Search Results (201)

This Y-chromosome study of Moroccan Jews, the largest conducted to date, analyzes the patrilineal origins of 288 men of genealogically verified Moroccan Jewish descent through the Avotaynu DNA Project, identifying 111 distinct founder lineages. The long-standing hypothesis of large-scale Berber Judaization has not previously been tested at full Y-chromosome resolution; our findings provide the first systematic evidence against it. Approximately 71% of founder lineages and 80% of individuals trace to haplogroups common in the Middle East. Only 4.5% of founder lineages are of autochthonous North African origin. Iberian-origin lineages account for 11% of Moroccan Jewish founder lineages reflecting sustained demographic and cultural exchange between Morocco and the Iberian Peninsula over many centuries. Split dates between Moroccan and Ashkenazi or Sephardic subclades cluster between the 5th and 8th centuries CE, suggesting that the ancestral lineages of contemporary Moroccan Jews were already present across the Mediterranean basin during late Antiquity and the early medieval period. Analysis of 190 distinct Moroccan Jewish surname roots identifies 29 polygenic and 30 monogenic surnames, and demonstrates that the linguistic origin of a surname, including surnames of Maghrebi morphology, does not necessarily reflect its bearer’s Y-chromosome ancestry. Unlike Ashkenazi Jews, Moroccan Jews show no evidence of a founder effect or genetic bottleneck, and display a remarkable patrilineal diversity. Among the individual lineages documented here are the first paleogenetic link between a contemporary Moroccan Jewish patriline and a victim of the 1348 Tàrrega pogrom, an Iberian/Ashkenazi split traceable to tenth-century al-Andalus, and an unexpected connection between a predominantly Moroccan Jewish lineage and the Saint Thomas Syrian Christian community of Kerala. Moroccan Jewish patrilineal heritage is overwhelmingly Middle Eastern in origin and has been preserved with remarkable continuity across two millennia of diaspora, persecution, and migration. Full article

SARS-CoV-2, the causative agent of COVID-19, emerged in late 2019 and rapidly developed into a global health crisis. In this study, we analysed 173,194 SARS-CoV-2 genomes from the GISAID database to explore the intra-continental dynamics and distribution of variants across Africa between 2020 and 2024. We have identified 1377 distinct lineages, which were classified by clade to assess associations with infection and mortality rate. So, we conducted a Shannon entropy analysis to confirm the diversity and we applied a Correspondence Analysis (CA). Our findings revealed that one of the deadliest in Africa during the Delta wave, lineage AY.45 predominated in the South Africa cluster, whereas AY.34.1 drove transmission in the Atlantic West Africa cluster, underscoring regional heterogeneity. Furthermore, early in the pandemic, men exhibited a 39% higher risk of infection compared to women (aOR: 1.39, 95% CI [1.34–1.45]), particularly in association with clade G. By contrast, later stages were dominated by clade GRA, which disproportionately affected the elderly (≥70 years; aOR: 1.39, 95% CI [1.33–1.45]) and children (0–9 years; aOR: 1.26, 95% CI [1.20–1.33]). Our analysis highlighted that the pandemic on the African continent unfolded as a mosaic of epidemics shaped by diverse variants and regional epidemiological contexts. These findings emphasize the importance of genomic surveillance to capture local epidemic signatures and inform region-specific public health strategies. Full article

