Biology subjects

Lawal, R. A.

Publications and source records attributed to Lawal, R. A..

7 recordsLinked to original sources

bioRxiv2023

Ancestral variation and its impact on wild house mouse genomes

Ancestral alleles are important contributors to adaptation and disease risk in populations. House mice emerged in and/or around the Indian subcontinent, but the genetic composition of this ancestral population and the extent to which ancestral variants contribute to contemporary global mouse diversity are poorly understood. To address these knowledge gaps, we assessed the origins and demographic patterning of global mouse diversity using a set of 169 wild mouse genome sequences from across the world. This dataset includes 37 mouse genomes from the broadly designated ancestral regions, providing crucial resources needed to evaluate the contributions and the impact of ancestral diversity on the genomic scale. We show that house mice emerged in the Indo-Pakistan region around 700 kya, with M. m. castaneus at the root of the M. musculus species. Migration out of the Indo-Pakistan homeland led to the subsequent emergence of the M. m. domesticus and M. m. musculus subspecies [~]360 and 260 kya, respectively. A modest fraction of ancestral alleles have persisted long-term across mouse populations through balancing selection, and we demonstrate that such regions are strongly enriched for genes with immune-related functions. Finally, we find widespread allele-sharing across Mus musculus lineages and show that this trend is largely due to incomplete lineage sorting, an interpretation contrary to some recent claims of pervasive subspecies introgression. Together, our work underscores the contributions of ancestral variants to contemporary house mouse diversity and adaptation, and refines our understanding of the natural evolutionary history of this important model species.

evolutionary biology↗

bioRxiv2023

Screening and isolation of protease-producing bacteria from wastewater samples in Obafemi Awolowo University (OAU) Campus, Ile-Ife, Nigeria.

BackgroundWastewater samples possess substantial potential as a valuable resource for the isolation of bacteria with the capacity to produce protease enzymes. Gaining insights into the proteolytic capabilities of these bacteria holds considerable significance for a wide range of industrial applications. Enhancing our understanding of the microbial diversity and protease production potential within wastewater can pave the way for the creation of customized enzymatic solutions tailored specifically for industrial needs. PurposeThe purpose of this study was to isolate and identify protease-producing bacteria from wastewater samples collected at Obafemi Awolowo University Campus in Nigeria. The study involved isolating bacteria from the wastewater, identifying them, evaluating their growth on protease-supporting agar, determining their proteolytic activities, and screening bacterial colonies for protease production using skim milk agar medium. MethodsWastewater samples were aseptically collected from various locations within Obafemi Awolowo University Campus, located in Ile-Ife, Osun State, Nigeria. Bacterial isolation from the wastewater was performed using the serial dilution technique. The samples were progressively diluted and plated onto nutrient agar media for bacterial growth. Skim milk agar media was specifically used to isolate protease-producing bacteria. Following the isolation, screening was conducted to identify potential protease-producing bacteria. Zonal inhibition methods were employed using skim milk agar media during the screening process. The objective was to select bacterial isolates that exhibited clear zones around their colonies, indicating protease activity. To identify the potential protease-producing bacteria, morphological and biochemical tests were conducted. These tests included observations of colonial morphology, cellular morphology, and biochemical characteristics. The Bergeys Manual was used as a reliable reference for taxonomic classification during the identification process. ResultsAmong the ten bacterial colonies obtained from the wastewater samples, eight exhibited clear zones, indicating protease activity. Morphological and biochemical tests identified the protease-producing bacteria as Bacillus spp. and Pseudomonas spp. Further characterization revealed that the Bacillus licheniformis isolate from Water Sample D1 (WSD1) displayed the highest protease activity. Bacillus subtilis isolates also showed significant protease production, while Pseudomonas spp. exhibited lower protease production. ConclusionsWastewater samples from the OAU Campus yielded protease-producing bacteria, with Bacillus licheniformis showing the highest activity. The findings highlight the industrial potential of the isolated Bacillus licheniformis strain and emphasize the significance of utilizing wastewater as a source for obtaining bacteria with protease production capabilities. Further studies on individual strains within the Bacillus and Pseudomonas genera may lead to the discovery of strains with enhanced protease production, enabling tailored enzymatic solutions for various industrial sectors. Overall, this study contributes to our understanding of protease-producing microorganisms.

microbiology↗

bioRxiv2022

Taxonomic assessment of two wild house mouse subspecies using whole genome sequencing

House mice (Mus musculus) are comprised of three primary subspecies. A large number of secondary subspecies have also been suggested on the basis of divergent morphology and molecular variation at limited numbers of markers. While the phylogenetic relationships among the primary M. musculus subspecies are well-defined, the relationships among the secondary subspecies, and their relationships to primary subspecies, remain poorly understood. Here, we integrate de novo genome sequencing of museum-stored specimens of house mice from one secondary subspecies (M. m. bactrianus) and publicly available genome sequences of house mice previously characterized as M. m. helgolandicus, with whole-genome sequences from diverse representatives of the three primary house mouse subspecies. We show that mice assigned to the secondary M. m. bactrianus and M. m. helgolandicus subspecies are not genetically differentiated from the contemporary M. m. castaneus and M. m. domesticus, respectively. Overall, our work suggests that the M. m. bactrianus and M. m. helgolandicus subspecies are not well-justified taxonomic entities, emphasizing the importance of leveraging whole-genome sequence data to inform subspecies designations. Additionally, our investigation has established experimental procedures for generating whole-genome sequences from air-dried museum specimens and provides key genomic resources to inform future genomic investigations of wild mouse diversity.

