Search Results (19)

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

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

When colonizing new ranges, plant populations may benefit from the absence of the checks imposed by the enemies, herbivores, and pathogens that regulated their numbers in their original range. Therefore, rates of plant damage or infestation by natural enemies are expected to be lower in the new range. Exposing both non-native and native plant populations in the native range, where native herbivores are present, can be used to test whether resistance mechanisms have diverged between populations. Datura stramonium is native to the Americas but widely distributed in Spain, where populations show lower herbivore damage than populations in the native range. We established experiments in two localities in the native range (Mexico), exposing two native and two non-native D. stramonium populations to natural herbivores. Plant performance differed between the localities, as did the abundance of the main specialist herbivore, Lema daturaphila. In Teotihuacán, where L. daturaphila is common, native plants had significantly more adult beetles and herbivore damage than non-native plants. The degree of infestation by the specialist seed predator Trichobaris soror differed among populations and between sites, but the native Ticumán population always had the lowest level of infestation. The Ticumán population also had the highest concentration of the alkaloid scopolamine. Scopolamine was negatively related to the number of eggs deposited by L. daturaphila in Teotihuacán. There was among-family variation in herbivore damage (resistance), alkaloid content (scopolamine), and infestation by L. daturaphila and T. soror, indicating genetic variation and potential for further evolution. Although native and non-native D. stramonium populations have not yet diverged in plant resistance/constitutive defense, the differences between ranges (and the two experimental sites) in the type and abundance of herbivores suggest that further research is needed on the role of resource availability and adaptive plasticity, specialized metabolites (induced, constitutive), and the relationship between genealogical origin and plant defense in both ranges. Full article

Based on the results of a preceding species-delimitation analysis for the diploid representatives of the genus Leucanthemum (Compositae, Anthemideae), the present study aims at the elaboration of a specific and subspecific taxonomic treatment of the tetraploid members of the genus. Following an integrative taxonomic approach, species-level decisions on eight predefined morphotaxon hypotheses were based on genetic/genealogical, morphological, ecological, and geographical differentiation patterns. ddRADseq fingerprinting and SNP-based clustering revealed genetic integrity for six of the eight morphotaxa, with no clear differentiation patterns observed between the widespread L. ircutianum subsp. ircutianum and the N Spanish (Cordillera Cantábrica) L. cantabricum and the S French L. delarbrei subsp. delabrei (northern Massif Central) and L. meridionale (western Massif Central). The inclusion of differentiation patterns in morphological (leaf dissection and shape), ecological (climatological and edaphic niches), and geographical respects (pair-wise tests of sympatry vs. allopatry) together with the application of a procedural protocol for species-rank decisions (the ‘Wettstein tesseract’) led to the proposal of an acknowledgement of the eight predefined morphotaxon hypotheses as six species (two of them with two subspecies). Nomenclatural consequences following from these results are drawn and lead to the following new combinations: Leucanthemum delarbrei subsp. meridionale (Legrand) Oberpr., T.Ott & Vogt, comb. nov. and Leucanthemum ruscinonense (Jeanb. & Timb.-Lagr.) Oberpr., T.Ott & Vogt, comb. et stat. nov. Full article

The Merino breed, which originates from Spain, is the most emblematic livestock breed in the world, since it is the first with a worldwide extension and has had an important impact on the genetic origin of several of the main current sheep populations. For this reason, it is of vital importance to typify the historical genetic lines of the original Spanish Merino breed and thereby ensure the conservation of its variability. In the present study, we used 337 purebred animals (males and females) registered in the Genealogical Book of the Native Merino Breed. All the animals were descendants of herds from six ancestral genetic lines (Maesso, Egea, Granda, López-Montenegro, Hidalgo, and Donoso). Significant differences were found in all the morphometric traits and indexes between the different genetic lines. Using discriminant analysis, 84% of the animals were classified correctly into their historical genetic lines. Furthermore, the distances between the lines, calculated by a cluster test, showed that Hidalgo, Maesso, and Donoso had the most clearly defined lines, while the Granda, López-Montenegro, and Egea lines were more similar to each other. All this demonstrates the rich genetic variability existing in the genuine gene pool of the Merino sheep breed. 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

