A comparison of protocols for isolating and extracting host DNA from caribou (Rangifer tarandus) fecal pellets

Determining age structure of populations is a valuable parameter in wildlife management, but is often difficult to obtain. Here, we tested a noninvasive method via fecal DNA, hormones, and pellet morphometrics to distinguish calf from adult in Central Mountain and Boreal woodland caribou (Rangifer tarandus caribou (Gmelin, 1788)) populations. Annual surveys of fall-sampled Central Mountain caribou were done in Jasper National Park, Alberta, between 2006 and 2011 and winter-sampled Boreal caribou were surveyed in the North Interlake area, Manitoba, between 2004 and 2010. Samples were amplified at 10 microsatellite loci to identify unique individuals and capture histories were used to identify putative calves and adults. Fecal pellets were measured for length, width, depth, dry mass, and analyzed for progesterone, estrogen, and testosterone concentrations. Results showed significant differences in fecal pellet size between putative calves and adults for both sexes and populations–seasons. Progesterone concentration was significantly higher in Jasper–fall and North Interlake–winter adult females. Testosterone was significantly higher in Jasper–fall adult males. North Interlake–winter males exhibited no significant difference in hormone concentrations between age classes. When applied to the entire Jasper data set, 98% of females and 88% of males were assigned to an age class. This study illustrates the possibilities of using noninvasive methods to determine an age class in wild ungulate populations.

Wind-power plants (WPs) within reindeer (Rangifer tarandus tarandus) habitat may have negative effects on reindeer habitat use. Avoidance effects towards a WP were tested by comparing reindeer distributions on a peninsula where a WP was built in 2006 with a control peninsula without a WP. Distributions were measured by direct observations during construction period, and in four subsequent years, and limited faecal pellet group counts along transects before, during and after the WP construction (2005–2010). We predicted higher reindeer density in the control than the WP peninsula and at increasing distances from the WP when controlling for habitat quality. We found no avoidance effects from the WP, with significantly more reindeer in the WP than the control peninsula. Faecal pellet group data supported a lack of negative effects towards the WP after construction compared to before, while area within 100 m from the access road to the WP was avoided during the construction period and for 3 years afterwards. Reindeer avoided low-quality habitat both in the control and WP peninsulas. Our study indicates that WP development might have minor effects on habitat use if built in poor habitats, at least for semi-domestic reindeer. Our results cannot be used to infer effects of a WP built in higher-quality habitats or where large-scale movements are less restrictive than on a peninsula. Disturbance effects of human infrastructure likely are context-dependent, and management should thus be careful in planning of WPs to minimize adverse effects.

Question: Are differences in landscape use of semi‐domesticated reindeer reflected in the vegetation of summer grazing grounds?Location: Alpine heaths, central east Sweden.Methods: Dry heath and grass heath vegetation plots with inferred grazing intensities (high, intermediate and low) were selected a priori from an interpolated pellet count map compiled in 2002. In each plot, faecal pellets were counted, environmental variables measured and vegetation sampled by listing presence and absence. Species composition was compared with a detrended correspondence analysis, and a canonical correspondence analysis was used to infer relations between species composition and environmental variables. Plots were also clustered to provide groupings for an indicator species analysis.Results: Significant differences in faecal pellet count were present between the highest and lowest grazing intensities for both vegetation types, showing that the pattern in the interpolated pellet maps was robust. Differences in species composition between grazing intensities were found for the dry heath only. Here, there was an apparent grazing gradient, with lichens and mosses in the low‐use plots and grasses and herbs in the high‐use plots. No such gradient was found for the grass heath.Conclusions: Within the dry heath vegetation type, grazing levels had a subtle effect on the vegetation, while no effects were seen in the grass heath, probably as a result of the dominance of more grazing‐tolerant graminoids. Even in the dry heath, species richness did not differ between grazing levels, but the relative abundances of species differed.

