Use of experimental translocations of Allegheny woodrat to decipher causal agents of decline

Impact of putatively beneficial genomic loci on gene expression in little brown bats (Myotis lucifugus, Le Conte, 1831) affected by white-nose syndrome

Genome-wide scans for selection have become a popular tool for investigating evolutionary responses in wildlife to emerging diseases. However, genome scans are susceptible to false positives and do little to demonstrate specific mechanisms by which loci impact survival. Linking putatively resistant genotypes to observable phenotypes increases confidence in genome scan results and provides evidence of survival mechanisms that can guide conservation and management efforts. Here we used an expression quantitative trait loci (eQTL) analysis to uncover relationships between gene expression and alleles associated with the survival of little brown bats (Myotis lucifugus) despite infection with the causative agent of white-nose syndrome. We found that 25 of the 63 single-nucleotide polymorphisms (SNPs) associated with survival were related to gene expression in wing tissue. The differentially expressed genes have functional annotations associated with the innate immune system, metabolism, circadian rhythms, and the cellular response to stress. In addition, we observed differential expression of multiple genes with survival implications related to loci in linkage disequilibrium with focal SNPs. Together, these findings support the selective function of these loci and suggest that part of the mechanism driving survival may be the alteration of immune and other responses in epithelial tissue.

Multi-generational benefits of genetic rescue

Genetic rescue-an increase in population fitness following the introduction of new alleles-has been proven to ameliorate inbreeding depression in small, isolated populations, yet is rarely applied as a conservation tool. A lingering question regarding genetic rescue in wildlife conservation is how long beneficial effects persist in admixed populations. Using data collected over 40 years from 1192 endangered Florida panthers (Puma concolor coryi) across nine generations, we show that the experimental genetic rescue implemented in 1995-via the release of eight female pumas from Texas-alleviated morphological, genetic, and demographic correlates of inbreeding depression, subsequently preventing extirpation of the population. We present unequivocal evidence, for the first time in any terrestrial vertebrate, that genetic and phenotypic benefits of genetic rescue remain in this population after five generations of admixture, which helped increase panther abundance (> fivefold) and genetic effective population size (> 20-fold). Additionally, even with extensive admixture, microsatellite allele frequencies in the population continue to support the distinctness of Florida panthers from other North American puma populations, including Texas. Although threats including habitat loss, human-wildlife conflict, and infectious diseases are challenges to many imperiled populations, our results suggest genetic rescue can serve as an effective, multi-generational tool for conservation of small, isolated populations facing extinction from inbreeding.

The evolutionary dynamics of local adaptations under genetic rescue is determined by mutational load and polygenicity

Inbred populations often suffer from increased mutational load and reduced fitness due to lower efficacy of purifying selection in groups with small effective population sizes. Genetic rescue (GR) is a conservation tool that is studied and deployed with the aim of increasing the fitness of such inbred populations by assisted migration of individuals from closely related outbred populations. The success of GR depends on several factors-such as their demographic history and distribution of dominance effects of mutations-that may vary across populations. While we understand the impact of these factors on the dynamics of GR, their impact on local adaptations remains unclear. To this end, we conduct a population genetics simulation study to evaluate the impact of trait complexity (Mendelian vs. polygenic), dominance effects, and demographic history on the efficacy of GR. We find that the impact on local adaptations depends highly on the mutational load at the time of GR, which is in turn shaped dynamically by interactions between demographic history and dominance effects of deleterious variation. Over time local adaptations are generally restored post-GR, though in the short term they are often compromised in the process of purging deleterious variation. We also show that while local adaptations are almost always fully restored, the degree to which ancestral genetic variation affecting the trait is replaced by donor variation can vary drastically and is especially high for complex traits. Our results provide insights on the impact of GR on trait evolution and considerations for the practical implementation of GR.

