Biology subjects

Musa, A. A.

Publications and source records attributed to Musa, A. A..

4 recordsLinked to original sources

bioRxiv2025

PyMSQ: a python package for fast Mendelian sampling (co)variance and haplotype-based similarity in genomic selection

BackgroundWhile genomic selection (GS) boosts rapid genetic gains by leveraging dense marker data for genomic estimated breeding values (GEBVs), prolonged application can reduce haplotype diversity and increase inbreeding. To address these risks, recent research has emphasized Mendelian sampling variance (MSV) and covariance (MSC), which capture within-family (co)variation not fully reflected in GEBVs. In parallel, theoretical advances have introduced a haplotype-based similarity measure that targets shared heterozygous segments, enabling more direct control over haplotype diversity--either standalone or in combination with conventional coancestry-based and genomic relationship matrices. ResultsWe present PyMSQ, an open-source Python package that implements two key developments: (1) a matrix-based approach for computing MSV and MSC in single-trait, multi-trait, and zygotic contexts, and (2) a haplotype-based similarity metric. By combining this matrix-based framework with optimized scientific libraries, PyMSQ achieves up to 332-fold faster computations than gamevar--a publicly available alternative--while preserving numerical accuracy. Using a Holstein-Friesian dataset, we demonstrate PyMSQs effectiveness in deriving MSV and MSC, as well as its novel similarity measure, which complements standard genomic relationship matrices by explicitly quantifying shared heterozygous segments rather than overall allele sharing, thereby providing additional insights for balancing immediate gains with long-term diversity. ConclusionBy facilitating the practical use of MSV, MSC, and a haplotype-based similarity metric, PyMSQ enables breeders and quantitative geneticists to adopt haplotype diversity constraints--whether as a standalone criterion or in synergy with optimal contribution selection. This framework opens new possibilities for preserving key haplotypic segments, ultimately supporting more sustainable genomic selection strategies. PyMSQ is freely available under an MIT License at https://github.com/aromemusa/PyMSQ.

genetics↗

bioRxiv2023

A similarity matrix for preserving haplotype diversity among parents in genomic selection

Mendelian sampling variability (MSV), determined by the heterozygosity and linkage phases of the parental haplotypes, quantifies the chance of producing offspring with high breeding values. Recent genomic selection criteria combine expected breeding values with MSV to maximize the chance of producing offspring with exceptional breeding values. These criteria, however, tend to select similar parents with high variability potential. Therefore, a measure of haplotype similarity is required to avoid this tendency and preserve diversity. Here, we derive this measure by pairing all potential gametes from two parents based on their segregating marker patterns. Subsequently, a similarity measure between two parents is defined as the absolute value of the covariance between the additive values of the paired gametes on a chromosome. A similarity matrix with absolute covariances as off-diagonal elements and MSVs as diagonal elements summarizes all pairwise similarities between parents. A parents similarity to itself equals its MSV. High similarity indicates that the parents share many heterozygous markers with large effects on a trait in the same linkage phase. The concept generalizes to multiple chromosomes, an aggregate genotype with multiple traits, and similarity between zygotes. We demonstrated the properties of the similarity matrix using empirical data. Through simulations, we showed that incorporating the matrix into genomic selection preserves up to 1630% more genetic variability and yields up to 7% more genetic gain relative to index selection in the long term. Although further research is needed, our results show that including similarity matrices preserves haplotype diversity and improves long-term genomic selection.

genetics↗

bioRxiv2020

Tsetse blood-meal sources, endosymbionts, and trypanosome infections provide insight into African trypanosomiasis transmission in the Maasai Mara National Reserve, a wildlife-human-livestock interface

