Degraded DNA from suboptimal field sampling is common in molecular ecology. However, its impact on techniques that use restriction site associated next-generation DNA sequencing (RADSeq, GBS) is unknown. We experimentally examined the effects of in situDNA degradation on data generation for a modified double-digest RADSeq approach (3RAD). We generated libraries using genomic DNA serially extracted from the muscle tissue of 8 individual lake whitefish (Coregonus clupeaformis) following 0-, 12-, 48- and 96-h incubation at room temperature posteuthanasia. This treatment of the tissue resulted in input DNA that ranged in quality from nearly intact to highly sheared. All samples were sequenced as a multiplexed pool on an Illumina MiSeq. Libraries created from low to moderately degraded DNA (12-48 h) performed well. In contrast, the number of RADtags per individual, number of variable sites, and percentage of identical RADtags retained were all dramatically reduced when libraries were made using highly degraded DNA (96-h group). This reduction in performance was largely due to a significant and unexpected loss of raw reads as a result of poor quality scores. Our findings remained consistent after changes in restriction enzymes, modified fold coverage values (2- to 16-fold), and additional read-length trimming. We conclude that starting DNA quality is an important consideration for RADSeq; however, the approach remains robust until genomic DNA is extensively degraded.

Animal populations at northern range limits may use habitat differently from those at range cores, requiring distinct conservation plans. Snakes are ectotherms that often have very specific requirements, but few studies have focused on the effect of northern latitudes on habitat selection by grassland snakes. We studied movement and habitat selection of 2 sympatric snake species at their northern range limits on the North American Great Plains: the eastern yellow‐bellied racer (Coluber constrictor flaviventris, hereafter racer), a Threatened species in Canada, and the bullsnake (Pituophis catenifer sayi), which is listed as Data Deficient. Both of these species are potentially vulnerable to extinction in Canada because of habitat loss. Snakes from our study populations traveled up to 10‐times farther from winter dens and occupied home ranges 3–104 times larger than populations further south. Both snake species moved from winter dens in the slopes of a major river valley to habitat in adjacent lowlands, including riparian zones (racers) and hilly areas with native grass species (bullsnakes). Multivariate modeling revealed that proximity to retreat sites was a significant predictor of snake site use for both species. Considering the need for winter dens and summering areas, our data suggest that snakes in northern latitudes should ideally have much larger protected areas compared to snakes near the core of their range. An alternative strategy is to conserve corridors linking wintering dens and summer habitats. Retreat sites such as burrows and shrubs are critical components of local habitat and should be included in conservation plans. © 2011 The Wildlife Society.

The grasslands of southwestern Saskatchewan, Canada are home to several snake species of conservation concern at the northern extreme of their geographic range. To aid conservation assessment and management planning for these snakes, we used radio‐telemetry, a geographic information system, and multivariate modeling to identify and compare macrohabitat selection by eastern yellow‐bellied racers (n = 33; Coluber constrictor flaviventris), bullsnakes (n = 16; Pituophis catenifer sayi), and prairie rattlesnakes (n = 23; Crotalus viridis). All 3 species shared communal hibernacula in the inactive winter season, but dispersed into different macrohabitats across the landscape during the spring and summer. Their home ranges varied in size by species and were dumbbell‐shaped with activity centers near hibernacula and in well‐defined summer grounds; activity centers were connected by narrow movement corridors. Racers strongly selected for riparian areas, bullsnakes selected for valley grassland habitats, and rattlesnakes selected for areas associated with prairie dog colonies. Some rattlesnakes traveled great distances (over 11 km) from the dens compared to the other species (bullsnake max. = 4 km; racer max. = 5 km), which may be a result of their selected macrohabitat being more patchily distributed in the landscape. Our results indicate that management plans for these snakes must consider the den area, corridors, and separate summering grounds, as well as differences in home range size and movement patterns for each species. © 2013 The Wildlife Society.

