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A Brief Overview of Survey Methodology

Prepared by: Robin Russell U.S. Geological Survey, National Wildlife Health Center, Madison, WI, ([email protected]);Todd Esque U.S. Geological Survey, Western Ecological Research Center, Henderson, NV, ([email protected]); Matthew Gompper Department of Fish, Wildlife and Conservation Ecology, New Mexico State University, Las Cruces, NM ([email protected]); Gary Roemer Department of Fish, Wildlife and Conservation Ecology, New Mexico State University, Las Cruces, NM, ([email protected])

Rabbit populations (including North American native or feral domestic species of the genera Brachylagus, Lepus, Oryctolagus and Sylvilagus) can be estimated from surveys using a variety of approaches. Below we provide a brief description of survey methods for , with additional details in the referenced literature. We cover survey methods that estimate presence/absence, relative abundance, abundance estimates from mark-recapture, and distance sampling. Choice of study design should depend on objectives and available resources. Please contact the authors for assistance with study designs that meet objectives within resource constraints. Consulting a statistician prior to beginning any surveillance program is recommended.

Presence/Absence

In general presence/absence estimates are used to elucidate patterns in how a species uses available habitat. Although not as sensitive to changes in abundance as other population-level metrics (see below), presence/absence can nonetheless be a useful tool for evaluating landscape-level changes in species distributions and resource use.

Presence/absence data can be summarized within the framework of occupancy modeling (MacKenzie et al. 2006). Occupancy estimates are generated from repeat visits to the same location over a short period of time within which the population can assume to be demographically and geographically closed (i.e. there is no reproduction, death, immigration or emigration). Occupancy is particularly useful for species that use a fixed location on a daily basis such as a hibernaculum, a pond, a roost, or a ‘form’ (a hollowed out nesting area/burrow). Selecting the scale at which occupancy is assessed for a species is an important consideration. Too large of a scale can result in a resolution that is not ecologically useful, while too small of an area will be more costly and result in a large number Black-jailed jackrabbit, Lepus of non-detections. When using transects to search for direct or indirect signs of californicus. Photo: Todd Esque. rabbits the length and width (that is, the search area and effective size of the transect), and distribution of transects is also important to consider and document. Occupancy estimates do not require that individual be marked. However, by marking individuals, estimates of both occupancy and abundance and/or density may be possible (see below). For rabbits several approaches have been successfully executed to estimate occupancy.

Occupancy estimation methods:

• Indirect (feces, tracks, burrows): By counting signs of rabbits along multiple transects established within a study area, indications of the presence or potential absence of rabbits can be collected. Along transects observers search for rabbit fecal pellets, latrines, tracks or burrows, and record locations of rabbit sign with GPS. Burrow locations can be surveyed for signs of recent activity to document presence/absence as well. Genetic analysis of fecal pellets can be used for species identification if similar species occupy an area. • Direct (cameras, captures, or visual) observations: Distributed camera traps, actual physical traps, or visual observations in defined areas such as along a transect can be used to “capture” animals and infer the presence/absence of rabbits. Care should be used in considering how best to distribute cameras, traps, or transects for visual surveys. Randomization of detectors should always be considered. Optimal approaches

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may differ as a function of the density of the species (when present) as well as the size of the study area. Stratification may be necessary to accurately estimate occupancy in different habitats. Spacing of the cameras, traps, or transects, may require experimentation for particular species and study sites. Home range (HR) estimates may be useful for determining camera or trap spacing.

Relative Abundance:

Relative Abundance surveys can be useful for comparing and contrasting populations when precise estimates of population size are not needed, and for elucidating patterns in habitat use when presence/absence fails to accurately or fully reflect observed distributions.

Methods of relative abundance estimation of rabbit populations:

• Road Surveys: Road surveys have long been used to assess the relative abundance of populations, and this is particularly true for lagomorphs. Surveys should be conducted by slowly driving roads and counting the number of individuals observed (typically per km) along a transect, often these surveys are conducted in the evening using spotlights. All surveys should be conducted at the same (or as similar as possible) time to control for seasonal or diurnal changes in activity/density of rabbits. By controlling for factors such as time of day or season, results of transect surveys can be compared over multiple years and/or sites. Foot surveys can be conducted in a similar fashion if roads are inaccessible. While at its simplest, road surveys provide count data, it is important to note Camera trap image of black-tailed jackrabbits. Photo courtesy of Gary Roemer. that they can also be designed to provide the type of data useful for distance sampling (see below). Repeated counts of animals made in a defined area such as a pond, a study site with a defined boundary, or a colony can be analyzed using N-mixture models (Royle 2004, Tilker et al. 2020).