BackgroundAfrican trypanosomiasis (AT) is a neglected disease of both humans and animals caused by Trypanosoma parasites, which are transmitted by obligate hematophagous tsetse flies (Glossina spp.). Understanding of AT transmission is hampered by limited knowledge on interactions of tsetse flies with their vertebrate hosts and the influence of endosymbionts on vector competence, especially in wildlife-human-livestock interfaces. We identified the tsetse species, their blood-meal sources, and the correlation between endosymbiont and trypanosome infection status in the trypanosome-endemic Maasai Mara National Reserve (MMNR) of Kenya. Methodology/Principal FindingsAmong 1167 tsetse flies (1136 Glossina pallidipes, 31 Glossina swynnertoni) collected from 10 sampling sites, 28 (2.4%) were positive by PCR for trypanosomes, majority (17/28) being Trypanosoma vivax. Blood-meal analyses based on high-resolution melting analysis of mitochondrial cytochrome c oxidase 1 and cytochrome b gene PCR products (n = 345) identified humans as the most common vertebrate host (37%), followed by hippopotamus (29.1%), African buffalo (26.3%), elephant (3.39%), and giraffe (0.84%). Trypanosome-infected flies had fed on hippopotamus and buffalo. Additionally, PCR analysis revealed that tsetse flies were more likely to be infected with trypanosomes if they were infected with the Sodalis glossinidius endosymbiont (P = 0.0022 Fishers exact test). Conclusions/SignificanceDiverse species of wildlife hosts may contribute to the maintenance of tsetse populations and/or persistent circulation of African trypanosomes in the MMNR. Although the African buffalo is known to be a key reservoir of AT, the higher proportion of hippopotamus blood-meals in trypanosomes-infected flies identified here indicates that other wildlife species may also be important to transmission cycles. No trypanosomes associated with human disease were identified, but the high proportion of human blood-meals identified are indicative of human African trypanosomiasis transmission risk. Furthermore, this work provides data showing that Sodalis endosymbionts can is associated with increased trypanosome infection rates in endemic ecologies. Author summaryHuman and animal African trypanosomiasis are neglected tropical diseases with potential to spread to new areas. Wild animals are important reservoirs for African trypanosomes and crucial in the emergence and re-emergence of AT. Vertebrate host-vector-parasite interactions are integral to trypanosome transmission. We investigated the vertebrate blood-meals and trypanosomes-endosymbionts co-infections in tsetse flies, which have been associated with reservoirs and vector competence, respectively, on AT transmission in Kenyas Maasai Mara National Reserve. We identified tsetse fly diversity, trypanosome and endosymbiont infection status, and vertebrate blood-meal hosts to infer potential transmission dynamics. We found that Glossina pallidipes was the major tsetse fly vector and that Trypanosoma vivax was the main trypanosome species circulating in the region. Humans, hippopotamus, and buffalo were the most frequented for blood-meals. Buffalo and hippopotamus blood-meals were identified in trypanosome infected flies. Feeding of the flies on both humans and wildlife may potentiate the risk of the human trypanosomiasis in this ecology. Additionally, we found that the endosymbiont Sodalis glossinidius is associated with higher trypanosome infection rates in wild tsetse flies. These findings emphasize the importance of understanding the interaction of tsetse flies with vertebrate blood-meal sources and their endosymbionts in the transmission and control of AT.

molecular biology↗

bioRxiv2020

Pathogens, endosymbionts, and blood-meal sources of host-seeking ticks in the fast-changing Maasai Mara wildlife ecosystem

BackgroundThe role of questing ticks in the epidemiology of tick-borne diseases in Kenyas Maasai Mara National Reserve (MMNR), an ecosystem with intensified human-wildlife-livestock interactions, remains poorly understood. Therefore, we carried out a survey of the diversity of questing ticks, their blood-meal hosts, and tick-borne pathogens to understand potential effects to human and livestock health. MethodsQuesting ticks were collected by flagging and hand picks from vegetation in 25 localities and identified based on morphologic and molecular criteria. We used PCR with high-resolution melting (HRM) analysis, and sequencing to identify Anaplasma, Babesia, Coxiella, Ehrlichia, Rickettsia, and Theileria pathogen diversities and blood meals in 231 tick pools. ResultsA total of 1,465 host-seeking ticks were collected, including Rhipicephalus appendiculatus (n = 1,125), Rhipicephalus pulchellus (n = 6), Rhipicephalus evertsi (n = 5), Amblyomma cf. gemma (n = 178), Amblyomma gemma (n = 145), Amblyomma variegatum (n = 4), Amblyomma sp. (n = 1), and Haemaphysalis leachi (n = 1). Remnant blood-meals from humans, wildebeest, and African buffalo were detected in Rh. appendiculatus, goat in Rh. evertsi, sheep in Am. gemma, and cattle in Am. variegatum. Rickettsia africae was detected in Am. gemma (1/25 pools) that had blood-meal remnant from sheep and Am. variegatum (4/25 pools) that had fed on cattle. Rickettsia spp. were found in Am. gemma (4/25 pools) and Rh. evertsi (1/4 pools). Anaplasma ovis was detected in Rh. appendiculatus (1/172 pools) and Rh. evertsi (1/4 pools), while Anaplasma bovis was detected in Rh. appendiculatus (1/172 pools). Theileria parva was detected in Rh. appendiculatus (27/172 pools). Babesia, Ehrlichia and Coxiella pathogens were not found in any ticks. Unexpectedly, diverse Coxiella sp. endosymbionts were detected in all tick genera (174/231 pools). ConclusionsThe data shows that ticks from the rapidly-changing MMNR are infected with zoonotic R.africae and unclassified Rickettsia spp, demonstrating the persistent risk of African tick-bite fever and other and Spotted Fever Group rickettsioses to local dwellers and visitors to the Maasai Mara ecosystem. Protozoan pathogens that may pose risk to livestock production were also identified. We also highlight possible existence of morphotypic variants of Amblyomma species, based on the observation of Ambyomma cf. gemma, which may be potential human parasites or emergent disease vectors. Our findings also demonstrate that questing ticks in this ecosystem have dynamic vertebrate blood sources including humans, wildlife and domestic animals, which may amplify transmission of tickborne zoonoses and livestock diseases. Further studies are needed to determine the role of Coxiella endosymbionts in tick physiology and vector competence.

molecular biology↗