Population genetic structure and history of fragmented remnant populations of the New England cottontail (Sylvilagus transitionalis)

FecalSeq enrichment with RAD Sequencing from non-invasive environmental samples holds promise for genetic monitoring of an imperiled lagomorph

Despite advances in genomic sequencing and bioinformatics, conservation genomics is still often hindered by a reliance on non-invasive samples. The presence of exogenous DNA and the low quantity and poor quality of DNA in non-invasive samples have been a roadblock to sequencing, thereby limiting the potential for genomic monitoring of endangered species. Recent molecular advances, such as host DNA enrichment, hold promise for facilitating sequencing from non-invasive samples. We used the FecalSeq method to enrich DNA extracted from wild-collected fecal pellets of the imperiled New England cottontail and identified SNPs from 3RAD Sequencing. We obtained SNPs from rabbit pellets, including pellets that were collected in poor environmental conditions and samples that performed poorly with microsatellites. Measures of sequencing success improved with greater amounts of starting DNA and 32% of samples generated SNP genotypes that passed quality control filtering. Genotyping error rates were high, however, and the approach was unable to consistently distinguish unique individuals or matching genotypes, while it was suitable for recovering the expected population structure. Pairing FecalSeq enrichment with RADseq is a promising low-cost method for monitoring wild populations using non-invasive samples in an environmental context, but it may be better suited for informing conservation through population genomics.

Separating Proactive Conservation from Species Listing Decisions

Proactive Conservation is a paradigm of natural resource management in the United States that encourages voluntary, collaborative efforts to restore species before they need to be protected through government regulations. This paradigm is widely used to conserve at-risk species today, and when used in conjunction with the Policy for Evaluation of Conservation Efforts (PECE), it allows for successful conservation actions to preclude listing of species under the Endangered Species Act (ESA). Despite the popularity of this paradigm, and recent flagship examples of its use (e.g., greater sage grouse, Centrocercus urophasianus), critical assessments of the outcomes of Proactive Conservation are lacking from the standpoint of species status and recovery metrics. Here, we provide such an evaluation, using the New England cottontail (Sylvilagus transitionalis), heralded as a success of Proactive Conservation efforts in the northeastern United States, as a case study. We review the history and current status of the species, based on the state of the science, in the context of the Conservation Initiative, and the 2015 PECE decision not to the list the species under the ESA. In addition to the impacts of the PECE decision on the New England cottontail conservation specifically, our review also evaluates the benefits and limits of the Proactive Conservation paradigm more broadly, and we make recommendations for its role in relation to ESA implementation for the future of at-risk species management. We find that the status and assurances for recovery under the PECE policy, presented at the time of the New England cottontail listing decision, were overly optimistic, and the status of the species has worsened in subsequent years. We suggest that use of PECE to avoid listing may occur because of the perception of the ESA as a punitive law and a misconception that it is a failure, although very few listed species have gone extinct. Redefining recovery to decouple it from delisting and instead link it to probability of persistence under recommended conservation measures would remove some of the stigma of listing, and it would strengthen the role of Species Status Assessments in endangered species conservation.

Carnivore occupancy within the early successional habitat of New England cottontails

Predation pressure from carnivores can shape ecological communities and have significant consequences for prey species that are declining or recovering from historical declines. New England cottontails Sylvilagus transitionalis are a species of Greatest Conservation Need in Connecticut (USA) and are experiencing continued declines associated with habitat loss. Restoration of early successional habitat is underway to address the most significant threat to their populations. However, one of the largest documented sources of mortality is associated with several key predators and remains a threat to recovery efforts. Our objectives were to develop species-specific occupancy estimates of carnivores in early successional habitat and relate our findings to the potential recovery of New England cottontails. We conducted camera surveys at 34 sites in early successional habitat in or near New England cottontail Focus Areas throughout Connecticut and used the program MARK to estimate occupancy and detectability from detection data. Key predators were found in early successional habitat, but their detectability was generally low. Occupancy was highest for coyotes Canis latrans and regional occupancy differed only for bobcats Lynx rufus. Covariates that influenced parameter estimates in our models included high road densities and the intensity of cottontail Sylvilagus detections. Expanding carnivores, particularly coyote and bobcat, may place additional pressure on New England cottontail recovery in the state, but restoration efforts that promote contiguous habitat and reduce isolated patches, where predation risk is higher, will improve their chances of a long-term recovery.

