Geology topics

Roderick B. Gagne

Publications and source records attributed to Roderick B. Gagne.

7 recordsLinked to original sources

USGS2025

Viral outbreak dynamics and evolution in wildlife at the interface with humans

In this study, we used a multi-faceted approach to understand patterns of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission and persistence in a wild white-tailed deer ( Odocoileus virginianus ) population. Serology data indicated transmission of SARS-CoV-2 and persistence during the seven-month sampling period. Traditional disease modelling based on deer-to-deer transmission indicated relatively low prevalence with an R 0 of 1.9 and recovery period of 7 days; however, individual-based modelling informed by GPS tracked-movement data captured a potential transmission event. Phylogenetic analyses revealed a recurring pattern of divergent groups of deer-derived sequences with human-derived sequences falling close to each deer-derived cluster. Further, human-derived sequences were frequently sampled months prior to the deer-derived sequences, indicating repeated human to deer spillover. Using multiple types of data as well as both fine and broad scale analyses, we have characterized a pattern of localized outbreaks of SARS-CoV-2 within white-tailed deer populations that are likely recurring due to frequent spillover events. Our results suggest that while deer-to-deer transmission occurs over small spatiotemporal scales, SARS-CoV-2 persistence over longer periods and across larger regions is likely driven by repeated spillover from human populations.

Pennsylvania↗

USGS2025

An enigmatic wild passerine mortality event in the eastern United States

The ability to rapidly respond to wildlife health events is essential. However, such events are often unpredictable, especially with anthropogenic disturbances and climate-related environmental changes driving unforeseen threats. Many events also are short-lived and go undocumented, making it difficult to draw on lessons learned from past investigations. We report on the response to a mortality event observed predominantly in wild passerines in the eastern United States. The event began in May 2021 when wildlife rehabilitators and private citizens reported large numbers of sick and dead juvenile birds, mostly presenting as single cases with neurologic signs and/or ocular and periocular lesions. Early efforts by rehabilitators, veterinarians, state and federal wildlife agencies, and universities helped gather public reports and fuel rapid responses by government agencies. Collective efforts included live bird and carcass collections; submission to diagnostic laboratories and evaluation; information sharing; and coordinated messaging to stakeholders and interested parties. Extensive diagnostic evaluations failed to identify a causative pathogen or other etiology, although congruent results across laboratories have helped drive further investigation into alternative causes, such as nutritional deficiencies. This report highlights the strengths of a multi-agency, interdisciplinary investigation while exposing the need for an operational framework with approaches and resources dedicated to wildlife health.

eastern United States↗

USGS2021

Translocations maintain genetic diversity and increase connectivity in sea otters, Enhydra lutris

Sea otters, Enhydra lutris , were once abundant along the nearshore areas of the North Pacific. The international maritime fur trade that ended in 1911 left 13 small remnant populations with low genetic diversity. Subsequent translocations into previously occupied habitat resulted in several reintroduced populations along the coast of North America. We sampled sea otters between 2008 and 2011 throughout much of their current range and used 19 nuclear microsatellite markers to evaluate genetic diversity, population structure, and connectivity between remnant and reintroduced populations. Average genetic diversity within populations was similar: observed heterozygosity 0.55 and 0.53, expected heterozygosity 0.56 and 0.52, unbiased expected heterozygosity 0.57 and 0.52, for reintroduced and remnant populations, respectively. Sea otter population structure was greatest between the Northern and Southern sea otters with further structuring in Northern sea otters into Western, Central, and Southeast populations (including the reintroduced populations). Migrant analyses suggest the successful reintroductions and growth of remnant groups have enhanced connectivity and gene flow between populations throughout many of the sampled Northern populations. We recommend that future management actions for the Southern sea otter focus on future reintroductions to fill the gap between the California and Washington populations ultimately restoring gene flow to the isolated California population.

North Pacific↗

USGS2021

Functional connectivity in a continuously distributed, migratory species as revealed by landscape genomics

Maintaining functional connectivity is critical for the long-term conservation of wildlife populations. Landscape genomics provides an opportunity to assess long-term functional connectivity by relating environmental variables to spatial patterns of genomic variation resulting from generations of movement, dispersal and mating behaviors. Identifying landscape features associated with gene flow at large geographic scales for highly mobile species is becoming increasingly possible due to more accessible genomic approaches, improved analytical methods and enhanced computational power. We characterized the genetic structure and diversity of migratory mule deer Odocoileus hemionus using 4051 single nucleotide polymorphisms in 406 individuals sampled across multiple habitats throughout Wyoming, USA. We then identified environmental variables associated with genomic variation within genetic groups and statewide using a stepwise approach to first evaluate nonlinear relationships of landscape resistance with genetic distances and then use mixed-effects modeling to choose top landscape genomic models. We identified three admixed genetic groups of mule deer and found that environmental variables associated with gene flow varied among genetic groups, revealing scale-dependent and regional variation in functional connectivity. At the statewide scale, more gene flow occurred in areas with low elevation and mixed habitat. In the southern genetic group, more gene flow occurred in areas with low elevation. In the northern genetic group, more gene flow occurred in grassland and forest habitats, while highways and energy infrastructure reduced gene flow. In the western genetic group, the null model of isolation by distance best represented genetic patterns. Overall, our findings highlight the role of different seasonal ranges on mule deer genetic connectivity, and show that anthropogenic features hinder connectivity. This study demonstrates the value of combining a large, genome-wide marker set with recent advances in landscape genomics to evaluate functional connectivity in a wide-ranging migratory species.