Forensic Genetic Genealogy (FGG) has fast become a popular tool in criminal investigations since it first emerged in 2018. FGG is a novel investigatory tool that has been applied to hundreds of unresolved cold cases in the United States to generate investigative leads and identify unknown individuals. Consumer DNA testing and the public’s increased curiosity about their own DNA and genetic ancestry, have greatly contributed to the availability of human genetic data. Genetic genealogy has been a field of study/interest for many years as both amateur and professional genetic genealogists use consumer DNA data to explore genetic connections in family trees. FGG encompasses this knowledge by applying advanced sequencing technologies to forensic DNA evidence samples and by performing genetic genealogy methods and genealogical research, to produce possible identities of unknown perpetrators of violent crimes and unidentified human remains. This combination of forensic genetics, genetic genealogy, and genealogical research has formed a new subdiscipline within the forensic sciences. This paper will summarize the individual disciplines that led to the emergence of FGG, its practice in forensic investigations, and current/future considerations for its use. Full article

Species delimitation—owing to the paramount role of the species rank in evolutionary, ecological, and nature conservation studies—is an essential contribution of taxonomy to biodiversity research. In an ‘integrative taxonomy’ approach to species delimitation on the diploid level, we searched for evolutionary significant units (the warps and wefts) that gave rise to the polyploid complex of European ox-eye daisies (Leucanthemum; Compositae-Anthemideae). Species discovery and validation methods based on genetic, ecological, geographical, and morphometric datasets were applied to test the currently accepted diploid morpho-species, i.e., morphologically delimited species, in Leucanthemum. Novel approaches were taken in the analyses of RADseq data (consensus clustering), morphometrics of reconstructed leaf silhouettes from digitized herbarium specimens, and quantification of species-distribution overlaps. We show that 17 of the 20 Leucanthemum morpho-species are supported by genetic evidence. The taxonomic rank of the remaining three morpho-species was resolved by combining genealogic, ecologic, geographic, and morphologic data in the framework of von Wettstein’s morpho-geographical species concept. We herewith provide a methodological pipeline for the species delimitation in an ‘integrative taxonomy’ fashion using sources of evidence from genealogical, morphological, ecological, and geographical data in the philosophy of De Queiroz’s “Unified Species Concept”. Full article

The racial identity literature has operationalized identity formation as progressive stage models, usually triggered by the experience of a negative race-based event. With the advent of new genealogical technology, it is imperative to include experiences that participants elect to experience (i.e., self-initiated or agentic encounter events). By using this perspective, identity processes become fluid and more expansive. In the context of this study, genetic ancestry tests are operationalized as a self-initiated encounter event. Participants (n = 8) were enrolled in an arts-in-education program that uses theater to explore Black Americans’ identities and family histories. This study used theater performance and modified life narrative interviews to understand how participation informed understandings of the self and others. Subsequent interviews highlighted how participants internalized the genetic test results and their participation within the group. Results indicated that, while participants were deeply invested in learning more about their ancestral roots, there were concerns related to the test results and their meaning for individuals. This study highlights that for the Black diaspora, identity is informed by ancestry and family history, as well as by interactions with created community members. Overall, this study opens the possibility for deeper exploration of racial identity formation within critical social psychology. Full article

We report the case of a 22-year-old male who visited a cardiologist after the first episode of atrial fibrillation (AF). Echocardiography and magnetic resonance imaging revealed decreased left ventricular (LV) systolic function with dilated LV. An intermittent second-degree AV (atrioventricular) block was detected during 24 h Holter monitoring. Genetic test revealed the pathogenic variant of the BAG3 (BLC2-associated athanogene 3) gene. Due to the high risk of heart failure (HF) progression and ventricular arrhythmias, an event recorder was implanted and a pathogenetic HF treatment was prescribed. The analysis of genealogy revealed that the patient’s father, at the age of 32, was diagnosed with dilated cardiomyopathy (DCM) and recurrent AF episodes. Genetic testing also confirmed a pathogenic variant of the BAG3 gene. Currently, with the optimal treatment of HF, the patient’s disease has been stable for three years and the condition is closely monitored on an outpatient basis. So, we demonstrate the importance of early detection for genetic testing and the unusual stability exhibited by the patient‘s optimal medical therapy for 3 years. Full article

