Evaluating mixed samples as a source of error in non-invasive genetic studies using microsatellites

Genetic Analysis and Status of Brown Bear Sub-Populations in Three National Parks of Greece Functioning as Strongholds for the Species’ Conservation

In order to optimize the appropriate conservation actions for the brown bear (Ursus arctos L.) population in Greece, we estimated the census (Nc) and effective (Ne) population size as well as the genetic status of brown bear sub-populations in three National Parks (NP): Prespa (MBPNP), Pindos (PINDNP), and Rhodopi (RMNP). The Prespa and Pindos sub-populations are located in western Greece and the Rhodopi population is located in eastern Greece. We extracted DNA from 472 hair samples and amplified through PCR 10 microsatellite loci. In total, 257 of 472 samples (54.5%) were genotyped for 6–10 microsatellite loci. Genetic analysis revealed that the Ne was 35, 118, and 61 individuals in MBPNP, PINDNP, and RMNP, respectively, while high levels of inbreeding were found in Prespa and Rhodopi but not in Pindos. Moreover, analysis of genetic structure showed that the Pindos population is genetically distinct, whereas Prespa and Rhodopi show mutual overlaps. Finally, we found a notable gene flow from Prespa to Rhodopi (10.19%) and from Rhodopi to Prespa (14.96%). Therefore, targeted actions for the conservation of the bears that live in the abovementioned areas must be undertaken, in order to ensure the species’ viability and to preserve the corridors that allow connectivity between the bear sub-populations in Greece.

Testing the effectiveness of genetic monitoring using genetic non-invasive sampling

Effective conservation requires accurate data on population genetic diversity, inbreeding, and genetic structure. Increasingly, scientists are adopting genetic non-invasive sampling (gNIS) as a cost-effective population-wide genetic monitoring approach. gNIS has, however, known limitations which may impact the accuracy of downstream genetic analyses. Here, using high-quality single nucleotide polymorphism (SNP) data from blood/tissue sampling of a free-ranging koala population (n = 430), we investigated how the reduced SNP panel size and call rate typical of genetic non-invasive samples (derived from experimental and field trials) impacts the accuracy of genetic measures, and also the effect of sampling intensity on these measures. We found that gNIS at small sample sizes (14% of population) can provide accurate population diversity measures, but slightly underestimated population inbreeding coefficients. Accurate measures of internal relatedness required at least 33% of the population to be sampled. Accurate geographic and genetic spatial autocorrelation analysis requires between 28% and 51% of the population to be sampled. We show that gNIS at low sample sizes can provide a powerful tool to aid conservation decision-making and provide recommendations for researchers looking to apply these techniques to free-ranging systems.

An efficient method for simultaneous species, individual, and sex identification via in-solution single nucleotide polymorphism capture from low-quality scat samples

Understanding predator population dynamics is important for conservation management because of the critical roles predators play within ecosystems. Noninvasive genetic sampling methods are useful for the study of predators like canids that can be difficult to capture or directly observe. Here, we introduce the FAECES* method (Fast and Accurate Enrichment of Canid Excrement for Species* and other analyses) which expands the toolbox for canid researchers and conservationists by using in-solution hybridization sequence capture to produce single nucleotide polymorphism (SNP) genotypes for multiple canid species from scat-derived DNA using a single enrichment. We designed a set of hybridization probes to genotype both coyotes (Canis latrans) and kit foxes (Vulpes macrotis) at hundreds of polymorphic SNP loci and we tested the probes on both tissues and field-collected scat samples. We enriched and genotyped by sequencing 52 coyote and 70 kit fox scats collected in and around a conservation easement in the Nevada Mojave Desert. We demonstrate that the FAECES* method produces genotypes capable of differentiating coyotes and kit foxes, identifying individuals and their sex, and estimating genetic diversity and effective population sizes, even using highly degraded, low-quantity DNA extracted from scat. We found that the study area harbours a large and diverse population of kit foxes and a relatively smaller population of coyotes. By replicating our methods in the future, conservationists can assess the impacts of management decisions on canid populations. The method can also be adapted and applied more broadly to enrich and sequence multiple loci from any species of interest using scat or other noninvasive genetic samples.

