Assessing trends
The regional monitoring program, initially developed and implemented in 2015, was designed to assess occupancy, changes in occupancy over time, and response to habitat management by New England cottontail (Shea et al.,
2019). After two years of implementation, the regional monitoring effort was shown to be ineffective in tracking occupancy trends due to low power to detect a large change in occupancy between years (Rittenhouse and Kovach,
2020). The initial survey protocol, established with a random sampling approach, failed to account for the extremely low occupancy rate of New England cottontails in suitable patches. The protocol was revised in 2017 to focus on surveying patches known to be occupied or in dispersal distance of patches known to be occupied; subsequently it yielded high power to document trends, and also revealed that a 50% decline in occupancy has occurred over the last decade (Rittenhouse and Kovach,
2020). With the improved survey design, the effort now provides information regarding occupancy, trends in occupancy, and responses to habitat management actions (Rittenhouse and Kovach,
2020).
Across all years of the regional monitoring effort (2016-2017 through 2020-2021 surveys), New England cottontail occupied 224 of 663 sites sampled and occurred exclusively (without eastern cottontail) on only 75 of those 224 sites (Table
1). When considered in context of the resiliency, representation, and redundancy tenets of species status assessments (USFWS,
2016), the New England cottontail does not appear to be resilient to current habitat and landscape conditions, extreme winter weather (Bauer et al.,
2020; Cheeseman et al.,
2021) nor to sympatry with eastern cottontail, as evidenced by the increasing proportion of co-occurrence with time (Table
1). Representation is low given the species’ narrow, specialized niche and concerns for low genetic diversity. Redundancy is also low and declining with only 224 sites (patches) in the remnant distribution occupied over the past 5 years (Table
1). Considering the relatively small number of known occupied patches range-wide (Table
1), alongside the relatively low patch-level densities, the range-wide population can be expected to be as low as 3000 individuals or less, range-wide. This is a startling low number for a lagomorph and substantially lower than the 17,000 individuals extrapolated from available shrubland, used as a population estimate in the 2015 listing decision (USFWS,
2015a). Further empirical evaluation of this range-wide population size is a key remaining uncertainty in the ongoing conservation effort. While population size is a difficult parameter to estimate for cottontails, given cryptic behaviors and low trap rates, it can be estimated by incorporating recently developed abundance estimation approaches into the existing monitoring program (Kristensen and Kovach,
2018). Current uncertainties in these estimates notwithstanding, the critically low abundances observed to date, in conjunction with the observed breakdown in metapopulation function (low survival, reproduction and dispersal; see above) pose imminent threats to population persistence.
Table 1
New England cottontail occurrence and co-occurrence with eastern cottontail from the regional monitoring effort spanning Connecticut, Massachusetts, Maine, New Hampshire, New York, and Rhode Island, USA, for the survey years 2016–2017 through 2020–2021 (Rittenhouse unpublished data [regional monitoring report for 2020–2021; New England Cottontail Regional Initiative
2021])
2016-2017 | 213 | 46 | 107 | 27 | 19 | 0.127 |
2017-2018 | 338 | 103 | 179 | 58 | 45 | 0.172 |
2018-2019 | 378 | 135 | 187 | 78 | 57 | 0.206 |
2019-2020 | 220 | 99 | 111 | 58 | 41 | 0.264 |
2020-2021 | 167 | 93 | 125 | 55 | 38 | 0.329 |
Total (all years) | 663 | 224 | 376 | 149 | 75 | 0.225 |
Response to Management
Widespread loss of shrublands has resulted in a heavy reliance on anthropogenically created successional shrublands by New England cottontails and a propensity for wildlife managers to create these shrublands to promote New England cottontails (Fuller and Tur,
2012). Yet, New England cottontail populations have failed to respond to these management efforts. Among managed patches, few support or provide suitable habitat for New England cottontail at present (Litvaitis et al.,
2021; Rittenhouse and Kovach,
2020). Many managed patches are too young, too small, too far from existing populations to support sustainable New England cottontail populations or sites simply do not possess the characteristics (e.g., soil, disturbance/management history) necessary to support shrubland development, and thus provide habitat (Litvaitis et al.,
2021). Occupancy remains higher in unmanaged patches than in patches managed for New England cottontail in three out of four years with data (Rittenhouse unpublished data [regional monitoring report for 2019-2020]). Colonization by New England cottontail has been observed in a minority of patches, consistent with dispersal limitations (Amaral et al.,
2016; Cheeseman,
2017; Cheeseman et al.,
2019b; Fenderson et al.,
2011; Fenderson et al.,
2014), while the number of sites occupied by New England cottontail have continued to decline (Rittenhouse and Kovach,
2020). New England cottontail density is not associated with patch management status in Maine and New Hampshire (Kovach and Bauer,
2021), nor is occupancy, range-wide (Bischoff, Rittenhouse and Rittenhouse, unpublished). Results from recent simulation modeling support this notion. Kovach and Bauer (
2021) found that a small, remnant population simulated with a 9-fold increase in habitat through restoration failed to achieve the conservation target size of 500 after 100 years. Only through habitat restoration combined with multiple population augmentations over time and optimistic vital rates (values representing the best-case scenario from the literature) was this simulated population able to increase to the 500-individual goal and persist. Simply put, the last 10 years are evidence that we do not have enough information to confidently suggest we can restore habitat to recover New England cottontails.
