Search Results (28)

Objectives: To analyze Colombia’s current human population, we employed a population genetics approach enriched by genealogical, demographic, cultural, and historical data to learn about its evolutionary history and to elucidate ethnic belonging and relationship patterns between its various population groups. Materials and Methods: This study relied on ten autosomal microsatellite markers (STRs) from 1364 individuals surveyed throughout the country. Aside from employing descriptive population genetics, substructure, and distance analysis, this investigation evaluated genealogical, demographic, cultural, and historical data gathered from fieldwork surveys. Results: We present a genetic diversity and ethnic belonging map of Colombia that suggests a nine-population classification (under Afro-descendant, Native American, and Admixed ethnicity labels) that reveals traces of evolutionary processes discussed in the light of the recent literature based on modern molecular markers. Colombia’s genetic trace from Africa varies among territories, as shown here by two differentiated Afro ancestral components, Chocó and San Andrés, in addition to the Afro admixture category. Some Native American peoples like the Wayúu, Zenú, Ticuna, Huitoto, and Cocama have a genetic configuration that remains relatively preserved. Nevertheless, other self-determined indigenous peoples who remain in their ancestral territories exhibit genetic introgression that is also reflected by their acculturation levels such as the Pijaos, Kankuamos, and Mokaná. The population classified as European admixture also shows an ancestral component that seems to be more fixed throughout neighboring territories but whose fluctuation depends on its specific demographic histories. Conclusions: This study combines STRs, a targeted sampling strategy, and advanced analytical tools to explore Colombia’s genetic diversity and evolutionary history. Locally, these findings enhance the understanding of genetics in a post-conflict society, crucial for human identification. Globally, they contribute to human population genetics, helping address evolutionary questions using data from diverse human ancestries and geographies. Full article

Background/Objectives: Dense genetic marker panels are increasingly used in kinship analysis for the identification of distant relatives. As more markers are available, it is possible to pinpoint IBD segments more precisely and more reliably, ultimately approaching close to continuously observed IBD. This study investigates the evidential value obtained for discrimination between common pedigree relationships if IBD is observed continuously across the autosomal genome without error. In the continuous case, the evidential value is limited only by the pedigree relationship and the recombination rates. Methods: We conducted simulations to generate IBD segments across the autosomal genome for individuals with defined pedigree relationships. The evidential value for relationship discrimination was then calculated exactly from the underlying model, assuming no genotyping error and full genome coverage. Results: The simulations show that the ability to distinguish pedigree relationships quickly diminishes as relationships become more distant. First cousins can be distinguished from second cousins with 99.9% accuracy which drops to 94% when distinguishing second and third cousins. Relationships with the same expected degree of relatedness can be discriminated using continuously observed IBD, although the effectiveness decreases with more distant relationships. Conclusions: Continuous IBD observation establishes a theoretical upper bound on the power to distinguish relationships if a large but finite number of markers is used. The findings provide a benchmark for evaluating kinship analyses based on finite genetic marker panels. Full article

This study systematically investigated the genetic characteristics and germplasm conservation strategies of Xinjiang Thompson Seedless grapes (Vitis vinifera Thompson Seedless) and Munake grapes (Vitis vinifera L. cv. Munake) using SSR molecular markers and whole-genome resequencing technology. A genetic diversity analysis of 165 Thompson Seedless accessions with 16 SSR markers identified 442 alleles (27.63 alleles per locus on average), with the expected heterozygosity (He = 0.76) and observed heterozygosity (Ho = 0.83) indicating moderate-to-low genetic diversity. A molecular variance analysis (AMOVA) further revealed that 96% of the genetic variation originated within populations, with minimal inter-population differentiation (Fst = 0.04). Phylogenetic reconstruction using SSR markers demonstrated significant genealogical associations between the two cultivars, supporting the hypothesis that Thompson Seedless may have originated from a domesticated lineage of Munake. The selected SSR markers exhibited high discriminatory power (PIC = 0.92), enabling the precise differentiation of accessions with closely related genetic backgrounds. Whole-genome resequencing identified 20,074,046 and 69,214,080 high-quality SNPs in 100 Thompson Seedless and 141 Munake accessions, respectively. Core germplasm banks were subsequently established: the Thompson Seedless core collection (25 accessions) captured 94% of genetic variation, reflecting genetic homogenization driven by intensive clonal cultivation, while the Munake core collection (42 accessions) retained 95% of allelic diversity and resolved regional synonym issues through highly polymorphic SNP markers. A comparative analysis revealed that Munake maintains higher genetic diversity due to natural gene flow, whereas Thompson Seedless faces heightened risks of genetic erosion from prolonged asexual propagation. These findings provide a theoretical foundation and technical framework for precise conservation, varietal improvement, and sustainable utilization of grape germplasm resources in Xinjiang. Full article