Applying genomic data in wildlife monitoring: Development guidelines for genotyping degraded samples with reduced single nucleotide polymorphism panels

The genomic era has led to an unprecedented increase in the availability of genome-wide data for a broad range of taxa. Wildlife management strives to make use of these vast resources to enable refined genetic assessments that enhance biodiversity conservation. However, as new genomic platforms emerge, problems remain in adapting the usually complex approaches for genotyping of noninvasively collected wildlife samples. Here, we provide practical guidelines for the standardized development of reduced single nucleotide polymorphism (SNP) panels applicable for microfluidic genotyping of degraded DNA samples, such as faeces or hairs. We demonstrate how microfluidic SNP panels can be optimized to efficiently monitor European wildcat (Felis silvestris S.) populations. We show how panels can be set up in a modular fashion to accommodate informative markers for relevant population genetics questions, such as individual identification, hybridization assessment and the detection of population structure. We discuss various aspects regarding the implementation of reduced SNP panels and provide a framework that will allow both molecular ecologists and practitioners to help bridge the gap between genomics and applied wildlife conservation.

Applying genomic data in wildlife monitoring: Development guidelines for genotyping degraded samples with reduced single nucleotide polymorphism panels

The genomic era has led to an unprecedented increase in the availability of genome-wide data for a broad range of taxa. Wildlife management strives to make use of these vast resources to enable refined genetic assessments that enhance biodiversity conservation. However, as new genomic platforms emerge, problems remain in adapting the usually complex approaches for genotyping of noninvasively collected wildlife samples. Here, we provide practical guidelines for the standardized development of reduced single nucleotide polymorphism (SNP) panels applicable for microfluidic genotyping of degraded DNA samples, such as faeces or hairs. We demonstrate how microfluidic SNP panels can be optimized to efficiently monitor European wildcat (Felis silvestris S.) populations. We show how panels can be set up in a modular fashion to accommodate informative markers for relevant population genetics questions, such as individual identification, hybridization assessment and the detection of population structure. We discuss various aspects regarding the implementation of reduced SNP panels and provide a framework that will allow both molecular ecologists and practitioners to help bridge the gap between genomics and applied wildlife conservation.

Individual identification via remote video verified by DNA analysis: a case study of the American black bear

Context Researchers and managers often use DNA analysis and remote photography to identify cryptic animals and estimate abundance. Remote video cameras are used less often but offer an increased ability to distinguish similar-looking individuals as well as to observe behavioural patterns that cannot be adequately captured with still photography. However, the use of this approach in species with minimally distinguishing marks has not been tested. Aims To determine the utility and accuracy of distinguishing characteristics of American black bears, Ursus americanus, observed on remote video for identifying individuals in an open population. Methods We compared individuals identified on video with individuals and their sex identified by DNA analysis of hairs collected from hair traps visited by the bears. Key results We found that remote video could be used to determine the number of male and female black bears sampled by the video cameras. Specifically, we matched 13 individual bear genotypes with 13 video identifications, one genotype for each individual. We correctly matched ~82% of video identifications with all 38 genotypes collected from hair traps. Conclusions We demonstrated that distinguishing characteristics of a cryptic animal in remote video can be used to accurately identify individuals. Remote video complements genetic analysis by providing information about habitat use and behaviour. Implications When remote video cameras can be used to identify individuals, a wealth of other information will subsequently be obtained. Multi-year video-based studies can show sex ratios, and relative physical condition; shed light on fine-scale habitat use, such as when and where animals feed and what they eat; and display social interactions and rare behaviours.

How Behavior of Nontarget Species Affects Perceived Accuracy of Scat Detection Dog Surveys

Detection dogs, specially trained domestic dogs (Canis familiaris), have become a valuable, noninvasive, conservation tool because they remove the dependence of attracting species to a particular location. Further, detection dogs locate samples independent of appearance, composition, or visibility allowing researchers to collect large sets of unbiased samples that can be used in complex ecological queries. One question not fully addressed is why samples from nontarget species are inadvertently collected during detection dog surveys. While a common explanation has been incomplete handler or dog training, our study aimed to explore alternative explanations. Our trials demonstrate that a scat’s genetic profile can be altered by interactions of nontarget species with target scat via urine-marking, coprophagy, and moving scats with their mouths, all pathways to contamination by nontarget species’ DNA. Because detection dogs are trained to locate odor independent of masking, the collection of samples with a mixed olfactory profile (target and nontarget) is possible. These scats will likely have characteristics of target species’ scats and are therefore only discovered faulty once genetic results indicate a nontarget species. While the collection of nontarget scats will not impact research conclusions so long as samples are DNA tested, we suggest ways to minimize their collection and associated costs.

Does kinship affect spatial organization in a small and isolated population of a solitary felid: The Eurasian lynx?

