Genetic Patterns Research Articles

Understanding the intrinsic biology of diffuse large B-cell lymphoma: recent advances and future prospects.

Diffuse large B-cell lymphoma (DLBCL) is the most common type of lymphoid tumor, and accounts for approximately 30-40% of non-Hodgkin lymphomas. Although the prognosis has significantly improved with the advent of rituximab combination chemotherapy in the early 2000s, recurrence still occurs in about 40% of cases. Even though chemotherapy with increased dose-intensity is used in recurrent cases, the prognosis of such patients remains poor. Thus, the development of personalized medicine, including molecular-targeted drugs, is required to improve the prognosis of DLBCL patients, and further understanding of the molecular pathogenesis of DLBCL is essential for this purpose. With recent advances in genetic analysis technology, unknown genetic abnormalities and gene expression patterns have been discovered, and based on these discoveries, progress is being made in elucidating and subdividing molecular pathologies. This article summarizes recent findings regarding molecular pathogenesis in DLBCL using transcriptome and genomics technologies, and outlines the path to personalized medicine.

A correlative study of the genomic underpinning of virulence traits and drug tolerance of Candida auris.

Candida auris is an opportunistic fungal pathogen with high mortality rates which presents a clear threat to public health. The risk of C. auris infection is high because it can colonize the body, resist antifungal treatment, and evade the immune system. The genetic mechanisms for these traits are not well known. Identifying them could lead to new targets for new treatments. To this end, we present an analysis of the genetics and gene expression patterns of C. auris carbon metabolism, drug resistance, and macrophage interaction. We chose to study two C. auris isolates simultaneously, one drug sensitive (B11220 from Clade II) and one drug resistant (B11221 from Clade III). Comparing the genomes, we confirm the previously reported finding that B11220 was missing a 12.8 kb region on chromosome VI. This region contains a gene cluster encoding proteins related to alternative sugar utilization. We show that B11221, which has the gene cluster, readily assimilates and utilizes D-galactose and L-rhamnose as compared to B11220, which harbors the deletion. B11221 exhibits increased adherence and drug resistance compared to B11220 when grown in these sugars. Transcriptomic analysis of both isolates grown on glucose or galactose showed that the gene cluster was upregulated when grown on D-galactose. These findings reinforce growing evidence of a link between metabolism and drug tolerance. B11221 resists phagocytosis by macrophages and exhibits decreased β-1,3-glucan exposure, a key determinant that allows Candida to evade the host immune system, as compared to B11220. In a transcriptomic analysis of both isolates co-cultured with macrophages, we find upregulation of genes associated with transport and transcription factors in B11221. Our studies show a positive correlation between membrane composition and immune evasion, alternate sugar utilization, and drug tolerance in C. auris.

Genetic Profile of Greek Indigenous Honey Bee Populations, Local Extinctions, Geographical Distinction, and Patterns, by Using mtDNA COI and Nuclear CSD Gene Analysis Markers

Evaluation and conservation of local genetic resources of the domestic honey bee populations is important, especially in regions with high diversity levels as well as high honey bee colony density. Greece is rich in honey bee biodiversity, hosting several subspecies, with the status of them being, though, doubtful. The purpose of the present study was to investigate the genetic relationships of both stationary and movable honey bee populations, originating from many location throughout Greece. Two molecular markers were utilized, namely, the conserved mitochondrial COI gene and the highly variable complementary sex determination (CSD) gene. Samples were collected from nine distant populations: eight populations from colonies that followed the traditional stationary beekeeping model and one following the modern migratory beekeeping model type, where the hives are transferred from place to place according to the season. Regardless the beekeeping model, all populations were characterized by sufficient genetic diversity indicating no signs of inbreeding or any bottleneck effects. Nevertheless, genetic differentiation and phylogenetic analysis in comparison with haplotypes obtained from GenBank revealed a genetic admixture pattern suggesting that movement causes genetic homogeneity, occasionally in the stable reared populations as well. Interestingly, two populations, namely, Kastoria and Protokklisi, belonging to A. m. macedonica population, were significantly differentiated, supporting the maintenance of their genetic integrity. Unfortunately, on the other hand, genetic structure of the populations from Crete (Sasalos population) provided evidence that the indigenous breed from the island, A. m. adami, has probably gone extinct. Future management strategies should focus on the conservation of the local genetic resources in which distinct genetic identity has been sustained.