• Pellet counts: Counts of rabbit feces (pellets) may also be used to assess relative abundance/relative density, in the absence of an ability to directly observe rabbits. By walking transects and counting pellets or groups of pellets, an assessment of relative abundance for each transect may be gained. Pellet counts can be converted into an abundance index, with a greater index value indicating a presumably higher population density in an area. There are a number of mechanisms for converting pellet counts from relative abundance estimates to absolute abundance estimates, including detailed work at a subset of sites to estimate actual population sizes (estimated via capture or non-invasive techniques outlined below) to determine the relationship between population density and the pellet count index. Direct observations of rabbits through visual counts or the methods outlined below are recommended over pellet indices.

Distance Sampling

Distance sampling has a long history of use for the estimation of density (Buckland et al. 1993). Distance sampling requires that the distance and angle to each sighted individual be recorded along with where the observation was made. Effective area sampled (i.e. transect width) is estimated from the data. Transect length may need to be adjusted for different species in different habitats; An important consideration is that estimation is difficult if population density is low and too few individuals are recorded.

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Figure. 1. Distribution of lagomorph transects and detections observed (red triangles) on White Sands National Park, New Mexico and subsequent estimates of landcover-specific lagomorph density estimated with a distance sampling method. All transects were randomly stratified by landcover type and repeatedly walked to observe lagomorphs. Adapted from Robinson (2013) and Robinson et al. (2014).

Methods for distance sampling of rabbit populations:

• Road or Transect Surveys: For lagomorphs, distance sampling involves set transects being surveyed either on foot or using slow moving vehicles such as the road surveys (noted above). An example of the type of information that can be gained through this approach is shown in Figure 1. Longshore et al. (2015) describe the field methods in detail for black-tailed jackrabbits and desert cottontails. As with other surveys, effort should be made to control for factors such as time of day and weather conditions when conducting surveys. Handheld spotlights can be used for night surveys. When an animal is observed, GPS location, time, species, bearing of the transect, bearing to the individual observed, distance to the individual observed (these data are taken with a compass and rangefinder, respectively, so the perpendicular distance from the road to the individual can be estimated), number of individuals, status (i.e., alive or dead), weather conditions and other habitat variables (relevant to the study) are typically recorded.

Abundance Estimation via Mark-Recapture and Similar Methods

Statistical approaches for extrapolating the size of animal populations have existed for over 50 years and over time have become increasingly sophisticated, allowing for more unbiased assessments of abundance as well as mechanisms for estimating the potential error or variance associated with the abundance estimates. Mark- recapture or capture-mark-recapture can provide estimates of animal abundance as well as survival rates, and potentially movements between populations. Here we outline several such approaches.

Methods of abundance estimation from marking and recapturing or resighting rabbit populations:

Mark-recapture, mark-resight, and spatial capture-recapture belong to a family of methods that require repeated observations of individual animals that are uniquely identified (either physical “recapture”, visual “resight” of known individuals, or collection of an individual’s genetic material, hair (with follicle), fecal material, etc. for identification). Spatial capture/recapture is an extension of mark-recapture where the specific locations (e.g., using GPS) of detections are recorded (i.e. traps, cameras, or capture locations). This information can be used to generate density estimates.

U.S. Geological Survey National Wildlife Health Center Department of the Interior • Mark-recapture: Physical capture of animals is an intensive process, that involves the capture, marking (with a unique identifier), and release of individual animals. Mark-recapture requires traps to be monitored for multiple days (or nights) to ensure an adequate sample of recaptures. Spatial-capture recapture employs the same concepts as mark-recapture but requires that the detector locations (either physical traps or cameras etc.) are recorded. As with other techniques the spacing of the traps is an important consideration (see Royle et al. 2014 for a comprehensive overview of spatial capture-recapture techniques). • Mark-resight: In areas where resighting animals is possible, mark- resight approaches may offer a less labor-intensive approach to abundance estimation. Rabbits can be captured using traps (box or cages), and marked with ear tags, pit tags, VHF-radio or Global Positioning (GPS) collars or with dyes (see Facka et al. 2010 for details on dye use). Mark-resight can be accomplished by walking transects and recording the identification of located animals, viewing marked animals from a stationary spot with binoculars or a spotting Camera trap image of Sylvilagus audobonii. Photo courtesy of scope, or photographing marked animals with a remote camera. Matt Gompper. • Genetic approaches: Non-invasive genetic approaches are often used to increase capture probabilities for rare species, or to reduce the stress of physical capture. Transects are visited and fecal or hair samples are collected when observed, or hair capture locations (i.e. hair snares) are deployed in a systematic grid. Individual identifications are made by genotyping the DNA gained from hair follicles or fecal samples. Transects are repeatedly sampled through re-visitation, allowing additional genetic samples to be collected, and estimates of detection probabilities to be generated. While non-invasive genetic approaches may reduce the labor-intensive aspects of field work, they require extensive laboratory work. Lab costs of genetic approaches need to be balanced against field costs for live trapping.