Scomber japonicus, commonly known as chub mackerel, is a fish species of economic significance in Korea, China, and Japan, whose natural abundance has reduced dramatically due to overfishing and environmental changes. To investigate the genetic differentiation and population structure of S. japonicus, a 359 base pair segment of the mitochondrial DNA (mtDNA) control region sequence was analyzed in 96 individuals sampled from three locations in Korean waters. Sixty-six haplotypes were recognized, of which 61 (92.42%) were population specific, whereas only five haplotypes were shared by multiple populations (8%). Two clades were revealed with low support values, and no specific genealogical branches were recognized according to geographical locations. Significant genetic differentiations, however, were detected among the three populations, with F_ST values (p < 0.05). These results indicate that populations of S. japonicus in Korean waters are genetically subdivided. Migration patterns, spawning site fidelity, and current temperature could be the possible causes of this subdivision. Consequently, it is thought that each of the genetically unique S. japonicus stocks found in Korean waters requires a different approach to management. Full article

Background/Objectives: Inferring genetic relationships based on genetic data has gained an increasing focus in the last years, in particular explained by the rise of forensic investigative genetic genealogy (FIGG) but also the introduction of expanded SNP panels in forensic genetics. A plethora of statistical methods are used throughout publications; in direct-to-consumer (DTC) testing, the shared segment approach is used, in screenings of relationships in medical genetic research, for instance, methods-of-moment estimators, e.g., estimation of the kinship coefficient, are used, and in forensic genetics, the likelihood and the likelihood ratio are commonly used to evaluate the genetic data under competing hypotheses. This current study aims to compare and contrast examples of the aforementioned statistical methods to infer relationships from genetic data. Methods/Results: This study includes some historical and some recently published panels of SNP markers to illustrate the strength and caveats of the statistical methods on different marker sets and a selection of pre-defined pairwise relationships, 1st through 7th degree. Extensive simulations are performed and subsequently subsetted based on the marker panels alluded to above. As has been shown in previous research, the likelihood ratio is most powerful, i.e., high correct classifications, when SNP data are sparse, say below 20,000 markers, whereas the windowed kinships and segment approaches are equally powerful when very dense SNP data are available, say >20,000 markers. In between lay approaches using method-of-moments estimators which perform well when the degree of relationship is below four but less so beyond, say, 4th degree relationships. The likelihood ratio is the only method that is easily adapted for non-pairwise tests and therefore has an additional depth not addressed in the current study. We furthermore perform a study of genotyping error rates and their impact on the different statistical methods employed to infer relationships, where the results show that error rates below 1% seem to have low impact across all methods, in particular for errors yielding false heterozygote genotypes. Full article

Due to their involvement in pathogen-mediated immune responses, the hypervariable genes of the Major Histocompatibility Complex (MHC) have become a paradigm for investigating the evolution and maintenance of genetic (adaptive) diversity, contextually providing insight into the viability of wild populations, which is meaningful for conservation. Here, we provide the first preliminary characterization of MHC polymorphism and evolution in trouts from Albania, a known hotspot of Salmonid diversity harboring ecologically and phylogenetically distinct native (threatened) taxa. Overall, 36 trout—including Lake Ohrid-endemic Salmo ohridanus and S. letnica, and both riverine and lacustrine native brown trout (the S. trutta complex) from the Drin-Skadar drainage—were genotyped at the MHC-DAB locus through next-generation amplicon sequencing. We identified 34 alleles (including 30 novel alleles), unveiling remarkable population/taxon MHC-DAB distinctiveness. Despite apparent functional (supertype) similarity, S. letnica and the S. trutta complex showed MHC-typical high sequence/allele diversity and evidence of global/codon-specific positive selection, particularly at antigen-binding sites. Conversely, deep-water-adapted S. ohridanus revealed unexpectedly reduced allelic/supertype diversity and relaxed selection. Evolution by reticulation and signals of trans-species polymorphism emerged from sequence genealogies. Further investigations and increased sampling will provide a deeper understanding of the evolutionary mechanisms yielding the observed pattern of MHC diversity across Albanian trout taxa and populations. Full article

