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Copyright of Conservation Biology is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

With the decline of bee populations worldwide, studies determining current wild bee distributions and diversity are increasingly important. Wild bee identification is often completed by experienced taxonomists or by genetic analysis. The current study was designed to compare two methods of identification including: (1) morphological identification by experienced taxonomists using images of field-collected wild bees and (2) genetic analysis of composite bee legs (multiple taxa) using metabarcoding. Bees were collected from conservation grasslands in eastern Iowa in summer 2019 and identified to the lowest taxonomic unit using both methods. Sanger sequencing of individual wild bee legs was used as a positive control for metabarcoding. Morphological identification of bees using images resulted in 36 unique taxa among 22 genera, and >80% of Bombus specimens were identified to species. Metabarcoding was limited to genus-level assignments among 18 genera but resolved some morphologically similar genera. Metabarcoding did not consistently detect all genera in the composite samples, including kleptoparasitic bees. Sanger sequencing showed similar presence or absence detection results as metabarcoding but provided species-level identifications for cryptic species (i.e., Lasioglossum). Genus-specific detections were more frequent with morphological identification than metabarcoding, but certain genera such as Ceratina and Halictus were identified equally well with metabarcoding and morphology. Genera with proportionately less tissue in a composite sample were less likely to be detected using metabarcoding. Image-based methods were limited by image quality and visible morphological features, while genetic methods were limited by databases, primers, and amplification at target loci. This study shows how an image-based identification method compares with genetic techniques, and how in combination, the methods provide valuable genus- and species-level information for wild bees while preserving tissue for other analyses. These methods could be improved and transferred to a field setting to advance our understanding of wild bee distributions and to expedite conservation research. [ABSTRACT FROM AUTHOR]

Avian mating strategies play a vital role in the demographic and genetic dynamics of a species and understanding avian reproductive tactics is important to conservation, population management and restoration. Classifications of avian mating strategies have historically been based on direct physical observations and tend to be rigid population‐level generalizations that overlook the variations inherent in most ecological systems. Based on limited empirical field observations, the American Black Swift Cypseloides niger borealis is considered to be a socially monogamous species with pair bonds lasting for many years. To test this hypothesis, we collected genomic DNA samples from banded swifts from six American Black Swift colonies in the western United States from 2004 to 2019 and isolated and developed primers for highly polymorphic microsatellite loci and used them to genotype our samples. Our parentage analysis revealed that sampled females never mated with the same male in subsequent years, suggesting that they are not sexually monogamous with a single partner for many years as previously hypothesized. [ABSTRACT FROM AUTHOR]

Sex ratio, and the extent to which it varies over time, is an important factor in the demography, management, and conservation of wildlife populations. Greater sage‐grouse Centrocercus urophasianus populations in western North America are monitored using counts of males at leks in spring. Population estimates derived from lek‐count data typically assume a constant, female‐biased sex ratio, yet few rigorous, empirically derived estimates of sex ratio are available to test that assumption. We estimated pre‐breeding sex ratio of greater sage‐grouse in a peripheral, geographically isolated population in northwestern Colorado during two consecutive winters using closed‐population, robust‐design, multi‐state, genetic mark–recapture models in program MARK. Sex ratio varied markedly between years, with estimates of 3.29 (95% CI: 2.36–4.59) females per male in winter 2012–2013 and 1.54 (95% CI: 1.22–1.95) females per male in winter 2013–2014. Rather than assuming a constant sex ratio, biologists should consider the potential for large annual variation in sex ratio of greater sage‐grouse populations when estimating population size or trend from male lek‐count data. [ABSTRACT FROM AUTHOR]

Genetic variation is a well‐known indicator of population fitness yet is not typically included in monitoring programs for sensitive species. Additionally, most programs monitor populations at one scale, which can lead to potential mismatches with ecological processes critical to species' conservation. Recently developed methods generating hierarchically nested population units (i.e., clusters of varying scales) for greater sage‐grouse (Centrocercus urophasianus) have identified population trend declines across spatiotemporal scales to help managers target areas for conservation. The same clusters used as a proxy for spatial scale can alert managers to local units (i.e., neighborhood‐scale) with low genetic diversity, further facilitating identification of management targets. We developed a genetic warning system utilizing previously developed hierarchical population units to identify management‐relevant areas with low genetic diversity within the greater sage‐grouse range. Within this warning system we characterized conservation concern thresholds based on values of genetic diversity and developed a statistical model for microsatellite data to robustly estimate these values for hierarchically nested populations. We found that 41 of 224 neighborhood‐scale clusters had low genetic diversity, 23 of which were coupled with documented local population trend decline. We also found evidence of cross‐scale low genetic diversity in the small and isolated Washington population, unlikely to be reversed through typical local management actions alone. The combination of low genetic diversity and a declining population suggests relatively high conservation concern. Our findings could further facilitate conservation action prioritization in combination with population trend assessments and (or) local information, and act as a base‐line of genetic diversity for future comparison. Importantly, the approach we used is broadly applicable across taxa. [ABSTRACT FROM AUTHOR]

