-Macaronesian endemism, represents the sole European species of the order Cyatheales. Considered a Tertiary relict of European Palaeotropical flora, its evolutionary history and genetic diversity, potentially influenced by presumed high clonal propagation, remain largely unknown. This study elucidates the phylogeographic history of C. macrocarpa, assessing the impact of vegetative reproduction on population dynamics and genetic variability. We provide genetic data from eight newly identified nuclear microsatellite loci and one plastid DNA region for 17 populations spanning the species' range, together with species distribution modeling data. Microsatellites reveal pervasive clonality in C. macrocarpa, which has varied among populations. We assess the impact of clonality on genetic diversity and evaluate how estimates of intra-population genetic diversity indices and genetic structuring are affected by the chosen definition of "individual" (focusing exclusively on genetically distinct individuals, genets, as opposed to considering all independent clonal replicates, ramets). We identify two main population groups, one in the northern Iberian Peninsula and the other in the Macaronesian archipelagos and southern Iberian Peninsula. Within each group, we found relict populations (in the Azores and the Cantabrian Cornice) as well as recent originated populations. This population structure suggests colonization dynamics in which recent populations originated from one or a few genets of relict populations and became established through intra-gametophytic self-fertilization and vegetative expansion. DAPC analysis facilitated the identification of alleles that most significantly contributed to the observed population structure. The current Andalusian populations appear to have originated from colonization events from the Azores and the Cantabrian Cornice. Our findings suggest that C. macrocarpa persisted through the Last Glacial Maximum in two refugia: the Azores and the Cantabrian Cornice. Colonization into new areas occurred presumably from these refuges, generating two large population groups with structured genetic diversity. This study underscores the significance of clonality in establishing new populations and shaping genetic structure.

Covering the bases: Population genomic structure of Lemnaminor and the cryptic species L. japonica in Switzerland.

Duckweeds, including the common duckweed Lemna minor, are increasingly used to test eco-evolutionary theories. Yet, despite its popularity and near-global distribution, the understanding of its population structure (and genetic variation therein) is still limited. It is essential that this is resolved, because of the impact genetic diversity has on experimental responses and scientific understanding. Through whole-genome sequencing, we assessed the genetic diversity and population genomic structure of 23 natural Lemna spp. populations from their natural range in Switzerland. We used two distinct analytical approaches, a reference-free kmer approach and the classical reference-based one. Two genetic clusters were identified across the described species distribution of L.minor, surprisingly corresponding to species-level divisions. The first cluster contained the targeted L. minor individuals and the second contained individuals from a cryptic species: Lemna japonica. Within the L. minor cluster, we identified a well-defined population structure with little intra-population genetic diversity (i.e., within ponds) but high inter-population diversity (i.e., between ponds). In L. japonica, the population structure was significantly weaker and genetic variation between a subset of populations was as low as within populations. This study revealed that L. japonica is more widespread than previously thought. Our findings signify that thorough genotype-to-phenotype analyses are needed in duckweed experimental ecology and evolution.

Analysis of the genetic diversity and genetic structure of Dermatophagoides farinae in different habitats using microsatellite markers

ABSTRACT The mite, Dermatophagoides farinae, is an allergen source that triggers allergy symptoms in humans. We studied how different habitats affect the genetic structure of D. farinae populations. We used 12 microsatellite loci to analyse the genetic structure of six D. farinae populations collected from four habitats: flour mill (FM), dormitory (DM), cotton mill (CM), and pillow (PL). The CM population had the highest genetic diversity (He = 0.641) while the FM population had less genetic diversity. AMOVA analysis showed 81% intrapopulation genetic variation and 19% interpopulation variation. The overall F ST value of the six populations was 0.18531, indicating significant population genetic differentiation. Significant genetic differentiation occurred between the FM population and the other three habitat populations. Bayesian clustering analysis showed that the FM population was divided into two clusters. UPGMA tree and PCoA data supported the above results and indicated that the D. farinae populations from CM, PL, and DM1 had similar genetic ancestors. It was speculated that D. farinae could spread through the cotton-pillow-dormitory route. This study showed that D. farinae may have undergone habitat-associated differentiation and provides measures for preventing the dispersal of D. farinae.