A novel SNP assay reveals increased genetic variability and abundance following translocations to a remnant Allegheny woodrat population

BACKGROUND

Allegheny woodrats (Neotoma magister) are found in metapopulations distributed throughout the Interior Highlands and Appalachia. Historically these metapopulations persisted as relatively fluid networks, enabling gene flow between subpopulations and recolonization of formerly extirpated regions. However, over the past 45 years, the abundance of Allegheny woodrats has declined throughout the species' range due to a combination of habitat destruction, declining hard mast availability, and roundworm parasitism. In an effort to initiate genetic rescue of a small, genetically depauperate subpopulation in New Jersey, woodrats were translocated from a genetically robust population in Pennsylvania (PA) in 2015, 2016 and 2017. Herein, we assess the efficacy of these translocations to restore genetic diversity within the recipient population.

RESULTS

We designed a novel 134 single nucleotide polymorphism panel, which was used to genotype the six woodrats translocated from PA and 82 individuals from the NJ population captured before and after the translocation events. These data indicated that a minimum of two translocated individuals successfully produced at least 13 offspring, who reproduced as well. Further, population-wide observed heterozygosity rose substantially following the first set of translocations, reached levels comparable to that of populations in Indiana and Ohio, and remained elevated over the subsequent years. Abundance also increased during the monitoring period, suggesting Pennsylvania translocations initiated genetic rescue of the New Jersey population.

CONCLUSIONS

Our results indicate, encouragingly, that very small numbers of translocated individuals can successfully restore the genetic diversity of a threatened population. Our work also highlights the challenges of managing very small populations, such as when translocated individuals have greater reproductive success relative to residents. Finally, we note that ongoing work with Allegheny woodrats may broadly shape our understanding of genetic rescue within metapopulations and across heterogeneous landscapes.

Genetic rescue in an inbred Arctic fox (Vulpes lagopus) population

Isolation of small populations can reduce fitness through inbreeding depression and impede population growth. Outcrossing with only a few unrelated individuals can increase demographic and genetic viability substantially, but few studies have documented such genetic rescue in natural mammal populations. We investigate the effects of immigration in a subpopulation of the endangered Scandinavian arctic fox (Vulpes lagopus), founded by six individuals and isolated for 9 years at an extremely small population size. Based on a long-term pedigree (105 litters, 543 individuals) combined with individual fitness traits, we found evidence for genetic rescue. Natural immigration and gene flow of three outbred males in 2010 resulted in a reduction in population average inbreeding coefficient (f), from 0.14 to 0.08 within 5 years. Genetic rescue was further supported by 1.9 times higher juvenile survival and 1.3 times higher breeding success in immigrant first-generation offspring compared with inbred offspring. Five years after immigration, the population had more than doubled in size and allelic richness increased by 41%. This is one of few studies that has documented genetic rescue in a natural mammal population suffering from inbreeding depression and contributes to a growing body of data demonstrating the vital connection between genetics and individual fitness.

Dynamics of Predator-Prey Metapopulations with Allee Effects

Allee effects increasingly are recognized as influential determinants of population dynamics, especially in disturbed landscapes. We developed a predator-prey metapopulation model to study the impact of an Allee effect on predator-prey. The model incorporates habitat destruction and predators with imperfect information about prey distribution. Criteria are established for the existence and stability of equilibria, and the possible existence of a limit cycle is discussed. Numerical bifurcation analysis of the model is carried out to examine the impact of Allee effects as well as other key processes on trophic dynamics. Inclusion of Allee effects produces a richer array of dynamics than earlier models in which it was absent. When prey interacts with generalist predators, Allee effects operate synergistically to depress prey populations. Allee effects are more likely to depress occupancy levels when destruction of habitat patches is moderate; at severe levels of destruction, Allee effects are swamped by demographic effects of habitat loss. Stronger Allee effects correspond to lower thresholds of predator colonization rates at which prey become extinct. We discuss implications of our model for conservation of rare species as well as pest management via biocontrol.

