Variation in the mitochondrial DNA of the<i>Sylvilagus</i>complex occupying the northeastern United States

Litvaitis, Marian K.; Lee, Woo-Jai; Litvaitis, John A.; Köcher, Thomas

doi:10.1139/z97-074

Cited by 20 publications

(14 citation statements)

References 30 publications

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“…To minimize bias associated with differences in resource use, traps were placed along transects spanning entire sites at rabbit sign or every 25 m in the absence of sign. We confirmed species identity for all cottontails using two restriction digests, performed on an amplified target section of mitochondrial DNA extracted from collected ear tissue as described by Ryan et al (2016) following modified protocols outlined by Litvaitis and Litvaitis (1996), Litvaitis, Litvaitis, Lee, and Kocher (1997), and Kovach, Litvaitis, and Litvaitis (2003).…”

Section: Location Data Acquisitionmentioning

confidence: 87%

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

Cheeseman

Ryan

Whipps

et al. 2018

Ecology and Evolution

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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.

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Section: Location Data Acquisitionmentioning

confidence: 87%

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

Cheeseman

Ryan

Whipps

et al. 2018

Ecology and Evolution

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“…For species identification, we performed polymerase chain reaction (PCR) in 25‐µL reaction volumes in AmpliTaq Gold® 360 Master Mix (Life Technologies, Grand Island, NY, USA), with 0.25 µM of each primer and 3 uL of template DNA. Mitochondrial DNA was targeted with primers L15934 and H16498 of Litvaitis et al (1997). The resulting product was restriction‐digested with NlaIII (New England Biolabs, Ipswich, MA, USA) as described by Kovach et al (2003), and confirmed by restriction digest with BfaI (New England Biolabs) as described by Litvaitis and Litvaitis (1996) and implemented in Kilpatrick et al (2013).…”

Section: Methodsmentioning

confidence: 99%

Evaluation of Cottontail Pellets Collected in Suboptimal Conditions for DNA Analysis

et al. 2020

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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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“…Using mtDNA D-loop sequence, Litvaitis et al (1997) found species-specific haplotypes formed distinct clusters in a phylogenetic analysis of New England and eastern cottontails. They concluded that hybridization did not occur in their sample of sympatric individuals.…”

Section: Introductionmentioning

confidence: 99%

“…Reciprocal monophyly, however, was not observed among haplotypes of the New England cottontail and the allopatric Appalachian cottontail (S. obscurus), which differ in chromosome number. This conflict among marker types was attributed to rapid fixation of chromosomal variants and retention of ancestral haplotypes rather than hybridization (Litvaitis et al 1997).…”

Section: Introductionmentioning

confidence: 99%

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Hybridization and polymorphic microsatellite markers for two lagomorph species (Genus Sylvilagus): implications for conservation

Berkman

Saltzgiver

Heist

et al. 2009

Conservation Genet Resour

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Eastern cottontails (Sylvilagus floridanus) are a prolific and popular game species in North America but have declined within the core of their range. Swamp rabbits (S. aquaticus) are sympatric with eastern cottontails and are a species of concern at the northern fringe of their range in Illinois. Although hybridization between these species may be a potential factor affecting their declines, no studies have yet been conducted to address this issue. We examined the potential for hybridization between sympatric eastern cottontails and swamp rabbits in Illinois by sequencing a portion of the mitochondrial 12S gene in 17 individuals of each species. Additionally, we developed six microsatellite markers for the eastern cottontail (7-13 alleles/locus) that also amplify in swamp rabbits (3-5 alleles/locus). We found fixed differences between species with haplotypes forming well-differentiated clades indicating a lack of hybridization. Hybridization between eastern cottontails and swamp rabbits does not appear to be affecting their declines. Misidentification due to ambiguous morphological characteristics of the two species occurred in an earlier study and in our own. We suggest the mitochondrial 12S gene may be a convenient molecular marker for the resolution of species identity questions. Information on microsatellites, occurrence of natural hybridization, and a molecular marker for species resolution will be useful for developing management plans for lagomorphs and focusing further research on factors affecting population status.

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Variation in the mitochondrial DNA of theSylvilaguscomplex occupying the northeastern United States

Cited by 20 publications

References 30 publications

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

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

Evaluation of Cottontail Pellets Collected in Suboptimal Conditions for DNA Analysis

Hybridization and polymorphic microsatellite markers for two lagomorph species (Genus Sylvilagus): implications for conservation

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