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Using Shrubland Mapping to Sample for New England Cottontails

Bill Buffum University of Rhode Island Department of Natural Resources Science January 2012

This report was prepared as part of a University of Rhode Island project entitled "Forest Management for Wildlife Habitat in Rhode Island" with funding from the University of Rhode Island and the United States Department of Agriculture through a McIntire-Stennis Cooperative Research Grant. Project partners include the Rhode Island Department of Environmental Management, the Rhode Island Agricultural Experiment Station and the Natural Resources Conservation Service. For more information on the project see: http://nrs.uri.edu/ce/Forestry.html Suggested citation: Buffum, B. 2012. Using Shrubland Mapping to Sample for New England Cottontails. Kingston, Rhode Island: Department of Natural Resources Science, University of Rhode Island. Photographs on cover page: New England cottontail (Lou Perrotti); Shrubland developing after clearcut (Bill Buffum). For questions about this report, contact Bill Buffum, Department of Natural Resources Science, University of Rhode Island, 13 Coastal Institute, Kingston RI 02881 ([email protected]).

Using Shrubland Mapping to Sample for New England Cottontails page 1

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1. Introduction During the winter of 2011 the University of Rhode Island (URI) initiated a study on the distribution, genetics and habitat requirements of New England Cottontail (Sylvilagus transitionalis) in Rhode Island in collaboration with the RI Department of Environmental Management (RIDEM) and the U.S. Fish and Wildlife Service (USFWS). The study collected cottontail pellets for genetic analysis in random sample locations which were identified by two models: (a) the habitat suitability index (HSI) model developed by Steve Fuller of the Wildlife Management Institute, and (b) an early successional habitat (ESH) model based on mapping of shrublands conducted at URI. This paper describes the process for developing the ESH model, the initial results, and the plan for 2012 sampling. Populations of New England Cottontail (NEC), Rhode Island’s only native cottontail, have been in decline for many years, and USFWS has listed NEC as a candidate for listing as an endangered species. A number of explanations have been offered for the decline, including competition with eastern cottontails (Sylvilagus floridanus), an introduced species that is more common in Rhode Island. However, habitat loss and fragmentation is considered to be the most important factor (Litvaitis 2006) The two species of cottontail are very similar in appearance and generally use the same habitats, although a study in western Connecticut reported that eastern cottontails tend to utilize shrubland habitat adjacent to open land while NEC tend to utilize shrubland surrounded by forest (Eabry 1968). DNA analysis of pellets is a most reliable, non-invasive method to distinguish between the two species. During the winter of 2011, URI managed a team of over 85 volunteers who surveyed more than 100 locations throughout the state and collected pellets for analysis in the URI Conservation Genetics Laboratory (Gottfried and Niebels 2011). 2. Selection of 2011 ESH Samples

In October 2011 a meeting was held at URI to plan the first season of NEC sampling.1 It was decided to generate two sets of random sample points and also sample all historical points where NEC had been detected in previous years. The first set of random points was generated by Andrew MacLauchlan of USFWS based on the HSI model developed by Steve Fuller of the Wildlife Management Institute. The second set of points was generated by Bill Buffum of URI based on a new ESH model described below.

The 2011 sample was stratified by three geographic areas, with more intensive sampling in Washington County. Islands not connected to the mainland by bridges were excluded. The planned number of sample sites for each region/model was as follows.

• Washington County: 75 random samples (50 HSI model, 25 ESH model) • Providence & Kent: 30 random samples (20 HSI model, 10 ESH model) • Bristol and Newport: 30 random samples (20 HSI model, 10 ESH model).

1 Attended by staff from URI, RIDEM and USFWS and the Natural Resources Conservation Service (NRCS).


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Additional points were provided to replace any points that were later determined to be unfeasible.