Wyoming↗

USGS2019

Urbanization reduces genetic connectivity in bobcats (Lynx rufus) at both intra- and interpopulation spatial scales

Urbanization is a major factor driving habitat fragmentation and connectivity loss in wildlife. However, the impacts of urbanization on connectivity can vary among species and even populations due to differences in local landscape characteristics, and our ability to detect these relationships may depend on the spatial scale at which they are measured. Bobcats ( Lynx rufus ) are relatively sensitive to urbanization and the status of bobcat populations is an important indicator of connectivity in urban coastal southern California. We genotyped 271 bobcats at 13,520 SNP loci to conduct a replicated landscape resistance analysis in five genetically distinct populations. We tested urban and natural factors potentially influencing individual connectivity in each population separately, as well as study–wide. Overall, landscape genomic effects were most frequently detected at the study–wide spatial scale, with urban land cover (measured as impervious surface) having negative effects and topographic roughness having positive effects on gene flow. The negative effect of urban land cover on connectivity was also evident when populations were analyzed separately despite varying substantially in spatial area and the proportion of urban development, confirming a pervasive impact of urbanization largely independent of spatial scale. The effect of urban development was strongest in one population where stream habitat had been lost to development, suggesting that riparian corridors may help mitigate reduced connectivity in urbanizing areas. Our results demonstrate the importance of replicating landscape genetic analyses across populations and considering how landscape genetic effects may vary with spatial scale and local landscape structure.

California↗

USGS2019

The expectations and challenges of wildlife disease research in the era of genomics: Forecasting with a horizon scan-like exercise

The outbreak and transmission of disease-causing pathogens are contributing to the unprecedented rate of biodiversity decline. Recent advances in genomics have coalesced into powerful tools to monitor, detect, and reconstruct the role of pathogens impacting wildlife populations. Wildlife researchers are thus uniquely positioned to merge ecological and evolutionary studies with genomic technologies to exploit unprecedented ‘Big Data’ tools in disease research; however, many researchers lack the training and expertise required to use these computationally intensive methodologies. To address this disparity, the inaugural ‘Genomics of Disease in Wildlife’ workshop assembled early to mid-career professionals with expertise across scientific disciplines (e.g., genomics, wildlife biology, veterinary sciences, and conservation management) for training in the application of genomic tools to wildlife disease research. A horizon scanning-like exercise, an activity to identify forthcoming trends and challenges, performed by the workshop participants identified and discussed five themes considered to be the most pressing to the application of genomics in wildlife disease research: i) “Improving Communication”, ii) “Methodological and Analytical Advancements”, iii) “Translation into Practice”, iv) “Integrating Landscape Ecology and Genomics”, and v) “Emerging New Questions”. Wide-ranging solutions from the horizon scan were international in scope, itemized both deficiencies and strengths in wildlife genomic initiatives, promoted the use of genomic technologies to unite wildlife and human disease research, and advocated best practices for optimal use of genomic tools in wildlife disease projects. The results offer a glimpse of the potential revolution in human and wildlife disease research possible through multi-disciplinary collaborations at local, regional, and global scales.

Journal of Heredity↗

USGS2017

Mitogenomes and relatedness do not predict frequency of tool-use by sea otters

Many ecological aspects of tool-use in sea otters are similar to those in Indo-Pacific bottlenose dolphins. Within an area, most tool-using dolphins share a single mitochondrial haplotype and are more related to each other than to the population as a whole. We asked whether sea otters in California showed similar genetic patterns by sequencing mitogenomes of 43 otters and genotyping 154 otters at 38 microsatellite loci. There were six variable sites in the mitogenome that yielded three haplotypes, one found in only a single individual. The other two haplotypes contained similar percentages (33 and 36%) of frequent tool-users and a variety of diet types. Microsatellite analyses showed that snail specialists, the diet specialist group that most frequently used tools, were no more related to each other than to the population as a whole. The lack of genetic association among tool-using sea otters compared with dolphins may result from the length of time each species has been using tools. Tool-use in dolphins appears to be a relatively recent innovation (less than 200 years) but sea otters have probably been using tools for many thousands or even millions of years.

Biology Letters↗