Genetic Testing Resources and Practice Patterns Among Pediatric Cardiomyopathy Programs.

The use of genetic testing has enhanced the diagnostic accuracy of heritable genetic cardiomyopathies. However, it remains unclear how genetic information is interpreted and incorporated into clinical practice for children with cardiomyopathy. The primary aim of this study was to understand how clinical practice differs regarding sequence variant classifications amongst pediatric cardiologists who treat children with cardiomyopathy. A secondary aim was to understand the availability of genetic testing and counseling resources across participating pediatric cardiomyopathy programs. An electronic survey was distributed to pediatric heart failure, cardiomyopathy, or heart transplantation physicians between August and September 2022. A total of 106 individual providers from 68 unique centers responded to the survey. Resources for genetic testing and genetic counseling vary among large pediatric cardiomyopathy programs. A minority of centers reported having a geneticist (N = 16, 23.5%) or a genetic counselor (N = 21, 31%) on faculty within the division of pediatric cardiology. A total of 9 centers reported having both (13%). Few centers (N = 13, 19%) have a formal process in place to re-engage patients who were previously discharged from cardiology follow-up if variant reclassification would alter clinical management. Clinical practice patterns were uniform in response to pathogenic or likely pathogenic variants but were more variable for variants of uncertain significance. Efforts to better incorporate genetic expertise and resources into the clinical practice of pediatric cardiomyopathy may help to standardize the interpretation of genetic information and better inform clinical decision-making surrounding heritable cardiomyopathies.

Whole Exome Sequencing as an Effective Molecular Diagnosis Tool for Craniofacial Fibrous Dysplasia with Ocular Complications

Purpose To summarize the clinical manifestations of craniofacial fibrous dysplasia (CFD) patients with ocular complications, and find effective methods to diagnose early. Methods Nine CFD patients with ocular complications, and their parents were recruited in this study. All patients underwent ocular and systemic examinations. Bone lesions from all patients and peripheral blood from patients and their parents were collected for whole exome sequencing (WES). According to the screening for low-frequency deleterious variants, and bioinformatics variants prediction software, possible disease-causing variants were found in multiple CFD patients. The variants were validated by Sanger sequencing. Trio analysis was performed to verify the genetic patterns of CFD. Results All patients were diagnosed with CFD, according to the clinical manifestations, classic radiographic appearance, and pathological biopsy. The main symptoms of the 9 CFD patients, included visual decline (9/9), craniofacial deformity (3/9) and strabismus (2/9), with few extraocular manifestations. The family backgrounds of all the CFD patients indicated that only the patient was affected, and their immediate family members were normal. GNAS variants were identified in all bone lesions from CFD patients, including two variant types: c.601C > T:p.R201C(6/9) and c.602G > A:p.R201H (3/9) in exon 8. The detection rate reached 100% by WES, but only 77.8% by Sanger sequencing. Interestingly, we found GNAS variants could not be detected in peripheral blood samples from CFD patients or their parents, and other potentially disease-causing gene variants related to CFD were not found. Conclusions For CFD patients with bone lesions involving the optic canal or sphenoid sinus regions, ocular symptoms should also be considered. Furthermore, we confirmed that CFD is not inherited, somatic variants in the GNAS gene are the main pathogenic gene causing CFD. Compared to the traditional methods in molecular genetic diagnosis of CFD, WES is more feasible and effective but limited in the type of samples.

Abstract PO4-08-05: Disparities in Genetic Testing Patterns and Positivity Among Patients with Breast Cancer in the CancerLINQ Real-World Oncology Database

