Genetic mark-recapture analysis of winter faecal pellets allows estimation of population size in Sage Grouse Centrocercus urophasianus

The Sage Grouse Centrocercus urophasianus is a species of conservation concern throughout its range in western North America. Since the 1950s, the high count of males at leks has been used as an index for monitoring populations. However, the relationship between this lek-count index and population size is unclear, and its reliability for assessing population trends has been questioned. We used non-invasive genetic mark-recapture analysis of faecal and feather samples to estimate pre-breeding population size for the Parachute-Piceance-Roan, a small, geographically isolated population of Sage Grouse in western Colorado, during two consecutive winters from 2012 to 2014. We estimated total pre-breeding population size as 335 (95% confidence interval (CI): 287–382) in the first winter and 745 (95% CI: 627–864) in the second, an approximate doubling in abundance between years. Although we also observed a large increase in the spring lek-count index between those years, high male count data poorly represented mark-recapture estimates of male abundance in each year. Our data suggest that lek counts are useful for detecting the direction and magnitude of large changes in Sage Grouse abundance over time but they may not reliably reflect small changes in abundance that may be relevant to small populations of conservation concern.     

A rangewide population genetic study of trumpeter swans

For management purposes, the range of naturally occurring trumpeter swans (Cygnus buccinator) has been divided into two populations, the Pacific Coast Population (PP) and the Rocky Mountain Population (RMP). Little is known about the distribution of genetic variation across the species’ range despite increasing pressure to make difficult management decisions regarding the two populations and flocks within them. To address this issue, we used rapidly evolving genetic markers (mitochondrial DNA sequence and 17 nuclear microsatellite loci) to elucidate the underlying genetic structure of the species. Data from both markers revealed a significant difference between the PP and RMP with the Yukon Territory as a likely area of overlap. Additionally, we found that the two populations have somewhat similar levels of genetic diversity (PP is slightly higher) suggesting that the PP underwent a population bottleneck similar to a well-documented one in the RMP. Both genetic structure and diversity results reveal that the Tri-State flock, a suspected unique, non-migratory flock, is not genetically different from the Canadian flock of the RMP and need not be treated as a unique population from a genetic standpoint. Finally, trumpeter swans appear to have much lower mitochondrial DNA variability than other waterfowl studied thus far which may suggest a previous, species-wide bottleneck.     

Population genetics reveals bidirectional fish movement across the Continental Divide via an interbasin water transfer

Interbasin water transfers are becoming an increasingly common tool to satisfy municipal and agricultural water demand, but their impacts on movement and gene flow of aquatic organisms are poorly understood. The Grand Ditch is an interbasin water transfer that diverts water from tributaries of the upper Colorado River on the west side of the Continental Divide to the upper Cache la Poudre River on the east side of the Continental Divide. We used single nucleotide polymorphisms to characterize population genetic structure in cutthroat trout (Oncorhynchus clarkii) and determine if fish utilize the Grand Ditch as a movement corridor. Samples were collected from two sites on the west side and three sites on the east side of the Continental Divide. We identified two or three genetic clusters, and relative migration rates and spatial distributions of admixed individuals indicated that the Grand Ditch facilitated bidirectional fish movement across the Continental Divide, a major biogeographic barrier. Previous studies have demonstrated ecological impacts of interbasin water transfers, but our study is one of the first to use genetics to understand how interbasin water transfers affect connectivity between previously isolated watersheds. We also discuss implications on native trout management and balancing water demand and biodiversity conservation.

     

Genetic consequences of trumpeter swan (Cygnus buccinator) reintroductions

Relocation programs are often initiated to restore threatened species to previously occupied portions of their range. A primary challenge of restoration efforts is to translocate individuals in a way that prevents loss of genetic diversity and decreases differentiation relative to source populations—a challenge that becomes increasingly difficult when remnant populations of the species are already genetically depauperate. Trumpeter swans were previously extirpated in the entire eastern half of their range. Physical translocations of birds over the last 70 years have restored the species to portions of its historical range. Despite the long history of management, there has been little monitoring of the genetic outcomes of these restoration attempts. We assessed the consequences of this reintroduction program by comparing patterns of genetic variation at 17 microsatellite loci across four restoration flocks (three wild-released, one captive) and their source populations. We found that a wild-released population established from a single source displayed a trend toward reduced genetic diversity relative to and significant genetic differentiation from its source population, though small founder population effects may also explain this pattern. Wild-released flocks restored from multiple populations maintained source levels of genetic variation and lacked significant differentiation from at least one of their sources. Further, the flock originating from a single source revealed significantly lower levels of genetic variation than those established from multiple sources. The distribution of genetic variation in the captive flock was similar to its source. While the case of trumpeter swans provides evidence that restorations from multiple versus single source populations may better preserve natural levels of genetic diversity, more studies are needed to understand the general applicability of this management strategy.     

