Biology subjects

Kilbride, E.

Publications and source records attributed to Kilbride, E..

5 recordsLinked to original sources

bioRxiv2025

Origins and diversity of Exmoor ponies: A mitogenome framework for assessing maternal lineage diversification in endangered pony breeds

In response to growing concerns over human-driven biodiversity loss, rewilding efforts increasingly employ semi-wild herbivores to restore ecosystems. The Exmoor pony is often cited as an ancient breed retaining primitive traits suited for such projects, yet its genetic history remains underexplored. We combined studbook records, mitochondrial DNA (mtDNA) D-loop, and whole mitogenome sequences to evaluate maternal lineage diversity for improved management recommendations and the phylogenetic placement of Exmoor ponies among modern and ancient breeds. We also assessed whether data from multiple breeds already available based on D-loop sequences could be organised into a useful framework for resolving the complex history of modern horse breeds. We identified eight mtDNA haplotypes among 88 Exmoor pony samples, representing all extant maternal lines. While phylogenetic trees based on D-loop sequences lacked resolution, clustering published sequences to a mitogenome-derived haplogroup framework allowed assessment of the distribution and relationships of lineages across diverse horse populations, including ancient DNA samples and Przelwalskis horses. The most basal lineages of Exmoors were traced back to the Pleistocene, supporting their ancient origin and status as a primitive population, with a possible ancestral role in the development of some modern breeds. The founder lineages were found to be polyphyletic, with more derived haplogroups representing subsequent mixture with other domestic horse breeds. Although nuclear genome sequencing is needed to fully assess levels of admixture, we identified new haplotypes, along with rare or basal haplotypes that could be prioritised for conservation in rewilding studies. Our results highlight the potential for broad testing of hypotheses about origins and relationships among horse breeds using short regions of DNA mapped onto a more robust phylogenetic framework resolved through comparison of whole mitogenomes.

evolutionary biology↗

bioRxiv2023

Balancing the scales: Impact of irrigation and pathogen burden on potato blackleg disease and soil microbial communities

Understanding the interaction between environmental conditions, crop yields, and soil health is crucial for sustainable agriculture in a changing climate. Management practices to limit disease are a balancing act. For example, in potato production, dry conditions favour common scab (Streptomyces spp.) and wet conditions favour blackleg disease (Pectobacterium spp.). The exact mechanisms involved and how these link to changes in the soil microbiome is unclear. Our objectives were to test how irrigation management and bacterial pathogen load in potato seed stocks impact: i) crop yields; ii) disease development (blackleg/common scab); and iii) soil microbial community dynamics. We used stocks of seed potatoes with varying Pectobacterium levels (Jelly [high load], Jelly [low load], and Estima [Zero - no Pectobacterium]). Stocks were grown under four irrigation regimes that differed in the timing and level of watering. The soil microbial communities were profiled using amplicon sequencing at 50% plant emergence and harvest and advanced bioinformatic analyses were used to correlate microbes to treatments and disease symptoms. Irrigation increased blackleg symptoms in the plots planted with stocks with low and high levels of Pectobacterium (22-34%) but not in the zero stock (2-6%). Not irrigating increased common scab symptoms (2-5%) and reduced crop yields. Irrigation did not impact the composition of the soil microbiome, but planting stock with a high Pectobacterium burden resulted in an increased abundance of Planctomycetota, Anaerolinea, and Acidobacteria species within the microbiome. Ensemble quotient analysis highlighted Anaerolinea as highly associated with blackleg symptoms in the field. We conclude that Pectobacterium pathogen load within seed stocks could have more substantial effects on soil communities than irrigation regimes.

microbiology↗

bioRxiv2023

Natural dispersal is better than translocation for reducing risks of inbreeding depression in eastern black rhinoceros (Diceros bicornis michaeli)

Due to ever increasing anthropogenic impacts, many species survive only in small and isolated populations. Active conservation management to reduce extinction risk includes: increasing habitat connectivity; translocations from captive populations; or intense surveillance of highly protected closed populations. The fitness of individuals born under these scenarios may vary due to differences in selection pressures. However, the genetic impacts of such strategies are rarely assessed. Using whole genome sequences from cohorts of the critically endangered eastern black rhinoceros as a model, we compare the consequences of past conservation efforts. We find that offspring of individuals that had either dispersed from native populations (FROH>100Kb = 0.13) or translocated from captive populations (FROH>100Kb = 0.08) showed lower inbreeding compared to closed populations (FROH>100Kb = 0.17). However, the frequency of highly deleterious mutations was higher for offspring resulting from translocation compared to the other groups and this load was sheltered by higher heterozygosity. This could increase risks of inbreeding depression if captive founders subsequently inbreed after translocation. In contrast, native dispersers reduced the negative effects of inbreeding without compromising the benefits of past purging of deleterious mutations. Our study highlights the importance of natural dispersal and reiterates the importance of maintaining habitat corridors between populations.

evolutionary biology↗

bioRxiv2023

Genetic diversity of the eastern black rhinoceros (Diceros bicornis michaeli) in Tanzania; implications for future conservation

In the past decade, there has been a drastic decline in the number of Eastern Black rhinoceros (black rhinoceros) (Diceros bicornis michaeli), primarily because of poaching across their natural habitats, leaving few individuals in small, isolated populations that are vulnerable to demographic extinction, disease epidemics, genetic drift and inbreeding. However, genetic consequences of the demographic decline on the remaining populations have not been investigated. Using the mitochondrial control region, this study investigated how current levels of genetic diversity relate to historical patterns, quantified genetic differentiation between extant populations and assessed the impacts of previous translocations on genetic diversity across populations. A total of 74 individual eastern black rhinoceroses were sampled from five extant populations in Tanzania and one neighbouring cross-border population in the Maasai Mara in Kenya. Six maternal haplotypes were identified, with an overall haplotype diversity of h=0.7 but low overall nucleotide diversity within populations ({pi} = 0.017) compared to historical populations from Tanzania ({pi} = 0.021). There was extensive variation in haplotype distribution between populations, with more variation exists within (65.5 %) than among the populations (35.5%), which may indicate lack of migration between populations. Specifically, some geographically close populations with different histories of introductions didnt share any haplotypes, suggesting that gene flow is currently restricted. The haplotypes were distributed among three east African haplogroups (CV, CE and EA) that have been described in previous studies, suggesting that multiple lineages have been preserved despite loss of haplotypes. One of the haplotypes was highly divergent and matched sequences previously classified as a subspecies that has not been recognised in recent years (D. b. ladoensis). We recommend that current levels of diversity be maintained by allowing natural movements of rhinoceroses between the populations, with the possibility of introducing additional variations by translocation of individuals between sites.

evolutionary biology↗

bioRxiv2020

Emergence of Lyme disease on treeless islands in Scotland, UK

Lyme disease (LD) is typically associated with forested habitats but has recently emerged on treeless islands in the Western Isles of Scotland. This has created a need to understand the environmental and human components of LD risk in open habitats. This study quantified both elements of LD risk and compared these between treeless islands with high and low LD incidence. We found high LD incidence was linked to higher prevalence in ticks (6.4% vs 0.4%) and increased human tick bite exposure. Most reported tick bites (72.7%) were within 1km of the home address and commonly in gardens. Residents on islands with high LD incidence reported increasing problems with ticks and suggested changing deer distribution as a potential driver. This study highlights the benefits to public health of an integrated approach to understand the factors contributing to LD emergence and a need to evaluate LD ecology in treeless habitats more broadly.

ecology↗