Abstract Introduction: Indications for hereditary genetic testing (GT) continue to expand among breast cancer patients (pts), with some guidelines suggesting offering germline GT to all pts diagnosed with breast cancer. The objective of this study was to explore patterns of germline GT and prevalence of pathogenic and likely pathogenic variant (PV) frequency by age, sex, race and ethnicity, and stage at diagnosis within a large, real world oncology database. Methods: The American Clinical Society for Oncology CancerLINQ Discovery breast dataset was used to identify pts with a stage 0-III breast cancer diagnosis who underwent breast surgery at initial diagnosis from 1990-2022. Genetic testing was identified as an available test result from at least one of the following genes: BRCA1/2, ATM, CHEK2, PALB2, TP53, BARD1, BRIP1, CDH1, MHL1, MSH2, MSH6, NF1, RAD51C, or RAD51D. Descriptive statistics were used for comparisons, and adjusted multivariable regression predicting receipt of GT was performed. Results: Overall, 76,978 pts with breast cancer were identified. Of these, 16,284 (21.1%) underwent GT. There were differences in the proportion of pts that underwent GT by age, sex, self-reported race and ethnicity, and stage at diagnosis (Table). Genetic testing decreased with increasing age (59.2% in < 40 vs 7.5% in >=70, p< 0.001) and was more common in men (45.9% vs 21.1% of women, p< 0.001). Genetic testing rates ranged from 18.1-27.7% by race and ethnicity (p< 0.001), with the lowest rates in Non-Hispanic Black (18.1%) and American Indian/Alaskan Native pts (18.2%) and the highest rate in Hispanic pts (27.7%). Genetic testing also differed by stage at diagnosis, with 19.3% of stage I pts vs 25.7% of stage III pts having genetic testing (p< 0.001). On multivariable analysis adjusted for age, sex, race and ethnicity, and stage, male sex was associated with increased likelihood of GT (OR 5.12, 95% CI 4.04-6.49 compared to female sex, p< 0.001) while increasing age (OR 0.05, 95% CI 0.04-0.06 in age >=70 compared to age < 40, p< 0.001) and Non-Hispanic Black or American Indian/Alaskan Native race and ethnicity were associated with decreased likelihood of GT (OR 0.69, 95% CI 0.65-0.73 for Non-Hispanic Black and OR 0.71, 95% CI 0.50-1.00 for American Indian/Alaskan Native pts, compared to Non-Hispanic White pts, p< 0.001); stage was not independently associated with GT. Among those that had GT, PVs were detected in 2,974 (18.3%) pts. PVs were more common in pts < 40 years (27.3% vs 15.0-17.6% in pts >=40, p< 0.001) and in men (26.4% vs 18.2% in women, p< 0.001). Compared by race and ethnicity, PVs were highest among American Indian/Alaskan Native patients (30.2%) and lowest in Non-Hispanic White and Asian/Pacific Islander patients (18.6% and 17.0%, respectively, p< 0.001). There was also a higher prevalence PVs with increasing stage (16.5% for stage 0 and 23.8% for stage III, p< 0.001). Among those with PVs, the distribution was as follows: BRCA1 n=937 (31.5%), BRCA2 n=1176 (39.5%), TP53 n=315 (10.6%), CHEK2 n=238 (8.0%), ATM n=214 (7.2%), and PALB2 n=200 (6.7%). Conclusions: Differences in patterns of GT and PV frequency by age, sex, race and ethnicity, and stage were prevalent. Importantly, despite lower rates of GT, PV frequencies were similar or higher among minority patients and similar among all pts aged 40 and older. Inclusive testing practices and expansion of genetic testing coverage are needed to work towards equitable access to and acceptance of genetic testing. Table. Genetic Testing And Positivity Rates Citation Format: Olga Kantor, Alyssa Jones, Brittany Bychkovsky, Alison Laws, Anna Weiss, Huma Rana, Judy Garber, Rochelle Scheib, Marianna Chavez, Erica Mayer, Tari King, Elizabeth Mittendorf. Disparities in Genetic Testing Patterns and Positivity Among Patients with Breast Cancer in the CancerLINQ Real-World Oncology Database [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-08-05.