Two Low Coverage Bird Genomes and a Comparison of Reference-Guided versus De Novo Genome Assemblies

As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novo genome assembly. We used low-coverage (∼3.5–5.5x) Illumina paired-end sequencing to assemble draft genomes of two bird species (the Gunnison Sage-Grouse, Centrocercus minimus, and the Clark''s Nutcracker, Nucifraga columbiana). We used these data to estimate de novo genome assemblies and reference-guided assemblies, and compared the information content and completeness of these assemblies by comparing CEGMA gene set representation, repeat element content, simple sequence repeat content, and GC isochore structure among assemblies. Our results demonstrate that even lower-coverage genome sequencing projects are capable of producing informative and useful genomic resources, particularly through the use of reference-guided assemblies.     

Rangewide genetic analysis of Lesser Prairie-Chicken reveals population structure,range expansion,and possible introgression

The distribution of the Lesser Prairie-Chicken (Tympanuchus pallidicinctus) has been markedly reduced due to loss and fragmentation of habitat. Portions of the historical range, however, have been recolonized and even expanded due to planting of conservation reserve program (CRP) fields that provide favorable vegetation structure for Lesser Prairie-Chickens. The source population(s) feeding the range expansion is unknown, yet has resulted in overlap between Lesser and Greater Prairie-Chickens (T. cupido) increasing the potential for hybridization. Our objectives were to characterize connectivity and genetic diversity among populations, identify source population(s) of recent range expansion, and examine hybridization with the Greater Prairie-Chicken. We analyzed 640 samples from across the range using 13 microsatellites. We identified three to four populations corresponding largely to ecoregions. The Shinnery Oak Prairie and Sand Sagebrush Prairie represented genetically distinct populations (F _ST > 0.034 and F _ST > 0.023 respectively). The Shortgrass/CRP Mosaic and Mixed Grass ecoregions appeared admixed (F _ST = 0.009). Genetic diversity was similar among ecoregions and N _e ranged from 142 (95 % CI 99–236) for the Shortgrass/CRP Mosaic to 296 (95 % CI 233–396) in the Mixed Grass Prairie. No recent migration was detected among ecoregions, except asymmetric dispersal from both the Mixed Grass Prairie and to a lesser extent the Sand Sagebrush Prairie north into adjacent Shortgrass/CRP Mosaic (m = 0.207, 95 % CI 0.116–0.298, m = 0.097, 95 % CI 0.010–0.183, respectively). Indices investigating potential hybridization in the Shortgrass/CRP Mosaic revealed that six of the 13 individuals with hybrid phenotypes were significantly admixed suggesting hybridization. Continued monitoring of diversity within and among ecoregions is warranted as are actions promoting genetic connectivity and range expansion.     

A multilocus population genetic survey of the greater sage-grouse across their range

The distribution and abundance of the greater sage-grouse (Centrocercus urophasianus) have declined dramatically, and as a result the species has become the focus of conservation efforts. We conducted a range-wide genetic survey of the species which included 46 populations and over 1000 individuals using both mitochondrial sequence data and data from seven nuclear microsatellites. Nested clade and structure analyses revealed that, in general, the greater sage-grouse populations follow an isolation-by-distance model of restricted gene flow. This suggests that movements of the greater sage-grouse are typically among neighbouring populations and not across the species, range. This may have important implications if management is considering translocations as they should involve neighbouring rather than distant populations to preserve any effects of local adaptation. We identified two populations in Washington with low levels of genetic variation that reflect severe habitat loss and dramatic population decline. Managers of these populations may consider augmentation from geographically close populations. One population (Lyon/Mono) on the southwestern edge of the species' range appears to have been isolated from all other greater sage-grouse populations. This population is sufficiently genetically distinct that it warrants protection and management as a separate unit. The genetic data presented here, in conjunction with large-scale demographic and habitat data, will provide an integrated approach to conservation efforts for the greater sage-grouse.     

Environmental DNA (eDNA) Sampling Improves Occurrence and Detection Estimates of Invasive Burmese Pythons

Environmental DNA (eDNA) methods are used to detect DNA that is shed into the aquatic environment by cryptic or low density species. Applied in eDNA studies, occupancy models can be used to estimate occurrence and detection probabilities and thereby account for imperfect detection. However, occupancy terminology has been applied inconsistently in eDNA studies, and many have calculated occurrence probabilities while not considering the effects of imperfect detection. Low detection of invasive giant constrictors using visual surveys and traps has hampered the estimation of occupancy and detection estimates needed for population management in southern Florida, USA. Giant constrictor snakes pose a threat to native species and the ecological restoration of the Florida Everglades. To assist with detection, we developed species-specific eDNA assays using quantitative PCR (qPCR) for the Burmese python (Python molurus bivittatus), Northern African python (P. sebae), boa constrictor (Boa constrictor), and the green (Eunectes murinus) and yellow anaconda (E. notaeus). Burmese pythons, Northern African pythons, and boa constrictors are established and reproducing, while the green and yellow anaconda have the potential to become established. We validated the python and boa constrictor assays using laboratory trials and tested all species in 21 field locations distributed in eight southern Florida regions. Burmese python eDNA was detected in 37 of 63 field sampling events; however, the other species were not detected. Although eDNA was heterogeneously distributed in the environment, occupancy models were able to provide the first estimates of detection probabilities, which were greater than 91%. Burmese python eDNA was detected along the leading northern edge of the known population boundary. The development of informative detection tools and eDNA occupancy models can improve conservation efforts in southern Florida and support more extensive studies of invasive constrictors. Generic sampling design and terminology are proposed to standardize and clarify interpretations of eDNA-based occupancy models.     