Background: Benthic invertebrate (BI) surveys have been widely used to characterize freshwater environmental quality but can be challenging to implement at desired spatial scales and frequency. Environmental DNA (eDNA) allows an alternative BI survey approach, one that can potentially be implemented more rapidly and cheaply than traditional methods. Methods: We evaluated eDNA analogs of BI metrics in the Potomac River watershed of the eastern United States. We first compared arthropod diversity detected with primers targeting mitochondrial 16S (mt16S) and cytochrome c oxidase 1 (cox1 or COI) loci to that detected by manual surveys conducted in parallel. We then evaluated spatial and temporal variation in arthropod diversity metrics with repeated sampling in three focal parks. We also investigated technical factors such as filter type used to capture eDNA and PCR inhibition treatment. Results: Our results indicate that genus-level assessment of eDNA compositions is achievable at both loci with modest technical noise, although database gaps remain substantial at mt16S for regional taxa. While the specific taxa identified by eDNA did not strongly overlap with paired manual surveys, some metrics derived from eDNA compositions were rank-correlated with previously derived biological indices of environmental quality. Repeated sampling revealed statistical differences between high- and low-quality sites based on taxonomic diversity, functional diversity, and tolerance scores weighted by taxon proportions in transformed counts. We conclude that eDNA compositions are efficient and informative of stream condition. Further development and validation of scoring schemes analogous to commonly used biological indices should allow increased application of the approach to management needs. [ABSTRACT FROM AUTHOR]

Characterizing genetic structure across a species' range is relevant for management and conservation as it can be used to define population boundaries and quantify connectivity. Wide-ranging species residing in continuously distributed habitat pose substantial challenges for the characterization of genetic structure as many analytical methods used are less effective when isolation by distance is an underlying biological pattern. Here, we illustrate strategies for overcoming these challenges using a species of significant conservation concern, the Greater Sage-grouse (Centrocercus urophasianus), providing a new method to identify centers of genetic differentiation and combining multiple methods to help inform management and conservation strategies for this and other such species. Our objectives were to (1) describe large-scale patterns of population genetic structure and gene flow and (2) to characterize genetic subpopulation centers across the range of Greater Sage-grouse. Samples from 2,134 individuals were genotyped at 15 microsatellite loci. Using standard STRUCTURE and spatial principal components analyses, we found evidence for four or six areas of large-scale genetic differentiation and, following our novel method, 12 subpopulation centers of differentiation. Gene flow was greater, and differentiation reduced in areas of contiguous habitat (eastern Montana, most of Wyoming, much of Oregon, Nevada, and parts of Idaho). As expected, areas of fragmented habitat such as in Utah (with 6 subpopulation centers) exhibited the greatest genetic differentiation and lowest effective migration. The subpopulation centers defined here could be monitored to maintain genetic diversity and connectivity with other subpopulation centers. Many areas outside subpopulation centers are contact zones where different genetic groups converge and could be priorities for maintaining overall connectivity. Our novel method and process of leveraging multiple different analyses to find common genetic patterns provides a path forward to characterizing genetic structure in wide-ranging, continuously distributed species. [ABSTRACT FROM AUTHOR]