Social organization in wild carnivores is mostly determined by patterns of family bonds, which may shape the degree of relatedness among individuals in the population. We studied kinship in a small and isolated population of a solitary carnivore, the Eurasian lynx (Lynx lynx) to evaluate its effect on spatial distribution of individuals. We investigated the relationship between spatial location and pair-wise kinship among 28 lynx individuals identified in 2004-2011 by telemetry, non-invasive sampling and genotyping with the use of 12 autosomal microsatellites in the Białowieża Primeval Forest, Poland. The average relatedness of the lynx population was relatively low (Lynch and Ritland's R = 0.03). Females were significantly more related to each other than males with other males. The inferred pedigree showed that the population was dominated by only 2 familial groups. We did not find significant correlations between the relatedness and the extent of home range overlap or the straight-line distances between the home ranges' central points. These results suggest that the dynamics of kinship in this solitary felid may not differ from the random mating processes described in social carnivores. Although the chances of random mating could be limited to a few resident males and females, the presence of unrelated floaters may provide a "breeding buffer" that may prevent an increase of relatedness and likely inbreeding in the population. This system is likely to fail in preserving genetic diversity in small, highly isolated populations; therefore, restoring habitat connectivity is crucial to ensure sufficient immigration from neighboring populations.

Environmental DNA from Residual Saliva for Efficient Noninvasive Genetic Monitoring of Brown Bears (Ursus arctos)

Noninvasive genetic sampling is an important tool in wildlife ecology and management, typically relying on hair snaring or scat sampling techniques, but hair snaring is labor and cost intensive, and scats yield relatively low quality DNA. New approaches utilizing environmental DNA (eDNA) may provide supplementary, cost-effective tools for noninvasive genetic sampling. We tested whether eDNA from residual saliva on partially-consumed Pacific salmon (Oncorhynchus spp.) carcasses might yield suitable DNA quality for noninvasive monitoring of brown bears (Ursus arctos). We compared the efficiency of monitoring brown bear populations using both fecal DNA and salivary eDNA collected from partially-consumed salmon carcasses in Southeast Alaska. We swabbed a range of tissue types from 156 partially-consumed salmon carcasses from a midseason run of lakeshore-spawning sockeye (O. nerka) and a late season run of stream-spawning chum (O. keta) salmon in 2014. We also swabbed a total of 272 scats from the same locations. Saliva swabs collected from the braincases of salmon had the best amplification rate, followed by swabs taken from individual bite holes. Saliva collected from salmon carcasses identified unique individuals more quickly and required much less labor to locate than scat samples. Salmon carcass swabbing is a promising method to aid in efficient and affordable monitoring of bear populations, and suggests that the swabbing of food remains or consumed baits from other animals may be an additional cost-effective and valuable tool in the study of the ecology and population biology of many elusive and/or wide-ranging species.

Guidelines for MSAT and SNP panels that lead to high-quality data for genetic mark–recapture studies

Molecular markers with inadequate power to discriminate among individuals can lead to false recaptures (shadows), and inaccurate genotyping can lead to missed recaptures (ghosts), potentially biasing genetic mark–recapture estimates. We used simulations to examine the impact of microsatellite (MSAT) and single nucleotide polymorphism (SNP) marker-set size, allelic frequency, multitubes approaches, and sample matching protocols on shadow and ghost events in genetic mark–recapture studies, presenting guidance on the specifications for MSAT and SNP marker panels, and sample matching protocols necessary to produce high-quality data. Shadow events are controllable by increasing the number of markers or by selecting markers with high discriminatory power; reasonably sized marker sets (e.g., ≥9 MSATs or ≥32 SNPs) of moderate allelic diversity lead to low probabilities of shadow errors. Ghost events are more challenging to control and low allelic dropout or false-allele error rates produced high rates of erroneous mismatches in mark–recapture sampling. Fortunately, error-tolerant matching protocols, which use information from positively matching loci between comparisons of samples, and multitubes protocols to achieve consensus genotypes are effective at eliminating ghost events. We present a case study on Pacific walrus, Odobenus rosmarus divergens (Illiger, 1815), using simulation results to inform genetic marker choices.