Abstract PO5-08-09: Li Fraumeni Syndrome in Breast Cancer Patients of Ceará/Brazil: correlations of genotype - fenotype

Abstract Introduction: Li Fraumeni Syndrome (LFS) is a rare condition determined by germline mutation of TP53 gene. LFS has penetrance near 100% with a broad spectrum of malignances such as breast, lung, sarcomas, choroid plexus, adrenocortical carcinomas, gliomas, leukemia and other starting from early childhood. Breast cancer is the most frequent cancer type of adults with LFS, followed by soft tissue sarcomas. Individuals with LFS has an aggressive prognosis of multiple neoplasms lifetime. In Brazil the most described variant of TP53 is c.1010G >A; p.R337H (the Brazilian variant). This variant affects predominantly individuals of South and Southeastern regions. Usually presents with the same spectrum of tumor of other variants however R337H presents lower penetrance, higher frequency of adrenocortical carcinomas, later onset of tumors. Ceará is a northeastern state of Brazil highly miscegenated distinct from populations of South where predominates European colonization. At Ceará originals there are no description of R337H. The present study describes Clinical and tumoral caractheristics of breast cancer patients with LFS of Cancer Reference Center of Ceará. Methods: from 2018 to 2021 breast cancer patients admitted in Instituto do Câncer do Ceará-ICC filling NCCN criteria for hereditary breast cancer were screened for germline variants. After assigned consent it was offer NGS germline genetic panel of 33 genes and clinical and pathologic data were recorded. Results: 460 BC patients were recruited, of them 6 had germline pathogenic mutation of TP53. Table 1 list these women and their variants. The mean age of the first tumor was 30 years (range 18-44), only one patient had no knowledge of familiar history (HF) of child and adults cancer, all the other listed HF of early onset of breast cancer, lung cancer, osteosarcoma, rabdomyosarcoma, GBM and gastrointestinal cancers. One had bilateral metachronic breast cancer, 3 of them had HER2 positive tumor, 1 had a metaplasic TNBC, and 1 had a Luminal B tumor. 2 variants were not found at populational database (a exons 2-10 microdeletion and a c.637C >T variant). About half of relatives recruited for genetic test confirmed to the carriers and 3 of them developed neoplasms (GBM and breast cancer). Two patient had early recurrence (one of them had a third tumor of ovarian – carcinosarcoma) and died at age of 30 and 39 years old. Conclusion: The Northeast of Brazil has a distint clinical and genetic pattern of LFS from the South. No R337H variant were found in our population. We identified different variants in all patients with LFS. The BC subtype more commom was HER2 positive. The bias of our study is the original objective that evolved determination of prevalence of hereditary breast and ovarian cancer. Based on these results we are now recruiting exclusively cancer patients with clinical criteria for LFS. Table 1 - LFS patients caractheristics Citation Format: Rosane Sant' Ana, Isabelle Joyce Fernandes, Maria Claudia Luciano, Maria Julia Bezerra, Flavio Bitencourt, Clarissa Albuquerquye, Paulo Goberlanio Silva, José Fernando De Moura, Francisca Fernanda Oliveira. Li Fraumeni Syndrome in Breast Cancer Patients of Ceará/Brazil: correlations of genotype - fenotype [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO5-08-09.

Characterization of genetic diversity in Curcuma longa L. cultivars using Start Codon Targeted (SCoT) markers

Curcuma longa L. (Family- Zingiberaceae), commonly called turmeric, is one of the most important commercial spices. Being a center of turmeric's diversity, India boasts of more than fifty cultivars with variable agronomic characters and curcumin content. However, the quest for calibrating their genetic variability remains debatable as popular molecular marker-based studies have yielded inconsistent results. A promising PCR-based approach, known as the Start Codon Targeted (SCoT)-PCR system has been established to be more efficient than random DNA marker systems because this technique can generate more information on genetic polymorphism patterns. Hence, the present study proposes to use Start Codon Targeted (SCoT) markers to assess inter-cultivar genetic diversity of turmeric. We report an orthogonal L16 (45) design-based approach to investigate the influence of five crucial factors (dNTPs, Taq DNA polymerase, primer, template DNA and annealing temperature of primer) on the efficiency of the polymerase chain reaction (PCR) for development of an optimized Start Codon Targeted (SCoT) amplification protocol using twenty-seven different cultivars of C. longa. The optimized PCR protocol yields best results with a 20 uL reaction mixture, containing 10×PCR Buffer (with 15 mM MgCl2), 2.5 mM dNTPs, 10 mM SCoT primer, Taq polymerase (2 U), template DNA (50 ng), which was verified by using twenty-five SCoT primers. This standardized rapid protocol of SCoT-PCR reported here was employed to examine genetic diversity among twenty-seven Indian cultivars of turmeric, revealing high range of polymorphism ranging from 81.25 % to 100 %. Unweighted pair group method of arithmetic averages (UPGMA) cluster analysis of the SCoT marker data segregated the twenty-seven cultivars into two main clusters. The first cluster comprised of nine cultivars (36 % of the cultivars) which was further divided into three sub-clusters and the second one consisted of eighteen cultivars (64 %) which further divided into four sub-clusters. From the results of this study, it can be inferred that the employment of SCoT markers can be an effective tool for analysing genetic variability, phylogenetic relationships and develop a rich genetic resource management system for C. longa cultivars.