Climate change is driving a northward shift in the distribution of North American wildlife, including ungulates. Temperate ungulates are host to a diversity of gastrointestinal nematode species, many of which are not found in wood¬ land and barren-ground caribou (Rangifer tarandus). Some of the most pathogenic of these parasites are those of the family Trichostrongylidae which are known to induce considerable morbidity and mortality in livestock globally. Although invasion of new trichostrongylid species to high latitudes may have significant impact on the health of naive (unexposed) caribou populations, the northern diversity and distribution of most species is unknown. In fact, our recent trichostrongylid survey of 20 wild ungulates in central Alberta and Saskatchewan revealed four new host and seven new geographic records. A challenge to determining parasite diversity is that many trichostrongyid eggs are morphologically indistin¬ guishable and post-mortem recovery and examination of adult nematodes is necessary to establish species identification. To better describe the diversity of parasite fauna that may infect northern caribou, we have developed a rapid, non-invasive tool, Single Stranded Conformation Polymorphism (SSCP), for broad-scale screening of cervid fecal pellets for trichostrongylid parasites. SSCP is a simple PCR-based technique that allows for species-specific electrophoretic discrimination using ITS-2 rDNA from parasite eggs. Trichostrongylid eggs in fecal pellets from three ecotypes of caribou, white-tailed deer (Odocoileus virginianus), mule deer (O. hemionus) and elk (Cervus elaphus) are being screened using SSCP to determine parasite diversity and range along two north-south transects in western Canada. Results outlining trichostrongylid diver¬ sity and distribution and implications for threatened woodland and barren-ground caribou populations will be reported. Baseline data on parasite biodiversity and distribution will provide a platform from which managers and veterinarians can monitor parasite range expansion in a warming climate and identify key parasite related risks.

EU SET TO APPROVE GERMAN AID FOR STENDAL MILL

Late Pleistocene Crocuta crocuta spelaea (Goldfuss, 1823) clans as prezewalski horse hunters and woolly rhinoceros scavengers at the open air commuting den and contemporary Neanderthal camp site Westeregeln (central Germany)

Proper management of threatened species requires knowledge of population sizes and structures, however current techniques to gather this information are generally impractical and costly and can be stressful on the animals. Non‐invasive methods that can produce high quality and accurate results are better alternatives. In winter 2010, we collected blood and fecal samples from 2 reindeer (Rangifer tarandus) populations (Kaamanen, Finland and Svalbard, Norway) to investigate the feasibility of using fecal progesterone metabolites to help estimate the reproductive status, the sex, and the age structures of the populations. We first examined the relationship between plasma progesterone and fecal progesterone metabolite concentrations. We further assessed whether fecal progesterone metabolite levels would clearly differ among calf, yearling, and adult and between pregnant and non‐pregnant females. We quantified fecal progesterone metabolites (using enzyme immunoassay) and plasma progesterone (using radio immunoassay) of females and males of different ages from the 2 herds. We found in both populations that fecal progesterone metabolite levels reflected plasma progesterone concentrations. However, the range of fecal progesterone metabolite concentration was much wider in Finland than in Svalbard, possibly due to differences in diet or body condition. We determined a threshold value of 1.31 ng/ml plasma progesterone and 2025.93 ng/g dried fecal progesterone metabolites to identify pregnant reindeer from non‐pregnant animals with 100% accuracy. We found a significant difference in fecal progesterone metabolite concentrations only between calves and yearlings/adults in Finland. We could not differentiate among males, non‐pregnant adults, or calves of either sex; therefore identification of sex may have to rely on the use of DNA techniques. Our results suggest that hormone concentration, in combination with fecal DNA and pellet morphometry techniques, may provide important population parameters and is a valuable tool for the monitoring of reindeer and may have an application for threatened populations of woodland caribou throughout the winter and early spring. © 2011 The Wildlife Society.

We describe an approach to estimation of the spatial distribution of reindeer (Rangifer tarandus). Spatial autocorrelation, inherent to the data describing the distribution of wildlife species, contains information that can be utilized to improve the effciency of field inventories. Our data included reindeer fecal pellet counts, satellite imagery and a digital terrain model. We applied ordinary logistic regression, autologistic regression, and the Gibbs sampler to predict spatial distribution of reindeer based on the combined data. A training set was used to compare the outcome for different field sampling designs for each method. Results suggested the possibility to reduce the number of plots by up to 75% with a 15% reduction in prediction accuracy (quality). We also showed that the Gibbs sampler outperformed, in terms of accuracy, the logistic regression. The outcome, however, was dependent on the spectral homogeneity of the area and on the relative position of the sampling design to the elevation curves. Our results justify the incorporation of spatial information when modeling the distribution of reindeer at finer scales (< 1 km).