Exploring the genetic diversity pattern of PvEBP/DBP2: A promising candidate for an effective Plasmodium vivax vaccine

Malaria remains a public health challenge. Since many control strategies have proven ineffective in eradicating this disease, new strategies are required, among which the design of a multivalent vaccine stands out. However, the effectiveness of this strategy has been hindered, among other reasons, by the genetic diversity observed in parasite antigens. In Plasmodium vivax, the Erythrocyte Binding Protein (PvEBP, also known as DBP2) is an alternate ligand to Duffy Binding Protein (DBP); given its structural resemblance to DBP, EBP/DBP2 is proposed as a promising antigen for inclusion in vaccine design. However, the extent of genetic diversity within the locus encoding this protein has not been comprehensively assessed. Thus, this study aimed to characterize the genetic diversity of the locus encoding the P. vivax EBP/DBP2 protein and to determine the evolutionary mechanisms modulating this diversity. Several intrapopulation genetic variation parameters were estimated using 36 gene sequences of PvEBP/DBP2 from Colombian P. vivax clinical isolates and 186 sequences available in databases. The study then evaluated the worldwide genetic structure and the evolutionary forces that may influence the observed patterns of genetic variation. It was found that the PvEBP/DBP2 gene exhibits one of the lowest levels of genetic diversity compared to other vaccine-candidate antigens. Four major haplotypes were shared worldwide. Analysis of the protein's 3D structure and epitope prediction identified five regions with potential antigenic properties. The results suggest that the PvEBP/DBP2 protein possesses ideal characteristics to be considered when designing a multivalent effective antimalarial vaccine against P. vivax.

Serpentine environment prevails over geographic distribution in shaping the genetic diversity of Medicago lupulina L.

Edaphic conditions of serpentine soils, naturally rich in heavy metals, act as a strong selection pressure that shapes specific metal-tolerant ecotypes. Medicago lupulina L. (black medick) is not only a widespread plant species that prefers calcareous and dry soil types but also grows at the borders of serpentine formations. It can also be found in waste and disturbed habitats. This is a species with reported phytoremediation potential, however, there is no published data regarding the impact of the environment on the genetic distribution of this species. The aim of our research was to explore how selection pressure of serpentine soils affects genetic diversity of M. lupulina and to test heavy-metal accumulation capacity of this species. Specimens of 11M. lupulina populations were collected from serpentine outcrops located in Central and Eastern Bosnia as well as from non-serpentine sites. Soil and plant samples were analyzed for the total contents of heavy metals using air-acetylene flame atomic absorption spectroscopy. Genetic diversity was analyzed using AFLP (Amplified Fragment Length Polymorphism) markers. Serpentine soils showed high nickel, cobalt, chromium and iron concentrations. Nickel and manganese concentrations in soil samples and plant material showed statistically significant correlation. Although plants in two populations show the ability to extract Ni, M. lupulina does not show hyperaccumulating properties. Despite severe selective pressure, genetic diversity in serpentine populations is not reduced. Analyses of intrapopulation and interpopulation genetic diversity showed significant genetic differentiation among populations which is not related to their geographic distance. Population from non-metalliferous soil showed clear separation from all other populations. Diversity data suggest that serpentine populations maintain genetic diversity by undetected mechanisms and that edaphic factors rather than geography influence genetic structure analyzed M. lupulina populations.