This article presents the findings of a scientific study investigating the efficacy of various assessment techniques used to evaluate the adaptability and productive qualities of Aberdeen Angus cattle on three prominent farms in the northern region of the Republic of Kazakhstan. A comprehensive analysis of the haematological and biochemical parameters of experimental groups of cattle with different genotypes (American, Canadian, and Estonian selection) was conducted. The studies revealed notable variability in haematological and biochemical indicators, contingent on the origin. Concurrently, the dynamics of the aforementioned indicators did not exceed the physiological norms. The modern allelofund was characterised with the help of microsatellite markers, and the level of genetic diversity of Aberdeen Angus cattle of different genotypes was estimated. The research uncovered the genealogical structure of the populations, the purity of the populations, the provenance, the polymorphism level, the heterozygosity indices, and the Wright fixation index (Fis). The genotyping of cattle of the Aberdeen Angus breed on 15 microsatellite markers yielded the establishment of 80 alleles in the Kolos-firm LLP, 77 alleles in the Vishnevskoe LLP, and 92 alleles in the Sever-Agro N LLP. The total expected heterozygosity was He = 0.673, while the observed heterozygosity was Ho = 0.710. Full article

Background/Objectives: Emerging forensic genetic applications, such as forensic investigative genetic genealogy (FIGG), advanced DNA phenotyping, and distant kinship inference, increasingly require dense SNP genotype datasets. However, forensic-grade DNA often contains missing genotypes due to its quality and quantity limitations, potentially hindering these applications. Genotype imputation, a method that predicts missing genotypes, is widely used in population and medical genetics, but its utility in forensic genetics has not been thoroughly explored. This study aims to assess the performance of genotype imputation in forensic contexts and determine the conditions under which it can be effectively applied. Methods: We employed a simulation-based approach to generate realistic forensic SNP genotype datasets with varying numbers, densities, and qualities of observed genotypes. Genotype imputation was performed using Beagle software, and the performance was evaluated based on the call rate and imputation accuracy across different datasets and imputation settings. Results: The results demonstrate that genotype imputation can significantly increase the number of SNP genotypes. However, imputation accuracy was dependent on factors such as the quality of the original genotype data and the characteristics of the reference population. Higher SNP density and fewer genotype errors generally resulted in improved imputation accuracy. Conclusions: This study highlights the potential of genotype imputation to enhance forensic SNP datasets but underscores the importance of optimizing imputation parameters and understanding the limitations of the original data. These findings will inform the future application of imputation in forensic genetics, supporting its integration into forensic workflows. Full article

Background: Forensic investigative genetic genealogy (FIGG) has developed rapidly in recent years and is considered a novel tool for crime investigation. However, crime scene samples are often of low quality and quantity and are challenging to analyze. Deciding which approach should be used for kinship inference in forensic practice remains a troubling problem for investigators. Methods: In this study, we selected four popular approaches—KING, IBS, TRUFFLE, and GERMLINE—comprising one method of moment (MoM) estimator and three identical by descent (IBD) segment-based tools and compared their performance at varying numbers of SNPs and levels of genotyping errors using both simulated and real family data. We also explored the possibility of making robust kinship inferences for samples with ultra-high genotyping errors by integrating MoM and the IBD segment-based methods. Results: The results showed that decreasing the number of SNPs had little effect on kinship inference when no fewer than 164 K SNPs were used for all four approaches. However, as the number decreased further, decreased efficiency was observed for the three IBD segment-based methods. Genotyping errors also had a significant effect on kinship inference, especially when they exceeded 1%. In contrast, MoM was much more robust to genotyping errors. Furthermore, the combination of the MoM and the IBD segment-based methods showed a higher overall accuracy, indicating its potential to improve the tolerance to genotyping errors. Conclusions: In conclusion, this study shows that different approaches have unique characteristics and should be selected for different scenarios. More importantly, the integration of the MoM and the IBD segment-based methods can improve the robustness of kinship inference and has great potential for applications in forensic practice. Full article