The raccoon (Procyon lotor (L., 1758)), a generalist mesocarnivore, has thrived in anthropogenically fragmented landscapes. In this study we utilized 13 microsatellites to analyze the population genetic structure in raccoons occupying an agriculturally fragmented habitat. Our analyses revealed low, but significant, levels of genetic structure ([F.sub.ST] = 0.022, P < 0.001) among 645 raccoons inhabiting 29 spatially distinct habitat patches (neighborhoods). We found no evidence for the presence of either isolation by distance or barriers. However, spatial autocorrelation revealed evidence for social structure at the raccoon-neighborhood scale. About 30% of the variance in levels of social structure among raccoon neighborhoods was explained by effects of habitat-patch size and the percentage of land cover represented by forest around the individual habitat patch. We found strong evidence of sex-biased dispersal using direct (parentage analysis) and indirect (relatedness and assignment indices) genetic estimators. However, our analysis revealed that among dispersing raccoons there was no difference in dispersal distance between sexes and that dispersal events are randomly distributed with respect to distance. Our study provides evidence that demographic and behavioral processes affecting raccoon spatial organization may be most critical at very fine scales of biological organization, such as within individual habitat patches. Le raton laveur (Procyon lotor (L., 1758)), un mesocarnivore generaliste, a prospere dans les paysages fragmentes par l'activite humaine. Nous utilisons, dans notre etude, 13 microsatellites pour determiner la structure genetique de la population chez des ratons laveurs qui vivent dans un habitat fragmente par l'agriculture. Nos analyses revelent des niveaux bas, mais significatifs, de structure genetique ([F.sub.ST] = 0,022, P < 0,001) parmi 645 ratons laveurs vivant dans 29 taches d'habitat distinctes (quartiers). Il n'y a aucune indication d'isolement par la distance, ni de barrieres. Cependant, l'autocorrelation spatiale donne des indications d'une structure sociale a l'echelle des quartiers de ratons laveurs. Environ 30 % de la variance des niveaux de structure sociale entre les quartiers de ratons laveurs s'explique par les effets de la taille de la tache d'habitat et le pourcentage de la couverture du sol autour des taches individuelles d'habitat qui est represente par de la foret. Des estimateurs genetiques directs (analyse de filiation) et indirects (indices de consanguinite et d'attribution) indiquent clairement une dispersion variable en fonction du sexe. Cependant, notre analyse revele que, parmi les ratons laveurs qui se dispersent, il n'y a pas de difference de distance de dispersion en fonction des sexes et que les evenements de dispersion sont repartis au hasard en fonction de la distance. Notre etude fournit des indications que les processus demographiques et comportementaux qui affectent l'organisation spatiale des ratons laveurs peuvent agir de la facon la plus critique aux echelles tres fines de l'organisation biologique, par exemple a l'interieur des taches individuelles d'habitat. [Traduit par la Redaction], Introduction Raccoons (Procyon lotor (L., 1758)) are mesocarnivores that have increased dramatically in numbers and distribution across much of North America, after a decline to relatively low levels in the [...]

Background. Hoary bats (Lasiurus cinereus) are among the bat species most commonly killed by wind turbine strikes in the midwestern United States. The impact of this mortality on species census size is not understood, due in part to the difficulty of estimating population size for this highly migratory and elusive species. Genetic effective population size (Ne) could provide an index of changing census population size if other factors affecting Ne are stable. Methods. Weused the NeEstimator package to derive effective breeding population size (Nb) estimates for two temporally spaced cohorts: 93 hoary bats collected in 2009-2010 and an additional 93 collected in 2017-2018. We sequenced restriction-site associated polymorphisms and generated a de novo genome assembly to guide the removal of sex-linked and multi-copy loci, as well as identify physically linked markers. Results. Analysis of the reference genome with psmc suggested at least a doubling of Ne in the last 100,000 years, likely exceeding Ne D 10,000 in the Holocene. Allele and genotype frequency analyses confirmed that the two cohorts were comparable, although some samples had unusually high or low observed heterozygosities. Additionally, the older cohort had lower mean coverage and greater variability in coverage, and batch effects of sampling locality were observed that were consistent with sample degradation. We therefore excluded samples with low coverage or outlier heterozygosity, as well as loci with sequence coverage far from the mode value, from the final data set. Prior to excluding these outliers, contemporary Nb estimates were significantly higher in the more recent cohort, but this finding was driven by high values for the 2018 sample year and low values for all other years. In the reduced data set, Nb did not differ significantly between cohorts. We found base substitutions to be strongly biased toward cytosine to thymine or the complement, and further partitioning loci by substitution type had a strong effect on Nb estimates. Minor allele frequency and base quality bias thresholds also had strong effects on Nb estimates. Instability of Nb with respect to common data filtering parameters and empirically identified factors prevented robust comparison of the two cohorts. Given that confidence intervals frequently included infinity as the stringency of data filtering increased, contemporary trends in Nb of North American hoary bats may not be tractable with the linkage disequilibrium method, at least using the protocol employed here. [ABSTRACT FROM AUTHOR]