Proper management of threatened populations requires prior knowledge of population sizes and structures, however, current techniques to gather this information are generally impractical, costly, and can be physically stressful for the animals. Non‐invasive methods (e.g. faecal sampling) that can produce high quality and accurate results are better alternatives. Using faecal samples collected from a Svalbard reindeer Rangifer tarandus platyrhynchus population in the winters of 2008 (N = 158) and 2009 (N = 161), we investigated and validated the feasibility of using faecal pellet sizes to differentiate between female calves, yearlings and adults. We found that pellets from adult females were longer than those from calves, and pellets from adults and yearlings were clearly wider than those from calves. With an accuracy of 91% correct classification, we did show that a combination of faecal pellet dimensions (length, width and depth), rather than a single dimension alone, can allow managers to clearly differentiate between age classes if pellets already identified as being from females are used. We also found a positive relationship between live weight and pellet size of the reindeer. Combined with DNA analysis to identify the gender of the animal that produced the faecal pellet, this information may provide important population parameters and be a valuable tool for the monitoring of various ungulate species including wild reindeer.

Conservation genomics is an important tool to manage threatened species under current biodiversity loss. Recent advances in sequencing technology mean that we can now use whole genomes to investigate demographic history, local adaptation, inbreeding, and more in unprecedented detail. However, for many rare and elusive species only non-invasive samples such as faeces can be obtained, making it difficult to take advantage of whole genome data. We present a method to extract DNA from the mucosal layer of faecal samples to reconstruct high coverage whole genomes using standard laboratory techniques, therefore in a cost-effective and efficient way. We use wild collected faecal pellets collected from wild caribou (Rangifer tarandus), a species undergoing declines in many parts of its range in Canada and subject to comprehensive conservation and population monitoring measures. We compare four faecal genomes to two tissue genomes sequenced in the same run. Quality metrics were similar between faecal and tissue samples with the main difference being the alignment success of raw reads to the reference genome likely due to differences in endogenous DNA content, affecting overall coverage. One of our faecal genomes was only reconstructed at low coverage (1.6X), however the other three obtained between 7 and 15X, compared to 19 and 25X for the tissue samples. We successfully reconstructed high-quality whole genomes from faecal DNA and, to our knowledge, are the first to obtain genome-wide data from wildlife faecal DNA in a non-primate species, representing an important advancement for non-invasive conservation genomics.

Correction: DNA metabarcoding of faecal pellets reveals high consumption of yew (<i>Taxus</i> spp.) by caribou (<i>Rangifer tarandus</i>) in a lichen-poor environment

Using multiple knowledge sources to interpret patterns of biodiversity can generate the comprehensive species characterizations that are required for effective conservation strategies. Caribou (Rangifer tarandus) display substantial intraspecific variation across their distribution and in the Sahtu Region of the Northwest Territories, Canada, three caribou types, each with a different conservation status, co-occur. Caribou are essential to the economies, culture, and livelihoods of northern indigenous peoples. Indigenous communities across the north are insisting that caribou research be community-driven and collaborative. In response to questions that arose through dialogue with five Sahtu Dene and Metis communities, we jointly developed a research approach to understand caribou differentiation and population structure. Our goal was to examine caribou variation through analysis of population genetics and an exploration of the relationships Dene and Metis people establish with animals within bioculturally diverse systems. To cultivate a research environment that supported legha gots'enete “learning together” we collaborated with Ɂehdzo Got'i ne (Renewable Resources Councils), elders, and an advisory group. Dene knowledge and categorization systems include a comprehensive understanding of the origin, behaviors, dynamic interactions, and spatial structure of caribou. Dene people classify to dzi “boreal woodland caribou” based on unique behaviors, habitat preferences, and morphology that differ from ɂekwe “barren-ground” or shuhta ɂepe “mountain” caribou. Similarly, genetic analysis of material (microsatellites and mitochondrial DNA) from caribou fecal pellets, collected in collaboration with community members during the winter, provided additional evidence for population differentiation that corresponded to the caribou types recognized by Dene people and produced insights into the evolutionary histories that contribute to the various forms. We developed culturally respectful and relevant descriptions of caribou variation through partnerships that respect the lives and experiences of people that depend on the land. By prioritizing mutual learning, researchers can broaden their understanding of biodiversity and establish a common language for collaboration.