Table 1. Numbering System for 2011 Samples

Series Region Model 1000 Washington County HSI 2000 Historic Points (all counties) --- 3000 Washington County ESH 4000 Providence/Kent Counties HSI 5000 Providence/Kent Counties ESH 6000 Bristol/Newport Counties HSI 7000 Bristol/Newport Counties ESH The 2011 ESH model was based on a recent mapping of shrubland in RI conducted as part of a study to analyze the sustainability of shrubland habitat (Buffum et al. 2011). Generation of points with the ESH model included the following process steps:

a) Start with all polygons of shrubland mapped in Rhode Island in the 2011 study. b) Exclude polygons on islands that are not connected to mainland by bridges. c) Exclude poorly drained shrubland, based on the "drainage" category of the Soil

Survey Geographic (SSURGO) Soil Polygons for the State of Rhode Island. SSURGO includes seven drainage categories, of which five are dryer than very poorly drained.2

d) Select polygons of shrubland with the appropriate drainage rating that have an area of at least 10 ha.

e) Exclude any polygon which overlapped with one of the "RI ranked parcels" identified by the HSI model.

f) Exclude the outer 25 meters of each polygon g) Exclude 50 meters from any historical point h) Generate random points within the remaining areas.

3. Preliminary Results of 2011 Sampling During the 2011 season, a total of 127 random sites were sampled, of which 62 sampling sites were "completed" by either finding pellets or visiting the site for at least three times without finding any pellets (Figure 1). Pellets were found in 56% of these sites. 2 The seven SSURGO drainage categories, ranging from poorly to well drained, are (1) permanently submerged, (2) very poorly drained, (3) poorly drained, (4) moderately well drained, (5) well drained, (6) somewhat excessively drained, and (7) excessively drained. The dataset is available at: http://www.edc.uri.edu/rigis/data/


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In addition to the samples collected at random points and known locations, another 274 "haphazard" samples were collected at non-random points. The only NEC detection in 2012 was in a haphazard site. Sampling will continue in 2012 at the 65 incomplete sites as well as at series of new random sites. Based on the findings from the 62 complete sites, the ESH model appears to be effective at selecting sites inhabited by Eastern Cottontails, with a higher rate of pellet detection than the HSI model or the historical sites where NEC was found in previous years (Table 3). However, it remains to be seen whether any model is more effective at identifying sites inhabited by NEC.

Source: Gottfried and Niebels 2011

Table 2. Results of 2011 Sampling from Completed Sites

Number of Completed Sites Percentage of sites

with pellets No pellets Pellets Total ESH Model 4 21 25 84% HSI Model 15 8 23 35% Historical Sites 8 6 14 43% Total 27 35 62 56%

Many of the 274 haphazard samples were collected in close proximity to each other, and can be divided into 63 geographic clusters. The number of samples per cluster ranged from 1 (20 clusters) to 31 (1 cluster) with an average of 4 samples per cluster. These sample sites were not randomly selected and locations without pellets were not recorded. Nevertheless, it is interesting to note that 49% of the clusters were located in areas that were mapped as shrubland with the drainage qualities of the ESH model. However, most of these clusters were located in patches that under 10 acres, whereas only 16% were located in patches ≥ 25 acres as per the ESH model. This confirms that the ESH model identifies sites that are likely to have cottontail, but that eastern cottontails also utilize many other habitat types, sometimes without any nearby shrubland. A preliminary analysis of the land use in three-acre circles around the sample points indicates that the plots where cottontail were detected were surrounded by more shrubland and less forest than the plots where cottontail were not detected (Figure 2). 3

3 For the random plots, the analysis was done for each individual plot. For the haphazard plots, the analysis was done by cluster, averaging all of the plots in each cluster. Land use information for this analysis was extracted from the RI Forest Habitat Map developed at URI - for more information about this map see Buffum (2012).