Background: Environmental DNA (eDNA) surveys are appealing options for monitoring aquatic biodiversity. While factors affecting eDNA persistence, capture and amplification have been heavily studied, watershed-scale surveys of fish communities and our confidence in such need further exploration. Methods: We characterized fish eDNA compositions using rapid, low-volume filtering with replicate and control samples scaled for a single Illumina MiSeq flow cell, using the mitochondrial 12S ribosomal RNA locus for taxonomic profiling. Our goals were to determine: (1) spatiotemporal variation in eDNA abundance, (2) the filtrate needed to achieve strong sequencing libraries, (3) the taxonomic resolution of 12S ribosomal sequences in the study environment, (4) the portion of the expected fish community detectable by 12S sequencing, (5) biases in species recovery, (6) correlations between eDNA compositions and catch per unit effort (CPUE) and (7) the extent that eDNA profiles reflect major watershed features. Our bioinformatic approach included (1) estimation of sequencing error from unambiguous mappings and simulation of taxonomic assignment error under various mapping criteria; (2) binning of species based on inferred assignment error rather than by taxonomic rank; and (3) visualization of mismatch distributions to facilitate discovery of distinct haplotypes attributed to the same reference. Our approach was implemented within the St. Regis River, NY, USA, which supports tribal and recreational fisheries and has been a target of restoration activities. We used a large record of St. Regis-specific observations to validate our assignments. Results: We found that 300 mL drawn through 25-mm cellulose nitrate filters yielded greater than 5 ng/µL DNA at most sites in summer, which was an approximate threshold for generating strong sequencing libraries in our hands. Using inferred sequence error rates, we binned 12S references for 110 species on a state checklist into 85 single-species bins and seven multispecies bins. Of 48 bins observed by capture survey in the St. Regis, we detected eDNA consistent with 40, with an additional four detections flagged as potential contaminants. Sixteen unobserved species detected by eDNA ranged from plausible to implausible based on distributional data, whereas six observed species had no 12S reference sequence. Summed log-ratio compositions of eDNA-detected taxa correlated with log(CPUE) (Pearson's R = 0.655, P < 0.001). Shifts in eDNA composition of several taxa and a genotypic shift in channel catfish (Ictalurus punctatus) coincided with the Hogansburg Dam, NY, USA. In summary, a simple filtering apparatus operated by field crews without prior expertise gave useful summaries of eDNA composition with minimal evidence of field contamination. 12S sequencing achieved useful taxonomic resolution despite the short marker length, and data exploration with standard bioinformatic tools clarified taxonomic uncertainty and sources of error. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Context: Translocation has become a widely used method to restore wildlife populations following extirpation. For some species, such as lekking grouse, which breed at traditional mating grounds, reproduction is linked to culturally established geographic locations. Cultural centres are lost upon extirpation, making restoration into otherwise rehabilitated habitats especially challenging. The process by which species with culturally dependent reproduction sometimes become re-established is poorly understood and merits investigation to improve conservation strategies. Historically, population restoration of North American lekking grouse (Tympanuchus spp. and Centrocercus spp.) via translocation has yielded poor results, in part because translocation sites lack leks, culturally determined breeding locations for which breeding adults form a high degree of philopatry. Columbian sharp-tailed grouse (Tympanuchus phasianellus columbianus ; CSTG) occurs in <10% of its historic range, but the existence of rehabilitated historic habitat provides for the potential of population restoration via translocation. Aims: We reintroduced CSTG to vacant habitat in north-central Nevada, USA, from 2013 to 2017, with concordant goals of promoting females to nest and males to lek. We tested the utility of performing artificial insemination (AI) on females before translocation and we conducted paternity analyses to understand male reproduction. Methods: We monitored females for the effects of AI on nest initiation, nest survival and egg fertility. We used post-hatch extra-embryonic membranes and other tissues to evaluate paternity of chicks produced at the restoration site. Key results: Artificial insemination had no effect on female survival or nest initiation, and did not fertilise any eggs within nine sampled clutches (n = 102 eggs). Most paternity was attributable to male residents that had survived for ≥1 year at the restoration site before the arrival of translocated females. Conclusions: Artificial insemination neither aided nor harmed female reproduction. A small number of translocated, resident adult males sired reproduction following female release. Implications: The presence of resident males at restoration sites may be more likely to result in post-translocation reproduction than is pre-translocation AI. Restoring CSTG to vacant habitat should focus on translocating females into suitable nesting habitat while simultaneously ensuring that reproductively capable males are available within or adjacent to the nesting habitat. We conducted a field trial of artificially inseminating (AI) translocated female Columbian sharp-tailed grouse (Tympanuchus phasianellus columbianus ; CSTG) to facilitate post-release reproduction at a restoration site. Specifically, we tested whether AI influenced nest initiation, adult survival and egg-fertility rates, and conducted genetic paternity analyses using eggshells. We found that AI did not influence any of the measured demographic rates and the majority of paternity assignments were attributed to relatively few locally established males. [ABSTRACT FROM AUTHOR]