Addressing the Early-Successional Habitat Needs of At-Risk Species on Privately Owned Lands in the Eastern United States

Public lands alone are insufficient to address the needs of most at-risk wildlife species in the U.S. As a result, a variety of voluntary incentive programs have emerged to recruit private landowners into conservation efforts that restore and manage the habitats needed by specific species. We review the role of one such effort, Working Lands for Wildlife (WLFW), initiated by the Natural Resources Conservation Service in partnership with the U.S. Fish and Wildlife Service. Using two at-risk species in the eastern U.S. (where private lands dominate), we show the substantial potential that WLFW has for restoring and maintaining needed habitats. Monitoring how effective these efforts are on populations of the target species has been challenging, and both monitoring and implementation are being modified in response to new information. Identifying landowner motivations is essential for developing long-term relationships and conservation success. As WLFW projects develop, they are moving toward a more holistic ecosystem approach, within which the conservation goals of at-risk species are embedded.

Location and Species Matters: Variable Influence of the Environment on the Gene Flow of Imperiled, Native and Invasive Cottontails

The environment plays an important role in the movement of individuals and their associated genes among populations, which facilitates gene flow. Gene flow can help maintain the genetic diversity both within and between populations and counter the negative impact of genetic drift, which can decrease the fitness of individuals. Sympatric species can have different habitat preferences, and thus can exhibit different patterns of genetic variability and population structure. The specialist-generalist variation hypothesis (SGVH) predicts that specialists will have lower genetic diversity, lower effective population sizes (Ne), and less gene flow among populations. In this study, we used spatially explicit, individual-based comparative approaches to test SGVH predictions in two sympatric cottontail species and identify environmental variables that influence their gene flow. New England cottontail (Sylvilagus transitionalis) is the only native cottontail in the Northeast US, an early successional habitat specialist, and a species of conservation concern. Eastern cottontail (S. floridanus) is an invasive species in the Northeast US and a habitat generalist. We characterized each species' genomic variation by developing double-digest Restriction-site Associated DNA sequence single nucleotide polymorphism markers, quantified their habitat with Geographic Information System environmental variables, and conducted our analyses at multiple scales. Surprisingly, both species had similar levels of genetic diversity and eastern cottontail's Ne was only higher than New England cottontail in one of three subregions. At a regional level, the population clusters of New England cottontail were more distinct than eastern cottontail, but the subregional levels showed more geographic areas of restricted gene flow for eastern cottontail than New England cottontail. In general, the environmental variables had the predicted effect on each species' gene flow. However, the most important environmental variable varied by subregion and species, which shows that location and species matter. Our results provide partial support for the SGVH and the identification of environmental variables that facilitate or impede gene flow can be used to help inform management decisions to conserve New England cottontail.

Spatial Use and Survival of Sympatric Populations of New England and Eastern Cottontails in Connecticut

The New England cottontail (NEC) Sylvilagus transitionalis is strongly associated with shrubland and early successional habitat and is the only cottontail native to the U.S. Northeast. The distribution and abundance of young forest habitat and NEC populations have declined. The eastern cottontail (EC) Sylvilagus floridanus was introduced into the U.S. Northeast in the early 1900s and uses similar habitat as NEC, but is expanding in distribution and abundance. Little information exists on spatial use, survival, and competition in sympatric populations of NEC and EC. Understanding differences in population demographics may identify important factors or relationships influencing population trends and aid in developing effective management strategies. Our objectives were to quantify home range and core area sizes, annual survival rates, minimum population densities, and range overlap for sympatric populations of NEC and EC at four sites in Connecticut. We monitored spatial use and survival rates of 107 radio-collared rabbits over a 10-y period. Mean annual home ranges and core areas were 10.9 and 2.5 ha for NEC and 5.6 and 1.6 ha for EC. Overlap in home range and core areas was greater within species than between species (NEC-EC). For both species and sex, home range size expanded from winter to breeding seasons. Survival rates were greater for NEC than for EC at all four sites, with predation as the major cause of mortality for both species. Space-use patterns suggest that the potential for EC to interfere with NEC reproduction is limited and avoidance or resource partitioning between species in the same patch may be occurring.