Genome-wide mining of diversity and evolutionary signatures revealed selective hotspots in Indian Sahiwal cattle

The Sahiwal cattle breed is the best indigenous dairy cattle breed, and it plays a pivotal role in the Indian dairy industry. This is due to its exceptional milk-producing potential, adaptability to local tropical conditions, and its resilience to ticks and diseases. The study aimed to identify selective sweeps and estimate intrapopulation genetic diversity parameters in Sahiwal cattle using ddRAD sequencing-based genotyping data from 82 individuals. After applying filtering criteria, 78,193 high-quality SNPs remained for further analysis. The population exhibited an average minor allele frequency of 0.221 ± 0.119. Genetic diversity metrics, including observed (0.597 ± 0.196) and expected heterozygosity (0.433 ± 0.096), nucleotide diversity (0.327 ± 0.114), the proportion of polymorphic SNPs (0.726), and allelic richness (1.323 ± 0.134), indicated ample genomic diversity within the breed. Furthermore, an effective population size of 74 was observed in the most recent generation. The overall mean linkage disequilibrium (r2) for pairwise SNPs was 0.269 ± 0.057. Moreover, a greater proportion of short Runs of Homozygosity (ROH) segments were observed suggesting that there may be low levels of recent inbreeding in this population. The genomic inbreeding coefficients, computed using different inbreeding estimates (FHOM, FUNI, FROH, and FGROM), ranged from −0.0289 to 0.0725. Subsequently, we found 146 regions undergoing selective sweeps using five distinct statistical tests: Tajima's D, CLR, |iHS|, |iHH12|, and ROH. These regions, located in non-overlapping 500 kb windows, were mapped and revealed various protein-coding genes associated with enhanced immune systems and disease resistance (IFNL3, IRF8, BLK), as well as production traits (NRXN1, PLCE1, GHR). Notably, we identified interleukin 2 (IL2) on Chr17: 35217075–35223276 as a gene linked to tick resistance and uncovered a cluster of genes (HSPA8, UBASH3B, ADAMTS18, CRTAM) associated with heat stress. These findings indicate the evolutionary impact of natural and artificial selection on the environmental adaptation of the Sahiwal cattle population.

Single-Nucleotide Variants in PADI2 and PADI4 and Ancestry Informative Markers in Interstitial Lung Disease and Rheumatoid Arthritis among a Mexican Mestizo Population

Rheumatoid arthritis (RA) is an autoimmune disease mainly characterized by joint inflammation. It presents extra-articular manifestations, with the lungs being one of the affected areas. Among these, damage to the pulmonary interstitium (Interstitial Lung Disease—ILD) has been linked to proteins involved in the inflammatory process and related to extracellular matrix deposition and lung fibrosis establishment. Peptidyl arginine deiminase enzymes (PAD), which carry out protein citrullination, play a role in this context. A genetic association analysis was conducted on genes encoding two PAD isoforms: PAD2 and PAD4. This analysis also included ancestry informative markers and protein level determination in samples from patients with RA, RA-associated ILD, and clinically healthy controls. Significant single nucleotide variants (SNV) and one haplotype were identified as susceptibility factors for RA-ILD development. Elevated levels of PAD4 were found in RA-ILD cases, while PADI2 showed an association with RA susceptibility. This work presents data obtained from previously published research. Population variability has been noticed in genetic association studies. We present data for 14 SNVs that show geographical and genetic variation across the Mexican population, which provides highly informative content and greater intrapopulation genetic diversity. Further investigations in the field should be considered in addition to AIMs. The data presented in this study were analyzed in association with SNV genotypes in PADI2 and PADI4 to assess susceptibility to ILD in RA, as well as with changes in PAD2 and PAD4 protein levels according to carrier genotype, in addition to the use of covariates such as ancestry markers.

