Analysis of Population Connectivity in Wyoming Greater Sage-grouse
The distribution and abundance of Greater Sage-grouse (Centrocercus urophasianus) have declined markedly throughout their entire range likely due to the loss, fragmentation, and degradation of sagebrush habitat. Although Wyoming contains the largest populations of Greater Sage-grouse, substantial impacts from recent energy development also threaten these populations. Knowledge of the impact of current energy development projects as well as other anthropogenic disturbances on Greater Sage-grouse populations and connectivity among them is unknown. The movement of individuals among subdivided populations is often essential for population persistence, yet can be hindered by various landscape features. The resulting population isolation can have serious negative impacts on population persistence. This task uses genetics techniques to (1) identify populations and connectivity levels among them, allowing wildlife managers to prioritize habitats for conservation, and (2) identify habitat and anthropogenic features that impair the connectivity among populations.
Degradation Rates of DNA Extracted from Fecal Samples for Use with Molecular Markers
Noninvasive genetic sampling of mountain lions (Felis concolor) is one of the few methods available that may provide realistic estimates of cougar populations in Colorado, which is something that has not been done successfully using traditional methods. Feces or scat samples could provide viable genetic material since epithelial cells shed from the intestinal tract appear in the feces. A marker system with the power to distinguish a small number of closely related individuals will also have sufficient power to distinguish among a large number of unrelated individuals. Before genetic sampling can be conducted, however, an assessment of potential genetic error rates must be made in order to appropriately design the sampling protocols and determine if such a method can provided reliable estimates. Using scat from captive cougars of known ages FORT scientists are subjecting samples to both controlled and uncontrolled environmental conditions in order to accurately assess the magnitude of error rates expected if scat samples are used for population estimations. Specifically, investigators are (1) evaluating differences in DNA quantity between a scat surface collection and a cross-sectional collection; (2) evaluating differences in DNA quantity from successive feces depositions to determine the variation in quantities of genetic material in scat; (3) quantifying differences in epithelial shedding rates; and (4) evaluating temporal, environmental, and seasonal effects on DNA quantity and quality for both controlled and uncontrolled conditions.
Investigation into the interaction between ecological and evolutionary responses to global change is an important aspect of climate change studies. An understanding of the genetic basis of phenotypes under selection allows for the prediction and mitigation of climate change effects on the viability of populations. To address this issue, USGS scientists are documenting changes in genetic diversity and allele frequencies in white-tailed ptarmigan from Mt. Evans, Colo., over a 40-year time span. They also are comparing current levels of diversity and patterns of allele frequencies within a northern population of the species on Vancouver Island, Canada. Further, they are attempting to identify genetic markers under selection and to determine whether these markers can be correlated with environmental changes associated with climate change. This study will employ genetics, stable isotope analysis, and traditional population demographics methodologies. This work is novel in that (1) investigators are probing climate change-related effects on an alpine species; (2) 40+ years of demographic data interspersed with tissue samples that further extend to the late 1930s are available; and (3) analyses are focused on identifying genes under selection, then merging demographic and genetic data with stable-isotope-inferred resource use to tell a comprehensive story about white-tailed ptarmigan population ecology in a changing alpine habitat.
Capture-recapture (CR) is a very important class of methods and models used to estimate population abundance, survival probabilities, and population trends of wildlife populations and to obtain movement information. A critical aspect of these methods is that the mark used on the animal must be unique, and permanent, for each individual animal. In just the past few years it has become feasible to consider using an individual's unique DNA as its mark. Such DNA "marking" has great potential advantages when "capture" can be related not to the animal but, for example, to hairs, feathers, or feces. Recognizing this potential, biologists have explored some aspects of DNA-based application of CR models (DNA-CR) to estimate population parameters. However, using DNA as a mark is not without problems from the standpoint of CR study design and analysis models. Experts in the area of CR theory are just beginning to develop rigorous inference methods to underlie and support these studies. Methods are urgently needed for designing studies wherein the data are appropriate for analysis, leading to proper, well-supported statistical inferences. To address this need, FORT geneticists will determine how well DNA markers work in mark-recapture studies to estimate population size and survival rates. Researchers will use a known set of samples (Gunnison Sage-grouse, Centrocercus minimus) to test the assumptions currently used in DNA capture-recapture studies and conduct a statistical-theoretical evaluation of this new application.
The purpose of this study is to further characterize a unique population of Sage Grouse, Centrocercus urophasianus, located around Lyon, Nevada, and Mono, California. This population was formerly determined to be genetically different from other Greater Sage-Grouse populations across the Rocky Mountain Region of North America. Previous genetic work focused on comparing all populations across the species' range, and therefore used relatively small sample sizes for the species characterization. For this study, FORT geneticists analyzed this unique population in greater detail by obtaining samples from locations within the population and analyzing those samples with the same mitochondrial and microsatellite loci used in the previous studies. Blood samples were collected by field researchers in 7 locations within the Lyon/Mono population. DNA was extracted from the blood, amplified using PCR with primers specific to the mitochondrial control region and the 7 microsatellite loci. Genetic data from all birds were then compared to each other and analyzed using statistical methods. Particular attention was paid to population extent and internal dynamics by drawing comparisons among specific regions within Lyon/Mono. The White Mountain population was found to be significantly distinct from all other Lyon/Mono populations, with other distinctions visible between the Long Valley and Parker Flat populations.