Gastrointestinal parasites of the New England cottontail rabbit (Sylvilagus transitionalis) and eastern cottontail rabbit (Sylvilagus floridanus) in the Hudson Valley, New York

The New England cottontail rabbit (NEC, Sylvilagus transitionalis) population has decreased dramatically in New York, USA, and the role of parasites in limiting the population has never been examined. The closely related and sympatric eastern cottontail rabbit (EC, Sylvilagus floridanus) was introduced into the range of NEC by humans and is currently thriving. This study aimed to investigate gastrointestinal parasites of the NEC and the EC and compare their parasite communities. Fecal pellets from 195 NEC and 125 EC were collected from the Hudson Valley, New York, in the winter of 2013-2014. Centrifugal fecal floats were performed in Sheather's sugar solution, and parasite ova and cysts were examined microscopically to identify gastrointestinal parasites present. For all pellets combined (n = 320), 91% were found to harbor at least 1 parasite species, with Eimeria species being the most common. Genetic analysis of pellets using microsatellite DNA identified 248 individual rabbits, with parasite prevalence (94%) similar to the prevalence estimate based on all pellets (91%). EC samples had a significantly higher (p < 0.05) parasite species richness (1.73, range 0-4) than NEC (1.20, range 0-3). EC and NEC shared 3 moderate to high (9-89%) prevalence parasites, in which EC prevalence was consistently higher. One parasite species was only found in NEC, and two were only found in EC, but the majority of these were of low abundance, precluding further statistical analyses.

Competition alters seasonal resource selection and promotes use of invasive shrubs by an imperiled native cottontail

Many ecosystems face multiple invaders, and interactions among invasive and native species may complicate conservation efforts for imperiled species. Examination of fine-scale resource selection can be used to detect patterns in habitat selection resulting from species interactions and assess the value of specific resources, including invasive plants, to wildlife. We used animal location data with mixed-effects resource selection models to examine seasonal competitive interactions and species-specific selection for forage and cover resources by an imperiled native lagomorph, the New England cottontail Sylvilagus transitionalis and its nonnative competitor, the eastern cottontail S. floridanus in the eastern Hudson Valley, NY. We found evidence that resource selection by New England cottontails depended on the relative prevalence of eastern cottontails to New England cottontails. Where eastern cottontails were less prevalent New England cottontail selected for resources characteristic of early successional shrublands. Where eastern cottontails were more prevalent, New England cottontails selected for resources characteristic of later successional shrublands. New England cottontail use of certain invasive shrubs depended on the prevalence of eastern cottontails relative to New England cottontails, suggesting response to invasive plants is confounded by interactions with a nonnative competitor. Our results further emphasize the need for conservation efforts to consider invasive management within the ecosystem context. We demonstrate the utility of resource selection studies to assist in this regard by exploring competitive interactions in the absence of removal studies, while simultaneously assessing the impact of habitat components such as invasive vegetation on species of conservation concern. Synthesis and applications Resource selection studies can be directly applied to inform ongoing species conservation where multiple invaders are present or where species interactions influence resource selection. Fine-scale assessments of resource selection, similar to those presented here, can be used to selectively manage habitat to benefit desired species within the ecosystem context.

Microsatellite marker development from next-generation sequencing in the New England cottontail (Sylvilagus transitionalis) and cross-amplification in the eastern cottontail (S. floridanus)

Objective

The New England cottontail (Sylvilagus transitionalis) is a species of high conservation priority in the Northeastern United States, and was a candidate for federal listing under the Endangered Species Act until a recent decision determined that conservation actions were sufficient to preclude listing. The aim of this study was to develop a suite of microsatellite loci to guide future research efforts such as the analysis of population genetic structure, genetic variation, dispersal, and genetic mark-recapture population estimation.

Results

Thirty-five microsatellite markers containing tri- and tetranucleotide sequences were developed from shotgun genomic sequencing of tissue from S. transitionalis, S. obscurus, and S. floridanus. These loci were screened in n = 33 wild S. transitionalis sampled from a population in eastern Massachusetts, USA. Thirty-two of the 35 loci were polymorphic with 2–6 alleles, and observed heterozygosities of 0.06–0.82. All loci conformed to Hardy–Weinberg Equilibrium proportions and there was no evidence of linkage disequilibrium or null alleles. Primers for 33 of the 35 loci amplified DNA extracted from n = 6 eastern cottontail (S. floridanus) samples, of which nine revealed putative species-diagnostic alleles. These loci will provide a useful tool for conservation genetics investigations of S. transitionalis and a potential diagnostic species assay for differentiating sympatric eastern and New England cottontails.