The latest Cretaceous saw the final diversification of dinosaurs before the K/Pg extinction. Discussions of end-Cretaceous dinosaur diversity have focused on well-sampled faunas from Laurasia; far less is known about dinosaurian faunas of the Southern Hemisphere, especially Africa. The late Maastrichtian Phosphates of Morocco provide a rare window into African dinosaur diversity. Abelisaurids, lambeosaurines, and titanosaurian sauropods are known. However, no diagnostic titanosaur remains have been recovered, leaving the affinities of these sauropods unclear. We describe Phosphatotitan khouribgaensis gen. et sp. nov., a new titanosaur from the Maastrichtian of Sidi Chennane, Khouribga Province. Phosphatotitan is represented by dorsal, sacral, and caudal vertebrae, and the pelvis. The new species differs from titanosaurs described from the Cretaceous of Africa and Europe but resembles South American Lognkosauria, and especially Patagotitan, in having short dorsal and caudal centra, expanded dorsal and caudal neural spines, and a broad pubis. Its small size relative to other Lognkosauria (3.5–4 tonnes) suggests a lineage selected for small size. The close relationships of Morocco’s titanosaurs and abelisaurids to South American species may reflect a wide distribution of these clades prior to the opening of the South Atlantic and the separation of Africa and South America ~100 Ma, while a complex pattern of oceanic dispersal may explain the presence of distinct saltasauroid lineages worldwide. The latest Cretaceous Gondwanan dinosaur faunas were highly endemic due to a combination of continental fragmentation, extinction, and dispersal, creating high endemism in southern continents and within Africa, suggesting that Maastrichtian dinosaur diversity is underestimated. Full article

Chikungunya virus (CHIKV) infection presents a wide spectrum of clinical outcomes, ranging from mild self-limiting disease to severe and fatal manifestations, which are influenced by both host and viral factors. Animal models are essential for elucidating CHIKV pathogenesis and for preclinical evaluation of antiviral strategies; however, a well-characterized model evaluating the effect of different viral doses in AG129 mice remains limited. In this study, we investigated the clinical, virological, and pathological outcomes of CHIKV infection in male AG129 mice inoculated intraperitoneally with different viral doses (10, 100, and 1000 PFU/mL) of a Brazilian strain belonging to the East/Central/South African (ECSA) lineage. Lower-dose inoculation (10 PFU/mL) resulted in a milder disease course, characterized by transient viremia, limited tissue viral dissemination, minimal histopathological alterations, partial survival, and viral clearance. In contrast, higher doses (≥100 PFU/mL) led to rapid systemic viral dissemination, severe histopathological damage in the spleen, liver, and kidneys, and uniform lethality. Viral RNA was detected in serum and multiple organs in a time-dependent manner, with limited differences among inoculum doses in most tissues. Notably, dose-related differences were observed in specific compartments and time points, particularly in hind-limb muscles at early time points and in serum at later stages. Full article

The European Middle Pleistocene represents a critical spatiotemporal interval in human evolution, marked by increasing morphological variability and ongoing debate regarding the evolutionary processes leading to the emergence of Neandertals. In particular, it remains unclear whether this variability reflects the coexistence of multiple evolutionary lineages within Europe or structured variation within a single, evolving lineage. Within this context, the site of Bilzingsleben (Thuringia, Germany) provides a key contribution to discussions of European Middle Pleistocene population structure. This study presents a detailed morphological assessment of the Bilzingsleben E7 mandibular fragment, integrating qualitative anatomical observations with quantitative analyses of discrete characters. The Bilzingsleben mandible was examined directly and evaluated within a broad comparative framework including European Middle Pleistocene hominins, Neandertals, and selected African and Asian specimens. Multivariate analyses, including Principal Coordinates Analysis (PCoA) and neighbor-joining cluster analysis based on Gower distances, were used to explore patterns of morphological affinity. Qualitative analysis indicates that the Bilzingsleben mandible exhibits a mosaic combination of predominantly primitive features—such as multiple mental foramina, marked lateral relief of the corpus, and a weakly developed submandibular fossa—together with a limited number of incipiently derived traits, including posterior extension of the corpus and a downward orientation of the digastric fossae. Quantitative results consistently place Bilzingsleben within the morphological variability of European Middle Pleistocene hominins but outside the compact Neandertal cluster. In the PCoA, Bilzingsleben occupies an intermediate (PCo1) and peripheral position (PCo2), contrasting with more centrally positioned specimens such as Mauer. Taken together, these results support an interpretation of Bilzingsleben as part of a European Middle Pleistocene set of populations exhibiting mosaic morphology, rather than considering Bilzingsleben as evidence for a distinct evolutionary lineage. When integrated with evidence from other anatomical elements from Bilzingsleben, the mandibular morphology supports interpreting this population within the broader evolutionary context of the Neandertal lineage. Full article