Examination of the Biology of Summer-Roosting Indiana Bats Using Genetic Tools
Despite being listed as an endangered species in 1967 with the full protection of the Endangered Species Act of 1973, the rangewide population of Indiana bat (Myotis sodalis) has declined by approximately half since listing. The decline has been particularly steep in the southern portion of the range, where managers lack basic information about Indiana bat population dynamics on the summer range. Traditional tracking techniques have not provided researchers with the ability to regularly monitor individual bats throughout a field season. Recently, however, advances in molecular genetic techniques have made it possible to uniquely identify animals using DNA as an individual mark in mark-recapture studies. Preliminary work at FORT has shown that DNA can be successfully (and non-invasively) extracted from Indiana bat fecal pellets collected from beneath roost trees. Further, a suite of highly polymorphic microsatellite loci has been isolated from this species and used to genotype individual Indiana bats. The optimization and success of these techniques now makes it possible to explore the relatedness of Indiana bat maternity colonies and also attempt to estimate population sizes using DNA. Because the need for accurate demographic and relatedness information is great for the management and recovery of the Indiana bat, FORT geneticists will use these techniques to uniquely identify individual bats to (1) investigate genetic relatedness and (2) support a trial mark-recapture study to estimate population size.
Genetic Characterization of Introduced Lynx in Colorado
Between 1999 and 2007, the Colorado Division of Wildlife released 218 lynx (Lynx canadensis) in the San Juan Mountains of southwestern Colorado. Prior to their release, genetic samples were obtained for each individual, and the animals' whereabouts and condition were monitored using radio-telemetry. In 2010, the Colorado Division of Wildlife (CDOW) designed an occupancy-modeling study to document the distribution and persistence (survival) of lynx in Colorado using non-invasive molecular techniques. Scientists in FORT's Molecular Ecology Lab are collaborating with the CDOW to uniquely identify lynx using DNA extracted from hair and scat samples.
Investigation of Family Relationships in Broad-tailed Hummingbirds Using Molecular Methods
Based on strong circumstantial evidence on numerous occasions, it is believed that adult female broad-tailed hummingbirds (Selasphorus platycercus) and one or both of her recently-fledged young remain together for two or more weeks after fledging. Due to proximity of banding sites to nesting areas in Rocky Mountain National Park, it cannot be accurately determined how long a family unit may remain together after beginning migration. The literature on broad-tailed hummingbirds reveals that the duration of maternal care beyond the first day is not observed. Therefore, the objectives of this study are to determine whether groups of broad-tailed hummingbirds observed migrating together are family groups using DNA analysis. FORT geneticists will isolate a set of polymorphic microsatellite loci directly from the broad-tailed hummingbird. These markers will then be used to determine the relatedness of individuals trapped together in Rocky Mountain National Park. Genotyping is achieved by extracting DNA from a tail feather from each trapped bird. Managers can use this information to monitor levels of genetic variability in populations.
Investigation of White-tailed Kite Population Bottleneck Using Museum Specimens
White-tailed Kite (Elanus leucurus) populations in North America have undergone dramatic fluctuations since early records of the species from the mid 1800s. Though common during the early expeditions of the western United States, by the turn of the century naturalists noted that White-tailed Kites were rare and suspected that the species was close to extinction. By the 1930s, the species was extirpated in the southeastern U.S. and was considered nearly extinct in California. But in the 1920-30s, kite numbers began to increase; by the 1940s, a trend toward recovery was apparent, with increasing numbers observed in subsequent decades. Today, the White-tailed Kite is a fairly common resident in California, with slowly increasing numbers in Texas, Florida, and Oregon, and in the middle Americas. It is unknown whether the kites in California are remnants of a few that survived the decline or whether another group of kites from South America colonized this region. This study compares DNA from kites sampled from museums that were collected before 1920 to DNA from modern samples. Results can determine not only the identity of the surviving kites but also the amount of genetic variability present, important information given that population bottlenecks typically leave extremely low levels of genetic variability.
Population Genetics of Wood Frogs in Rocky Mountain National Park
Wood frogs (Rana sylvatica) are considered to be a species of conservation concern and have been listed as an endangered species in the State of Colorado. Population sizes have been declining, likely due to habitat loss associated with hydrological changes, disease, and other environmental factors. A pilot study conducted by FORT scientists on wood frogs in this region showed that there were some significant differences among ponds (contrary to published work on wood frogs in other states), suggesting that there may be reduced levels of gene flow within Rocky Mountain National Park due to changes in hydrology. For this study, a much more rigorous and complete sample of wood frogs in Rocky Mountain National Park will be collected by FORT scientists. A new sampling regime will be implemented to circumvent previous problems associated with sampling closely related individuals. In this study, DNA will be extracted from eggs and 8-14 microsatellite loci will be amplified for each individual.
With the populations of many migratory birds and other animals on the decline, understanding their migrations and seasonal movements is often critical for devising conservation strategies. Today, new approaches being explored for tracking animals are based on intrinsic markers. Two groups of intrinsic markers that have promise are stable isotopes and genetic markers, particularly if used together. This pilot project will explore the use of both stable isotopes and two kinds of genetic markers, mitochondrial DNA and microsatellites, to understand the movements of Clark's nutcrackers (Nucifraga Columbiana), a bird whose population numbers and movements are sensitive to losses of high-elevation forest in the western U.S. and Canada. Clark's nutcrackers are of particular interest since they forage primarily on the seeds of whitebark and limber pine, two tree species affected by pine beetle outbreaks and blister rust. By combining genetic and isotopic techniques to understand patterns in population structure and movements of birds, this study potentially will provide information to help develop conservation strategies for nutcrackers. The study also pioneers an application of combined intrinsic marker techniques. The objectives of this study are to examine molecular markers (mitochondrial and nuclear DNA) in individual birds to determine whether there is regional differentiation in nutcracker populations. If we discover cases where specimens collected in geographically disparate locations are genetically similar, then chemical markers (stable and radio isotope values that are transferred to animals via food or water) will be employed to determine whether that individual can be linked to a geographic location where genetically similar individuals are more abundant.