Assessing polar bear (Ursus maritimus) population structure in the Hudson Bay region using SNPs

Defining subpopulations using genetics has traditionally used data from microsatellite markers to investigate population structure; however, single‐nucleotide polymorphisms (SNPs) have emerged as a tool for detection of fine‐scale structure. In Hudson Bay, Canada, three polar bear (Ursus maritimus) subpopulations (Foxe Basin (FB), Southern Hudson Bay (SH), and Western Hudson Bay (WH)) have been delineated based on mark–recapture studies, radiotelemetry and satellite telemetry, return of marked animals in the subsistence harvest, and population genetics using microsatellites. We used SNPs to detect fine‐scale population structure in polar bears from the Hudson Bay region and compared our results to the current designations using 414 individuals genotyped at 2,603 SNPs. Analyses based on discriminant analysis of principal components (DAPC) and STRUCTURE support the presence of four genetic clusters: (i) Western—including individuals sampled in WH, SH (excluding Akimiski Island in James Bay), and southern FB (south of Southampton Island); (ii) Northern—individuals sampled in northern FB (Baffin Island) and Davis Strait (DS) (Labrador coast); (iii) Southeast—individuals from SH (Akimiski Island in James Bay); and (iv) Northeast—individuals from DS (Baffin Island). Population structure differed from microsatellite studies and current management designations demonstrating the value of using SNPs for fine‐scale population delineation in polar bears.

REFERENCE AND BASELINE HEMATOCRIT MEASURES FOR THE THREATENED NEW ENGLAND COTTONTAIL (SYLVILAGUS TRANSITIONALIS) AND COMPARISON WITH SYMPATRIC EASTERN COTTONTAIL (SYLVILAGUS FLORIDANUS) RABBITS

From June 2014 to June 2015, capillary tube collections of blood were obtained concurrently with ear clips of trapped free-ranging, globally vulnerable New England cottontails (NEC; Sylvilagus transitionalis) and eastern cottontail rabbits (EC; Sylvilagus floridanus) in the Hudson Valley region of New York, United States. Species identification (NEC, EC) and sex (NEC) were determined genetically using a mitochondrial DNA assay and Y chromosome marker, respectively. Hematocrit values were obtained using a microhematocrit centrifuge. We provide the reference values 35.15-49.55 (2.5 and 97.5 percentiles) and 90% confidence intervals (CI) [lower: 33.00, 36.08; upper: 46.95, 51.00], for hematocrit of NEC. The mean hematocrit for NEC was 42.35% (SE = 0.58, n = 47) and a comparative contemporaneous mean in the same area for EC [39.96 (SE = 0.81, n = 26)], which was significantly different from NEC (P = 0.02). There was a significant sex difference for NEC [male: 43.99 (SE = 1.02, n = 28); female: 39.92 (SE = 0.78, n = 19), P < 0.0001], though not for EC.

Anthropogenic Habitats Facilitate Dispersal of an Early Successional Obligate: Implications for Restoration of an Endangered Ecosystem

Landscape modification and habitat fragmentation disrupt the connectivity of natural landscapes, with major consequences for biodiversity. Species that require patchily distributed habitats, such as those that specialize on early successional ecosystems, must disperse through a landscape matrix with unsuitable habitat types. We evaluated landscape effects on dispersal of an early successional obligate, the New England cottontail (Sylvilagus transitionalis). Using a landscape genetics approach, we identified barriers and facilitators of gene flow and connectivity corridors for a population of cottontails in the northeastern United States. We modeled dispersal in relation to landscape structure and composition and tested hypotheses about the influence of habitat fragmentation on gene flow. Anthropogenic and natural shrubland habitats facilitated gene flow, while the remainder of the matrix, particularly development and forest, impeded gene flow. The relative influence of matrix habitats differed between study areas in relation to a fragmentation gradient. Barrier features had higher explanatory power in the more fragmented site, while facilitating features were important in the less fragmented site. Landscape models that included a simultaneous barrier and facilitating effect of roads had higher explanatory power than models that considered either effect separately, supporting the hypothesis that roads act as both barriers and facilitators at all spatial scales. The inclusion of LiDAR-identified shrubland habitat improved the fit of our facilitator models. Corridor analyses using circuit and least cost path approaches revealed the importance of anthropogenic, linear features for restoring connectivity between the study areas. In fragmented landscapes, human-modified habitats may enhance functional connectivity by providing suitable dispersal conduits for early successional specialists.

