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1. Adaptive divergence despite low effective population size in a peripherally isolated population of the pygmy rabbit, Brachylagus idahoensis

   https://doi.org/10.1111/mec.16040  

   Byer, Nathan W.; Holding, Matthew L.; Crowell, Miranda M.; Pierson, Todd W.; Dilts, Thomas E.; Larrucea, Eveline S.; Shoemaker, Kevin T.; Matocq, Marjorie D. (July 2021, Molecular Ecology)

   Abstract Local adaptation can occur when spatially separated populations are subjected to contrasting environmental conditions. Historically, understanding the genetic basis of adaptation has been difficult, but increased availability of genome‐wide markers facilitates studies of local adaptation in non‐model organisms of conservation concern. The pygmy rabbit (Brachylagus idahoensis) is an imperiled lagomorph that relies on sagebrush for forage and cover. This reliance has led to widespread population declines following reductions in the distribution of sagebrush, leading to geographic separation between populations. In this study, we used >20,000 single nucleotide polymorphisms, genotype‐environment association methods, and demographic modeling to examine neutral genetic variation and local adaptation in the pygmy rabbit in Nevada and California. We identified 308 loci as outliers, many of which had functional annotations related to metabolism of plant secondary compounds. Likewise, patterns of spatial variation in outlier loci were correlated with landscape and climatic variables including proximity to streams, sagebrush cover, and precipitation. We found that populations in the Mono Basin of California probably diverged from other Great Basin populations during late Pleistocene climate oscillations, and that this region is adaptively differentiated from other regions in the southern Great Basin despite limited gene flow and low effective population size. Our results demonstrate that peripherally isolated populations can maintain adaptive divergence. 

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2. Food quality, security, and thermal refuge influence the use of microsites and patches by pygmy rabbits ( Brachylagus idahoensis ) across landscapes and seasons

   https://doi.org/10.1002/ece3.8892  

   Olsoy, Peter J.; Milling, Charlotte R.; Nobler, Jordan D.; Camp, Meghan J.; Shipley, Lisa A.; Forbey, Jennifer S.; Rachlow, Janet L.; Thornton, Daniel H. (May 2022, Ecology and Evolution)

   Abstract How intensely animals use habitat features depends on their functional properties (i.e., how the feature influences fitness) and the spatial and temporal scale considered. For herbivores, habitat use is expected to reflect the competing risks of starvation, predation, and thermal stress, but the relative influence of each functional property is expected to vary in space and time. We examined how a dietary and habitat specialist, the pygmy rabbit (Brachylagus idahoensis), used these functional properties of its sagebrush habitat—food quality, security, and thermal refuge—at two hierarchical spatial scales (microsite and patch) across two seasons (winter and summer). At the microsite and patch scales, we determined which plant functional traits predicted the number of bites (i.e., foraging) by pygmy rabbits and the number of their fecal pellets (i.e., general habitat use). Pygmy rabbits used microsites and patches more intensely that had higher crude protein and aerial concealment cover and were closer to burrows. Food quality was more influential when rabbits used microsites within patches. Security was more influential in winter than summer, and more at Cedar Gulch than Camas. However, the influence of functional properties depended on phytochemical and structural properties of sagebrush and was not spatiotemporally consistent. These results show function‐dependent habitat use that varied according to specific activities by a central‐place browsing herbivore. Making spatially explicit predictions of the relative value of habitat features that influence different types of habitat use (i.e., foraging, hiding, and thermoregulating) will improve how we predict patterns of habitat use by herbivores and how we monitor and manage functional traits within habitats for wildlife. 

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3. Terrain Features and Architecture of Wolverine (Gulo gulo) Resting Burrows and Reproductive Dens on Arctic Tundra

   https://doi.org/10.14430/arctic75576  

   Glass, Thomas W.; Breed, Greg A.; Laird, Cristina R.; Magoun, Audrey J.; Robards, Martin D.; Williams, Cory T.; Kielland, Knut (September 2022, ARCTIC)

   Burrowing species rely on subterranean and subnivean sites to fulfill important life-history and behavioral processes, including predator avoidance, thermoregulation, resting, and reproduction. For these species, burrow architecture can affect the quality and success of such processes, since characteristics like tunnel width and chamber depth influence access by predators, thermal insulation, and energy spent digging. Wolverines (Gulo gulo) living in Arctic tundra environments dig burrows in snow during winter for resting sites and reproductive dens, but there are few published descriptions of such burrows. We visited 114 resting burrows and describe associated architectural characteristics and non-snow structure. Additionally, we describe characteristics of 15 reproductive den sites that we visited during winter and summer. Although many resting burrows were solely excavated in snow, most incorporated terrain structures including cliffs, talus, river shelf ice, thermokarst caves, and stream cutbanks. Burrows typically consisted of a single tunnel leading to a single chamber, though some burrows had multiple entrances, branching tunnels, or both. Tunnels in resting burrows were shorter than those in reproductive dens, and resting chambers were typically located at the deepest part of the burrow. Reproductive dens were associated with snowdrift-forming terrain features such as streambeds, cutbanks on lake edges, thermokarst caves, and boulders. Understanding such characteristics of Arctic wolverine resting and reproductive structures is critical for assessing anthropogenic impacts as snowpack undergoes climate-driven shifts. 