Additional Resources

• Ballinger, A. and Morgan, D.G., 2002. Validating two methods for monitoring population size of the (Oryctolagus cuniculus). Wildlife Research 29:431-437. • Bauer, M.L., B. Ferry, H. Holman, and A.I. Kovach. 2020. Monitoring a reintroduction with noninvasive genetic sampling. Wildlife Society Bulletin 44:110-121. • Bosch, A.M., Benson, K.J. and Mead, A.J., 2016. Declining frequency of road-killed rabbits in central Georgia. Georgia Journal of Science 74:2. • Brown, S.C., Wells, K., Roy‐Dufresne, E., Campbell, S., Cooke, B., Cox, T. and Fordham, D.A., 2020. Models of spatiotemporal variation in rabbit abundance reveal management hot spots for an invasive species. Ecological Applications 30:p.e02083. • Brubaker, D.R., A.I. Kovach, M.J. Ducey, W. Jakubas and K. O’Brien. 2014. Factors influencing detection in occupancy surveys of a threatened lagomorph. Wildlife Society Bulletin 38:513-523. • Buckland, S.T., Anderson, D.R., Burnham, K.P. and Laake, J.L. 1993. Distance Sampling: Estimating abundance of biological populations. Chapman and Hall, London. 446 pp. • Cheng, E., K. Hodges, R. Sollmann, and L.S. Mills. 2017. Genetic sampling for estimating density of common species. Ecology and Evolution 7:6210-6219. • Cypher, B.L., Bjurlin, C.D. and Nelson, J.L., 2018. Comparison of rabbit abundance survey techniques in arid habitats. California Fish and Game. 104:19-27. • DeMay, S.M., P.A. Becker, J.L. Rachlow, and L.P. Waits. 2017. Genetic monitoring of an recovery: demographic and genetic trends for reintroduced pygmy rabbits (Brachylagus idahoensis). Journal of Mammalogy 98:350-364. • Eaton, MJ., P.T. Hughes, J.D. Nichols, A. Morkill, and C. Anderson. 2011. Spatial patterns of the Lower Keys . Journal of Wildlife Management 75:1186-1193. • Efford, M. G. 2020. secr: Spatially explicit capture-recapture models. R package version 4.2.2. https://CRAN.R-project.org/package=secr