Revealing biomarkers and major pathways between SARS-CoV-2 and SARS-like viruses using transcriptomics analysis

SARS-CoV-2 is the causative agent of Coronavirus Disease 2019 (COVID-19). It is common for patients with COVID-19 to present with fatigue, fever, cough, loss of taste and smell, headache, and other clinical manifestations. Several studies have proved that the transmission pathogenicity, genetic patterns of SARS and SARS-CoV-2 are very similar. In this research, we attempted to investigate the transcriptional signature of SARS-CoV-2 in vitro and in vivo, with SARS viruses. Differentially expressed genes (DEG) were identified through analyzing three datasets (GSE147507, GSE17400, and GSE150316). After identification the common DEG between each dataset were applied for pathways as well as gene ontology analysis to comprehend their compatibility. These common DEGs were also employed to generate the protein-protein interaction network, gene regulatory network, and gene co-expression network. The networks illustrated, how genes are regulated by various transcription factors and miRNAs. Overexpression's of many genes are linked to comorbid disorders, malignant cell growth, inflammatory cytokine, and chemokine activation. Finally, some drugs were predicted based on these highly expressed genes, which may have a significant impact on reducing the burden of these diseases in the future.

Distribution of nose types among Igbos of South-East Nigeria

Background: The nose is an important aesthetic unit that is essential in defining the facial appearance of an individual and also helps in identifying a tribe or race. Understanding the distribution of nose types within the Igbo population is crucial for elucidating patterns of human diversity, population genetics, and evolutionary anthropology. The aims of this study were to determine some nasal parameters of Igbo adults, analyze the distribution of the types, check sexual dimorphism, and to correlate the parameters with age, height, weight and body mass index (BMI) respectively Materials and Methods: This was a descriptive cross-sectional study of 312 Igbos in Enugu of Southeastern Nigeria using cluster sampling. The nasal dimensions were measured with digital Vernier’s calipers and the nasal indices were calculated. Weight and height were also measured and BMI calculated. All data were collated and analyzed. Results: The mean age was 37.05 (±15.83). The age range was 20 to 69 years and they were grouped into 20 – 29 years group, 30 – 39, 40 – 49, 50 – 59 and 60 – 69 years groups. The range nasal height was 37.24 - 57.63mm for males, while range for females was 32.43 - 52.97mm. The range for nasal width was 37.04 - 51.29mm for males and 32.93 - 48.52mm for females. The mean nasal widths of males were significantly wider than those of females in all age groups respectively (p < 0.01). The mean nasal indices for males and females were 91.91 (platyrrhine) and 86.26 (platyrrhine) respectively. Majority of the sample population had platyrrhine nose (67%) while 32% of them had mesorrhine nose and only 1% of them had leptorrhine nose. There was a significant positive correlation between height of nose and width of nose of adult Igbos with their age, height and weight (p value <0.01) and a significant negative correlation with body mass index (p <0.01). Conclusion: This study provides valuable insights into the distribution of nose types among the Igbo people of South-East Nigeria. We have characterized the prevalence of different nose types and explored potential associations with demographic and anthropometric factors. The major nose type of Igbos is platyrrhine, while the minor one is mesorrhine. Knowledge of nasal parameters are applied in forensic studies; and in surgeries involving the nose, and this ensures that individuals do not lose their identities even after extensive nasal surgeries.

Bridging Genetic Insights with Neuroimaging in Autism Spectrum Disorder-A Systematic Review.