This study investigates the role of naming practices as cultural repositories that preserve family, lineage, and community identity. It explores how anthroponymy encodes histories of ancestry, migration, settlement, and sociopolitical organisation in two West African societies, Dàgáárè-speaking communities and Yorùbá communities. Adopting a comparative onomastic ethnographic approach, this research analyses names among the two selected cultures. Data is drawn from interviews, school registers, attendance sheets, and cultural practices, with emphasis on how names record genealogical descent, settlement histories, occupational roles, spiritual affiliations, and ethical expectations. In Dàgáárè and Yorùbá culture, bal/baloo yoe (clan names) and lineage names identify descent from founding ancestors, document migration and settlement, mark ritual responsibilities, memorialise historical events, and regulate kinship and marriage through totemic and spiritual identities. This study argues that names in Dàgáárè- and Yorùbá-speaking societies operate as cultural texts that preserve and transmit heritage across generations. The significant implications extend to linguistics, anthropology, and heritage studies, where names can be leveraged as tools for cultural preservation and historical analysis. Full article

Background: Ecuador is a genetically diverse population setting shaped by long-term interactions among Native American, European, and African populations across distinct ecological regions. Although multiple studies have examined ancestry patterns in Ecuadorian populations, the available evidence remains fragmented and methodologically heterogeneous. Objective: To systematically identify, critically appraise, and synthesize published studies on genetic ancestry and population structure in Ecuador. Methods: A systematic review was conducted in accordance with PRISMA 2020. Searches were performed in PubMed/MEDLINE, Scopus, Web of Science Core Collection, SciELO, and Google Scholar through 31 January 2026. Eligible studies reported extractable ancestry-related data from Ecuadorian populations using autosomal, mitochondrial DNA, Y-chromosomal, or other ancestry-relevant genetic markers. Methodological quality was assessed using an adapted Joanna Briggs Institute framework. Owing to substantial heterogeneity across marker systems, sampling strategies, and ancestry inference methods, findings were synthesized qualitatively rather than by meta-analysis. Results: Of 1243 records identified, 12 studies met the inclusion criteria. Across marker systems, the evidence consistently supported a three-way admixture framework involving Native American, European, and African ancestry components, together with substantial regional and population-specific heterogeneity. Autosomal studies generally showed higher Native American ancestry in Highland and Native American populations, whereas African ancestry was more prominent in Afro-Ecuadorian and some Coastal populations. Uniparental markers further supported persistent sex-biased admixture, with predominant Native American maternal lineages and comparatively greater European or African paternal contributions depending on region and population history. Conclusions: Ecuadorian populations share a broad three-way admixture framework, but with marked internal heterogeneity across regions and population groups. These findings highlight the importance of geographic and demographic context in ancestry interpretation and the need for larger, more balanced, and methodologically standardized genomic studies in Ecuador. Full article