Figure 1. Map of 2011 NEC Survey Locations


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The three acre circle size for the analysis was selected to represent the home range of eastern cottontails, which has been estimated as ranging from 0.5 - 40 acres in Massachusetts (Mass Wildlife 2012) and 2.3 - 40 acres in New York (AEC 2012). Figure 2 also suggests that the random sampling process encouraged the researchers to venture into large patches of shrubland, while the haphazard sampling tended to take place in more accessible agriculture and developed areas. Figure 2. Land Use in Three-acre Circles Around 2011 Sample points

The median percentage of the surrounding three acres plots covered with shrubland was significantly higher for sample plots where pellets were detected (both random and haphazard) than in the plots where pellets were not detected.4 In contrast, the median percentage of the surrounding three acres plots covered with forest was significantly lower for sample plots where pellets were detected (both random and haphazard) than in the plots where pellets were not detected.

4 Statistical analysis was carried out with the Mann-Whitney U test because the distributions were not normal.

-10%

0%

10%

20%

30%

40%

50%

60%

70%

Forest Shrubland Agriculture and Grassland

Developed Other

Percent of 3 acre circles (mean) around sample

points of each land use type

Random sites - no pellets detected

Random sites - pellets detected

Haphazard sites - pellets detected


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4. Extent of Shrubland Habitat in Rhode Island According to the ESH model, 96 patches of suitable shrubland habitat exist in Rhode Island with an average patchsize of 52 acres and total area of 5,039 acres. However, an analysis of shrubland extent in 2008 found that the total area of patches of at least 25 acres increases by 53% if patches less than 100 feet apart are combined (Buffum 2011).5 The same study also noted that the extensive area of wetlands in Rhode Island may play an important role in increasing the connectivity of shrubland patches for New England cottontail. The state includes 60,112 acres of wetland which are classified by the National Wetlands Inventory as including wetland shrubland or forest. Even non-shrubland wetlands often contain a dense understory that could be used by cottontail as corridors between shrubland patches. The total area of cottontail habitat increases by 16% if patches connected by wetlands are combined and by 73% if patches connected by wetlands and patches less than 100 feet from other patches are combined. For an illustration of how these types of connectivity increase the extent of habitat, see Figure 3. 5. Selection of 2012 ESH Samples

In December 2011 a meeting was held at URI to plan the second season of NEC sampling.6 It was decided to generate two more sets of random sample points based on the ESH and HSI models. The ESH model was used to generate the first set of points in 2012, and the HSI model was used to generate additional points that were at least 100 meters from one of the ESH points.

The 2012 sampling will focus on the southeast and southwest portions of the state.

• Southwest RI: defined as areas in RI ≤ 5 miles from the Connecticut border that fall in the towns of Westerly, Hopkinton, Exeter, West Greenwich and Coventry. This region was subdivided into five equal sub-regions.

• Southeast RI: defined as the towns of Little Compton and Tiverton

The planned number of sample sites for each region/model follows, but additional points were provided to replace any points that were later determined to be unfeasible.

• Southwest RI (north portion):10 random samples (5 HSI model, 5 ESH model) • Southwest RI (north-central):10 random samples (5 HSI model, 5 ESH model) • Southwest RI (central portion):10 random samples (5 HSI model, 5 ESH model) • Southwest RI (south-central): 10 random samples (5 HSI model, 5 ESH model) • Southwest RI (south portion): 10 random samples (5 HSI model, 5 ESH model) • Little Compton: 10 random samples (5 HSI model, 5 ESH model) • Tiverton: 10 random samples (5 HSI model, 5 ESH model)

5 The area between patches is excluded from the area calculation. 6 Attended by staff from URI, NRCS, RIDEM and USFWS.

Using Shrubland Mapping to Sample for New England Cottontails page 6 Figure 3. Extent of cottontail habitat with different connectivity scenarios

1. Cottontail habitat: patchsize > 25 acres 2. Cottontail habitat: patchsize > 25 acres if connected by wetlands

3. Cottontail habitat: patchsize > 25 acres if 4. Cottontail habitat: patchsize > 25 acres if connected by 50 ft shrubland buffer connected by 50 ft. shrubland buffer or wetlands

Notes: Source: Buffum (2011) Based on 2008 shrubland data and ESH Model. Shrubland: red outline; NWI Wetlands: solid blue Location: Little Compton, RI. Imagery: 2008_RI911