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4. Integrating anthropogenic factors into regional‐scale species distribution models—A novel application in the imperiled sagebrush biome

   https://doi.org/10.1111/gcb.14728  

   Requena‐Mullor, Juan M.; Maguire, Kaitlin C.; Shinneman, Douglas J.; Caughlin, Timothy Trevor (July 2019, Global Change Biology)

   Abstract Species distribution models (SDMs) that rely on regional‐scale environmental variables will play a key role in forecasting species occurrence in the face of climate change. However, in the Anthropocene, a number of local‐scale anthropogenic variables, including wildfire history, land‐use change, invasive species, and ecological restoration practices can override regional‐scale variables to drive patterns of species distribution. Incorporating these human‐induced factors into SDMs remains a major research challenge, in part because spatial variability in these factors occurs at fine scales, rendering prediction over regional extents problematic. Here, we used big sagebrush (Artemisia tridentataNutt.) as a model species to explore whether including human‐induced factors improves the fit of the SDM. We applied a Bayesian hurdle spatial approach using 21,753 data points of field‐sampled vegetation obtained from the LANDFIRE program to model sagebrush occurrence and cover by incorporating fire history metrics and restoration treatments from 1980 to 2015 throughout the Great Basin of North America. Models including fire attributes and restoration treatments performed better than those including only climate and topographic variables. Number of fires and fire occurrence had the strongest relative effects on big sagebrush occurrence and cover, respectively. The models predicted that the probability of big sagebrush occurrence decreases by 1.2% (95% CI: −6.9%, 0.6%) when one fire occurs and cover decreases by 44.7% (95% CI: −47.9%, −41.3%) if at least one fire occurred over the 36 year period of record. Restoration practices increased the probability of big sagebrush occurrence but had minimal effect on cover. Our results demonstrate the potential value of including disturbance and land management along with climate in models to predict species distributions. As an increasing number of datasets representing land‐use history become available, we anticipate that our modeling framework will have broad relevance across a range of biomes and species. 

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5. Biotic and abiotic factors affecting Atlantic ghost crab (Ocypode quadrata) spatiotemporal activity at an important shorebird nesting site in Virginia

   https://doi.org/10.1371/journal.pone.0307821  

   Call, Mikayla N; Pongnon, Rasheed S; Wails, Christy N; Karpanty, Sarah M; Lapenta, Kristy C; Wilke, Alexandra L; Boettcher, Ruth; Alvino, Camille R; Fraser, James D (August 2024, PLOS ONE)

   Romanach, Stephanie S (Ed.)

   Atlantic ghost crabs (Ocypode quadrata) are predators of beach-nesting shorebird nests and chicks on the United States’ Atlantic and Gulf coasts. Ghost crabs may also disturb birds, altering foraging, habitat use, or nest and brood attendance patterns. Shorebird conservation strategies often involve predator and disturbance management to improve reproductive success, but efforts rarely target ghost crabs. Despite the threat to shorebird reproductive success, ghost crabs are a poorly understood part of the beach ecosystem and additional knowledge about ghost crab habitat selection is needed to inform shorebird conservation. We monitored ghost crab activity, defined as burrow abundance, throughout the shorebird breeding season on Metompkin Island, Virginia, an important breeding site for piping plovers (Charadrius melodus) and American oystercatchers (Haematopus palliatus). We counted burrows at shorebird nests and random locations throughout the breeding season and investigated whether ghost crab activity was greater at nest sites relative to random locations without shorebird nests. While we observed burrows at all nest sites (n= 63 nests), we found that burrow counts were lower at piping plover nests with shell cover, relative to random locations with no shell cover. Ghost crabs may avoid piping plover nest sites due to anti-predator behaviors from incubating adults or differences in microhabitat characteristics selected by piping plovers. We also investigated the effects of habitat type, date, and air temperature on the abundance of ghost crab burrows. We found that while crab burrows were present across the barrier island landscape, there were more burrows in sandy, undisturbed habitats behind the dunes, relative to wave-disturbed beach. Additionally, ghost crab activity increased later in the shorebird breeding season. Understanding when and where ghost crabs are most likely to be active in the landscape can aid decision-making to benefit imperiled shorebird populations. 

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