Genetic diversity and forensic parameters of autosomal STR markers included Investigator® HDplex panel in the general population of the Russian Federation

Modern STR multiplexes used for parentage and kinship testing typically contain 20–30 informative loci. However, in certain cases, additional markers are necessary to address uncertainties and inconclusive cases. The Investigator® HDplex multiplex includes loci that are often utilized as supplementary markers and are not part of the standard STR identification systems. In our study, we examined a total of 558 unrelated individuals from 76 geographically distinct localities across all eight Federal Districts of the Russian Federation. We present key forensic parameters and allele frequencies obtained from this analysis. We evaluated the intra-population genetic diversity among the Federal District populations and compared the general population of the Russian Federation with populations from various regions around the world. SE33 exhibited the highest level of polymorphism, with 48 detected alleles, while D4S2366 and D6S474 displayed the fewest alleles (7). Heterozygosity values across all loci ranged from 0.7616 for D4S2366 to 0.9337 for SE33. We did not observe any significant deviation from the Hardy-Weinberg Equilibrium for the loci studied. The maximum FST value between the Russian sub-populations was 0.003. Comparison of the general population of the Russian Federation with populations from Europe, Asia, Africa, and South America, largely supported the historical relationship between the studied population and their respective biogeography.

Insights on Pinna nobilis population genetic structure in the Aegean and Ionian Sea.

The fan mussel Pinna nobilis Linnaeus, 1758 is an endemic species of the Mediterranean Sea, protected by international agreements. It is one of the largest bivalves in the world, playing an important role in the benthic communities; yet it has been recently characterized as Critically Endangered by the IUCN, due to mass mortality events. In this context, the assessment of the genetic variation of the remaining P. nobilis populations and the evaluation of connectivity among them are crucial elements for the conservation of the species. For this purpose, samples were collected from six regions of the Eastern Mediterranean Sea; the Islands of Karpathos, Lesvos and Crete; the Chalkidiki and Attica Peninsulas; and the Amvrakikos Gulf. Sampling was performed either by collecting tissue from the individuals or by using a non-invasive method, i.e., by scraping the inside of their shells aiming to collect their mucus and thus avoid stress induction to them. Conventional molecular techniques with the use of the COI and 16S rRNA mitochondrial markers were selected for the depiction of the intra-population genetic variability. The analyses included 104 samples from the present study and publicly available sequences of individuals across the whole Mediterranean Sea. The results of this work (a) suggest the use of eDNA as an efficient sampling method for protected bivalves and (b) shed light to the genetic structure of P. nobilis population in the Eastern Mediterranean; this latter knowledge might prove to be fundamental for the species conservation and hence the ecosystem resilience. The haplotype analyses reinforced the evidence that there is a certain degree of connectivity among the distinct regions of the Mediterranean; yet there is evidence of population distinction within the basin, namely between the Western and the Eastern basins. The combination of both genetic markers in the same analysis along with the inclusion of a large number of individuals produced more robust results, revealing a group of haplotypes being present only in the Eastern Mediterranean and providing insights for the species' most suitable conservation management.

Genetic structure of Rhodeus sinensis reflects historical imprints of East Asian paleo-drainages

ABSTRACT A complete reconstruction of the history regarding the distribution of a species requires a separate analysis of the events before and after colonizing the current distribution. In a freshwater species, the historical pattern of linkages between water systems, as an event before colonization, can be determined by examining the phylogenetic relationship between the populations from different drainages. Given the insular nature of freshwater systems, on the other hand, intra-population genetic diversity is largely related to the effective sizes of the first colonizing populations and the habitat capacities. This study analyzed the genetic diversity and structure of Rhodeus sinensis, a freshwater acheilognathid inhabiting the southern and western parts of the Korean Peninsula using two mitochondrial and twenty microsatellite loci. Korean R. sinensis appears to have originated from mainland China along the paleo-Yellow river across the vast continental shelf of the Yellow Sea and first colonized the west coast of the Korean Peninsula, based on phylogenetic data obtained from mitochondrial loci. These west coast populations have remained relatively small, and populations that migrated south appear to have thrived in the southwestern part of the peninsula, where the populations thereby displayed relatively high genetic diversity. Southern populations appear to have been formed by the movement of relatively small numbers following geological fluctuations, which likely have left traces of genetic drift throughout history, as also reflected in our results. The population of this species on the southeast coast of the peninsula appears to have been established by anthropogenic translocation.

