An evaluation of field and noninvasive genetic methods for estimating Eurasian otter population size

Low signs of territorial behavior in the Eurasian otter during low-water conditions in a Mediterranean river

The Eurasian otter Lutra lutra is a territorial semi-aquatic carnivore usually found at low densities in rivers, coastal areas, and wetlands. Its diet is based on prey associated with aquatic environments. Mediterranean rivers are highly seasonal, and suffer reduced flow during the summer, resulting in isolated river sections (pools) that sometimes can be left with a minimal amount of water, leading to concentrations of food for otters. To our knowledge, this process, which was known to field naturalists, has not been accurately described, nor have otter densities been estimated under these conditions. In this study, we describe the population size and movements of an aggregation of otters in an isolated pool in the Guadiana River in the Tablas de Daimiel National Park (central Spain), which progressively dried out during the spring-summer of 2022, in a context of low connectivity due to the absence of circulating water in the Guadiana and Gigüela rivers. Using non-invasive genetic sampling of 120 spraints collected along 79.4 km of sampling transects and spatial capture-recapture methods, we estimated the otter density at 1.71 individuals/km of river channel length (4.21 individuals/km2) in a progressively drying river pool, up to five times higher than previously described in the Iberian Peninsula. The movement patterns obtained with the spatial capture-recapture model are not quite different from those described in low density, which seems to indicate a wide home range overlap, with low signs of territoriality.

Identification of three Asian otter species (Aonyx cinereus, Lutra sumatrana, and Lutrogale perspicillata) using a novel noninvasive PCR-RFLP analysis

Four species of otters occur in tropical Asia, and all face multiple threats to their survival. Studies of distribution and population trends of these otter species in Asia, where they occur sympatrically, are complicated by their elusive nature and difficulties with reliable identification of species in field surveys. In Malaysia, only three species, the smooth-coated otter, Asian small-clawed otter, and hairy-nosed otter have been reliably reported as residents. We designed a replicable and cost-efficient PCR-RFLP protocol to identify these three species. Using published reference sequences of mitochondrial regions, we designed and tested three PCR-RFLP protocols on DNA extracted from reference samples and 33 spraints of wild otters collected along the North Central Selangor Coast of Malaysia. We amplified and sequenced two fragments (450 and 200 bp) of the mt D-loop region and a 300-bp fragment of the mt ND4 gene using primer sets TanaD, TanaD-Mod, and OTR-ND4, respectively. Amplification products were digested with restriction enzymes to generate species-specific RFLP profiles. We analyzed the costs of all three protocols and compared these with the costs of sequencing for species identification. Amplification success was highest for the smallest PCR product, with the TanaD-Mod primer amplifying DNA from all 33 spraints. TanaD and OTR-ND4 primers amplified DNA from 60.6% and 63.6% spraints, respectively. PCR products of TanaD-Mod provided the expected species-specific RFLP profile for 32 (97%) of the spraints. PCR products of OTR-ND4 provided the expected RFLP profile for all 21 samples that amplified, but TanaD produced spurious bands and inconsistent RFLP profiles. The OTR-ND4 primer-enzyme protocol was the least expensive (437 USD) for processing 100 samples, followed by TanaD-Mod (455 USD). We suggest the use of both OTR-ND4 and TanaD-Mod protocols that show potential for highly efficient and reliable species identification from noninvasive genetic sampling of three Asian otter species. We expect our novel noninvasive PCR-RFLP analysis methods to facilitate population monitoring, ecological and behavioral studies on otters in tropical and subtropical Asia.