evolutionary biology↗

bioRxiv2021

Selection shapes the landscape of functional variation in wild house mice

BackgroundThrough human-aided dispersal, house mice have recently colonized new and diverse habitats across the globe, promoting the emergence of new traits that confer adaptive advantages in distinct environments. Despite their status as the premiere mammalian model system, the impact of this demographic and selective history on the global patterning of disease-relevant trait variation in wild mouse populations is poorly understood. ResultsHere, we leveraged 154 whole-genome sequences from diverse wild house mouse populations, subspecies, and species to survey the geographic organization of functional variation and systematically identify signals of positive selection. We show that a significant proportion of wild mouse variation is private to single populations, including numerous predicted functional alleles. In addition, we report strong signals of positive selection at numerous genes associated with both complex and Mendelian diseases in humans. Notably, we detect a significant excess of selection signals at disease-associated genes relative to null expectations, pointing to the important role of adaptation in shaping the landscape of functional variation in wild mouse populations. We also uncover strong signals of selection at multiple genes involved in starch digestion, including Mgam and Amy1. We speculate that the successful emergence of the human-mouse commensalism may have been facilitated, in part, by dietary adaptations at these loci. Finally, our work uncovers multiple cryptic structural variants that manifest as putative signals of positive selection, highlighting an important and under-appreciated source of false-positive signals in genome-wide selection scans. ConclusionsOverall, our findings underscore the role of adaptation in shaping wild mouse genetic variation at human disease-associated genes. Our work highlights the biomedical relevance of wild mouse genetic diversity and unsdercores the potential for targeted sampling of mice from specific populations as a strategy for developing effective new mouse models of both rare and common human diseases.

evolutionary biology↗

bioRxiv2020

Population and species diversity at mouse centromere satellites

Centromeres are satellite-rich chromatin domains that are essential for chromosome segregation. Centromere satellites evolve rapidly between species but little is known about population-level diversity across these loci. We developed a k-mer based method to quantify centromere copy number and sequence variation from whole genome sequencing data. We applied this method to diverse inbred and wild house mouse (genus Mus) genomes and uncover pronounced variation in centromere architecture between strains and populations. We show that patterns of centromere diversity do not mirror the known ancestry of inbred strains, revealing a remarkably rapid rate of centromere sequence evolution. We document increased satellite homogeneity and copy number in inbred compared to wild mice, suggesting that inbreeding remodels mouse centromere architecture. Our results highlight the power of k-mer based approaches for probing variation across repetitive regions and provide the first in-depth, phylogenetic portrait of centromere variation across Mus musculus.

genomics↗

bioRxiv2020

Sexual dimorphism in the meiotic requirement for PRDM9: a mammalian evolutionary safeguard

In many mammals, genomic sites for recombination are determined by histone methyltransferase PRMD9. Mice lacking PRDM9 are infertile, but instances of fertility or semi-fertility in the absence of PRDM9 have been reported in mice, canines and a human female. Such findings raise the question of how the loss of PRDM9 is circumvented to maintain reproductive fitness. We show that genetic background and sex-specific modifiers can obviate the requirement for PRDM9 in mice. Specifically, the meiotic DNA damage checkpoint protein CHK2 acts as a modifier allowing female-specific fertility in the absence of PRDM9. We also report that in the absence of PRDM9, a PRDM9-independent recombination system is compatible with female meiosis and fertility, suggesting sex-specific regulation of meiotic recombination, a finding with implications for speciation. One Sentence SummarySex-specific modulation of a meiotic DNA damage checkpoint limits the requirement for PRDM9 in mammalian fertility.

genetics↗

bioRxiv2019

The wild species genome ancestry of domestic chickens

Hybridization and/or introgression play a key role in the evolutionary history of animal species. It is commonly observed in several orders in wild birds. The domestic chicken Gallus gallus domesticus is the commonest livestock species exploited for the benefit of mankind. The origin of its diversity remains unsettled. Here, we report a genome-wide analyses for signatures of introgression within domestic village chicken. We first established the genome-wide phylogeny and divergence time across the genus Gallus, showing the sister relationships between Grey junglefowl G. sonneratii and Ceylon junglefowl G. lafayettii and that the Green junglefowl is the first diverging lineage within the genus Gallus. Then, by analysing the whole-genome sequences of geographically diverse chicken populations, we reveal extensive bidirectional introgression between Grey junglefowl and domestic chicken and to a much less extent with Ceylon junglefowl. A single case of Green junglefowl G. varius introgression was identified. These introgressed regions include biological functions related to the control of gene expression. Our results show that while the Red junglefowl is the main ancestral species, introgressive hybridization episodes have impacted the genome and contributed to the diversity of domestic chicken, although likely at different level across its geographic range.

evolutionary biology↗