Use of environmental DNA (eDNA) to assess distributions of aquatic and semi-aquatic macroorganisms is promising, but sampling schemes may need to be tailored to specific objectives. Given the potentially high variance in aquatic eDNA among replicate grab samples, compositing smaller water volumes collected over a period of time may be more effective for some applications. In this study, we compared eDNA profiles from composite water samples aggregated over three hours with grab water samples. Both sampling patterns were performed with identical autosamplers paired at two different sites in a headwater stream environment, augmented with exogenous fish eDNA from an upstream rearing facility. Samples were filtered through 0.8 μm cellulose nitrate filters and DNA was extracted with a cetyl trimethylammonium bromide procedure. Eukaryotic and bacterial community profiles were derived by amplicon sequencing of 12S ribosomal, 16S ribosomal, and cytochrome oxidase I loci. Operational taxa were assigned to genus with a lowest common ancestor approach for eukaryotes and to family with the RDP Classifier software for prokaryotes. Eukaryotic community profiles were more consistent with composite sampling than grab sampling. Downstream, rarefaction curves suggested faster taxon accumulation for composite samples, and estimated richness was higher for composite samples as a set than for grab samples. Upstream, composite sampling produced lower estimated richness than grab samples, but with overlapping standard errors. Furthermore, a bimodal pattern of richness as a function of sequence counts suggested the impact of clumped particles on upstream samples. Bacterial profiles were insensitive to sample method, consistent with the more even dispersion expected for bacteria compared with eukaryotic eDNA. Overall, samples composited over 3 h performed equal to or better than triplicate grab sampling for quantitative community metrics, despite the higher total sequencing effort provided to grab replicates. On the other hand, taxon-specific detection rates did not differ appreciably and the two methods gave similar estimates of the ratio of the common fish genera Salmo and Coregonus at each site. Unexpectedly, Salmo eDNA dropped out substantially faster than Coregonus eDNA between the two sites regardless of sampling method, suggesting that differential settling affects the estimation of relative abundance. We identified bacterial patterns that were associated with eukaryotic diversity, suggesting potential roles as biomarkers of sample representativeness. [ABSTRACT FROM AUTHOR]

Genetic mark-recapture methods are increasingly being used to estimate demographic parameters in species where traditional techniques are problematic or imprecise. The federally endangered Indiana bat Myotis sodalis has declined dramatically and threats such as white-nose syndrome continue to afflict this species. To date, important demographic information for Indiana bats has been difficult to estimate precisely using traditional techniques such as emergence counts. Successful management and protection of Indiana bats requires better methods to estimate population sizes and survival rates throughout the year, particularly during summer when these bats reproduce and are widely dispersed away from their winter hibernacula. In addition, the familial makeup of maternity colonies is unknown, yet important for understanding local and regional population dynamics. We had four objectives in this study. For the first two objectives we investigated the potential use of DNA from fecal samples (fecal DNA) collected at roosts to obtain genetically based mark-recapture estimates of 1) colony size and 2) survival rates, for an Indiana bat maternity colony in Indianapolis, Indiana. The third objective was to compare our genetically based colony-size estimates with emergence counts conducted at the same roost tree to evaluate the genetic mark-recapture method. Our fourth objective was to use fecal DNA to estimate levels of relatedness among individuals sampled at the roost. In the summer of 2008, we collected fecal pellets and conducted emergence counts at a prominent roost tree during three time periods each lasting 7 or 8 d. We genotyped fecal DNA using five highly polymorphic microsatellite loci to identify individuals and used a robust-design mark-recapture approach to estimate survival rates as well as colony size at the roost tree. Emergence count estimates at the roost tree ranged from 100 to 215, whereas genetic mark-recapture estimates were higher, ranging from 122 to 266 and more precise. Apparent survival was 0.994 (SE ¼ 0.04) between sampling periods suggesting that few bats died or permanently emigrated during the course of the study. Relatedness estimates, r, between all pairs of individuals averaged 0.055 ranging from 0 to 0.779, indicating that most individuals were not closely related. We demonstrate here the promise of using fecal DNA to estimate demographic information for Indiana bats and potentially other bat species. [ABSTRACT FROM AUTHOR]

Abstract: Fecal DNA collected noninvasively can provide valuable information about genetic and ecological characteristics. This approach has rarely been used for equids, despite the need for conservation of endangered species and management of abundant feral populations. We examined factors affecting the efficacy of using equid fecal samples for conservation genetics. First, we evaluated two fecal collection methods (paper bag vs. ethanol). Then, we investigated how time since deposition and month of collection impacted microsatellite amplification success and genotyping errors. Between May and November 2014, we collected feral horse fecal samples of known age each month in a feral horse Herd Management Area in western Colorado and documented deterioration in the field with photographs. Samples collected and dried in paper bags had significantly higher amplification rates than those collected and stored in ethanol. There was little difference in the number of loci that amplified per sample between fresh fecal piles and those that had been exposed to the environment for up to 2 months (in samples collected in paper bags). After 2 months of exposure, amplification success declined. When comparing fresh (0–2 months) and old (3–6 months) fecal piles, samples from fresh piles had more matching genotypes across samples, better amplification success and less allelic dropout. Samples defecated during the summer and collected within 2 months of deposition had highest number of genotypes matching among samples, and lowest rates of amplification failure and allelic dropout. Due to the digestive system and amount of fecal material produced by equids, as well as their occurrence in arid ecosystems, we suggest that they are particularly good candidates for noninvasive sampling using fecal DNA. [ABSTRACT FROM AUTHOR]