Human Immunodeficiency Virus Type 1 (HIV-1), the causative agent of the acquired immune deficiency syndrome (AIDS), originated from zoonotic transmissions of simian immunodeficiency viruses (SIVs) infecting African great apes, following complex cross-species transmission events and virus–host co-evolution. These processes were accompanied by multiple viral adaptations, particularly within structural and accessory genes, enabling evasion of host restriction factors and long-term viral persistence. In 1988, an antisense open reading frame (ORF) overlapping the env gene was proposed and subsequently confirmed by the identification of antisense transcripts and the antisense protein (ASP). An “intact” ASP ORF (defined as >150 codons) is predominantly conserved in pandemic HIV-1 group M viruses and shows evidence of positive selection, suggesting a selective advantage. Increasing evidence supports the hypothesis that the asp gene emerged de novo during the evolution of group M and contributed to viral adaptation and global spread in humans. This review combines a narrative review of the literature with original in silico analyses of HIV-1 and SIV sequences retrieved from the Los Alamos National Laboratory database. We systematically reassessed the distribution, length variability and conservation of the ASP ORF across HIV-1 groups (M, N, O, P), subtypes, circulating recombinant forms (CRFs), unique recombinant forms (URFs) and related SIV lineages. Our updated analyses confirmed the strong association between the presence of an “intact” ASP ORF and pandemic HIV-1 group M lineages, while revealing rare but notable antisense ORFs in selected SIVcpz and SIVgor strains. By integrating evolutionary, epidemiological and sequence-based evidence, we aim to clarify the origin and maintenance of the ASP ORF and to contextualize its emergence within the broader framework of overlapping gene evolution, de novo gene birth and the selective pressures shaping viral fitness and pandemic potential. Full article

African swine fever (ASF) has been a persistent threat to Eurasian pig populations since its emergence in 2007. The disease has become endemic in numerous countries, including Poland, Germany, Romania, Hungary, Italy, the Philippines, and several others. Epidemiological data reveals that over 99% of outbreaks are attributed to a highly virulent hemadsorbing virus belonging to genotype II. Traditional genotyping methods, primarily relying on the B646L gene, have faced significant limitations in providing a comprehensive understanding of virus dissemination patterns. Previous attempts to identify a universal marker for tracking virus spread through analysis of the CVR locus of the B602L gene and the I73R/I329L locus failed to produce a coherent picture of the virus’s geographical distribution across Eurasia. To address these challenges, a comprehensive study was conducted involving the analysis of 250 ASFV isolates/strains from 25 countries across Europe and Asia between 2007 and 2024. This research led to the development of a novel sub-genotyping algorithm for ASFV genotype II. The study identified four topotypes: «CAU1», «EU1», «EU2», and «ASIA1». Within these topotypes, 31 genetic lineages were detected, each characterized by specific single-nucleotide polymorphisms (SNPs). Based on the comparison of two methods of sub-genotyping Eurasian ASFVs—the classification by Gallardo C. et al. (2023) based on genetic variations of 6 loci, and the proposed classification into topotypes and genetic lineages using whole-genomes—it was established that the multigenic approach has insufficient resolution. At the same time, significant differences were observed at the level of whole-genomes. The creation of a new spatiotemporal classification has significant applications in international surveillance of ASF outbreaks, local disease monitoring, and investigation of new infection cases. Full article

This study investigated the genetic diversity and population structure of five Hainan indigenous pig breeds (147 individuals from 7 populations representing 5 breeds: 3 Duntou pig subpopulations (DT-DZ, DT-SJ, and DT-SG) and four additional breeds (Wuzhishan, Wenchang, Lingao, and Tunchang)) to address germplasm conservation needs driven by exotic crossbreeding, African swine fever, and inadequate genetic evaluation. After strict quality screening, we used 147 qualified samples for microsatellite genotyping and 104 samples for mtDNA D-loop sequencing. The analyses integrated 17 FAO-recommended microsatellite markers and mtDNA D-loop sequencing. In total, 15 out of 17 loci exhibited high polymorphism (PIC > 0.6), with Wuzhishan pigs exhibiting the highest genetic diversity (He = 0.666, I = 1.279). Pairwise Fst values indicated significant genetic differentiation among all populations (p < 0.05), and AMOVA attributed 87.32% of the genetic variation to within-population differences. Three complementary clustering methods (UPGMA, PCoA, and STRUCTURE with the optimal K value of 2 identified via the ΔK algorithm) divided the populations into two clades, clearly separating the Duntou subpopulations from other breeds. mtDNA D-loop sequencing of 104 individuals yielded a 1175 bp fragment, identifying 12 haplotypes and a high haplotype diversity (Hd = 0.688) low nucleotide diversity (π = 0.00193) pattern; Lingao pigs showed no genetic variation, while Duntou and Wuzhishan pigs had the highest Hd. NJ phylogenetic analysis indicated that Hainan pigs form an independent subclade within Chinese indigenous pigs, closely related to Luchuan pigs. These findings confirm the high overall genetic diversity and distinct population-level divergence in Hainan pigs, with Duntou pigs representing a unique lineage. This work provides a scientific basis for targeted conservation strategies, including prioritizing the conservation of Duntou and Wuzhishan pigs and restoring genetic variation in Lingao pigs. Full article