Genetic Diversity in Peripheral Pedunculate Oak (Quercus robur L.) Provenances—Potential Climate Change Mitigators in the Center of Distribution despite Challenges in Natural Populations

Croatian pedunculate oak (Quercus robur L.) populations represent southern range peripheral populations, often viewed as sources of valuable diversity and drought-resistant ecotypes. At the same time, they endure stronger selection pressures as a result of climate change. The leaves of 20 individuals per population (17) were sampled in a field trial and analyzed using 10 nuclear and 9 chloroplast SSRs to determine the level of intrapopulation genetic variability and genetic differentiation. Analysis with nSSRs revealed deviation from HWE in seven populations. AMOVA showed a high intra-population diversity (98.53%) and a small but statistically significant inter-population differentiation. Isolation by distance explained 19.6% of differentiation. Average FST between populations was low (0.013) compared with usual values for peripheral populations. Populations were rich in cpSSR haplotypes, confirming the hotspot of diversity caused by the encounter of recolonization routes. Unbiased haplotype diversity (HE) from 9 chloroplast SSRs and 325 individuals was (HE = 0.440). Sixty-six different haplotypes were grouped in three maternal lineages by both a median-joining network and a neighbor-joining algorithm. AMOVA for cpSSRs showed statistically significant diversity among populations (70.23%), suggesting genetic differentiation, but also a probable anthropogenic effect. AMOVA of nSSRs within and between lineages showed that original recolonization patterns of nuclear diversity were subsequently erased by gene flow.

Phylogeographic inference for Bichromomyia flaviscutellata sensu stricto (Diptera: Psychodidae: Phebotominae) from the Brazilian Amazon rainforest, based on the 3' region of the COI gene.

Bichromomyia flaviscutellata (Mangabeira, 1942) sensu stricto (Diptera: Psychodidae) has been recognized as the main vector of Leishmania amazonensis in the Brazilian Amazon. For this reason, it is of paramount importance to understand the distribution of genetic diversity of populations of this vector, particularly the genetic structure and gene flow, for its management and control efforts. This study investigated the phylogeographic structure of five B. flaviscutellata s.s. populations from the central Brazilian Amazon region by analyzing 1,141 bp fragment of the 3' region of the COI gene. A total of 85 specimens of B. flaviscutellata s.s. were sequenced from Manaus (14), Rio Preto da Eva (10), Pitinga (14), Novo Airão (21), and Autazes (26); all in the state of Amazonas. The dataset yielded 59 haplotypes, most of them connected to each other in the main network. There were high levels of intrapopulation genetic variability (h = 0.945 ± 0.035 - 0.978 ± 0.054). The genetic distance values among populations varied from moderate (0.0873) to very high (0.3535), and all comparisons were significant, as well as the hierarchical analysis (ΦST = 0.2145). In contrast, these comparisons revealed a high number of shared sites (Ss = 6-34) and no difference in fixed sites (Sf = 0) among populations indicating absence of historical isolation. The Mantel test indicated that 67.92% (r = 0.6792; P = 0.06) of the genetic structure observed in B. flaviscutellata s.s. cannot be explained by the isolation-by-distance (IBD) model. This genetic structure, weakly explained by the IBD, may be due mainly by the forest habitat fragmentation and the low dispersal (flight) capacity of sand flies. Both factors could lead to population fragmentation and isolation, which promote genetic differentiation. Taken together, these findings suggest that the genetic structure observed in the studied populations of B. flaviscutellata s.s. is likely generated by microevolutionary processes acting at the population level at the present time and, therefore, evolutionary lineages were not recognized among the populations analyzed.