Many aspects of parasite biology critically depend on their hosts, and understanding how host‐parasite populations are co‐structured can help improve our understanding of the ecology of parasites, their hosts, and host‐parasite interactions. This study utilized genetic data collected from raccoons (Procyon lotor), and a specialist parasite, the raccoon tick (Ixodes texanus), to test for genetic co‐structuring of host‐parasite populations at both landscape and host scales. At the landscape scale, our analyses revealed a significant correlation between genetic and geographic distance matrices (i.e., isolation by distance) in ticks, but not their hosts. While there are several mechanisms that could lead to a stronger pattern of isolation by distance in tick vs. raccoon datasets, our analyses suggest that at least one reason for the above pattern is the substantial increase in statistical power (due to the ≈8‐fold increase in sample size) afforded by sampling parasites. Host‐scale analyses indicated higher relatedness between ticks sampled from related vs. unrelated raccoons trapped within the same habitat patch, a pattern likely driven by increased contact rates between related hosts. By utilizing fine‐scale genetic data from both parasites and hosts, our analyses help improve our understanding of epidemiology and host ecology. [ABSTRACT FROM AUTHOR]

Given the significance of animal dispersal to population dynamics and geographic variability, understanding how dispersal is impacted by landscape patterns has major ecological and conservation importance. Speaking to the importance of dispersal, the use of linear mixed models to compare genetic differentiation with pairwise resistance derived from landscape resistance surfaces has presented new opportunities to disentangle the menagerie of factors behind effective dispersal across a given landscape. Here, we combine these approaches with novel resistance surface parameterization to determine how the distribution of high- and low-quality seasonal habitat and individual landscape components shape patterns of gene flow for the greater sage-grouse ( Centrocercus urophasianus) across Wyoming. We found that pairwise resistance derived from the distribution of low-quality nesting and winter, but not summer, seasonal habitat had the strongest correlation with genetic differentiation. Although the patterns were not as strong as with habitat distribution, multivariate models with sagebrush cover and landscape ruggedness or forest cover and ruggedness similarly had a much stronger fit with genetic differentiation than an undifferentiated landscape. In most cases, landscape resistance surfaces transformed with 17.33-km-diameter moving windows were preferred, suggesting small-scale differences in habitat were unimportant at this large spatial extent. Despite the emergence of these overall patterns, there were differences in the selection of top models depending on the model selection criteria, suggesting research into the most appropriate criteria for landscape genetics is required. Overall, our results highlight the importance of differences in seasonal habitat preferences to patterns of gene flow and suggest the combination of habitat suitability modeling and linear mixed models with our resistance parameterization is a powerful approach to discerning the effects of landscape on gene flow. [ABSTRACT FROM AUTHOR]

Copyright of Condor: Ornithological Applications is the property of Oxford University Press / USA and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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Identification of microsatellites, or simple sequence repeats (SSRs), can be a time-consuming and costly investment requiring enrichment, cloning, and sequencing of candidate loci. Recently, however, high throughput sequencing (with or without prior enrichment for specific SSR loci) has been utilized to identify SSR loci. The direct "Seq-to-SSR" approach has an advantage over enrichment-based strategies in that it does not require a priori selection of particular motifs, or prior knowledge of genomic SSR content. It has been more expensive per SSR locus recovered, however, particularly for genomes with few SSR loci, such as bird genomes. The longer but relatively more expensive 454 reads have been preferred over less expensive Illumina reads. Here, we use Illumina paired-end sequence data to identify potentially amplifiable SSR loci (PALs) from a snake (the Burmese python, Python molurus bivittatus), and directly compare these results to those from 454 data. We also compare the python results to results from Illumina sequencing of two bird genomes (Gunnison Sage-grouse, Centrocercus minimus, and Clark's Nutcracker, Nucifraga columbiana), which have considerably fewer SSRs than the python. We show that direct Illumina Seq-to-SSR can identify and characterize thousands of potentially amplifiable SSR loci for as little as $10 per sample - a fraction of the cost of 454 sequencing. Given that Illumina Seq-to-SSR is effective, inexpensive, and reliable even for species such as birds that have few SSR loci, it seems that there are now few situations for which prior hybridization is justifiable. [ABSTRACT FROM AUTHOR]