Thermal pollution from industrial processes can have negative impacts on the spawning and development of cold-water fish. Point sources of thermal effluent may need to be managed to avoid affecting discrete populations. Correspondingly, we examined fine-scale ecological and genetic population structure of two whitefish species (Coregonus clupeaformis and Prosopium cylindraceum) on Lake Huron, Canada, in the immediate vicinity of thermal effluent from nuclear power generation. Niche metrics using δ13C and δ15N stable isotopes showed high levels of overlap (48.6 to 94.5%) in resource use by adult fish captured in areas affected by thermal effluent compared to nearby reference locations. Isotopic niche size, a metric of resource use diversity, was 1.3- to 2.8-fold higher than reference values in some thermally affected areas, indicative of fish mixing. Microsatellite analyses of genetic population structure (Fst, STRUCTURE and DAPC) indicated that fish captured at all locations in the vicinity of the power plant were part of a larger population extending beyond the study area. In concert, ecological and genetic markers do not support the presence of an evolutionarily significant unit in the vicinity of the power plant. Thus, future research should focus on the potential impacts of thermal emissions on development and recruitment.

The behaviour of snakes makes them vulnerable to road mortality, which may have conservation implications for some species. We examined factors affecting road mortality of snakes around Grasslands National Park of Canada (GNP), Saskatchewan, an area inhabited by a unique snake community within Canada, including the threatened Eastern Yellow-bellied Racer (Coluber constrictor flaviventris). Systematic surveys (n = 45) of roads in the Grasslands National Park area in 2009 yielded 36 dead and 18 live snakes. Multivariate modelling revealed that proximity to hibernacula was positively correlated with presence of snakes on roads. Paved roads had disproportionately higher numbers of snake mortalities, suggesting that traffic patterns are a bigger risk factor than road use per se. Some radio-tracked Eastern Yellow-bellied Racers (2 of 17; 12%) and Bullsnakes (Pituophis catenifer sayi) (4 of 5; 80%) captured at emergence from hibernacula had road areas in their home ranges. These individuals equipped with radio-transmitters used roads and immediately adjacent areas significantly more than expected, based on their availability, suggesting possible selection for roads. Strategies to reduce road mortality of snakes should focus on key stretches of roads, such as those near winter hibernacula or riparian zones. The placement of paved roads in sensitive areas like those in and around Grasslands National Park should be carefully considered to minimize snake mortality.

No abstract

On the North American Great Plains, several snake species reach their northern range limit where they rely on sparsely distributed hibernacula located in major river valleys. Independent colonization histories for the river valleys and barriers to gene flow caused by the lack of suitable habitat between them may have produced genetically differentiated snake populations. To test this hypothesis, we used 10 microsatellite loci to examine the population structure of two species of conservation concern in Canada: the eastern yellow-bellied racer (Coluber constrictor flaviventris) and bullsnake (Pituophis catenifer sayi) in 3 major river valleys in southern Saskatchewan. Fixation indices (FST) showed that populations in river valleys were significantly differentiated for both species (racers, FST = 0.096, P = 0.001; bullsnakes FST = 0.045–0.157, P = 0.001). Bayesian assignment (STRUCTURE) and ordination (DAPC) strongly supported genetically differentiated groups in the geographically distinct river valleys. Finer-scale subdivision of populations within river valleys was not apparent based on our data, but is a topic that should be investigated further. Our findings highlight the importance of major river valleys for snakes at the northern extent of their ranges, and raise the possibility that populations in each river valley may warrant separate management strategies.

We isolated and characterized 16 microsatellite loci from the Louisiana pine snake, Pituophis ruthveni. Loci were screened in 24 individuals from locations throughout its distribution in Louisiana and Texas. The number of alleles per locus ranged from 4 to 12, observed heterozygosity ranged from 0.200 to 0.875, and the probability of identity ranged from 0.043 to 0.298. We examined cross-species amplification at these loci in P. catenifer (bullsnakes and gopher snakes) and P. melanoleucus (pine snakes). These new markers provide tools for examining the conservation genetics of this species complex. Louisiana pine snakes face numerous threats: population densities are extremely low and their natural habitat has been severely altered and fragmented. In southern Canada, P. catenifer is at the northern extreme of its range and limited by the availability of suitable over-wintering sites.