Despite the undefinition of the origins of Ca de Rater (CR) and Ca de Bestiar (CB) dogs, references to these endangered autochthonous breeds highlighted their ratting/pet and shepherding/guard skills for centuries. Genealogical historical records were traced back to founders. Founder number in the reference population (146 and 53 for CR and CB, respectively), historical and reference maximum generations traced (eight and seven for CR and CB, respectively), and historical average number of complete generations (1.04 for both breeds) were determined. Structure assessment revealed the existence of subpopulations regarding criteria such as breeders (75 and 17), breeder location (32 and eight), owners (368 and 198), and owner location (73 and 51) for CR and CB, respectively. Average inbreeding (F) within breed subpopulations ranged from 0.27–1.20% for CB breeders and the rest of subpopulation criteria for both breeds, respectively, except for CB owners and owner location. F ranged from 0.27–1.41% for CB historical population and CR current population, respectively. The study of genetic diversity revealed a relatively similar genetic background between subpopulations. Average coancestry between and within breeds suggested a similar evolutionary process. However, Mann–Whitney U test determined significant differences for diversity parameters (F, ΔR, coancestry, nonrandom mating degree, maximum, complete, and equivalent generations, ΔF, and genetic conservation index) between breeds and their functionalities. Conclusively, functionality in dog breeds may determine the genetic diversity evolution of endangered breeds, even when these share the same geographic isolation conditions. Full article

The insufficient number of available simple sequence repeats (SSRs) inhibits genetic research on and molecular breeding of Paeonia lactiflora, a flowering crop with great economic value. The objective of this study was to develop SSRs for P. lactiflora with Illumina RNA sequencing and assess the role of SSRs in gene regulation. The results showed that dinucleotides with AG/CT repeats were the most abundant type of repeat motif in P. lactiflora and were preferentially distributed in untranslated regions. Significant differences in SSR size were observed among motif types and locations. A large number of unigenes containing SSRs participated in catalytic activity, metabolic processes and cellular processes, and 28.16% of all transcription factors and 21.74% of hub genes for inflorescence stem straightness were found to contain SSRs. Successful amplification was achieved with 89.05% of 960 pairs of SSR primers, 55.83% of which were polymorphic, and most of the 46 tested primers had a high level of transferability to the genus Paeonia. Principal component and cluster dendrogram analyses produced results consistent with known genealogical relationships. This study provides a set of SSRs with abundant information for future accession identification, marker-trait association and molecular assisted breeding in P. lactiflora. Full article

Direct-to-consumer genetic ancestry testing is a new and growing industry that has gained widespread media coverage and public interest. Its scientific base is in the fields of population and evolutionary genetics and it has benefitted considerably from recent advances in rapid and cost-effective DNA typing technologies. There is a considerable body of scientific literature on the use of genetic data to make inferences about human population history, although publications on inferring the ancestry of specific individuals are rarer. Population geneticists have questioned the scientific validity of some population history inference approaches, particularly those of a more interpretative nature. These controversies have spilled over into commercial genetic ancestry testing, with some companies making sensational claims about their products. One such company—BritainsDNA—made a number of dubious claims both directly to its customers and in the media. Here we outline our scientific concerns, document the exchanges between us, BritainsDNA and the BBC, and discuss the issues raised about media promotion of commercial enterprises, academic freedom of expression, science and pseudoscience and the genetic ancestry testing industry. We provide a detailed account of this case as a resource for historians and sociologists of science, and to shape public understanding, media reporting and scientific scrutiny of the commercial use of population and evolutionary genetics. Full article

With the overwhelming popularity of genealogy-themed television series, genetic genealogy testing, online subscription services for research, and the enduring aphorism of Sankofa, people of African descent are consistently dispelling the long-avowed assertion that the ancestry of the enslaved in the United States and their descendants is, for the most part, unknowable. [...] Full article

This article explores ways in which advances in genetic testing have both facilitated and democratized genealogical research for individuals in search of their “roots” or ethnic heritage. These advances coincide with the quests of people of African descent to pinpoint their precise origins and ethnic backgrounds in Africa, revelations that have been denied to many African descendants in the diaspora from slavery times to the present. Genetics and DNA as the “great truth teller”, however, frequently yield results that go contrary to expectations. In this article, the author explores at a personal level the tensions that the “Genetic Revolution” produces between biology and society. Full article