Quaternary climatic oscillations greatly influenced the present-day population genetic structure of animals and plants. For species with high dispersal and reproductive potential, phylogeographic patterns resulting from historical processes can be cryptic, overshadowed by contemporary processes. Here we report a study of the phylogeography of Odocoileus hemionus, a large, vagile ungulate common throughout western North America. We examined sequence variation of mitochondrial DNA (control region and cytochrome b) within and among 70 natural populations across the entire range of the species. Among the 1766 individual animals surveyed, we recovered 496 haplotypes. Although fine-scale phylogenetic structure was weakly resolved using phylogenetic methods, network analysis clearly revealed the presence of 12 distinct haplogroups. The spatial distribution of haplogroups showed a strong genetic discontinuity between the two morphological types of O. hemionus, mule deer and black-tailed deer, east and west of the Cascade Mountains in the Pacific Northwest. Within the mule deer lineage, we identified several haplogroups that expanded before or during the Last Glacial Maximum, suggesting that mule deer persisted in multiple refugia south of the ice sheets. Patterns of genetic diversity within the black-tailed deer lineage suggest a single refugium along the Pacific Northwest coast, and refute the hypothesis that black-tailed deer persisted in one or more northern refugia. Our data suggest that black-tailed deer recolonized areas in accordance with the pattern of glacial retreat, with initial recolonization northward along a coastal route and secondary recolonization inland. [ABSTRACT FROM AUTHOR]

The eastern gray squirrel ( Sciurus carolinensis) often serves as a model organism for investigations of wildlife ecology. The authors developed 11 polymorphic microsatellite markers to facilitate future research questions. The number of alleles per locus ranged from three to ten and observed heterozygosities ranged from 0.143 to 0.786. Interspecific screening revealed that several loci were polymorphic in Sciurus niger (eight loci) and Tamiasciurus hudsonicus (four loci). These markers will aid in investigations of movements, social structure and mating tactics of eastern gray squirrel populations. [ABSTRACT FROM AUTHOR]

Clark's nutcrackers are important seed dispersers for two widely-distributed western North American conifers, whitebark pine and limber pine, which are declining due to outbreaks of mountain pine beetle and white pine blister rust. Because nutcracker seed dispersal services are key to maintaining viable populations of these imperiled pines, knowledge of movement patterns of Clark's nutcrackers helps managers understand local extinction risks for these trees. To investigate population structure within Clark's nutcracker, we developed primers for and characterized 13 polymorphic microsatellite loci. In a screen of 22 individuals from one population, levels of variability ranged from 6 to 15 alleles. No loci were found to be linked, although 4 loci revealed significant departures from Hardy-Weinberg equilibrium and evidence of null alleles. These microsatellite loci will enable population genetic analyses of Clark's nutcrackers, which could provide insights into the spatial relationships between nutcrackers and the trees they help disperse. [ABSTRACT FROM AUTHOR]

Twenty one polymorphic microsatellite loci for the Japanese dace ( Tribolodon hakonensis) were isolated and characterized. The number of observed alleles per locus in 32 individuals ranged from 3 to 30. The observed and expected heterozygosities ranged from 0.125 to 0.969 and from 0.175 to 0.973, respectively. All loci conformed to Hardy-Weinberg equilibrium, no linkage disequilibrium was observed between pairs of loci and no loci showed evidence of null alleles. These microsatellite loci will be useful for investigating the intraspecific genetic variation and population structure of this species. [ABSTRACT FROM AUTHOR]

The Broad-tailed Hummingbird ( Selaphorus platycercus) breeds at higher elevations in the central and southern Rockies, eastern California, and Mexico and has been studied for 8 years in Rocky Mountain National Park, Colorado. Questions regarding the relatedness of Broad-tailed Hummingbirds banded together and then recaptured in close time proximity in later years led us to isolate and develop primers for 10 polymorphic microsatellite loci. In a screen of 25 individuals from a population in Rocky Mountain National Park, the 10 loci were found to have levels of variability ranging from two to 16 alleles. No loci were found to depart from linkage disequilibrium, although two loci revealed significant departures from Hardy-Weinberg equilibrium. These 10 microsatellite loci will be applicable for population genetic analyses, investigation of mating systems and relatedness, and may help gain insight into the migration timing and routes for this species. [ABSTRACT FROM AUTHOR]

