Genetic sampling for estimating density of common species.

Understanding population dynamics requires reliable estimates of population density, yet this basic information is often surprisingly difficult to obtain. With rare or difficult-to-capture species, genetic surveys from noninvasive collection of hair or scat has proved cost-efficient for estimating densities. Here, we explored whether noninvasive genetic sampling (NGS) also offers promise for sampling a relatively common species, the snowshoe hare (Lepus americanus Erxleben, 1777), in comparison with traditional live trapping. We optimized a protocol for single-session NGS sampling of hares. We compared spatial capture-recapture population estimates from live trapping to estimates derived from NGS, and assessed NGS costs. NGS provided population estimates similar to those derived from live trapping, but a higher density of sampling plots was required for NGS. The optimal NGS protocol for our study entailed deploying 160 sampling plots for 4 days and genotyping one pellet per plot. NGS laboratory costs ranged from approximately $670 to $3000 USD per field site. While live trapping does not incur laboratory costs, its field costs can be considerably higher than for NGS, especially when study sites are difficult to access. We conclude that NGS can work for common species, but that it will require field and laboratory pilot testing to develop cost-effective sampling protocols.

Legacies of past exploitation and climate affect mammalian sexes differently on the roof of the world - the case of wild yaks.

In polar environments, a lack of empirical knowledge about biodiversity prompts reliance on species distribution models to predict future change, yet these ignore the role of biotic interactions including the role of long past human exploitation. To explore how mammals of extreme elevation respond to glacial recession and past harvest, we combined our fieldwork with remote sensing and used analyses of ~60 expeditions from 1850-1925 to represent baseline conditions for wildlife before heavy exploitation on the Tibetan Plateau. Focusing on endangered wild yaks (Bos mutus), we document female changes in habitat use across time whereupon they increasingly relied on steeper post-glacial terrain, and currently have a 20x greater dependence on winter snow patches than males. Our twin findings­that the sexes of a cold-adapted species respond differently to modern climate forcing and long-past exploitation­indicate that effective conservation planning will require knowledge of the interplay between past and future if we will assure persistence of the region's biodiversity.

The hidden history of the snowshoe hare, Lepus americanus: extensive mitochondrial DNA introgression inferred from multilocus genetic variation.

Hybridization drives the evolutionary trajectory of many species or local populations, and assessing the geographic extent and genetic impact of interspecific gene flow may provide invaluable clues to understand population divergence or the adaptive relevance of admixture. In North America, hares (Lepus spp.) are key species for ecosystem dynamics and their evolutionary history may have been affected by hybridization. Here we reconstructed the speciation history of the three most widespread hares in North America - the snowshoe hare (Lepus americanus), the white-tailed jackrabbit (L. townsendii) and the black-tailed jackrabbit (L. californicus) - by analysing sequence variation at eight nuclear markers and one mitochondrial DNA (mtDNA) locus (6240 bp; 94 specimens). A multilocus-multispecies coalescent-based phylogeny suggests that L. americanus diverged ~2.7 Ma and that L. californicus and L. townsendii split more recently (~1.2 Ma). Within L. americanus, a deep history of cryptic divergence (~2.0 Ma) was inferred, which coincides with major speciation events in other North American species. While the isolation-with-migration model suggested that nuclear gene flow was generally rare or absent among species or major genetic groups, coalescent simulations of mtDNA divergence revealed historical mtDNA introgression from L. californicus into the Pacific Northwest populations of L. americanus. This finding marks a history of past reticulation between these species, which may have affected other parts of the genome and influence the adaptive potential of hares during climate change.

Conservation implications of the evolutionary history and genetic diversity hotspots of the snowshoe hare.

