Biology subjects

Taylor, R. L.

Publications and source records attributed to Taylor, R. L..

4 recordsLinked to original sources

bioRxiv2024

Assessing the Sustainability of Pacific Walrus Harvest in a Changing Environment

Harvest sustainability is a primary goal of wildlife management and conservation, and in a changing world it is increasingly important to consider environmental drivers of population dynamics alongside harvest in cohesive management plans. This is particularly pertinent for harvested species that are acutely experiencing effects of climate change. The Pacific walrus (Odobenus rosmarus divergens), a critical traditional subsistence resource for indigenous communities, is simultaneously subject to rapid habitat loss associated with diminishing sea ice and an increasing anthropogenic footprint in the Arctic. We developed a theta-logistic population modeling-management framework to evaluate various harvest scenarios combined with four potential climate/disturbance scenarios (ranging from optimistic-pessimistic) which simulates Pacific walrus population dynamics to the end of the 21st century. We considered two types of harvest strategies: (1) adaptive harvest scenarios wherein harvest is calculated as a percentage of the population and annual harvests are updated at set intervals as the population is reassessed, and (2) non-adaptive harvest scenarios wherein annual harvest remains constant. All climate/disturbance scenarios indicated declines of varying severity in Pacific walrus abundance to the end of the 21st century, even in the absence of harvest. However, we found that an adaptive annual harvest of 1.23% of the independent-aged female subset of the population (e.g., 1,280 independent-aged females harvested in 2020, representing contemporary harvest levels) met our criterion for sustainability (>70% probability of maintaining population abundance above maximum net productivity level) under all climate/disturbance scenarios, accepting a medium risk tolerance level of 25%. This suggests that the present rate of Pacific walrus harvest is sustainable and will continue to be--provided the harvest adapts to match changes in population dynamics. Our simulations suggest that a sustainable non-adaptive harvest is also possible, but only at low levels if the population declines as expected. Applying a constant annual harvest of 1,280 independent-aged females (equivalent to contemporary harvest levels of 1.23) exceeded our criterion for sustainability and resulted in a >5% chance of quasi-extinction by the end of the 21st century under three of the four climate/disturbance scenarios we evaluated. Our results highlight the importance of adaptive co-management strategies, and we suggest such modeling frameworks are useful for managing for harvest sustainability in a changing climate.

ecology↗

bioRxiv2023

Assessing the Population Consequences of Disturbance and Climate Change for the Pacific Walrus

Climate change and anthropogenic disturbance are increasingly affecting wildlife at a global scale. Predicting how varying types and degrees of disturbance may interact to influence population dynamics is a key management challenge. Population Consequences of Disturbance (PCoD) models provide a framework to link effects of anthropogenic disturbance on an individuals behavior and physiology to population-level changes. Bioenergetic models often constitute the basis of these frameworks, wherein an individuals daily energy balance is simulated over the course of its lifetime, allowing many individuals to be subjected to different environmental conditions and ultimately simulate population-level vital rates under varying degrees of disturbance. In the present study, we develop a Pacific walrus (Odobenus rosmarus divergens) PCoD model to encompass the population-level effects of both anthropogenic disturbance and climate change. Pacific walruses are an Arctic/subarctic ice-associated pinniped. As the Arctic has become increasingly ice-free with climate change, walruses spend more time on land-based (rather than ice-based) haulouts from which they must expend more energy to reach foraging areas, and where they have a greater risk of predation and disturbance-based mortalities. Concurrently, sea ice loss is increasing the anthropogenic footprint in Arctic regions (e.g., fisheries, shipping, energy exploration) which creates additional disturbance. We developed a bioenergetic Dynamic Energy Budget (DEB) model for the Pacific walrus and applied it to four scenarios (ranging from optimistic-pessimistic) which incorporate different global sea ice model projections along with varying degrees of anthropogenic disturbance. All scenarios indicated a decline in Pacific walrus carrying capacity and population growth rate (and thus overall abundance) to the end of the 21st century, but demonstrated that the intensity of that decline could be mitigated by global efforts to reduce carbon emissions (i.e., lessening the rate of sea ice loss) and local management and conservation efforts to protect sensitive habitat areas. In summary, we introduced a flexible PCoD modelling framework in a novel context which will prove useful to researchers studying walruses and other species similarly threatened by rapid environmental change.

ecology↗

bioRxiv2020

New pathogenic variants and insights into pathogenic mechanisms in GRK1-related Oguchi disease.

PurposeBiallelic mutations in G-Protein coupled receptor kinase 1 (GRK1) cause Oguchi disease, a rare subtype of congenital stationary night blindness (CSNB). The purpose of this study was to identify pathogenic GRK1 variants and use in-depth bioinformatic analyses to evaluate how their impact on protein structure could lead to pathogenicity. MethodsPatients genomic DNA was sequenced by whole genome, whole exome or focused exome sequencing. Pathogenic variants, published and novel, were compared to nondisease associated missense variants. The impact of GRK1 missense variants at the protein level were then predicted using a series of computational tools. ResultsWe identified eleven previously unpublished cases with biallelic pathogenic GRK1 variants, including seven novel variants, and reviewed all GRK1 pathogenic variants. Further structure-based scoring revealed a hotspot for missense variants in the kinase domain. Additionally, to aid future clinical interpretation, we identified the bioinformatics tools best able to differentiate pathogenic from non-pathogenic variants. ConclusionWe identified new GRK1 pathogenic variants in Oguchi disease patients and investigated how disease-causing variants may impede protein function, giving new insights into the mechanisms of pathogenicity. All pathogenic GRK1 variants described to date have been collated into a Leiden Open Variation Database (http://dna2.leeds.ac.uk/GRK1_LOVD/genes/GRK1).

genetics↗

bioRxiv2020

Regulatory architecture of the RCA gene cluster captures an intragenic TAD boundary and enhancer elements in B cells

The Regulators of Complement Activation (RCA) gene cluster comprises several tandemly arranged genes with shared functions within the immune system. RCA members, such as complement receptor 2 (CR2), are well-established susceptibility genes in complex autoimmune diseases. Altered expression of RCA genes has been demonstrated at both the functional and genetic level, but the mechanisms underlying their regulation are not fully characterised. We aimed to investigate the structural organisation of the RCA gene cluster to identify key regulatory elements that influence the expression of CR2 and other genes in this immunomodulatory region. Using 4C, we captured extensive CTCF-mediated chromatin looping across the RCA gene cluster in B cells and showed these were organised into two topologically associated domains (TADs). Interestingly, an inter-TAD boundary was located within the CR1 gene at a well-characterised segmental duplication. Additionally, we mapped numerous gene-gene and gene-enhancer interactions across the region, revealing extensive co-regulation. Importantly, we identified an intergenic enhancer and functionally demonstrated this element upregulates two RCA members (CR2 and CD55) in B cells. We have uncovered novel, long-range mechanisms whereby autoimmune disease susceptibility may be influenced by genetic variants, thus highlighting the important contribution of chromatin topology to gene regulation and complex genetic disease. SIGNIFICANCEThe complement system is a complex network of protein effectors and regulators that play a key role in immunity. Several regulators of complement response are clustered within Regulators of Complement Activation (RCA) gene family. Its members are all functionally, structurally, and genetically related. However, the functional relevance of this close gene organisation is unknown. We show that the clustering of the RCA members is due to shared long-range regulatory elements and physical chromatin looping. We also reveal that the RCA genes are divided into two adjacent chromatin domains and a domain boundary falls within the body of an expressed gene (CR1). Overall, our findings in the RCA cluster offer insights into their evolution, biology and roles in disease.

genetics↗