Prescriptive Evolution to Conserve and Manage Biodiversity

We are witnessing a global, but unplanned, evolutionary experiment with the biodiversity of the planet. Anthropogenic disturbances such as habitat degradation and climate change result in evolutionary mismatch between the environments to which species are adapted and those in which they now exist. The impacts of unmanaged evolution are pervasive, but approaches to address them have received little attention. We review the evolutionary challenges of managing populations in the Anthropocene and introduce the concept of prescriptive evolution, which considers how evolutionary processes may be leveraged to proactively promote wise management. We advocate the planned management of evolutionary processes and explore the advantages of evolutionary interventions to preserve and sustain biodiversity. We show how an evolutionary perspective to conserving biodiversity is fundamental to effective management. Finally, we advocate building frameworks for decision-making, monitoring, and implementation at the boundary between management and evolutionary science to enhance conservation outcomes.

Allegheny woodrat (Neotoma magister) captive propagation to promote recovery of declining populations

The Allegheny woodrat (Neotoma magister) is endemic to the eastern United States with local distributions restricted to rocky habitats within deciduous forests. Over the last 40 years, woodrats have declined precipitously due to an array of human-mediated pressures. There is growing interest in the captive propagation of woodrats as a tool to promote in situ conservation, but their solitary social structure, territorial behavior, and low fecundity present challenges for the attainment of levels of ex situ reproduction sufficient to support reintroduction programs. In 2009 we established a captive breeding program with 12 wild-caught individuals (4.8) collected from Indiana and Pennsylvania. Restricting breeding to wild-caught individuals, over 26 months we produced 19 litters comprised of 43 pups (26.17), of which 40 (24.16) survived to weaning. In sum, wild-caught individuals readily habituated to the captive environment and the low fecundity of woodrats was offset by high survival rates for both adults and juveniles. Therefore, when managed appropriately, captive Allegheny woodrat populations should be capable of supporting the release of surplus individuals to augment in situ conservation measures.

Parasites and the conservation of small populations: The case of Baylisascaris procyonis

Human demands on natural resources result in landscape changes that facilitate the emergence of disease. Most emerging diseases are zoonotic, and some of these pathogens play a role in the decline of vulnerable wildlife species. Baylisascaris procyonis, the common roundworm parasite of raccoons (Procyon lotor), is a well recognized zoonotic infection that has many of the properties associated with a pathogen capable of driving extinction. It is highly non-specific and frequently pathogenic with regard to paratenic hosts, which contact eggs of B. procyonis at raccoon latrines. Eggs accumulate at latrines and remain viable for many years. Transmission of B. procyonis is sensitive to changes in land-use, and fragmented habitats increase contact rates between raccoons, potential paratenic hosts, and the parasite. Raccoons, and subsequently B. procyonis, have been introduced to Europe and Japan, where naïve vertebrates may be exposed to the parasite. Finally, domestic animals and exotic pets can carry patent infections with B. procyonis, thus increasing environmental contamination beyond raccoon latrines, and expanding the area of risk to potential paratenic hosts. This parasite can potentially contribute to extinctions of vulnerable species, as exemplified by the case of the Allegheny woodrat (Neotoma magister), a species that has experienced local declines and extinctions that are linked to B. procyonis. Conservation strategies for vulnerable species should consider the transmission ecology of parasitic pathogens, like B. procyonis.

Parasite zoonoses and wildlife: One Health, spillover and human activity

This review examines parasite zoonoses and wildlife in the context of the One Health triad that encompasses humans, domestic animals, wildlife and the changing ecosystems in which they live. Human (anthropogenic) activities influence the flow of all parasite infections within the One Health triad and the nature and impact of resulting spillover events are examined. Examples of spillover from wildlife to humans and/or domestic animals, and vice versa, are discussed, as well as emerging issues, particularly the need for parasite surveillance of wildlife populations. Emphasis is given to Trypanosoma cruzi and related species in Australian wildlife, Trichinella, Echinococcus, Giardia, Baylisascaris, Toxoplasma and Leishmania.