Captive Breeding and Reintroductions
A captive breeding program was established in 2011 with the goal of supplying 500 rabbits for reintroduction per year (New England Cottontail Regional Initiative,
2014). These efforts now include two zoos, two outdoor pens and two island breeding colonies (New England Cottontail Regional Initiative,
2019). While these efforts have successfully produced 382 kits from 2011-2021 (including 2 strong years producing 96 in 2018 and 70 in 2019, followed by the COVID-19 pandemic limited breeding and releases in 2020 and 2021), initial production goals have yet to be realized (New England Cottontail Regional Initiative, 2017,
2018,
2019). These successes have been limited in part due to a combination of logistical constraints, limited zoo and pen resources/capacity, and uncertainties regarding sustainable take from island populations, as well as knowledge gaps regarding small litter size and low juvenile survival to weaning that may limit these efforts.
Captively-bred New England cottontails have been reintroduced in groups of 7-21 individuals across 2-5 years at five sites – Great Swamp and Ninigret NWR in RI, Bellamy Wildlife Management Area and Rollinsford in NH, and Wells Reserve in Maine. Reproduction in the wild (of both founders and their wild-born offspring) has been observed in at least three reintroduction sites, however, post-release and annual survival is highly variable, as is reproductive contribution among founding individuals. Achieving a self-sustaining population requires persistent effort, and without annual augmentation via new releases, some monitored populations declined to low numbers after an initial period of growth, with biased sex ratio and a loss of genetic diversity (Bauer et al.
2020, Bauer and Kovach unpublished data). In two recent releases, dispersal into the surrounding landscape has occurred at the time of the writing of this paper, potentially indicating a more robust landscape-level response (Bauer & Kovach, unpublished data). These findings underscore the challenges of bringing back an extirpated population in a landscape devoid of neighboring occupied patches; such connectivity is critical in a metapopulation context to provide dispersers and gene flow to offset winter mortality and bolster genetic diversity (Bauer et al.,
2020). The small numbers of individuals released and the small habitat patches available for reintroduction provide further challenges for these efforts. Other successful lagomorph reintroductions have released orders of magnitude larger numbers of individuals, because high mortality and low rates of successful establishment are common (DeMay et al.,
2017; Watland et al.,
2007).
Limits to Population Growth
Integrating the most current knowledge of status, threats and remaining uncertainties, we have identified a number of factors that appear to be limiting growth and recovery of New England cottontail populations. First, stochastic factors – demographic, genetic and environmental––are at play in the remnant, small populations. Random demographic fluctuations result in skewed sex ratios (Bauer et al.,
2020), and winter storms, especially late spring snows, lead to stochastic mortality events (Bauer et al.,
2020; Cheeseman et al.,
2021). Genetic bottlenecks have reduced genetic diversity and continued ongoing genetic drift in isolated populations may result in loss of important adaptive alleles (Cheeseman et al.,
2019b; Fenderson et al.,
2011; Fenderson et al.,
2014). High relatedness of individuals on small patches, with limited dispersal, suggests inbreeding may be ongoing, although the latter has not been confirmed with fine-scale genetic data. Low heterozygosity and inbreeding may limit population growth through reduced fitness, survival and reproduction (Saccheri et al.,
1998).
Low vital rates are another primary factor limiting population growth. Additionally, mortality rates may be elevated above evolutionary baselines due to habitat degradation (i.e., invasive plants, small patch size), increased tick burdens with climate change, and the naturalization of novel predators like coyote and recovery of native predators like bobcat and fisher (Broman et al.,
2014; Cheeseman et al.,
2021; Gompper,
2002; Hapeman et al.,
2011; Ogden et al.,
2021). Further, density dependent effects that release small populations from predation pressure by generalist predators (e.g., predator population regulation, prey switching) may not operate in favor of New England cottontail where the similar but more abundant eastern cottontail is present. In such cases, it is possible for predation to drive the species with a lower survival capacity to extinction (Korobeinikov and Wake,
1999). Further, population expansion, including into managed patches, is limited by low colonization rates––a result of low vagility, low habitat availability, and a highly fragmented matrix. This is particularly concerning as many shrublands are ephemeral and, thus, suitable patches are continuously lost to natural forest succession. Without colonization of new patches to balance ongoing patch extinctions, populations will continue to decline.