Different Adaptive Potential of Norway Spruce Ecotypes in Response to Climate Change in Czech Long-Term Lowland Experiment

As a result of climate change, Norway spruce (Picea abies [L.] Karst.) is dying across Europe. One of the primary reasons for this is the cultivation of unsuitable spruce provenances and ecotypes. This study deals with the growth and genetics of the ecotypes of Norway spruce, the most important tree species of the Czech Republic. At the study site, namely Cukrák, an experimental site was established in 1964 to plant three basic spruce ecotypes: low-elevation (LE), medium-elevation (ME) and high-elevation (HE) ecotype. A dendrometric inventory, dendrochronological sampling and genetic analyses were carried out on individual trees in 45 to 46 years old spruce stands. The ME ecotype was the most productive in terms of its carbon sequestration potential, while the HE ecotype had the lowest radial growth. All ecotypes exhibited a noteworthy negative correlation between tree-ring growth and seasonal temperature, annual temperature, previous year September to current year August temperature, June to July temperature, as well as individual monthly temperatures from previous May to current August. The relationship of annual and seasonal precipitation to growth was significant only for the LE and ME ecotypes, but precipitation from previous year September to current year August and precipitation from current June to July were the most significant for all ecotypes, where the ME had the highest r value. The HE ecotype does not adapt well to a dry climate and appears to be unsuitable compared to the other ecotypes under the studied conditions. This study also documented intra-population genetic variation within years of low growth, as evidenced by significant clonal heritability. The selection of the appropriate spruce ecotypes is essential for the stability and production of future stands and should become an important pillar of forest adaptation to climate change.

Genetic Variation of Ceiba pentandra (L.) Gaertn. from Three Populations in West Sumatra, Indonesia Based on RAPD Markers

Ceiba pentandra (L.) Gaertn. is one of the cotton-producing plants. However, there is a population decline in some areas, resulting in a decrease in genetic variation. This study aims to determine intrapopulation and interpopulation genetic variation and genetic differentiation of C. pentandra in three populations in West Sumatra. The research was conducted with the descriptive method using molecular data and sample collection with the survey method. Analysis of genetic variation using RAPD (Random Amplified Polymorphic DNA) markers on 15 individual plants collected from three populations, namely Solok, Pesisir Selatan, and Padang Pariaman. The results showed that primers OPA-01, OPA-02, and OPB-10 could detect polymorphism. The value of intrapopulation genetic variation was highest in the South Coastal population (H = 0.1857) and lowest in the Solok population (H = 0.1228). Interpopulation genetic variation (DST = 0.0326) was lower than intrapopulation genetic variation (Hs = 0.1607), with a low genetic differentiation value (GST = 0.1686) and a high gene flow value (Nm = 2.4660). Cluster analysis showed that the Pesisir Selatan and Solok populations had the farthest genetic distances (0.0580). UPGMA analysis shows that accessions do not cluster specifically based on their population.

Assessment of genetic differences in animals as exemplified by representatives of the genus <i>Camelus</i>

Data on the genetic variability of genomic DNA from two species of camels (Dromedary and Bactrian) are presented. It is noted that these animal species are of great importance in a number of southern countries, they are used as farm animals (milk, meat, wool), as draft, riding and sports animals. At present, much attention is paid to the study of camels in order to identify their genetic characteristics that can be used in breeding work. One of the research methods is multilocus analysis using labeled oligonucleotide probes. The latter selectively hybridize in separate regions of genomic DNA, leading to the appearance of specific genetic profiles characteristic of each individual. Labeling the probe with digoxigenin makes it possible to detect the results of hybridization on the filter. After the reaction of molecular hybridization of the probe with genomic DNA of camels, from 3 to 15 DNA fragments were detected, while the pattern of hybridization was very different in Dromedaries and Bactrians, which indicates a significant genetic difference in the organization of genomes. The coefficient of similarity of individuals in Bactrians was significantly higher than in Dromedaries (0.48 versus 0.39); interspecific similarity coefficient in this parameter was only 0.13. The calculation of the genetic distance between populations gave a rather high value of 0.305, which is significantly higher than the previously obtained data on cattle (from 0.05 to 0.10). Intrapopulation genetic diversity was assessed by the criterion of average heterozygosity. Calculations showed greater genetic diversity in the dromedary population (H = 0.72), which was indirectly confirmed by a lower similarity coefficient in this group of animals.