(1) Background. Parabuthus liosoma is one of the largest buthid scorpion species and is endemic to Saudi Arabia and Yemen. This study provides the first DNA barcoding and phylogenetic analysis of P. liosoma from Saudi Arabia, contributing to global efforts in arachnid molecular identification and biodiversity documentation. (2) Methods. The whole genome was extracted from nine adult individuals of P. liosoma, collected from Farasan Island, southwest of Saudi Arabia. A portion of the mitochondrial DNA, specifically, the cytochrome oxidase subunit I gene (COI) sequences, was amplified and sequenced and subjected to genetic and phylogenetic analyses. (3) Results. The DNA barcoding results revealed a high level of genetic variability within P. liosoma, aiding in species identification and supporting its utility as a molecular tool for scorpion taxonomy. In addition, our results reveal a monophyletic relationship among Parabuthus species, with a clear distinction between Arabian and African lineages. (4) Conclusions. This study highlights the effectiveness of DNA barcoding as a reliable tool for species identification and taxonomy and enhances our knowledge of the evolutionary history and geographic distribution of Parabuthus scorpions. However, further research is required to elucidate the complex phylogenetic relationships within this genus. Full article

This study investigates the genomic basis of immune adaptation in the transparent glass catfish (Kv: Kryptopterus vitreolus), focusing on the loss of the Toll-like receptor 21 (TLR21) gene. Comparative genomic analysis with closely related non-transparent North African catfish (Cg: Clarias gariepinus) revealed 11 TLR genes in the latter, while only 8 TLR genes (KvTLR1, 2, 3, 5, 7, 9, 13, and 20) were retained in the glass catfish, with TLR21 specifically absent. Collinearity analysis confirmed that the genomic region containing TLR21 is conserved across eight siluriform species, with loss exclusively in the glass catfish, supporting its lineage-specific absence. Structural expansion was notable in KvTLR5, KvTLR7, and KvTLR20. Molecular docking indicated that binding stability between CpG oligonucleotides and TLR21 varies significantly, with CpG-B 1681 showing the strongest interaction, which highlights sequence-dependent ligand recognition. Interestingly, absence of the TLR1 gene in another transparent teleost, the X-ray tetra (Pristella maxillaris), suggests that transparent fishes may share an evolutionary trend of lineage-specific TLR gene loss. Together, these findings reveal a distinctive evolutionary trajectory in the innate immune receptor family of transparent fishes and provide new molecular insights into their adaptive immune strategies. These insights will benefit the academic community by improving comparative frameworks for fish innate immunity, and they may inform disease prevention and health management strategies in aquaculture and the ornamental fish trade. Full article