Scale-dependent effects of a heterogeneous landscape on genetic differentiation in the Central American squirrel monkey (Saimiri oerstedii)

Landscape genetic studies offer a fine-scale understanding of how habitat heterogeneity influences population genetic structure. We examined population genetic structure and conducted a landscape genetic analysis for the endangered Central American Squirrel Monkey (Saimiri oerstedii) that lives in the fragmented, human-modified habitats of the Central Pacific region of Costa Rica. We analyzed non-invasively collected fecal samples from 244 individuals from 14 groups for 16 microsatellite markers. We found two geographically separate genetic clusters in the Central Pacific region with evidence of recent gene flow among them. We also found significant differentiation among groups of S. o. citrinellus using pairwise F_ST comparisons. These groups are in fragments of secondary forest separated by unsuitable “matrix” habitats such as cattle pasture, commercial African oil palm plantations, and human residential areas. We used an individual-based landscape genetic approach to measure spatial patterns of genetic variance while taking into account landscape heterogeneity. We found that large, commercial oil palm plantations represent moderate barriers to gene flow between populations, but cattle pastures, rivers, and residential areas do not. However, the influence of oil palm plantations on genetic variance was diminished when we restricted analyses to within population pairs, suggesting that their effect is scale-dependent and manifests during longer dispersal events among populations. We show that when landscape genetic methods are applied rigorously and at the right scale, they are sensitive enough to track population processes even in species with long, overlapping generations such as primates. Thus landscape genetic approaches are extremely valuable for the conservation management of a diverse array of endangered species in heterogeneous, human-modified habitats. Our results also stress the importance of explicitly considering the heterogeneity of matrix habitats in landscape genetic studies, instead of assuming that all matrix habitats have a uniform effect on population genetic processes.

Estimating Size and Trend of the North Interlake Woodland Caribou Population Using Fecal-DNA and Capture-Recapture Models

A critical step in recovery efforts for endangered and threatened species is the monitoring of population demographic parameters. As part of these efforts, we evaluated the use of fecal-DNA based capture–recapture methods to estimate population sizes and population rate of change for the North Interlake woodland caribou herd (Rangifer tarandus caribou), Manitoba, Canada. This herd is part of the boreal population of woodland caribou, listed as threatened under the federal Species at Risk Act (2003) and the provincial Manitoba Endangered Species Act (2006). Between 2004 and 2009 (9 surveys), we collected 1,080 fecal samples and identified 180 unique genotypes (102 females and 78 males). We used a robust design survey plan with 2 surveys in most years and analysed the data with Program MARK to estimate encounter rates (p), apparent survival rates (ϕ), rates of population change (λ), and population sizes (N). We estimated these demographic parameters for males and females and for 2 genetic clusters within the North Interlake. The population size estimates were larger for the Lower than the Upper North Interlake area and the proportion of males was lower in the Lower (33%) than the Upper North Interlake (49%). Population rate of change for the entire North Interlake area (2005–2009) using the robust design Pradel model was significantly <1.0 (λ = 0.90, 95% CI: 0.82–0.99) and varied between sex and area with the highest being for males in Lower North Interlake (λ = 0.98, 95% CI: 0.83–1.13) and the lowest being for females in Upper North Interlake (λ = 0.83, 95% CI: 0.69–0.97). The additivity of λ between sex and area is supported on the log scale and translates into males having a λ that is 0.09 greater than females and independent of sex, Lower North Interlake having a λ that is 0.06 greater than Upper North Interlake. Population estimates paralleled these declining trends, which correspond to trends observed in other fragmented populations of woodland caribou along the southern part of their range. The results of this study clearly demonstrate the applicability and success of non-invasive genetic sampling in monitoring populations of woodland caribou. © 2012 The Wildlife Society.

Genetic evidence for dispersal by both sexes in the Central American Squirrel Monkey, Saimiri oerstedii citrinellus

Sex-biased dispersal (SBD) is common in many vertebrates, including primates. However, dispersal patterns in New World primates may vary among closely related taxa or populations in different local environments. Here, we test for SBD in an endangered New World primate, the Central American Squirrel Monkey (Saimiri oerstedii citrinellus). Previous studies of behavioral ecology suggest predominantly female dispersal in S.o. oerstedii in the Southern Pacific region of Costa Rica. However, our genetic data do not support strongly female-biased dispersal in S.o. citrinellus in the Central Pacific region. Our tests for SBD using microsatellite data including comparisons of isolation-by-distance, AI(c) , and F(ST) values between males and females were not significant. Also, we found greater population genetic structure in mitochondrial markers than in microsatellite markers, indicative of predominantly male dispersal. We conclude that both sexes disperse in S.o. citrinellus, and that males probably disperse over longer distances. We discuss how spatial and temporal variation among local populations should be taken into account when studying dispersal patterns and especially sex bias.