This study investigates the genealogical and demographic trends of the Massese sheep breed in Tuscany from 2001 to 2021. The Herd Book kept by the Italian Sheep and Goat Breeders Association (Asso.Na.Pa) provided the data. The descriptive statistics were analyzed using JMP software. The pedigree parameters of a total of 311,056 animals (whole population—WP) were analyzed using CFC, ENDOG, and Pedigree viewer software. A total of 24,586 animals born in the period 2007–2021 represented the Reference Population (RP), and 18,554 animals the Base Population (BP). The demographic results showed an inconsistent trend of offspring registration. This study showed a short period of productivity for both ewes and rams, with means of 1.47 and 19.2 registered newborn ewes and rams, respectively. The genealogical analysis revealed incomplete data, highlighting inaccurate assessments of the relationships among the animals, and inbreeding with large differences among provinces. The average inbreeding coefficient in the WP was 1.16%, and it was 2.26% in the RP. The total number of inbreds was 2790 in the WP, with an average F_PED of 13.56%, and 2713 in the RP, with an average F_PED of 12.82%. The use of pedigree data is a key and economical approach to calculating inbreeding and relationship coefficients. It is the primary step in genetic management, playing a crucial role in the preservation of a breed. The regular updating of genealogical data is the first step to ensuring the conservation of animal genetic resources, and this study is compromised by the lack of such updates. Full article

Investigating the genetic diversity and population structure of wheat germplasm is crucial for understanding the underlying variability essential for breeding programs and germplasm preservation. This research aims to contribute novel insights with respect to the genetic makeup and relationships among these wheat genotypes, shedding light on the diversity present within the Turkish wheat germplasm. In this study, iPBS-retrotransposon markers were employed to analyze 58 wheat genotypes, encompassing 54 landraces and 4 cultivars sourced from Türkiye. These markers serve as genetic indicators that can be used to evaluate genetic variation, build genealogical trees, and comprehend evolutionary connections. The PCR products were visualized on agarose gel, and bands were scored as present/absent. The ten iPBS primers collectively yielded an average of 16.3 alleles, generating a total of 163 polymorphic bands. The number of alleles produced by individual markers ranged from 4 (iPBS-2386) to 29 (iPBS-2219). The genetic parameters were calculated using the popgen and powermarker programs. The genetic relationships and population structures were assessed using the ntsys and structure programs. Polymorphism information content (PIC) per marker varied from 0.13 (iPBS-2390) to 0.29 (iPBS-2386), with an average value of 0.22. Shannon’s information index (I) was calculated as 1.48, while the number of effective alleles (Ne) and Nei’s genetic diversity (H) were determined to be 0.26 and 0.31, respectively. Genotype numbers 3 (Triticum dicoccum) and 10 (Triticum monococcum) exhibited the maximum genetic distance of 0.1292, signifying the highest genetic disparity. Population structure analysis revealed the segregation of genotypes into three distinct subpopulations. Notably, a substantial portion of genotypes clustered within populations correlated with the wheat species. This population structure result was consistent with the categorization of genotypes based on wheat species. The comprehensive assessment revealed noteworthy insights with respect to allele distribution, polymorphism content, and population differentiation, offering valuable implications for wheat breeding strategies and germplasm conservation efforts. In addition, the iPBS markers and wheat genotypes employed in this study hold significant potential for applications in wheat breeding research and germplasm preservation. Full article

Although Malaysia is considered free of human malaria, there has been a growing number of Plasmodium knowlesi cases. This alarming trend highlighted the need for our understanding of this parasite and its associated vectors, especially considering the role of genetic diversity in the adaptation and evolution among vectors in endemic areas, which is currently a significant knowledge gap in their fundamental biology. Thus, this study aimed to investigate the genetic diversity of Anopheles balabacensis, Anopheles cracens, Anopheles introlatus, and Anopheles latens—the vectors for P. knowlesi malaria in Malaysia. Based on cytochrome c oxidase 1 (CO1) and internal transcribed spacer 2 (ITS2) markers, the genealogic networks of An. latens showed a separation of the haplotypes between Peninsular Malaysia and Malaysia Borneo, forming two distinct clusters. Additionally, the genetic distances between these clusters were high (2.3–5.2% for CO1) and (2.3–4.7% for ITS2), indicating the likely presence of two distinct species or cryptic species within An. latens. In contrast, no distinct clusters were observed in An. cracens, An. balabacensis, or An. introlatus, implying a lack of pronounced genetic differentiation among their populations. It is worth noting that there were varying levels of polymorphism observed across the different subpopulations, highlighting some levels of genetic variation within these mosquito species. Nevertheless, further analyses revealed that all four species have undergone demographic expansion, suggesting population growth and potential range expansion for these vectors in this region. Full article

