Clayton T. Lamb

Novel genomic resources for a climate change sensitive mammal: characterization of the American pika transcriptome.

BackgroundWhen faced with climate change, species must either shift their home range or adapt in situ in order to maintain optimal physiological balance with their environment. The American pika (Ochotona princeps) is a small alpine mammal with limited dispersal capacity and low tolerance for thermal stress. As a result, pikas have become an important system for examining biotic responses to changing climatic conditions. Previous research using amplified fragment length polymorphisms (AFLPs) has revealed evidence for environmental-mediated selection in O. princeps populations distributed along elevation gradients, yet the anonymity of AFLP loci and lack of available genomic resources precluded the identification of associated gene regions. Here, we harnessed next-generation sequencing technology in order to characterize the American pika transcriptome and identify a large suite of single nucleotide polymorphisms (SNPs), which can be used to elucidate elevation- and site-specific patterns of sequence variation.ResultsWe constructed pooled cDNA libraries of O. princeps from high (1400m) and low (300m) elevation sites along a previously established transect in British Columbia. Transcriptome sequencing using the Roche 454 GS FLX titanium platform generated 780 million base pairs of data, which were assembled into 7,325 high coverage contigs. These contigs were used to identify 24,261 novel SNP loci. Using high resolution melt analysis, we developed 17 of these SNPs into genotyping assays, which were validated with independent DNA samples from British Columbia Canada and Oregon State USA. In addition, we detected haplotypes in the NADH dehydrogenase subunit 5 of the mitochondrial genome that were fixed and different among elevations, suggesting that this may be an informative target gene for studying the role of cellular respiration in local adaptation. We also identified contigs that were unique to each elevation, including a high elevation-specific contig that was a positive match with the hemoglobin alpha chain from the plateau pika, a species restricted to high elevation steppes in Asia. Elevation-specific contigs may represent candidate regions subject to differential levels of gene expression along this elevation gradient.ConclusionsTo our knowledge, this is the first broad-scale, transcriptome-level study conducted within the Ochotonidae, providing novel genomic resources for studying pika ecology, behaviour and population history.

Factors influencing detection of grizzly bears at genetic sampling sites

Abstract Recent advances in genetic approaches have facilitated genetic marking in capture–recapture (CR) experiments. Individuals can now be identified through non-invasive sampling and multi-locus genotyping instead of physical capture. In non-invasive studies where collection sites are used, detection depends on whether (1) an individual deposits a sample at the collection site, and (2) an individual can be genetically identified from the sample. Here we evaluate factors influencing detection of grizzly bears (Ursus arctos) at hair-sampling sites from 4 genetic CR projects (2006–2012) in British Columbia, Canada, and provide recommendations for maximizing detection in future studies. We found significant effects of trap type (bait site vs. rub object), sex, and season on the detection of grizzly bears. Bait-site detection was approximately 5-fold greater than detection at rub objects; and bait sites generally detected the sexes equally, whereas rub-tree detection was strongly male-biased. At rub objects, males had a 7-fold greater detection during the breeding season compared with females. Genotyping success increased with the number of hair follicles in the sample and decreased with the duration between trap checks. Rainfall was correlated with trap duration and was also negatively related to genotyping success. Samples with little genetic material (<2 guard hair, or <15 underfur) had low genotyping success and are best avoided, especially if samples with more follicles exist. Rub objects are an efficient sampling method but we caution investigators that these traps, unless deployed in large numbers, imperfectly detect female bears. The combined effect of trap type, sex, and season on a bear visiting a site, paired with the effects of hair quality, quantity, and sampling duration or rainfall on genotyping success, produced a range of detection spanning 2 orders of magnitude, highlighting the imperative for investigators to consider these factors for CR projects.

Effects of habitat quality and access management on the density of a recovering grizzly bear population