Although thought to be rare, hybridization with eastern cottontail has recently been documented (New England cottontail Regional Initiative,
2018,
2021). These recent observations may indicate rates of hybridization are increasing in areas where New England cottontail is on the decline and in low numbers on a patch and where eastern cottontails are newly colonizing an area previously occupied by New England cottontails only. Wasted reproductive effort from such inter-specific mating (failed or successful) further impedes a positive population trajectory on local patches, and recent evidence that F1 hybrids can reproduce (New England Cottontail Regional Initiative,
2018,
2021) raise additional questions about potential threats of genetic introgression.
Acute, and potentially severe infections with bacterial and viral pathogens are also of concern for cottontail rabbits. Notable examples are
Francisella tularensis (cause of tularemia) and the rabbit hemorrhagic disease virus serotype 2 (RHDV2). The bacterium
F. tularensis is highly infectious and zoonotic, with rabbits considered a natural reservoir and amplifying host (Brown et al.,
2015; Hestvik et al.,
2015; Petersen and Schriefer,
2005; Wobeser et al.,
2009). Virulence varies by bacterial strain, but the more virulent strains, which are common in the United States, can cause mortality within 1 week of exposure (Brown et al.,
2015). In a study of a wild population of eastern cottontails in Illinois, where tularemia was enzootic, Woolf et al. (
1993) reported almost a third of collared animals succumbed to this disease during the study period, illustrating the potentially devastating effects such infections can have. Arthropods are known vectors of
F. tularensis, and particularly ticks (Brown et al.,
2015; Hestvik et al.,
2015), which is relevant for New England cottontails given the tick burdens mentioned above. Studies on tularemia specifically in New England cottontails are lacking, but a recent news article reports a case on Patience Island, Rhode Island (News,
2021).
The most recent threat, RHDV2, may be the most serious one to the future persistence of remnant New England cottontails. Rabbit hemorrhagic disease virus is well documented in European rabbits and has a high fatality rate at 70-100% (Dalton et al.,
2012; Kerr and Donnelly,
2013). Cases in the United States have been reported sporadically (Kerr and Donnelly,
2013; McIntosh et al.,
2007) but a recent outbreak in wild rabbits in the Southwestern US has sparked concerns of more extensive spread (Asin et al.,
2021). Biosecurity and minimizing the spread of this virus has been emphasized (USGS,
2020a,
b,
c) because once established, the disease can be devastating. Reports on the susceptibility of
Sylvilagus species to RHDV2 vary. The recent cases in the United States include several cottontails including the eastern cottontail, desert cottontail (
Sylvilagus audubonii), and mountain cottontail (
Sylvilagus nuttallii) (Asin et al.,
2021; Lankton et al.,
2021). Because of its overlapping range with the New England cottontail, the eastern cottontail could be an important reservoir of infection if RDHV2 were to spread to the Northeast. These findings suggest that the potential risk to New England cottontail could be high.
In summary, in 2015, the 12-month finding identified habitat loss as the most significant threat to New England cottontail, with predation, competition with eastern cottontails and small population size noted as contributing factors. In our review, we have emphasized numerous additional factors, primarily biological (low vital rates, connectivity, genetic variation, hybridization, parasites and disease), that contribute to the continued decline of the species. Thus, it is now evident that habitat restoration alone is insufficient to reverse the population decline of the New England cottontail, at least in the near term.
A more successful path toward recovery will require long-term commitments and a multi-scale approach to management, where we not only consider habitat within the patch, but the arrangement of patches on the landscape and intervening matrix, with landscape-level planning that considers succession dynamics in this system. It will also require dedicated resources to facilitate an enhanced captive breeding effort that produces and releases hundreds of rabbits annually on the landscape, until populations stabilize and become self-sustaining. Existing simulation models (Bauer
2018; Kovach and Bauer,
2021) can be used to predict numbers and rates of releases required for successful reintroductions, as well as for managing removals from captive breeding colonies. Once these reintroductions and augmentations stabilize, it is conceivable that further captive breeding may not be needed, if habitat management can maintain these rebuilt populations. Successful recovery will also require an improved understanding of and mitigation of threats, as they evolve, and the incorporation of new knowledge into management, as it becomes available. Doing so will require dedicated funding for research and adaptive management experimentation, and potentially bringing in guidance from experts outside of the current initiative, to move beyond ad hoc approaches. Continued, consistent support for the monitoring program is also critical for tracking trends and understanding their causes; expanding monitoring to assess abundance in addition to occupancy will be important to accurately evaluate population status. Recent declines in financial support of the monitoring program and future uncertainties about funding priorities in the face of the shift away from a dedicated New England Cottontail Conservation Initiative toward a broader Young Forest Initiative must be addressed. In the big picture, open recognition of the conservation reliant nature of the New England cottontail, and accordingly, a long-term strategy for its conservation, with consistent resource commitments, is necessary.