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• Fidino, M., J. L. Simonis, S. B. Magle.2019. A multistate dynamic occupancy model to estimate local colonization–extinction rates and patterns of co‐occurrence between two or more interacting species. Methods in Ecology and Evolution 10: 233-244. • Fiske, I., and R. Chandler. 2011. unmarked: An R Package for Fitting Hierarchical Models of Wildlife Occurrence and Abundance. Journal of Statistical Software, 43(10), 1-23. http://www.jstatsoft.org/v43/i10/. • Guerrero-Casado, J., Ström, H., Hilström, L., Prada, L.M., Carpio, A.J. and Tortosa, F.S., 2020. Assessment of the suitability of latrine counts as an indirect method by which to estimate the abundance of European rabbit populations at high and low abundance. European Journal of Wildlife Research, 66:10. • Homyack, J.A., Harrison, D.J., Litvaitis, J.A. and Krohn, W.B., 2006. Quantifying densities of snowshoe in Maine using pellet plots. Wildlife Society Bulletin 34:74-80. • Hodges, K.E. and Mills, L.S., 2008. Designing fecal pellet surveys for snowshoe hares. Forest Ecology and Management 256:1918-1926. • Hunt, V.M., Magle, S.B., Vargas, C., Brown, A.W., Lonsdorf, E.V., Sacerdote, A.B., Sorley, E.J. and Santymire, R.M., 2014. Survival, abundance, and capture rate of rabbits in an urban park. Urban Ecosystems 17:547-560. • Laake, J. Laake, J.L. (2013). RMark: An R Interface for Analysis of Capture-Recapture Data with MARK. AFSC Processed Rep 2013-01, 25p. Alaska Fish. Sci. Cent., NOAA, Natl. Mar. Fish. Serv., 7600 Sand Point Way NE, Seattle WA 98115. • Larrucea, E.S., and P. F. Brussard. 2008. Habitat selection and current distribution of the in Nevada and California, USA. Journal of Mammalogy 89: 691–699, • Litvaitis, J.A., J. P. Tash, M. K. Litvaitis, M. N. Marchand, A. I. Kovach and R. Innes, 2006. A range-wide survey to determine the current distribution of New England Cottontails. Wildlife Society Bulletin 34:1190- 1197. • Longshore, K., T. C. Esque, and K. E. Nussear. 2017. An assessment of food habits, prey availability, and nesting success of golden eagles within the Desert Renewable Energy Conservation Plan Area. California Energy Commission. Publication number: CEC-500-2017-003. • MacKenzie, D. I., J.D. Nichols, M.E. Seamans, and R.J. Gutiérrez. 2009. Modeling species occurrence dynamics with multiple states and imperfect detection. Ecology, 90: 823–835. • MacKenzie, D.I., J. D. Nichols, J. Andrew Royle, K.H. Pollock, L.L. Bailey, and J. E. Hines 2006. Occupancy estimation and modeling: inferring patterns and dynamics of species occurrence. Elsevier. • McDonald, T., J. Carlisle, and A. McDonald. 2019. Rdistance: Distance-Sampling analyses for density and abundance estimation. R package version 2.1.3 https://CRAN.R-project.org/package=Rdistance • Nielson, S. Wakamiya, and C. Nielsen. Viability and patch occupancy of a metapopulation at the northern edge of its distribution. Biological Conservation 141:1043-1054. • Nichols, J.D., J.E. Hines, D. I. Mackenzie, M.E. Seamans, and R.J. Gutiérrez. 2007. Occupancy estimation and modeling with multiple states and state uncertainty. Ecology, 88: 1395–1400. • Planillo, A. and Malo, J.E., 2018. Infrastructure features outperform environmental variables explaining rabbit abundance around motorways. Ecology and Evolution 8: 942-952. • Price, A.J. and J. L. Rachlow. 2011. Development of an index of abundance for pygmy rabbit populations. Journal of Wildlife Management 75:929-937. • Robinson, Q. H. 2013. The application of occupancy modeling to evaluate intraguild predation in a model carnivore system. Thesis. New Mexico State University, Las Cruces, New Mexico. • Robinson, Q. H., D. Bustos, and G. W. Roemer. 2014. The application of occupancy modeling to evaluate intraguild predation in a model carnivore system. Ecology 95:3112-3123. • Rouco, C., Santoro, S., Delibes-Mateos, M. and Villafuerte, R., 2016. Optimization and accuracy of faecal pellet count estimates of population size: The case of European rabbits in extensive breeding nuclei. Ecological Indicators 64: 212-216. • Royle, A., R. Chandler, R. Sollmann, and B. Gardner. 2014. Spatial Capture Recapture. Elsevier. • Royle, J.A. 2004. N-Mixture models for estimating population size from spatially replicated counts. Biometrics 60: 108–115.

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• Royle, J.A., R.B. Chandler, C. Yackulic, and J.D. Nichols. 2012. Likelihood analysis of species occurrence probability from presence-only data for modelling species distributions Methods in Ecology and Evolution. 3: 545-554 • Sarmento, P., J. Crus, A. Paula, C. Eira, M. Capinha, I. Ambrósio, C. Ferreira and C. Fonseca. 2012. Occupancy, colonization and extinction patterns of rabbit populations: implications for Iberian lynx conservation. European Journal of Wildlife Research 58:523–533. • Shannon, G., Lewis, J. S., & Gerber, B. D. 2014. Recommended survey designs for occupancy modelling using motion-activated cameras: insights from empirical wildlife data. PeerJ 2: e532. • Sutherland, C., A. Royle, and D. Linden 2019. oSCR: Multi-Session Sex-Structured Spatial Capture- Recapture Models. R package version 0.42.0. • Tilker, A., A. Nguyen, J. F. Abrams, T.B. Hagwat, M.L.T. Van Nguyen et al. 2018. A little-known endemic caught in the South-east Asian extinction crisis: the Annamite striped rabbit (Nesolagus timminsi). Oryx 10.1017/S0030605318000534 • Wilson, T.L., J.B. Odei, M.B. Hooten, and T.C. Edwards. 2010. Hierarchical spatial models for predicting pygmy rabbit distribution and relative abundance. Journal of Applied Ecology 47: 401–409

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