Feral Horse Space Use and Genetic Characteristics from Fecal DNA

Feral horses (Equus ferus caballus) in the western United States are managed by the Bureau of Land Management (BLM) and United States Forest Service in designated areas on public lands with a goal of maintaining populations in balance with multiple uses of the landscape. Small, isolated populations can be at risk of extirpation from stochastic events and deleterious genetic effects resulting from inbreeding and reduced heterozygosity. The genetic diversity of feral horse herds is periodically monitored using blood or hair samples collected during management gathers (i.e., occasions when the herd is rounded up). We conducted a study to examine genetic characteristics of the feral horse population at the BLM Little Book Cliffs Herd Management Area (HMA) in Colorado, USA, using non-invasively collected fecal samples. Additionally, we explored whether genotypes could be used to document space use and potential sub-population development. We used a random sampling scheme, walking transects in sampling areas covering most of the HMA to find and collect fecal samples of all ages, except those that were deteriorating. We collected >1,800 fecal samples from across the study area in May, August, and October 2014. We then identified unique individuals using a suite of microsatellite loci. Our estimates of genetic diversity from fecal samples were higher than those reported from blood and hair samples taken during recent horse gathers, likely because our sample size and spatial distribution was larger. Genotypes revealed that some individuals were found only in certain parts of the study area and at a higher proportion than random; thus, they could be considered residents in those sampling areas. Using discriminant function analyses, we detected 5 genetic groups in the sample population, but these did not correspond to individuals in specific parts of the study area. Our results support the use of fecal DNA to augment direct observations of horse presence and could be used to detect habitat use and areas of high density. Non-invasive techniques such as fecal DNA sampling can help managers decide whether new individuals need to be translocated to a closed population to maintain genetic diversity without the human safety and animal welfare concerns associated with gathers and invasive techniques. © 2021 The Wildlife Society.     

Using Fecal DNA and Closed-Capture Models to Estimate Feral Horse Population Size

Accurate population estimates provide the foundation for managing feral horses (Equus caballus ferus) across the western United States. Certain feral horse populations are protected by the Wild and Free-Roaming Horses and Burros Act of 1971 and managed by the Bureau of Land Management (BLM) or the United States Forest Service on designated herd management areas (HMAs) or wild horse territories, respectively. Horses are managed to achieve an appropriate management level (AML), which represents the number of horses determined by BLM to contribute to a thriving natural ecological balance and avoid deterioration of the range. To achieve AML for each HMA, BLM resource managers need accurate and precise population estimates. We tested the use of non-invasive fecal samples in a genetic capture-recapture framework to estimate population size in a closed horse population at the Little Book Cliffs HMA, Colorado, USA, with a known size of 153 individuals. We collected 1,957 samples over 3 independent sampling periods in 2014 and amplified them at 8 microsatellite loci. We applied mark-recapture models to determine population size using 954 samples that amplified at all 8 loci. We subsampled and reanalyzed our dataset to simulate different data collection protocols and evaluated effects on accuracy and precision of estimates using N-mixture modeling, full likelihood closed-capture modeling, and capwire single-occasion modeling that used data from all 3 sampling periods. Our model results were accurate and precise for analyses that used data from all 3 occasions; however, capwire single-occasion modeling was not accurate when we analyzed each sampling period separately. For all subsampling analysis scenarios, reducing sample size decreased precision, whether by reducing number of field staff, field days, or geographic areas surveyed on each period. Reducing spatial coverage of the survey area did not result in accurate population estimates and only marginally lowered the number of samples that would need to be collected to maintain accuracy. Because laboratory analysis contributes the greatest expense for this method ($80 U.S./sample), reducing fecal sample size is advantageous. Our results demonstrate that non-invasive sampling combined with good survey design and careful genetic and capture-recapture analyses can provide an alternative method to estimate the number of feral horses in a closed population. This method may be especially appropriate in situations where aerial inventories are not practical or accurate because of low sighting conditions. But the higher costs associated with laboratory sample analyses may reduce the method's feasibility compared to helicopter surveys. © 2021 The Wildlife Society. This article has been contributed to by US Government employees and their work is in the public domain in the USA.