Autism Spectrum Disorder (ASD) is an early onset neurodevelopmental disorder characterized by impaired social interaction and communication, and repetitive patterns of behavior. Family studies show that ASD is highly heritable, and hundreds of genes have previously been implicated in the disorder; however, the etiology is still not fully clear. Brain imaging and electroencephalography (EEG) are key techniques that study alterations in brain structure and function. Combined with genetic analysis, these techniques have the potential to help in the clarification of the neurobiological mechanisms contributing to ASD and help in defining novel therapeutic targets. To further understand what is known today regarding the impact of genetic variants in the brain alterations observed in individuals with ASD, a systematic review was carried out using Pubmed and EBSCO databases and following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. This review shows that specific genetic variants and altered patterns of gene expression in individuals with ASD may have an effect on brain circuits associated with face processing and social cognition, and contribute to excitation-inhibition imbalances and to anomalies in brain volumes.

Population, culture history, and the dynamics of change in European prehistory★

AbstractDespite many attacks on its shortcomings, culture history has remained in practice the dominant framework for describing and interpreting European prehistory. It has gained even more salience in recent years because the new information coming from ancient DNA about the genetic ancestry of individuals in prehistory seems to show that this correlates closely with the cultural affiliation of the archaeological material with which they are found, raising concerns that old and discredited links between biological and cultural identity are being revived. This article argues that exploring the links between cultural and genetic ancestry does not need to fall into these errors if it takes its theory and methods from the discipline of cultural evolution and rejects characterization of the relationship in terms of ‘ethnic groups’. This involves describing the archaeological record in more fine‐grained, less essentialist ways and at the same time linking the archaeological and genetic patterns to histories of the rise and decline of populations and the interactions between them.

Genetic diversity patterns within and among varieties of Korean orchardgrass (Dactylis glomerata L.) based on SSR and EST-SSR analysis

Genetic diversity patterns within and among varieties of Korean orchardgrass (Dactylis glomerata L.) based on SSR and EST-SSR analysis

Exploration of genetic variability in Garcinia [<i>Garcinia gummi-gutta</i> L.(Robson)] germplasm based on growth, yield and quality traits

Eleven Garcinia germplasm along with local check of Pechiparai were evaluated and underwent principal component analysis to assess genetic divergence and variation patterns during 2019 to 2022. The first two principal components, contributing significant Eigen values, explained 71.20% of the total variability. The Acc. Gg 9 was the top performer, exhibiting favourable yield and growth traits with lower pest and disease incidence, high biochemical compounds viz., hydroxy citric acid and tartaric acid compared to local check. Cluster analysis revealed four major clusters, offering diversity for breeding programs. Correlation studies highlighted traits such as number of fruits per tree, rind thickness, and tartaric acid showing significant positive correlations with yield per tree. Selection based on identified key traits was deemed crucial for enhancing effectiveness. Additionally, DNA fingerprinting analysis indicated the potential use of RAPD markers (OPA03570) for differentiating Kudampuli cultivar PPI (K) 1 from the local check. Overall, the present investigation provides insights into optimizing Garcinia breeding programs, emphasizing trait-based selection and DNA fingerprinting for varietal differentiation.

Effects of past riverine connectivity on the population structure and species distribution of ‘Geophagus’ brasiliensis (Cichlidae) complex in a Neotropical hotspot

Abstract Once fishes and rivers are intrinsically connected, historical events such as river captures and the reconfiguration of palaeodrainages affect population structure and species distribution. However, direct evidence of these events remains limited. We aimed to directly infer putative connections between adjacent river basins to understand genetic and geographical patterns in populations and species of the ‘Geophagus’ brasiliensis complex. For that, we analysed 174 sequences of the mitochondrial gene cytochrome c oxidase subunit I (COI) from five species along 35 sites within and near a coastal basin in northeastern Brazil. Based on haplotype network, palaeodrainage reconstruction, geological inferences of river captures and analyses of molecular variance (AMOVAs), we tested how the genetic structure could be associated with variable patterns of habitat connectivity through time. In general, high levels of genetic variation were identified, including shared haplotypes among drainages for most species. AMOVA suggested that drainage rearrangements between adjacent basins were the main drivers of genetic diversification in the ‘G.’ brasiliensis complex. Our study refuted dispersal routes via the continental shelf, whereas eight putative river captures suggested historical connections that enabled gene flow among drainages until recent interruption. These results provide novel insights on the role of riverscape evolution on the biogeography of neotropical ichthyofauna.

