Baobab Index

Non-native rodents serve as bridges between anthropogenic and natural landscapes. They have expanded across the planet alongside humans while bringing competition, predation, and pathogens, such as poxviruses, to naïve ecosystems. Although rodents serve as reservoirs for multiple zoonotic poxviruses, limited research has focused on rodents for identification of unknown poxviruses. Here, we characterized a divergent metagenome-assembled poxvirus, madamurpox virus, from the oral swab of a black rat in southeastern Madagascar. While madamurpox virus shares a phylogenetic relationship with human-infecting molluscum contagiosum virus and bat-associated Rousettus poxvirus, madamurpox virus presents extensive genetic variation and represents a putative new species and genus in the Chordopoxvirinae subfamily. Further, although madamurpox virus has a similar genome organization to molluscum contagiosum virus and Rousettus poxvirus, madamurpox virus lacks key immune modulators seen in molluscum contagiosum virus. Our findings highlight that substantial unexplored poxvirus diversity likely exists in rodents, with globally distributed, non-native rodent populations of increased interest.

Intestinal infections remain highly prevalent among children living in rural, resource-limited settings, where repeated exposure to environmental pathogens begins early in life. In such contexts, enteric infections often represent chronic colonization rather than acute disease, frequently involving simultaneous carriage of parasitic and bacterial pathogens. Despite growing interest in intestinal co-infections, data on parasitic-bacterial co-occurrence, particularly among asymptomatic children in endemic settings, remain limited. Madagascar, characterized by high endemicity of intestinal parasites and major gaps in water and sanitation infrastructure, provides a relevant setting to investigate these patterns. A community-based cross-sectional study was conducted among 242 children under 15 years of age from three rural communities in northwestern Madagascar. Stool samples were examined using light microscopy for intestinal parasites and real-time PCR for selected protozoan and bacterial enteropathogens. At least one intestinal pathogen was detected in 64.9% of children. Parasitic infections predominated (46.7%), with Giardia intestinalis identified as the most common pathogen (43.4%), while bacterial enteropathogens were detected in 23.1% of participants, mainly Campylobacter spp. and diarrheagenic Escherichia coli. Mixed infections were frequent: 23.6% of children harbored two or more pathogens, and parasitic-bacterial co-infections accounted for a substantial proportion of detected cases. Notably, most infections-including mixed infections-were asymptomatic. Infection patterns varied across study sites and were associated with environmental exposures such as water source, sanitation access, contact with livestock, and exposure to surface water. Intestinal parasitic-bacterial co-infections are common among children in rural Madagascar and often occur without overt clinical symptoms. These findings highlight the limitations of symptom-based and single-pathogen diagnostic approaches in endemic settings. Integrated diagnostic strategies combining microscopy and molecular methods, together with improvements in water and sanitation infrastructure, are essential to address the hidden burden of chronic intestinal infections in vulnerable pediatric populations.

Madagascar-endemic chameleons with large, conspicuous occipital lobes currently comprise 12 species that were traditionally classified in the phenetic Calumma cucullatum group. We here use a combination of DNA sequences from Restriction-Associated DNA sequencing (RADseq), museomics shotgun sequencing from historical name-bearing types, and Sanger-sequenced mitochondrial and nuclear gene fragments, to revisit the phylogeny and species delimitation in this group. We find robust phylogenomic evidence for polyphyly of the group, with C. cucullatum sister to the C. furcifer group, and species of the C. nasutum group intercalated between C. malthe and the remainder of ingroup species. Furthermore, according to our mitochondrial tree, C. tsycorne does not belong to the group. Several species such as C. brevicorne and C. malthe are recovered as paraphyletic in the mitochondrial tree while being unambiguously monophyletic in the phylogenomic tree; this mito-nuclear discordance may reflect ancestral introgressive hybridization. In our phylogenomic estimations, most currently recognized species are inferred as deep monophyletic lineages, and the RADseq clustering analysis recovered these as well-defined units. Exceptions were C. jejy, which is placed as sister taxon to the morphologically distinct C. peltierorum with rather shallow sequence divergence, and the C. brevicorne / C. crypticum complex. Combining molecular and morphological data suggests that populations of C. malthe from northern Madagascar represent a distinct species, here described as C. krystalae sp. nov. Our data reveal that chameleons, despite their elaborate phenotypic differences used in intraspecific signalling and their interspecific genital differences, can be characterized by complex evolutionary patterns probably involving hybridization and introgression.