With climate warming, the ranges of many boreal species are expected to shift northward and to fragment in southern peripheral ranges. To understand the conservation implications of losing southern populations, we examined range-wide genetic diversity of the snowshoe hare (Lepus americanus), an important prey species that drives boreal ecosystem dynamics. We analysed microsatellite (8 loci) and mitochondrial DNA sequence (cytochrome b and control region) variation in almost 1000 snowshoe hares. A hierarchical structure analysis of the microsatellite data suggests initial subdivision in two groups, Boreal and southwestern. The southwestern group further splits into Greater Pacific Northwest and U.S. Rockies. The genealogical information retrieved from mtDNA is congruent with the three highly differentiated and divergent groups of snowshoe hares. These groups can correspond with evolutionarily significant units that might have evolved in separate refugia south and east of the Pleistocene ice sheets. Genetic diversity was highest at mid-latitudes of the species' range, and genetic uniqueness was greatest in southern populations, consistent with substructuring inferred from both mtDNA and microsatellite analyses at finer levels of analysis. Surprisingly, snowshoe hares in the Greater Pacific Northwest mtDNA lineage were more closely related to black-tailed jackrabbits (Lepus californicus) than to other snowshoe hares, which may result from secondary introgression or shared ancestral polymorphism. Given the genetic distinctiveness of southern populations and minimal gene flow with their northern neighbours, fragmentation and loss of southern boreal habitats could mean loss of many unique alleles and reduced evolutionary potential.

Optimism and challenge for science-based conservation of migratory species in and out of U.S. National Parks.

Public agencies sometimes seek outside guidance when capacity to achieve their mission is limited. Through a cooperative agreement and collaborations with the U.S. National Park Service (NPS), we developed recommendations for a conservation program for migratory species. Although NPS manages ∼ 36 million hectares of land and water in 401 units, there is no centralized program to conserve wild animals reliant on NPS units that also migrate hundreds to thousands of kilometers beyond parks. Migrations are imperiled by habitat destruction, unsustainable harvest, climate change, and other impediments. A successful program to counter these challenges requires public support, national and international outreach, and flourishing migrant populations. We recommended two initial steps. First, in the short term, launch or build on a suite of projects for high-profile migratory species that can serve as proof to demonstrate the centrality of NPS units to conservation at different scales. Second, over the longer term, build new capacity to conserve migratory species. Capacity building will entail increasing the limited knowledge among park staff about how and where species or populations migrate, conditions that enable migration, and identifying species' needs and resolving them both within and beyond parks. Building capacity will also require ensuring that park superintendents and staff at all levels support conservation beyond statutory borders. Until additional diverse stakeholders and a broader American public realize what can be lost and do more to protect it and engage more with land management agencies to implement actions that facilitate conservation, long distance migrations are increasingly likely to become phenomena of the past.

Impacts of simulated livestock grazing on Utah prairie dogs (Cynomys parvidens) in a low productivity ecosystem.

Allometric foraging theory suggests that herbivores of greatly differing size should co-exist through niche segregation, but a few studies of large-small herbivore foraging relationships have reported competitive interactions. This study addresses the potential roles of habitat productivity and large herbivore grazing intensities on large-small herbivore foraging interactions. We examined effects of different intensity simulated grazing treatments on forage abundance and quality for Utah prairie dogs (Cynomys parvidens) in a low productivity ecosystem, and consequent effects on prairie dog individual growth rates, foraging preferences, and activity budgets. We hypothesized that simulated grazing would have predominantly facilitative impacts on Utah prairie dogs, as was found for black-tailed prairie dogs in higher productivity ecosystems. To test this hypothesis, we measured the effects of simulated grazing on forage nitrogen, digestibility, and biomass. Simulated grazing increased average forage nitrogen and digestibility while decreasing forage biomass. These effects were associated with reduced individual growth rates, increased juvenile foraging time, and reduced juvenile vigilance. Results suggest that the negative effects of reduced vegetation biomass greatly outweighed positive treatment effects in this study. However, prairie dogs in the moderate intensity defoliation treatment showed some preference for "grazed" plots over "ungrazed" plots, and this preference increased with time. Our study lends support to the idea that habitat productivity and herbivore densities may mediate shifts between facilitative and competitive interactions between different-sized herbivores.