Benchmarking kinship estimation tools for ancient genomes using pedigree simulations.

There is growing interest in uncovering genetic kinship patterns in past societies using low-coverage palaeogenomes. Here, we benchmark four tools for kinship estimation with such data: lcMLkin, NgsRelate, KIN, and READ, which differ in their input, IBD estimation methods, and statistical approaches. We used pedigree and ancient genome sequence simulations to evaluate these tools when only a limited number (1 to 50 K, with minor allele frequency ≥0.01) of shared SNPs are available. The performance of all four tools was comparable using ≥20 K SNPs. We found that first-degree related pairs can be accurately classified even with 1 K SNPs, with 85% F1 scores using READ and 96% using NgsRelate or lcMLkin. Distinguishing third-degree relatives from unrelated pairs or second-degree relatives was also possible with high accuracy (F1 > 90%) with 5 K SNPs using NgsRelate and lcMLkin, while READ and KIN showed lower success (69 and 79% respectively). Meanwhile, noise in population allele frequencies and inbreeding (first-cousin mating) led to deviations in kinship coefficients, with different sensitivities across tools. We conclude that using multiple tools in parallel might be an effective approach to achieve robust estimates on ultra-low-coverage genomes.

Patrilineal segmentary systems provide a peaceful explanation for the post-Neolithic Y-chromosome bottleneck

Studies have found a pronounced decline in male effective population sizes worldwide around 3000–5000 years ago. This bottleneck was not observed for female effective population sizes, which continued to increase over time. Until now, this remarkable genetic pattern was interpreted as the result of an ancient structuring of human populations into patrilineal groups (gathering closely related males) violently competing with each other. In this scenario, violence is responsible for the repeated extinctions of patrilineal groups, leading to a significant reduction in male effective population size. Here, we propose an alternative hypothesis by modelling a segmentary patrilineal system based on anthropological literature. We show that variance in reproductive success between patrilineal groups, combined with lineal fission (i.e., the splitting of a group into two new groups of patrilineally related individuals), can lead to a substantial reduction in the male effective population size without resorting to the violence hypothesis. Thus, a peaceful explanation involving ancient changes in social structures, linked to global changes in subsistence systems, may be sufficient to explain the reported decline in Y-chromosome diversity.

Genomic Diversity and Recombination Analysis of the Spike Protein Gene from Selected Human Coronaviruses.

Human coronaviruses (HCoVs) are seriously associated with respiratory diseases in humans and animals. The first human pathogenic SARS-CoV emerged in 2002-2003. The second was MERS-CoV, reported from Jeddah, the Kingdom of Saudi Arabia, in 2012, and the third one was SARS-CoV-2, identified from Wuhan City, China, in late December 2019. The HCoV-Spike (S) gene has the highest mutation/insertion/deletion rate and has been the most utilized target for vaccine/antiviral development. In this manuscript, we discuss the genetic diversity, phylogenetic relationships, and recombination patterns of selected HCoVs with emphasis on the S protein gene of MERS-CoV and SARS-CoV-2 to elucidate the possible emergence of new variants/strains of coronavirus in the near future. The findings showed that MERS-CoV and SARS-CoV-2 have significant sequence identity with the selected HCoVs. The phylogenetic tree analysis formed a separate cluster for each HCoV. The recombination pattern analysis showed that the HCoV-NL63-Japan was a probable recombinant. The HCoV-NL63-USA was identified as a major parent while the HCoV-NL63-Netherland was identified as a minor parent. The recombination breakpoints start in the viral genome at the 142 nucleotide position and end at the 1082 nucleotide position with a 99% CI and Bonferroni-corrected p-value of 0.05. The findings of this study provide insightful information about HCoV-S gene diversity, recombination, and evolutionary patterns. Based on these data, it can be concluded that the possible emergence of new strains/variants of HCoV is imminent.

