Biology subjects

Northrup, J. M.

Publications and source records attributed to Northrup, J. M..

8 recordsLinked to original sources

bioRxiv2026

Measuring American black bear genetic load in fixed structural variants and runs of homozygosity

Populations living in geographically isolated regions are expected to have reduced gene flow, increased genetic drift, and elevated levels of inbreeding, influencing both genetic load and possibly the distribution of structural variants. The American black bear (Ursus americanus) is widely found across Ontario, Canada, where populations inhabit diverse landscapes ranging from relatively intact contiguous forested landscapes to isolated regions such as the Saugeen Peninsula. Here, we investigated the population genomic history across five Ontario black bear populations using a combination of short-read (SR) and long-read (LR) sequencing data. We compared population genetic metrics including nucleotide diversity ({pi}), Tajimas D, runs of homozygosity (ROH), and genome-wide structural variants (SVs) to assess population health and identify signatures of isolation. Our results showed that the isolated Saugeen Peninsula population is genetically distinct and exhibited reduced nucleotide diversity, greater ROH and SV abundance compared with mainland populations. The population also showed elevated genetic load in all genomic features, suggesting increased exposure of deleterious variation that are expressed in ROH and population specific SVs. We further discuss the integration of ROH, SVs and genetic load in conservation assessments.

genomics↗

bioRxiv2025

Environmental and temporal factors affecting record white-tailed deer antler characteristics in Ontario, Canada

White-tailed deer (Odocoileus virginianus) are an ecologically and economically important species in North America. Their antlers, one of their most recognizable features, are used for dominance displays, mate attraction, and defense, with size and shape being key determinants of success. Antler characteristics are influenced by a combination of genetics, age and environmental factors, notably habitat quality and resource availability. In this study, we explored how diverse environmental factors, including climate and land cover composition, impact antler size, tine configuration, and the distribution of record-scoring white-tailed deer across Ontario, Canada, using hunter-submitted data from long-term antler scoring records. We used conditional autoregressive (CAR) models to examine these relationships and found that warmer temperatures the year of harvest were positively associated with larger antlers and more record deer in a given county, while winter precipitation the year of harvest was negatively associated with these characteristics, likely due to reduced forage availability or increased energy expenditure during more severe winters. Rangeland and forest land cover types were positively associated with increased antler size and tine number. We observed no temporal changes in antler size in Ontario, contrasting with broader trends observed in North America. These results show how local environmental conditions and land cover composition influence antler traits and the distribution of record white-tailed deer, highlighting the complexity of environmental influences on trait variation.

ecology↗

bioRxiv2025

The heritability of migration behaviours in a wide-ranging ungulate

Migration behaviour is thought to be declining globally in the face of rapid human-mediated environmental change. While many species exhibit individual plasticity in their migratory behaviour, not all species demonstrate the level of plasticity necessary to adjust to novel conditions. Selection on heritable behaviours might therefore play an important role in the maintenance of migratory phenotypes for some species. Using GPS and genomic data from 242 individuals (256 animal-years) in a pedigree-free quantitative genetic approach, we estimated heritability, repeatability, and sources of environmental variation for migration traits in migrating mule deer (Odocoileus hemionus). We also estimated heritability of body size to ensure validity of our results. Heritability estimates of body size traits were comparable to the current estimates for ungulate body size. We found low heritability for broad patterns of migration timing, distance, and duration, but high heritability for movement rate along the migratory route. Our findings suggest that wild mule deer populations have the potential to respond to selection pressure generated by human activity or global environmental changes through microevolutionary changes in migration behaviours. Significance StatementMigration behaviour is critical for the reproduction and survival of a wide variety of taxa, yet there have been global declines in migrations in the face of rapid human-mediated environmental change. Despite our understanding that variation in migration behaviour has both genetic and environmental components, studies quantifying the sources of genetic variation contributing to migration phenotypes are lacking. Our study provides, to our knowledge, the first empirical evidence of heritability in a migration behaviour in ungulates. These results have implications for the evolution and maintenance of migration behaviours in natural populations.

genetics↗

bioRxiv2023

Epigenetic clocks, sex markers, and age-class diagnostics in three harvested large mammals

The development of epigenetic clocks, or the DNA methylation-based inference of age, is an emerging tool for ageing in free ranging populations. In this study, we developed epigenetic clocks for three species of large mammals that are the focus of extensive management throughout their range: white-tailed deer, black bear, and mountain goat. We quantified differential DNA methylation patterns at over 30,000 cytosine-guanine sites (CpGs) from tissue samples (N=141) of all three species. We used a penalized regression model (elastic net) to build highly explanatory (black bear r = 0.95; white-tailed deer r = 0.99; mountain goat r = 0.97) and robust (black bear Median Absolute Error or MAE = 1.33; white-tailed deer MAE = 0.29; mountain goat MAE = 0.61) models of age (clocks). We also characterized individual CpG sites within each species that demonstrated clear differences in methylation levels between age classes and sex, which can be used to develop a suite of accessible diagnostic markers. Our results demonstrate promising tools for the large-scale estimation of age in wild animals, which have the potential to contribute to wildlife monitoring by providing easily obtainable representations of age structure in managed populations.