Plague remains a major public health concern in Madagascar. In the Central Highlands, where the disease is still endemic, the black rat (Rattus rattus) is the main reservoir of the causative agent Yersinia pestis. Understanding its population dynamics and structure is therefore crucial to inform control strategies, as dispersal may greatly limit the effectiveness of local interventions during outbreaks. In this context, our study investigates the genetic structure of R. rattus populations at a fine geographical scale and across two different years. Sampling was conducted in six villages of the Azobenzene district, both inside houses and in habitat outside villages. A total of 480 individuals, captured in March - May 2019 and 2020, were genotyped at 18 microsatellite loci. Our results showed that genetic diversity levels were relatively similar among villages and years. However, subpopulations living outside villages displayed significantly higher genetic diversity and lower genetic differentiation levels than those from inside houses, indicating larger effective population sizes outside villages in the cultivated habitats. These findings suggest more restricted movement among rat subpopulations from the houses, and greater connectivity among subpopulations living outside villages. However, overall genetic differentiation was rather low, suggesting extensive dispersal of rats at the scale of the district, facilitating rapid recolonization after local control efforts. Because of the recolonization problem, an integrated approach combining flea control inside houses together with measures to reduce human-rodent contact would thus appear more appropriate than rodent control only to limit plague transmission.

Madagascar's lemurs are globally unique primates, yet many nocturnal taxa remain poorly studied. Among them, the eastern woolly lemur (Avahi laniger) is widespread across the island's northern and central-eastern rainforests, but little is known about its ecology outside protected areas. We surveyed 18 unprotected forests, representing about one third of the species' range, to evaluate its occurrence, population density, habitat use, and interactions with local communities. Using 97 nocturnal line transects (291.8 km of survey effort) combined with vegetation assessments and 208 interviews, we found A. laniger at all study sites. Estimated population density was 41.3 individuals/km2, which is at the lower margin of reported values for the genus. Encounter rates did not differ significantly along a gradient of forest degradation (undisturbed to highly logged primary forest), suggesting some tolerance to structural degradation. However, use of fallow-derived habitats was restricted to sites with the early successional tree Harungana madagascariensis, highlighting the importance of vertical structures and specific food plants. Morphological measurements showed no evidence of reduced body condition compared to populations in protected areas. Interviews revealed broad local knowledge of the species (73% recognition), occasional and opportunistic hunting, and low prevalence of taboos against consumption. Notably, hunting could be linked to locally reduced abundances. We demonstrate that A. laniger persists across a gradient of human-modified landscapes, if vertical forest structures and food resources remain available. Conservation strategies should therefore include forested areas not generally considered suitable for lemurs (e.g., agroforests), while strictly preventing hunting to ensure population viability under ongoing habitat fragmentation.

Novel species of fungi described in this study include those from various countries as follows:

East African cattle, including Malagasy native cattle (ZMA), are generally thought to have been shaped by admixture between African taurine and Asian indicine lineages, but the detailed position and formation history of ZMA within this broader diversity remain unclear. We analyzed worldwide SNP data from 145 cattle populations comprising 4093 individuals using principal component analysis (PCA), pairwise weighted F

Freshwater eels (genus Anguilla) are of major biological and commercial interest due to their complex catadromous life cycle and as a high-value fishery resource, but the biology of tropical species is still poorly understood. This study investigates the genetic integrity, diversity and population structure of three species of tropical eels (Anguilla marmorata, A. bicolor and A. mossambica) in the western Indian Ocean, based on partial nucleotide sequences of the mtDNA control region (n = 107 samples) and the nuclear GTH2b gene (n = 91 samples) for individuals collected from two freshwater systems in northern Madagascar. No first-generation hybrids between the studied species were found, despite frequent heterozygosities at the nuclear locus. For the mtDNA control region, all species were characterized by high haplotype diversity (ranging between 0.992 and 0.996) and nucleotide diversity (ranging between 0.035 and 0.059), patterns that are consistent with a historical population expansion during the late Pleistocene as inferred from demographic modelling. In line with previous studies, we confirmed distinct mtDNA haplogroups in A. marmorata and A. bicolor which can be attributed to the partial and/or past separation of populations across the Indian Ocean, whereas the western Indian Ocean endemic A. mossambica revealed no structure. Our findings align with existing evidence for spawning areas in the western Indian Ocean for all three species, with A. marmorata partially separated from eastern Indian Ocean populations and A. bicolor showing higher connectivity. Our findings will aid in the future management of local anguillid stocks.