Caribou (Rangifer tarandus) are declining worldwide. Across Canada, numerous populations have been extirpated over the past 50 years. In many cases, the mechanism of these declines is unsustainable predation exacerbated by apparent competition. Apparent competition occurs when alternate prey species, primarily deer (Odocoileus spp.) and moose (Alces americanus), increase in distribution and abundance, resulting in increased populations of predators (e.g., wolves (Canis lupus), cougar (Puma concolor), bears (Ursus spp.)) that are shared with caribou. Despite the role of white-tailed deer (Odocoileus virginianus) in apparent competition and caribou declines, relatively little is known about the resource use of this ungulate, or other apparent competitors, in west-central Alberta, Canada. I used GPS-collar locations from 2018–2022 in west-central Alberta to compare the habitat selection of whitetailed deer and mountain caribou. I then used DNA metabarcoding of fecal pellets collected in 2016 and 2022 to evaluate the diet of white-tailed deer and mountain caribou, as well as mule deer (O. hemionus), moose, and elk (Cervus canadensis) during winter. I found anthropogenic and environmental factors that may contribute to spatial overlap, or separation, between whitetailed deer and mountain caribou. Deer avoided areas with greater snow cover during winter and selected for forage availability during summer. Conversely, caribou had a non-significant response to snow cover and avoided valley bottoms but selected for ridgelines (alpine) during both seasons. I found relatively little overlap among the winter diet of the five sympatric ungulates. However, certain forage items including the Fabaceae and Lentibulariaceae families were abundant in the diet of all five ungulates and may result in shared resource use. I found DNA of lichenicolous fungi in the diet of caribou, but also white-tailed and mule deer, moose, and elk. My results provide new information on how deer, moose, and elk use the landscape in west-central Alberta, and how that compares to mountain caribou. Similarities in the spatial and diet overlap of sympatric ungulates can help inform strategies designed to mitigate the impacts of apparent competition for caribou.,

&lt;p&gt;In many Norwegian alpine and tundra areas sheep and reindeer graze sympatrically. Areas covered with dung or urine may have consequences for reindeer pasture utilization. Experiments were conducted on 5 stall fed male reindeer calves where animals were individually presenred with two troughs (experimental and control) containing 200 g of concentrate. Fresh and dry sheep and reindeer pellets (50 g wet weight) were mixed with the concentrate in the experimental trough and the aversive response was tested against the control. Both fresh sheep (P &amp;lt; 0.0001) and reindeer (P &amp;lt; 0.0001) pellets were associated with aversive response by reindeer. A similar response was found for dry sheep (P = 0.006) and dry reindeer (P = 0.0009) pellets. Similar trials were conducted using sheep and reindeer urine (20 g sprayed evenly on the food) and the aversive response by reindeer was tested against the control (sprayed with 20 g of water). Both sheep and reindeer urine stimulated an aversive response by reindeer {P = 0.03 for both tests). The differences in the aversive response of reindeer ro fresh sheep and reindeer pellets, dry sheep and reindeer pellets and sheep and reindeer urine were also tested. No differences by reindeer were found between sheep and reindeer pellets, either for fresh (P = 0.28) or dry (P = 0.07), or between food treated with sheep and reindeer urine (P = 0.28). Possible habituation to sheep and reindeer pellets was tested using 8 consecutive trials with dry pellets, followed by 2 additional trials when dry pellets were soaked in water. This was done to simulate natural dry periods followed by rain showers. Habituation effects were found in trials with dry sheep and reindeer pellets. Subsequent trials with fecal pellets soaked in water significantly reduced food intake when compared with the last habituation trial with dry pellets (P &amp;lt; 0.05).&lt;/p&gt;

Conservation genomics is an important tool to manage threatened species under current biodiversity loss. Recent advances in sequencing technology mean that we can now use whole genomes to investigate demographic history, local adaptation, inbreeding, and more in unprecedented detail. However, for many rare and elusive species only non-invasive samples such as faeces can be obtained, making it difficult to take advantage of whole genome data. We present a method to extract DNA from the mucosal layer of faecal samples to re-sequence high coverage whole genomes using standard laboratory techniques. We use wild collected faecal pellets collected from caribou (Rangifer tarandus), a species undergoing declines in many parts of its range in Canada and subject to comprehensive conservation and population monitoring measures. We compare four faecal genomes to two tissue genomes sequenced in the same run. Quality metrics were similar between faecal and tissue samples with the main difference being the alignment success of raw reads to the reference genome due to differences in low quality and endogenous DNA content, affecting overall coverage. One of our faecal genomes was only re-sequenced at low coverage (1.6 ×), however the other three obtained between 7 and 15 ×, compared to 19 and 25 × for the tissue samples. We successfully re-sequenced high-quality whole genomes from faecal DNA and are one of the first to obtain genome-wide data from wildlife faecal DNA in a non-primate species. Our work represents an important advancement for non-invasive conservation genomics.