Long-Term Noninvasive Genetic Monitoring Guides Recovery of the Endangered Columbia Basin Pygmy Rabbits (Brachylagus idahoensis)

Abstract

Background/Objectives: Loss and fragmentation of habitat from agricultural conversion led to the near extirpation of the pygmy rabbit (Brachylagus idahoensis Merriam, 1891) population in the Columbia Basin (CB) of Washington, USA. Recovery efforts began in 2002 and included captive breeding, translocations from other regions for genetic rescue, and reintroduction into native habitat in three sites: Sagebrush Flat (SBF), Beezley Hills (BH), and Chester Butte (CHB). Methods: We used noninvasive and invasive genetic sampling to evaluate demographic and population genetic parameters on three translocated populations of pygmy rabbits over eight years (2011-2020). For each population, our goal was to use fecal DNA sampling and 19 microsatellite loci to monitor spatial distribution, apparent survival rates, genetic diversity, reproduction, effective population size, and the persistence of CB ancestry. Over the course of this study, 1978 rabbits were reintroduced as part of a cooperative conservation effort between state and federal agencies. Results: Through winter and summer monitoring surveys, we detected 168 released rabbits and 420 wild-born rabbits in SBF, 13 released rabbits and 2 wild-born in BH, and 16 released rabbits in CHB. Observed heterozygosity (H_o) values ranged from 0.62-0.84 (SBF), 0.59-0.80 (BH), and 0.73-0.77 (CHB). Allelic richness (AR) ranged from 4.67-5.35 (SBF), 3.71-5.41 (BH), and 3.69-4.65 (CHB). Effective population (N_e) within SBF varied from 12.3 (2012) to 44.3 (2017). CB ancestry persisted in all three wild populations, ranging from 15 to 27%. CB ancestry persisted in 99% of wild-born juveniles identified in SBF. Apparent survival of juvenile rabbits differed across years (1-39%) and was positively associated with release date, release weight, and genetic diversity. Survival of adults (0-43%) was positively influenced by release day, with some evidence that genetic diversity also positively influenced adult apparent survival. Conclusions: Noninvasive genetic sampling has proven to be an effective and efficient tool in monitoring this reintroduced population, assessing both demographic and genetic factors. This data has helped managers address the goals of the Columbia Basin recovery program of establishing multiple sustainable wild populations within the sagebrush steppe habitat of Washington.

Keywords: Brachylagus idahoensis; genetic monitoring; native populations; noninvasive genetic sampling; pygmy rabbits; wildlife.

Figure 1

(Left) Pygmy rabbit distribution across the western United States Taken from Smith et al. (46). (Right) Geographic location of the reintroduced Columbia Basin pygmy rabbit (Brachylagus idahoensis) populations in Washington, USA, and locations of Sagebrush Flat, Beezley Hills, and Chester Butte recovery areas.

Figure 2

Location of Sagebrush Flat (SBF) wildlife area in Washington, USA, Conservation Reserve Program habitat (CRP), and active pygmy rabbit (B. idahoensis) burrows (•) identified during winter monitoring surveys during (a) winter 2012–2013, (b) winter 2013–2014, (c) winter 2014–2015, (d) winter 2015–2016, (e) winter 2016–2017, (f) winter 2017–2018, (g) summer 2018, (h) winter 2018–2019, and (i) winter 2019–2020. Area to the left of SBF represents private land.

Figure 3

Predicted probabilities of apparent survival rates for pygmy rabbits (B. idahoensis) introduced into the central WA for significant variables in each model. (a) Juvenile survival rate by release weight for released juveniles in the Sagebrush Flat recover area (SBF), (b) juvenile survival rate by release day for released juveniles in SBF, (c) juvenile survival rate by homozygosity for released juveniles in SBF, (d) adult survival rate by release weight for released adults in SBF, (e) juvenile survival rate by release day for juveniles released into pens in the Beezley Hills and Chester Butte recovery areas. Predicted probabilities plots were generated from top models for juvenile and adult survival.