An Analysis of Overstory Tree Canopy Cover in Sites Occupied by Native and Introduced Cottontails in the Northeastern United States with Recommendations for Habitat Management for New England Cottontail

The New England cottontail (Sylvilagus transitionalis) is a high conservation priority in the Northeastern United States and has been listed as a candidate species under the Endangered Species Act. Loss of early successional habitat is the most common explanation for the decline of the species, which is considered to require habitat with dense low vegetation and limited overstory tree canopy. Federal and state wildlife agencies actively encourage landowners to create this habitat type by clearcutting blocks of forest. However, there are recent indications that the species also occupies sites with moderate overstory tree canopy cover. This is important because many landowners have negative views about clearcutting and are more willing to adopt silvicultural approaches that retain some overstory trees. Furthermore, it is possible that clearcuts with no overstory canopy cover may attract the eastern cottontail (S. floridanus), an introduced species with an expanding range. The objective of our study was to provide guidance for future efforts to create habitat that would be more favorable for New England cottontail than eastern cottontail in areas where the two species are sympatric. We analyzed canopy cover at 336 cottontail locations in five states using maximum entropy modelling and other statistical methods. We found that New England cottontail occupied sites with a mean overstory tree canopy cover of 58% (SE±1.36), and was less likely than eastern cottontail to occupy sites with lower overstory canopy cover and more likely to occupy sites with higher overstory canopy cover. Our findings suggest that silvicultural approaches that retain some overstory canopy cover may be appropriate for creating habitat for New England cottontail. We believe that our results will help inform critical management decisions for the conservation of New England cottontail, and that our methodology can be applied to analyses of habitat use of other critical wildlife species.

A multiscale analysis of gene flow for the New England cottontail, an imperiled habitat specialist in a fragmented landscape

Landscape features of anthropogenic or natural origin can influence organisms' dispersal patterns and the connectivity of populations. Understanding these relationships is of broad interest in ecology and evolutionary biology and provides key insights for habitat conservation planning at the landscape scale. This knowledge is germane to restoration efforts for the New England cottontail (Sylvilagus transitionalis), an early successional habitat specialist of conservation concern. We evaluated local population structure and measures of genetic diversity of a geographically isolated population of cottontails in the northeastern United States. We also conducted a multiscale landscape genetic analysis, in which we assessed genetic discontinuities relative to the landscape and developed several resistance models to test hypotheses about landscape features that promote or inhibit cottontail dispersal within and across the local populations. Bayesian clustering identified four genetically distinct populations, with very little migration among them, and additional substructure within one of those populations. These populations had private alleles, low genetic diversity, critically low effective population sizes (3.2-36.7), and evidence of recent genetic bottlenecks. Major highways and a river were found to limit cottontail dispersal and to separate populations. The habitat along roadsides, railroad beds, and utility corridors, on the other hand, was found to facilitate cottontail movement among patches. The relative importance of dispersal barriers and facilitators on gene flow varied among populations in relation to landscape composition, demonstrating the complexity and context dependency of factors influencing gene flow and highlighting the importance of replication and scale in landscape genetic studies. Our findings provide information for the design of restoration landscapes for the New England cottontail and also highlight the dual influence of roads, as both barriers and facilitators of dispersal for an early successional habitat specialist in a fragmented landscape.

Effects of structural connectivity on fine scale population genetic structure of muskrat, Ondatra zibethicus

In heterogeneous landscapes, physical barriers and loss of structural connectivity have been shown to reduce gene flow and therefore lead to population structuring. In this study, we assessed the influence of landscape features on population genetic structure and gene flow of a semiaquatic species, the muskrat. A total of 97 muskrats were sampled from three watersheds near Sudbury, Ontario, Canada. We estimated population genetic structure using 11 microsatellite loci and identified a single genetic cluster and no genetic differences were found among the watersheds as a result of high levels of gene flow. At finer scales, we assessed the correlation between individual pairwise genetic distances and Euclidean distance as well as different models of least cost path (LCP). We used a range of cost values for the landscape types in order to build our LCP models. We found a positive relationship between genetic distance and least cost distance when we considered roads as corridors for movements. Open landscapes and urban areas seemed to restrict but not prevent gene flow within the study area. Our study underlines the high-dispersal ability of generalist species in their use of landscape and highlights how landscape features often considered barriers to animal movements are corridors for other species.