Genetic diversity and population structure of indigenous guinea fowl (Numida meleagris) in Benin using simple sequence repeat markers.

This study aimed to assess the genetic diversity and population structure of 12 guinea fowl phenotypes from three climatic zones (Guinean, Sudano-Guinean and Sudanian) of Benin. A total of 96 adult guinea fowl, aged at least 6months, were selected for blood sampling. Fragment analysis was carried out using 17 polymorphic microsatellite markers. The informative marker combinations revealed a total of 83alleles across all loci, with an average of 5alleles per locus and a mean polymorphic information content (PIC) of0.793. This study showed an observed heterozygosity of0.492. The inbreeding coefficient values ranged from0.086 in white phenotype to0.226 in cinnamon, showing a deficit of heterozygotes, suggesting a moderate inbreeding level. A relatively low population differentiation was observed, with a mean fixation index(Fst) value of0.033. The short genetic distances between phenotypes, unlike the strong genetic identities, revealed high genetic proximity between the 12 phenotypes of indigenous guinea fowl in Benin. These data indicate the existence of a single indigenous guinea fowl population with high intra-population genetic diversity with respect to climatic zones or phenotypes. This study will help in the selection of parental breeding stock for genetic improvement programs, as well as in the conservation for biodiversity maintenance and sustainable use of the indigenous guinea fowl in the study zones in Benin.

Genetic diversity and forensic parameters of autosomal STR markers included PowerPlex® CS7 panel in the general population of the Russian Federation

PowerPlex® CS7 multiplex is commonly used as a source of supplementary markers in parentage and kinship studies. We analysed a total of 687 unrelated individuals from 94 geographically different localities across all Federal Districts of the Russian Federation and provide forensically important parameters and allele frequencies. The paper also presents results of an intra-population genetic diversity study between the populations of the Federal Districts and comparison with populations from various regions of the world.

Community-wide correlations between species richness, abundance and population genomic diversity in a freshwater biodiversity hotspot.

Understanding patterns of diversity across macro (e.g. species-level) and micro (e.g. molecular-level) scales can shed light on community function and stability by elucidating the abiotic and biotic drivers of diversity within ecological communities. We examined the relationships among taxonomic and genetic metrics of diversity in freshwater mussels (Bivalvia: Unionidae), an ecologically important and species-rich group in the southeastern United States. Using quantitative community surveys and reduced-representation genome sequencing across 22 sites in seven rivers and two river basins, we surveyed 68 mussel species and sequenced 23 of these species to characterize intrapopulation genetic variation. We tested for the presence of species diversity-abundance correlations (i.e. the more-individuals hypothesis, MIH), species-genetic diversity correlations (SGDCs) and abundance-genetic diversity correlations (AGDCs) across all sites to evaluate relationships between different metrics of diversity. Sites with greater cumulative multispecies density (a standardized metric of abundance) had a greater number of species, consistent with the MIH hypothesis. Intrapopulation genetic diversity was strongly associated with the density of most species, indicating the presence of AGDCs. However, there was no consistent evidence for SGDCs. Although sites with greater overall densities of mussels had greater species richness, sites with higher genetic diversity did not always exhibit positive correlations with species richness, suggesting that there are spatial and evolutionary scales at which the processes influencing community-level diversity and intraspecific diversity differ. Our work reveals the importance of local abundance as indicator (and possibly a driver) of intrapopulation genetic diversity.