O1 Regulation of genes by telomere length over long distances Jerry W. Shay O2 The microtubule destabilizer KIF2A regulates the postnatal establishment of neuronal circuits in addition to prenatal cell survival, cell migration, and axon elongation, and its loss leading to malformation of cortical development and severe epilepsy Noriko Homma, Ruyun Zhou, Muhammad Imran Naseer, Adeel G. Chaudhary, Mohammed Al-Qahtani, Nobutaka Hirokawa O3 Integration of metagenomics and metabolomics in gut microbiome research Maryam Goudarzi, Albert J. Fornace Jr. O4 A unique integrated system to discern pathogenesis of central nervous system tumors Saleh Baeesa, Deema Hussain, Mohammed Bangash, Fahad Alghamdi, Hans-Juergen Schulten, Angel Carracedo, Ishaq Khan, Hanadi Qashqari, Nawal Madkhali, Mohamad Saka, Kulvinder S. Saini, Awatif Jamal, Jaudah Al-Maghrabi, Adel Abuzenadah, Adeel Chaudhary, Mohammed Al Qahtani, Ghazi Damanhouri O5 RPL27A is a target of miR-595 and deficiency contributes to ribosomal dysgenesis Heba Alkhatabi O6 Next generation DNA sequencing panels for haemostatic and platelet disorders and for Fanconi anaemia in routine diagnostic service Anne Goodeve, Laura Crookes, Nikolas Niksic, Nicholas Beauchamp O7 Targeted sequencing panels and their utilization in personalized medicine Adel M. Abuzenadah O8 International biobanking in the era of precision medicine Jim Vaught O9 Biobank and biodata for clinical and forensic applications Bruce Budowle, Mourad Assidi, Abdelbaset Buhmeida O10 Tissue microarray technique: a powerful adjunct tool for molecular profiling of solid tumors Jaudah Al-Maghrabi O11 The CEGMR biobanking unit: achievements, challenges and future plans Abdelbaset Buhmeida, Mourad Assidi, Leena Merdad O12 Phylomedicine of tumors Sudhir Kumar, Sayaka Miura, Karen Gomez O13 Clinical implementation of pharmacogenomics for colorectal cancer treatment Angel Carracedo, Mahmood Rasool O14 From association to causality: translation of GWAS findings for genomic medicine Ahmed Rebai O15 E-GRASP: an interactive database and web application for efficient analysis of disease-associated genetic information Sajjad Karim, Hend F Nour Eldin, Heba Abusamra, Elham M Alhathli, Nada Salem, Mohammed H Al-Qahtani, Sudhir Kumar O16 The supercomputer facility “AZIZ” at KAU: utility and future prospects Hossam Faheem O17 New research into the causes of male infertility Ashok Agarwa O18 The Klinefelter syndrome: recent progress in pathophysiology and management Eberhard Nieschlag, Joachim Wistuba, Oliver S. Damm, Mohd A. Beg, Taha A. Abdel-Meguid, Hisham A. Mosli, Osama S. Bajouh, Adel M. Abuzenadah, Mohammed H. Al-Qahtani O19 A new look to reproductive medicine in the era of genomics Serdar Coskun P1 Wnt signalling receptors expression in Saudi breast cancer patients Muhammad Abu-Elmagd, Abdelbaset Buhmeida, Ashraf Dallol, Jaudah Al-Maghrabi, Sahar Hakamy, Wejdan Al-Qahtani, Asia Al-Harbi, Shireen Hussain, Mourad Assidi, Mohammed Al-Qahtani, Adel Abuzenadah P2 Analysis of oxidative stress interactome during spermatogenesis: a systems biology approach to reproduction Burak Ozkosem, Rick DuBois P3 Interleukin-18 gene variants are strongly associated with idiopathic recurrent pregnancy loss. Safia S Messaoudi, Maryam T Dandana, Touhami Mahjoub, Wassim Y Almawi P4 Effect of environmental factors on gene-gene and gene-environment reactions: model and theoretical study applied to environmental interventions using genotype S. Abdalla, M. Nabil Al-Aama P5 Genomics and transcriptomic analysis of imatinib resistance in gastrointestinal stromal tumor Asmaa Elzawahry, Tsuyoshi Takahashi, Sachiyo Mimaki, Eisaku Furukawa, Rie Nakatsuka, Isao Kurosaka, Takahiko Nishigaki, Hiromi Nakamura, Satoshi Serada, Tetsuji Naka, Seiichi Hirota, Tatsuhiro Shibata, Katsuya Tsuchihara, Toshirou Nishida, Mamoru Kato P6

The Danakil Depression in northeastern Africa represents one of the harshest arid environments on Earth, yet two genera of fishes, Danakilia (Cichlidae) and Aphanius (Cyprinodontidae), share its sparse aquatic habitats. The evolutionary history of these fishes is investigated here in the context of genetic, geological and paleoenvironmental information. We collected samples from seven sites and assessed phylogeographic relationships using concatenated COI and cytb mtDNA genes. Danakilia morphospecies show low differentiation at mitochondrial markers, but variation is partitioned between a northern cluster containing D. dinicolai plus three undescribed riverine populations, and a southern cluster including two creek populations of D. franchettii separated by the hypersaline waters of Lake Afrera. Aphanius displayed four genetically distinct clades (A. stiassnyae in Lake Afrera; one distributed across the entire area; one in Lake Abaeded; and one in the Shukoray River), but without clear large-scale geographic structure. However, Danakil Aphanius are clearly differentiated from A. dispar sensu stricto from the Sinai Peninsula. Geological evidence suggests that after the Late Pleistocene closure of the Danakil-Red Sea connection, increased post-glacial groundwater availability caused the formation of a brackish paleo-lake flooding the entire region below the -50 m contour. Fish populations previously isolated in coastal oases during glaciation were able to mix in the paleo-lake. Subsequently, in a more arid phase starting ∼7300 BP, paleo-lake regression isolated fishes in separate drainages, triggering their still ongoing diversification.