Population assignment of migratory Westslope Cutthroat Trout (WCT) in the Clark Fork–Pend Oreille River basin

AbstractObjectiveThe Clark Fork–Pend Oreille River basin of northeastern Washington and the Idaho Panhandle historically supported a robust metapopulation of the Westslope Cutthroat Trout (WCT) Oncorhynchus lewisi, a western native salmonid of high cultural and economic value. The construction of impassible hydroelectric dams and smaller instream barriers has prevented the return of migratory WCT to spawning tributaries, leading to the fragmentation of this metapopulation over the past 100 years. One such impassible barrier is Albeni Falls Dam (AFD) near Newport, Washington, which was completed without fish passage capabilities in 1955. We sought to examine large‐scale genetic patterns in the study area and determine the most likely spawning tributary of origin for migratory WCT captured below AFD.MethodsWe created a genetic baseline representative of populations within the Clark Fork–Pend Oreille River basin from upstream and downstream of the dam using 191 biallelic single‐nucleotide polymorphism genetic markers. Our data set included 124 collections, which allowed for an examination of population structure and hatchery influence across the study area and provided a robust tool for population assignment. Population assignment tests were conducted using the program RUBIAS.ResultPopulation assignment tests were successful for all pure WCT of unknown origin despite potential influence from hatchery lineages across the study area. Of 83 migratory WCT captured below AFD, approximately 80% were assigned to tributaries upstream of AFD with a posterior assignment probability of at least 90%. Only one fish was assigned to a tributary downstream of AFD.ConclusionOur results indicate that AFD disrupts the natural metapopulation dynamics of WCT populations in the basin. Passage for WCT at this barrier would reestablish metapopulation connectivity within the basin by allowing migratory individuals to make genetic contributions to populations upstream of the dam.

Genetic potential and inheritance pattern of agronomic traits in faba bean under free and infested Orobanche soil conditions

BackgroundOrobanche is an obligate parasite on faba bean in the Mediterranean region, causes considerable yield losses. Breeding tolerant faba bean genotypes to Orobanche is pivotal to sustain production and ensuring global food security, particularly considering the challenges posed by population growth. In the present study, seven faba bean lines and four testers were used in a line×tester mating design during 2020–2021 and 2021–2022 growing seasons. The eleven parents and their 28 F1 crosses were evaluated under Orobanche free and naturally infested soils.ResultsThe results demonstrated considerable variations among the evaluated genotypes, wide diversity among the parental materials, and heterotic effects for all studied agronomic traits under Orobanche-free and infested soils. Orbanche infestation displayed a significant adverse impact on all the studied agronomic traits. The genotypes Line1, Line2, Line3, and Line5 displayed superior performance under Orobanche-infested conditions and recorded the highest values of all studied agronomic traits. Additionally, Line1, Line2, Line3, Line5, and Line7 exhibited desirable significant GCA for most evaluated traits under the two infestation conditions. The obtained crosses displayed significant negative or positive heterosis for studied agronomic characters such as plant height, number of branches per plant, number of pods per plant, number of seeds per plant, and seed weight per plant were observed. Furthermore, specific cross combinations such as Line2×Sakha3, Line3×Nubaria5, Line7 × Nubaria5, Line6×Nubaria1, Line5×Sakha3, Line1×Sakha3, and Line1 × Nubaria5 exhibited superior performance in seed yield and contributing traits under Orobanche-infested conditions. Moreover, these specific crosses showed superior efficacy in reducing dry weight of Orobanche spikes. The results obtained from GGE biplot analysis closely aligned with those from the line×tester procedure, affirming the significance of GGE biplot as a valuable statistical tool for assessing genotype combining ability in line× tester data. Both additive and non-additive gene actions were reported to be predominantly involved in the inheritance of the studied agronomic traits in faba bean.ConclusionsThe detected genetic diversity within the evaluated faba bean genotypes and their developed crosses exhibits substantial potential for improving faba bean productivity under Orobanche-infested conditions. The parental genotypes, Line1, Line2, Line3, Line5, and Line7, were identified as effective and promising combiners. Moreover, the developed crosses Line2×Sakha3, Line3×Nubaria5, Line7×Nubaria5, Line6×Nubaria1, Line5×Sakha3, Line1×Sakha3, and Line1×Nubaria5 could be considered valuable candidates for developing high-yielding and tolerant faba bean genotypes to Orobanche.