genomics↗

bioRxiv2023

The dynamic interaction between predator and prey drives mesopredator movement and foraging ecology

Prey availability and predation risk drive animal distribution, movement, and foraging ecology, yet studies rarely analyze multiple predator-prey levels together. Understanding how predators optimize risk-reward tradeoffs is important for species conservation and management, especially in systems facing extreme ecosystem change. We examined how top-down (modelled polar bear habitat selection) and bottom-up (modeled fish diversity) processes influence the habitat selection, movement, and foraging behavior of 26 ringed seals (greater than 70,000 dives and 10,000 locations over 877 seal days). Our results suggest that polar bears spatially restrict seal movements and reduce the time seals spend foraging, potentially decreasing foraging success. Seals were more likely to be present and dive longer in high-predation risk areas when prey diversity was high. Further, seal habitat selection models excluding polar bears overestimated core space use. These findings illustrate the dynamic tradeoffs that mesopredators make when balancing predation risk and resource acquisition.

ecology↗

bioRxiv2022

Genomic correlates for migratory direction in a free-ranging cervid

Animal migrations are some of the most ubiquitous and one of the most threatened ecological processes. A wide range of migratory behaviours occur in nature, and this behaviour is not uniform between and within species, where even individuals in the same population can exhibit differentiation. While the environment largely drives migratory behaviour, it is necessary to understand the genetic mechanisms influencing migration to elucidate the adaptive potential of migratory species to cope with novel conditions and adapt to environmental change. In this study, we identified genes associated with migratory traits by undertaking pooled genome-wide scans on a natural population of a facultatively migrating ungulate. We identified genomic regions associated with variation in migratory direction in the study population, including FTM1, a gene linked to the formation of lipids, and DPPA3, a gene linked to epigenetic modifications of the maternal line. Such a genetic basis for migratory traits can have implications on heritability of behaviour and the flexibility of individuals to change their behaviour in the face of stochastic changes in their environment.

genomics↗

bioRxiv2020

Characterizing the demographic history and prion protein variation to infer susceptibility to chronic wasting disease in a naïve population of white-tailed deer (Odocoileus virginianus)

Assessments of the adaptive potential in natural populations are essential for understanding and predicting responses to environmental stressors like climate change and infectious disease. Species face a range of stressors in human-dominated landscapes, often with contrasting effects. White-tailed deer (deer) are expanding in the northern part of their range following decreasing winter severity and increasing forage availability. Chronic wasting disease (CWD), a prion disease affecting cervids, is likewise expanding and represents a major threat to deer and other cervids. We obtained tissue samples from free-ranging deer across their native range in Ontario, Canada which has yet to detect CWD in wild populations of cervids. We used high-throughput sequencing to assess neutral genomic variation, and variation in the PRNP gene that is partly responsible for the protein misfolding when deer contract CWD. Neutral variation revealed a high number of rare alleles and no population structure, and demographic models suggested a rapid historical population expansion. Allele frequencies of PRNP variants associated with CWD susceptibility and disease progression were evenly distributed across the landscape and consistent with deer populations not infected with CWD. We then estimated the selection coefficient of CWD, with simulations showing an observable and rapid shift in PRNP allele frequencies that coincides with the start of a novel CWD epidemic. Sustained surveillance of genomic and PRNP variation can be a useful tool for CWD-free regions where deer are managed for ecological and economic benefits.

molecular biology↗

bioRxiv2017

A Comment On Priors For Bayesian Occupancy Models

Understanding patterns of species occurrence and the processes underlying these patterns is fundamental to the study of ecology. One of the more commonly used approaches to investigate species occurrence patterns is occupancy modeling, which can account for imperfect detection of a species during surveys. In recent years, there has been a proliferation of Bayesian modeling in ecology, which includes fitting Bayesian occupancy models. The Bayesian framework is appealing to ecologists for many reasons, including the ability to incorporate prior information through the specification of prior distributions on parameters. While ecologists often intend to choose priors so that they are \"uninformative\"; or \";vague\";, such priors can easily be unintentionally highly informative. Here we report on how the specification of a \"vague\" normally distributed (i.e., Gaussian) prior on coefficients in Bayesian occupancy models can unintentionally influence parameter estimation. Using both simulation and empirical examples, we illustrate how this issue likely compromises inference about species-habitat relationships. While the occurrence of this issue likely depends on the data set, researchers fitting Bayesian occupancy models should conduct sensitivity analyses to ensure intended inference, or use priors other than those most commonly used in the literature. We provide further suggestions for addressing this issue in occupancy studies, and an online tool for exploring this issue under different contexts.

ecology↗