Advancement to hair-sampling surveys of a medium-sized mammal: DNA-based individual identification and population estimation of a rare Australian marsupial, the spotted-tailed quoll (Dasyurus maculatus)

Context. Enumeration of cryptic/rare or widely distributed mammal species is exceedingly difficult for wildlife managers using standard survey methods. Individual identification via non-invasive hair-DNA methods offers great promise in extending the information available from hairs collected to survey for presence/absence of a species. However, surprisingly few wildlife studies have attempted this because of potential limitations with the field method and genetic samples. Aim. The applicability of hair DNA to identify individuals and estimate numbers was assessed for a rare, medium-sized Australian marsupial carnivore, the spotted-tailed quoll (Dasyurus maculatus). Methods. Hair samples were obtained remotely in the field with baited hair-sampling devices (known as handi-glaze hair tubes) that permit multiple visitations by individuals and species. A hierarchical approach developed and applied to the DNA extraction and PCR protocol, based on single and four pooled hairs of each collected sample, was used to assess genotype reliability (cross-species DNA mixing, allelic dropout and false allele errors) and enumerate the local study population. These results were compared against a concurrent live-cage trapping survey that was equivalent in scale and trap density to enable a rigorous evaluation of the efficiency and reliability of the DNA-based hair-sampling technique. Key results. Of the 288 hair devices deployed, 52 (18%) captured spotted-tailed quoll hair and the majority (90%) of these samples provided adequate DNA to genetically profile individuals at 10 microsatellite loci and a sexing marker. The hierarchical approach provided a feasible way to verify whether cross-species DNA mixing had occurred in the pooled-hair DNA extracts by comparing the results against the independent single-hair DNA extract, and assess genotyping reliability of both DNA concentrations. Fewer individuals were detected using hair-sampling (n = 16) than live-trapping (n = 21), despite hair-sampling occurring over a longer period (40 cf. 26 nights). Conclusions. The population-level information gained by the DNA-based technologies adds considerable value to the remote hair-sampling method which up until the present study had been used to detect the presence of medium-sized mammals. Our study demonstrated the utility of the DNA-based hair-sampling method to identify spotted-tailed quoll individuals and for surveying local populations. However, improvements to the hair-sampling method, such as increasing the density of stations or the provision of a food reward, should be considered to enhance sampling efficiency to allow the enumeration of local populations. Implications. The use of remote hair-sampling devices that permit multiple visitations and do not require daily collection can be feasible and reliable to genetically identify individuals when coupled with appropriate strategies. By combining single- and pooled-hair DNA extracts, a good compromise between laboratory efficiency and data integrity is afforded.

Review of capture-recapture methods applicable to noninvasive genetic sampling

The use of noninvasive genetic sampling to identify individual animals for capture-recapture studies has become widespread in the past decade. Strong emphasis has been placed on the field protocols and genetic analyses with fruitful results. Little attention has been paid to the capture-recapture application for this specific type of data beyond stating the effects of assumption violations. Here, we review the broad class of capture-recapture methods that are available for use with DNA-based capture-recapture data, noting the array of biologically interesting parameters such as survival, emigration rates, state transition rates and the finite rate of population change that can be estimated from such data. We highlight recent developments in capture-recapture theory specifically designed for noninvasive genetic sampling data.

Noninvasive genotyping and Mendelian analysis of microsatellites in African savannah elephants

We obtained fresh dung samples from 202 (133 mother-offspring pairs) savannah elephants (Loxodonta africana) in Samburu, Kenya, and genotyped them at 20 microsatellite loci to assess genotyping success and errors. A total of 98.6% consensus genotypes was successfully obtained, with allelic dropout and false allele rates at 1.6% (n = 46) and 0.9% (n = 37) of heterozygous and total consensus genotypes, respectively, and an overall genotyping error rate of 2.5% based on repeat typing. Mendelian analysis revealed consistent inheritance in all but 38 allelic pairs from mother-offspring, giving an average mismatch error rate of 2.06%, a possible result of null alleles, mutations, genotyping errors, or inaccuracy in maternity assignment. We detected no evidence for large allele dropout, stuttering, or scoring error in the dataset and significant Hardy-Weinberg deviations at only two loci due to heterozygosity deficiency. Across loci, null allele frequencies were low (range: 0.000-0.042) and below the 0.20 threshold that would significantly bias individual-based studies. The high genotyping success and low errors observed in this study demonstrate reliability of the method employed and underscore the application of simple pedigrees in noninvasive studies. Since none of the sires were included in this study, the error rates presented are just estimates.