Primers for 10 microsatellite loci were developed specifically to amplify low quantity and quality DNA in the endangered Indiana Bat ( Myotis sodalis). In a screen of 20 individuals from a population in Missouri, the 10 loci were found to have levels of variability ranging from seven to 18 alleles. No loci were found to be linked, although two loci revealed significant departures from Hardy-Weinberg equilibrium. These microsatellite loci will be applicable for population genetic analyses and for use in mark-recapture studies that utilize DNA collected non-invasively from fecal pellets, which will ultimately aid in management efforts. [ABSTRACT FROM AUTHOR]

In order to analyze population genetic structure at multiple spatial scales, 12 polymorphic microsatellite loci were developed for the eastern hellbender ( Cryptobranchus alleganiensis alleganiensis). The number of alleles per locus ranged from 6 to 12 (mean of 9.25 per locus) and the observed heterozygosity ranged from 0.645 to 0.935 among 31 individuals. Two loci exhibited significant deviations from Hardy-Weinberg equilibrium. No evidence for linkage disequilibrium was detected between pairs of loci. These markers will be used to examine population genetic structure across the geographic range of this declining species. [ABSTRACT FROM AUTHOR]

Twenty-one polymorphic microsatellite markers were developed for the Virginia opossum ( Didelphis virginiana). The number of alleles ranged from two to 13 and observed heterozygosities ranged from 0.464 to 0.964. Significant heterozygote deficiencies were observed at three loci and null alleles were detected at five loci. Evidence for gametic disequilibrium was observed between three sets of paired loci after a sequential Bonferroni correction was applied. These markers will enable us to investigate the mating tactics, movement behaviour and social structure of Virginia opossum populations inhabiting fragmented agricultural landscapes. [ABSTRACT FROM AUTHOR]

Twelve polymorphic microsatellite loci were developed for the American dog tick ( Dermacentor variabilis), an important vector of infectious diseases in humans and animals. Four multiplexed panels comprising the loci were developed and 45 ticks collected from two raccoons ( Procyon lotor) were genotyped. The number of alleles per locus ranged from nine to 30, and single locus heterozygosities ranged from 0.18 to 0.93. Data generated using these markers will further our understanding of factors affecting gene flow in D. variabilis, thus helping to elucidate the transmission dynamics of diseases associated with this vector. [ABSTRACT FROM AUTHOR]

Fourteen polymorphic microsatellite loci were developed for the raccoon tick ( Ixodes texanus). Three multiplexed panels comprising the loci were developed and 50 ticks collected from two infected raccoons ( Procyon lotor) were genotyped. The number of alleles per locus ranged from five to 22, and single locus heterozygosities ranged from 0.46 to 0.94. Future research will further our understanding of I. texanus biology and help in elucidating the effects of life-history variation on parasite population genetic structure, using I. texanus as a model organism. [ABSTRACT FROM AUTHOR]

In order to complement ecological information with genetic data we isolated and characterized 14 polymorphic microsatellite markers from raccoons ( Procyon lotor). Three multiplexed panels comprising the loci were developed and 29 individuals from a contiguous habitat patch in northern Indiana, USA were genotyped. The number of alleles per locus ranged from four to 18, and overall heterozygosities ranged from 0.31 to 1.00. One locus was identified as possibly being X-linked, since males appeared to be hemizygous. Data generated using these markers will be used to further our understanding of small-scale raccoon population dynamics in a highly fragmented landscape. [ABSTRACT FROM AUTHOR]

Eastern chipmunks are small forest rodents for which ecological data at multiple spatial scales exist, but no molecular markers have been developed that provide adequate resolution to examine genetic structure at fine scales in this species. Thus, we developed 12 variable microsatellite loci, which amplified in three multiplexed reactions, and screened them in 27 individuals from northern Indiana, USA. Observed heterozygosities across loci ranged from 0.26 to 0.91 and number of alleles per locus ranged from three to 10. We will use these markers along with ecological data to understand population dynamics of eastern chipmunks at small spatial scales. [ABSTRACT FROM AUTHOR]

We describe 10 novel North American river otter ( Lontra canadensis) polymorphic microsatellite loci. Individuals from two river drainages in New York were sampled, and the number of alleles per locus ranged from two to 12 (Drainage 1) and two to 10 (Drainage 2). Observed heterozygosities ranged from 0.21 to 0.83 (Drainage 1) and 0.20 to 0.80 (Drainage 2). Preliminary screening revealed that loci amplified in five other mustelids [ Martes pennanti ( n = 6), Martes fiona ( n = 8), Mustela frenata ( n = 8), Mustela erminea ( n = 8) and Mustela vison ( n = 5)]. [ABSTRACT FROM AUTHOR]