Background/Objectives: Segmental duplications (SDs) are major drivers of genome evolution and structural variation in primates, particularly within acrocentric chromosomes, where rDNA arrays and duplicated sequences are densely clustered. However, the evolutionary dynamics of rDNA-linked SDs across great ape lineages have remained poorly characterized due to longstanding technical limitations in genome assembly. Here, we investigate the organization, copy number variation, and evolutionary conservation of acrocentric SDs in great apes by integrating fluorescence in situ hybridization (FISH) with comparative analyses of telomere-to-telomere (T2T) genome assemblies. Methods: Using eight human-derived fosmid probes targeting SD-enriched regions flanking rDNA arrays, we analyzed multiple individuals from chimpanzee, bonobo, gorilla, and both Bornean and Sumatran orangutans. Results: Our FISH analyses revealed extensive lineage-specific variation in SD copy number and chromosomal distribution, with pronounced heteromorphism in African great apes, particularly gorillas, and more conserved patterns in orangutans. Several SDs showed fixed duplications across species, while others exhibited high levels of polymorphism and individual-specific organization. Conclusions: Comparison with T2T assemblies confirmed consistent genomic localization for a subset of probes, whereas others displayed partial discordance, highlighting the persistent challenges in resolving highly repetitive and structurally dynamic regions even with state-of-the-art assemblies. Genome-wide analyses further revealed species-specific enrichment of SDs on rDNA-bearing chromosomes, with chimpanzees and bonobos showing higher proportions than gorillas, and contrasting patterns between the two orangutan species. Overall, our results demonstrate that rDNA-linked SDs represent highly dynamic genomic compartments that have undergone differential expansion and remodeling during great ape evolution. These regions contribute substantially to inter- and intra-species structural variation and provide a mechanistic substrate for lineage-specific genome evolution, underscoring the importance of integrating cytogenetic and T2T-based approaches to fully capture the complexity of duplicated genomic landscapes. Full article

Orbea is a morphologically diverse lineage within the subtribe Stapeliinae, yet plastome evolution in Arabian taxa remains insufficiently characterized. This study reports the first complete chloroplast genomes of Orbea sprengeri subsp. commutata and O. wissmannii var. eremastrum and investigates plastome structure, sequence variability, and phylogenetic relationships across tribe Ceropegieae. Chloroplast genomes were assembled, annotated, and compared with 13 published plastomes representing major Ceropegieae lineages. Both Arabian plastomes displayed the typical quadripartite structure and identical gene content of 114 unique genes, including 80 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. However, O. wissmannii var. eremastrum exhibited pronounced structural divergence, possessing the largest plastome recorded for the tribe (170,054 bp), an 8.9 kb expansion of the inverted repeat regions, and an 8.4 kb inversion spanning the ndhG–ndhF region. Comparative analyses revealed conserved gene order across Ceropegieae but identified six highly variable loci (accD, clpP, ndhF, ycf1, psbM–trnD, and rpl32–trnL) as potential DNA barcodes. Selection pressure analyses indicated strong purifying selection across most genes, with localized adaptive signals in accD, ndhE, ycf1, and ycf2. Phylogenomic reconstruction consistently resolved the two Arabian Orbea taxa as a distinct clade separate from the African O. variegata. This study fills a gap in Ceropegieae plastid genomics and underscores the importance of sequencing additional Orbea species to capture the full extent of genomic variation within this diverse genus. Full article

The incidence of tuberculosis disease (TBD) in New Brunswick (NB) is low but has been rising over the past decade. Analyzing these trends can help identify specific risk factors and transmission patterns to guide targeted public health strategies. This study aimed to provide a comprehensive and detailed characterization of TBD in NB by examining data from 1 January 2002, to 31 December 2024. All TB patients with Mycobacterium tuberculosis complex (MTBC) clinical isolates identified in NB healthcare facilities were eligible for inclusion in the study. We analyzed demographic, drug susceptibility, and 24-locus Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem Repeat (MIRU-VNTR) data from 166 patients. Most MTBC isolates were pan-susceptible to first-line anti-tuberculosis drugs (90.9–98.1%), with 2.4% showing multidrug resistance. The MIRU-VNTR demonstrated a high discriminatory power of 0.9982 and a low clustering rate of 20.4%. Two samples from the same patient, collected seven years apart, showed different genetic profiles, suggesting that the second episode was a new infection. The most prevalent MTBC lineage was East African Indian (n = 23, 13%). This study provides early insights into TB trends in NB, including what may be the first recorded case of TB reinfection in NB. Our findings will help guide future TB research, policies, and public health interventions in the region. Full article