Hierarchical population structure of a rare lagomorph indicates recent fragmentation has disrupted metapopulation function

Cheeseman, Amanda E.; Cohen, Jonathan B.; Whipps, Christopher M.; Kovach, Adrienne I.; Ryan, Sadie J.

doi:10.1007/s10592-019-01206-z

Cited by 13 publications

(22 citation statements)

References 66 publications

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“…1). In prior years, December 2013 to March 2015, we collected pellets on snow as described by Cheeseman et al (2019) and used these for comparison with samples collected in less ideal weather conditions of 2016.…”

Section: Methodsmentioning

confidence: 99%

“…The winter 2015–2016 study was conducted in the lower Hudson Valley, New York, at 2 sites located in Putnam County. Sampling in the winters of 2013–2014 and 2014–2015 included collections at several sites across 4 counties, as described in Cheeseman et al (2019). New England and eastern cottontails were sympatric throughout the region; snowshoe hare was not present within the study area.…”

Section: Study Areamentioning

confidence: 99%

“…Success of such noninvasive genetic monitoring efforts depends on the quality and composition of collected scats (Broquet et al 2007, Murphy et al 2007, Woodruff et al 2015) and methods used to process them (Wehausen et al 2004). In the northeastern United States, occupancy of sampling areas by the New England cottontail ( Sylvilagus transitionalis ) is regularly monitored by genetic analysis of rabbit fecal pellets to determine its presence or absence, and distinguish it from the congeneric eastern cottontail ( S. floridanus ) and snowshoe hare ( Lepus americanus ; Kovach et al 2003; Fenderson et al 2011, 2014; Kilpatrick et al 2013; Brubaker et al 2014; Cheeseman et al 2019). The New England cottontail is of particular interest, because this once widespread rabbit now occupies fragmented habitats in only a small proportion of its historical range (Nelson 1909, Litvaitis 1993).…”

mentioning

confidence: 99%

“…This method is able to distinguish among New England cottontail, eastern cottontail, and snowshoe hare pellets, and may be used in combination with a secondary confirmation (Litvaitis and Litvaitis 1996). Cottontail pellets may also be genetically tested to identify individual rabbits, targeting nuclear microsatellite DNA to obtain a multilocus genotype, which can be used to make population abundance estimations and evaluate genetic connectivity of cottontail populations (Fenderson et al 2011, 2014; Berkman et al 2015; Cheeseman et al 2019). Similar monitoring techniques have been used for other imperiled lagomorph species such as pygmy rabbits ( Brachylagus idahoensis ; Adams et al 2011, DeMay et al 2013).…”

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confidence: 99%

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Evaluation of Cottontail Pellets Collected in Suboptimal Conditions for DNA Analysis

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Occupancy monitoring of the New England cottontail (Sylvilagus transitionalis) relies on collections of fecal pellets made following a snowfall, and subsequent genetic screening to distinguish New England cottontail pellets from those of the eastern cottontail (S. floridanus) and snowshoe hare (Lepus americanus). In years when snowy conditions are not common, less frequent sampling may result in data gaps at long‐term monitoring sites, and jeopardize ongoing field research projects that rely on genetic data from fecal pellets. Such conditions occurred in the lower Hudson Valley, New York, USA, in the winter of 2015–2016, during which we collected pellets from the ground to evaluate performance of genetic testing relative to pellet quality. Pellets were categorized on overall appearance of degradation, assigned a pellet quality score, and then genetically analyzed to identify species using mitochondrial DNA. The pellets identified as being from New England cottontail were further evaluated targeting nuclear microsatellite DNA to obtain a multilocus genotype to identify individual rabbits. Species identification was possible for 89% of the highest quality pellets from the ground, and 68% in the most degraded pellets. A complete multilocus genotype was obtained in 79% of the least degraded pellets, but only 14% of the most degraded pellets. Certain genetic loci strongly influenced this success rate, with some performing better than others. Pellets collected from snow were still most reliable with 100% identified to species, and >97% of New England cottontail with a complete multilocus genotype. Thus, if researchers are genotyping rabbit pellets for applications such as abundance estimations, only the higher quality pellets from the ground or those collected from snow will likely be useful. For occupancy monitoring, a wider range of pellets may be acceptable for species identification, with the understanding that there is a tradeoff with pellet quality and successful DNA analysis. These results indicate that sampling from the ground and qualitative assessment of pellet quality using our categorization scheme is a viable method for New England cottontail monitoring in years with less snow. © 2020 The Wildlife Society.

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Section: Methodsmentioning

confidence: 99%

Section: Study Areamentioning

confidence: 99%

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Evaluation of Cottontail Pellets Collected in Suboptimal Conditions for DNA Analysis

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“…Today, New England cottontails are isolated into 5 geographically and genetically distinct regional populations (Litvaitis et al 2006, Fenderson et al 2011. Further subdivisions occur within each of these geographic areas, resulting in small, local metapopulations, in which extinctions and recolonizations occur independently from each other (Fenderson et al 2011(Fenderson et al , 2014Bauer 2018;Cheeseman et al 2019).…”

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Monitoring a New England Cottontail Reintroduction with Noninvasive Genetic Sampling

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Careful monitoring of reintroduced threatened species is essential for informing conservation strategies and evaluating reintroduction efforts in an adaptive management context. We used noninvasive genetic sampling to monitor a reintroduction of a threatened shrubland specialist, the New England cottontail (Sylvilagus transitionalis), in southeastern New Hampshire, USA. We monitored the apparent survival and breeding success of founder individuals and tracked changes in population size and genetic diversity for 5 years following an initial reintroduction in 2013. We released 42 rabbits, documented 29 unique offspring in years following releases through noninvasive surveys, and identified 6 founder individuals and 9 recruited offspring that bred. Apparent survival of founders was variable and greatest in the first year of the reintroduction. Predation was the primary cause of mortality and greatest in the first month after release and after heavy snowfall. Population size remained small but relatively stable until a stochastic decline in the fourth year following reintroduction, followed by a slight rebound after population augmentation and offspring production by wild‐born rabbits. Genetic diversity increased after the initial founders with diverse genetic backgrounds were released and then they and their subsequent offspring bred. We documented successful dispersal 700 m from the release site to a high‐quality patch of habitat, which remained occupied throughout the study. For New England cottontail reintroductions to be successful in the long term, releases will be needed at multiple patches within dispersal distance, and habitat corridors need to be restored among patches to create a functioning metapopulation. For small or isolated reintroduced populations, continued intensive monitoring is needed to detect stochastic declines in population size or changes in sex ratios and guide subsequent management reactions via additional reintroductions or population augmentations. Noninvasive genetic sampling is a valuable tool to monitor reintroductions of the New England cottontail and other threatened species to provide managers with detailed information to inform decision‐making in an adaptive management framework. © 2020 The Wildlife Society.

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Is conservation based on best available science creating an ecological trap for an imperiled lagomorph?

Cheeseman

Cohen

Ryan

et al. 2020

Ecology and Evolution

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Hierarchical population structure of a rare lagomorph indicates recent fragmentation has disrupted metapopulation function

Cited by 13 publications

References 66 publications

Evaluation of Cottontail Pellets Collected in Suboptimal Conditions for DNA Analysis

Evaluation of Cottontail Pellets Collected in Suboptimal Conditions for DNA Analysis

Monitoring a New England Cottontail Reintroduction with Noninvasive Genetic Sampling

Is conservation based on best available science creating an ecological trap for an imperiled lagomorph?

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