Handling Editor: Kelly Marnewick Abstract 1. Human activities have dramatic effects on the distribution and abundance of wildlife. Increased road densities and human presence in wilderness areas have elevated human-caused mortality of grizzly bears and reduced bears’ use. Management agencies frequently attempt to reduce human-caused mortality by managing road density and thus human access, but the effectiveness of these actions is rarely assessed. 2. We combined systematic, DNA-based mark–recapture techniques with spatially explicit capture–recapture models to estimate population size of a threatened grizzly bear population (Kettle–Granby), following management actions to recover this population. We tested the effects of habitat and road density on grizzly bear population density. We tested both a linear and threshold-based road density metric and investigated the effect of current access management (closing roads to the public). 3. We documented an c. 50% increase in bear density since 1997 suggesting increased landscape and species conservation from management agencies played a significant role in that increase. However, bear density was lower where road densities exceeded 0.6 km/km2 and higher where motorised vehicle access had been restricted. The highest bear densities were in areas with large tracts of few or no roads and high habitat quality. Access management bolstered bear density in small areas by 27%. 4. Synthesis and applications. Our spatially explicit capture–recapture analysis demonstrates that population recovery is possible in a multi-use landscape when management actions target priority areas. We suggest that road density is a useful surrogate for the negative effects of human land use on grizzly bear populations, but spatial configuration of roads must still be considered. Reducing roads will increase grizzly bear density, but restricting vehicle access can also achieve this goal. We demonstrate that a policy target of reducing human access by managing road density below 0.6 km/km2, while ensuring areas of high habitat quality have no roads, is a reasonable compromise between the need for road access and population recovery goals. Targeting closures to areas of highest habitat quality would benefit grizzly bear population recovery the most.

Invest long term in Canada's wilderness

Increasing global demand for Canadas resources is eroding the countrys iconic wilderness, intact ecosystems, and rich megafaunal diversity ([ 1 ][1], [ 2 ][2]). To meet its 2020 commitments to the United Nations Convention on Biological Diversity (CBD), Canada must protect 17% of its terrestrial

Tweet success? Scientific communication correlates with increased citations in Ecology and Conservation

Science communication is seen as critical for the disciplines of ecology and conservation, where research products are often used to shape policy and decision making. Scientists are increasing their online media communication, via social media and news. Such media engagement has been thought to influence or predict traditional metrics of scholarship, such as citation rates. Here, we measure the association between citation rates and the Altmetric Attention Score—an indicator of the amount and reach of the attention an article has received—along with other forms of bibliometric performance (year published, journal impact factor, and article type). We found that Attention Score was positively correlated with citation rates. However, in recent years, we detected increasing media exposure did not relate to the equivalent citations as in earlier years; signalling a diminishing return on investment. Citations correlated with journal impact factors up to ∼13, but then plateaued, demonstrating that maximizing citations does not require publishing in the highest-impact journals. We conclude that ecology and conservation researchers can increase exposure of their research through social media engagement and, simultaneously, enhance their performance under traditional measures of scholarly activity.

Estimating unrecorded human-caused mortalities of grizzly bears in the Flathead Valley, British Columbia, Canada

Managing the number of grizzly bear (Ursus arctos) mortalities to a sustainable level is fundamental to bear conservation. All known grizzly bear deaths are recorded by management agencies but the number of human-caused grizzly bear deaths that are not recorded is generally unknown, causing considerable uncertainty in the total number of mortalities. Here, we compare the number of bears killed legally by hunters to the number killed by people for all other reasons, for bears wearing functioning radiocollars and for uncollared bears recorded in the British Columbia (BC) government mortality database for the Flathead Valley in southeast BC. Between 1980 and 2016, permitted hunters killed 10 collared bears and 12 (9 known, 3 suspected) were killed by people for other reasons. This ratio differed (p < 0.0001) from the uncollared bears in the government database where 71 were killed by hunters while only 10 were killed for other reasons. We estimate that 88% (95% CI; 67–96%) of the human-caused mortalities that were not by permitted hunters were unreported. The study area may have low reporting rates because it is >40 km on a gravel road from a Conservation Officer office, so reporting is difficult and there are no human residences so there is little concern of a neighbor contacting an officer. Our results are likely indicative of other places that are road-accessed but far from settlements. We discuss the implications of sampling individuals for collaring and the possible implications of wearing a collar on the animal’s fate.

Density-dependent signaling: An alternative hypothesis on the function of chemical signaling in a non-territorial solitary carnivore

Brown bears are known to use rubbing behavior as a means of chemical communication, but the function of this signaling is unclear. One hypothesis that has gained support is that male bears rub to communicate dominance to other males. We tested the communication of dominance hypothesis in a low-density brown bear population in southeast British Columbia. We contrasted rubbing rates for male and female bears during and after the breeding season using ten years of DNA-mark-recapture data for 643 individuals. Here we demonstrate that male brown bears rub 60% more during the breeding than the non-breeding season, while female rubbing had no seasonal trends. Per capita rub rates by males were, on average, 2.7 times higher than females. Our results suggest that the function of rubbing in the Rocky Mountains may not only be to communicate dominance, but also to self-advertise for mate attraction. We propose that the role of chemical communication in this species may be density-dependent, where the need to self-advertise for mating is inversely related to population density and communicating for dominance increases with population density. We suggest that future endeavors to elucidate the function of rubbing should sample the behavior across a range of population densities using camera trap and genotypic data.