Genealogical research usually begins with the discovery of affinity among individual humans. Such kinship is induced by direct observation, as well as by hearsay (indirect observation) that can be independently confirmed. Those who want to continue investigating a case history after the observational mode of fact-finding is no longer sustainable have no other choice than to switch to the discovery of consanguineous relationships. This involves a paradigm shift, where investigation dramatically changes from observation to inference, from inductive to deductive reasoning. Individuation is important in characterizing the personhood of an individual, but those same facts are of little empirical value in establishing the unification of a family. In addition, genealogists rely on marriage as an observable source of evidence for unification. However, this extrapolation is not completely convincing because marriage does not take into account the uncertainty of paternity. Individual parents usually descend from different parts of family history, which suggests genealogists should evaluate cultural factors responsible for non-random mating in attempting to infer consanguinity. For example, there is the incest taboo, a cultural convention which addresses the abnormal genetic consequences of inbreeding. Other non-random mating factors of a more general nature may also be identified in the unification of genetically different individuals. Here, for example, causality is expected in cultural principles that are of a cohesive and integrative nature. Those kinds of evidence may determine an unmarried pair’s earliest engagement and may also be responsible for the origin and maintenance of the marriage relationship, even throughout post-reproductive life. Lastly, current genealogical research is severely infected with confirmation bias, and from which it must be protected if it is to achieve the status of a scientific discipline. Critical rationalism provides a solution to that kind of problem. It is with remediation in mind, as it applies to all of the aforementioned issues, that genealogical systematics is characterized. Full article

This article describes new algorithms that allow for viewing genetic sequences in the form of their multispectral images. We presented examples of the construction of such mappings with a demonstration of the practical problems of comparative genomics. New DNA visualization tools seem promising, thanks to their informativeness and representativeness. The research illustrates how a novel sort of multispectral mapping, based on decomposition in several parametric spaces, can be created for comparative genetics. This appears to be a crucial step in the investigation of the genetic coding phenomenon and in practical activities, such as forensics, genetic testing, genealogical analysis, etc. The article gives examples of multispectral parametric sets for various types of coordinate systems. We build mappings using binary sub-alphabets of purine/pyrimidine and keto/amino. We presented 2D and 3D renderings in different characteristic spaces: structural, integral, cyclic, spherical, and third-order spherical. This research is based on the method previously developed by the author for visualizing genetic information based on new molecular genetic algorithms. One of the types of mappings, namely two-dimensional, is an object of discrete geometry, a symmetrical square matrix of high dimension. The fundamental properties of symmetry, which are traced on these mappings, allow us to speak about the close connection between the phenomenon of genetic coding and symmetry when using the developed mathematical apparatus for representing large volumes of complexly organized molecular genetic information. Full article

In horses, demographic patterns are complex due to historical migrations and eventful breeding histories. Particularly puzzling is the ancestry of the North African horse, a founding horse breed, shaped by numerous influences throughout history. A genetic marker particularly suitable to investigate the paternal demographic history of populations is the non-recombining male-specific region of the Y chromosome (MSY). Using a recently established horse MSY haplotype (HT) topology and KASP™ genotyping, we illustrate MSY HT spectra of 119 Barb and Arab-Barb males, collected from the Maghreb region and European subpopulations. All detected HTs belonged to the Crown haplogroup, and the broad MSY spectrum reflects the wide variety of influential stallions throughout the breed’s history. Distinct HTs and regional disparities were characterized and a remarkable number of early introduced lineages were observed. The data indicate recent refinement with Thoroughbred and Arabian patrilines, while 57% of the dataset supports historical migrations between North Africa and the Iberian Peninsula. In the Barb horse, we detected the HT linked to Godolphin Arabian, one of the Thoroughbred founders. Hence, we shed new light on the question of the ancestry of one Thoroughbred patriline. We show the strength of the horse Y chromosome as a genealogical tool, enlighten recent paternal history of North African horses, and set the foundation for future studies on the breed and the formation of conservation breeding programs. Full article