Table 3. Numbering System for 2012 Samples

Series Region Model 8100 Zone 1Southwest RI (South) ESH 8200 Zone 2 Southwest RI (South Central) ESH 8300 Zone 3 Southwest RI (Central) ESH 8400 Zone 4 Southwest RI (North Central) ESH 8500 Zone 5 Southwest RI (North) ESH 8600 Little Compton ESH 8700 Tiverton ESH 9000 Zone 1Southwest RI (South) HSI 9200 Zone 2 Southwest RI (South Central) HSI 9300 Zone 3 Southwest RI (Central) HSI 9400 Zone 4 Southwest RI (North Central) HSI 9500 Zone 5 Southwest RI (North) HSI 9600 Little Compton HSI 9700 Tiverton HSI The 2012 ESH model was similar to that of 2011 with the following differences:

a) The polygons of shrubland had been updated based on the new 2011 imagery available on RIGIS.

b) Due to the limited number of large shrubland patches in the southwest portion of the state, the minimum size of shrubland polygons was reduced from 10 to 4 ha (10 acres), and the 25 meter internal buffer was not excluded as in 2011.

c) It was not necessary to exclude polygons which overlapped with one of the "RI ranked parcels" identified by the HSI model, since this year the ESH samples were identified before HSI sites, and the HSI sample excludes sites with 100 meters of an ESH sample.

d) A minimum distance of 100 meters between random points was established. 6. Future Analyses Hopefully the 2012 sampling will detect some more NEC. If not, it can be decided whether it is worthwhile to conduct a study of eastern cottontail. A GIS analysis of the landscape around the sample areas could complement the detailed vegetation analysis that Amy Gottfried is currently doing. The completion of a larger sample of random points would allow a GIS analysis of more specific land use categories (whereas the current analysis merged six forest types into one general forest category). An expanded analysis could also cover larger areas around the sample plots and consider additional variables such as fragmentation and the amount of edge.


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7. References AEC 2012. Eastern Cottontail: Adirondack Ecological Center. Based on Saunders, D. A. 1988. Adirondack Mammals. State University of New York, College of Environmental Science and Forestry. 216pp. www.esf.edu/aec/adks/mammals/cottontail.htm. Accessed 13 Jan 2012. Buffum B, McWilliams SM and August PV. 2011. A spatial analysis of forest management and its contribution to maintaining the extent of shrubland habitat in southern New England, United States. Forest Ecology and Management 262: 775–1785 (doi:10.1016/j.foreco.2011.07.024). Available at: http://nrs.uri.edu/ce/Reports.html. Buffum B. 2011. Can forest management maintain the extent of shrubland habitat in Rhode Island? A spatial analysis. Kingston, Rhode Island: Department of Natural Resources Science, University of Rhode Island. Available at: http://nrs.uri.edu/ce/Reports.html. Buffum B. 2012. A new Tool for Mapping Forest Habitats in Rhode Island. Kingston Rhode Island: Department of Natural Resources Science, University of Rhode Island. Available at: htpp://nrs.uri.edu/ce/Reports.html. Eabry S. 1968. An ecological study of Sylvilagus Transitionalis and S. Floridanus of northeastern Connecticut. Storrs, CT: University of Connecticut. 70 p. Gottfried A and Niebels M. 2011. Habitat, Distribution and Genetics of the New England Cottontail. Department of Natural Resource Science, University of Rhode Island. http://nrs.uri.edu/ce/Cottontail.html. Accessed 13 January, 2011. MassWildlife 2012. Cottontails in Massachusetts. Massachusetts Division of Fisheries & Wildlife. www.mass.gov/dfwele/dfw/wildlife/living/living_with_cottontails.htm. Accessed 13 January 2012. Litvaitis JA and Tash JP. 2006. Status, Habitat Features Associated With Remnant Populations, and Identification of Sites for Restoration and Translocation of New England Cottontails, Final Report to the U.S. Fish and Wildlife Service, New England Field Office. Durham, NH: Department Of Natural Resources, University of New Hampshire.

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