A Noninvasive Genetic Insight into the Spatial and Social Organization of an Endangered Population of the Eurasian Otter (Lutra lutra, Mustelidae, Carnivora)

The Eurasian otter is endangered in Italy, only surviving in southern river basins. The spatial and social structure of a population living at the border of the current range was explored through a noninvasive genetic study along 174 km of the Sangro river. Sampling was conducted in 2011 and 2012, collecting spraints and anal jellies at 62 marking sites. Samples were successfully genotyped at 13 nuclear microsatellites and the ZFX/ZFY locus for molecular sexing, resulting in 14 distinct genotypes (4 females, 2 possible females, 8 males), from 35 marking sites. Mean captures/recaptures rate was 3.8 captures/individual, with males being recaptured more frequently than females. Spatial overlap among individuals was analyzed through a linear regression model fitted against sibship categories and sex pairing. Nine out of the fourteen genotyped individuals belonged to three full-sib clusters, while five individuals had no full-sibs in the population. Full-sibs overlapped more than half-sibs, while male–male pairs showed significantly higher spatial overlap than both male–female and female–female pairs. Estimated mean density was 0.152 otters/km and 2.4 individuals/10 × 10 km grid cell. Accordingly, the 3440 grid cells of otter occurrence in Italy could likely host about 8000 otters, suggesting the current population has become larger than the minimum viable population size.

Noninvasive Genetic Assessment Is an Effective Wildlife Research Tool When Compared with Other Approaches

Wildlife research has been indispensable for increasing our insight into ecosystem functioning as well as for designing effective conservation measures under the currently high rates of biodiversity loss. Genetic and genomic analyses might be able to yield the same information on, e.g., population size, health, or diet composition as other wildlife research methods, and even provide additional data that would not be possible to obtain by alternative means. Moreover, if DNA is collected non-invasively, this technique has only minimal or no impact on animal welfare. Nevertheless, the implementation rate of noninvasive genetic assessment in wildlife studies has been rather low. This might be caused by the perceived inefficiency of DNA material obtained non-invasively in comparison with DNA obtained from blood or tissues, or poorer performance in comparison with other approaches used in wildlife research. Therefore, the aim of this review was to evaluate the performance of noninvasive genetic assessment in comparison with other methods across different types of wildlife studies. Through a search of three scientific databases, 113 relevant studies were identified, published between the years 1997 and 2020. Overall, most of the studies (94%) reported equivalent or superior performance of noninvasive genetic assessment when compared with either invasive genetic sampling or another research method. It might be also cheaper and more time-efficient than other techniques. In conclusion, noninvasive genetic assessment is a highly effective research approach, whose efficacy and performance are likely to improve even further in the future with the development of optimized protocols.

Factors influencing genotyping success and genotyping error rate of Eurasian otter (Lutra lutra) faeces collected in temperate Central Europe

The use of non-invasively collected DNA source material for genetic and genomic applications is usually characterized by low target DNA concentration and quality, genotyping errors and cost-intensive lab procedures. However, for otters (Lutrinae) as elusive species of conservation concern, genetic non-invasive sampling has become an important tool to study their ecology and demography. To increase cost-efficiency of monitoring programmes and to promote the expansion of genomic approaches to non-invasive samples, we aimed to refine sample collection and preparation. Therefore, we examined the effects of intrinsic sample characteristics (including diet), environmental conditions in the field and sample treatment in the molecular laboratory on the success of genotyping and allelic dropout (ADO) rates using microsatellite markers in 1970 fresh Eurasian otter (Lutra lutra) scats. Using fresh samples only, we probably eliminated one of the most important impediments of genotyping DNA from otter faecal samples beforehand. But, we observed higher genotyping success and lower ADO rates for anal glad secretions and faecal samples containing high proportions of mucus. Moist conditions during sample collection may promote DNA degradation and PCR inhibition, leading to decreased genotyping success rates. ADO was further affected by the type of extraction kit. However, a high proportion of variance remaining unexplained by our models implied that additional parameters were acting (amount of PCR inhibitors, non-uniform distribution of intestinal cells, efficiency of PCRs, specific microclimate at marking sites). We summarized influential factors maximizing genotyping quality of otter scats and give recommendations for sample collection, storage and DNA extraction based on our results and current literature.

Marking behaviour and census of Eurasian otters (Lutra lutra) in riverine habitats: what can scat abundances and non-invasive genetic sampling tell us about otter numbers?

Growing human-wildlife conflicts and legal conservation obligations increased the need for precise information on Eurasian otter (Lutra lutra) population parameters for species status assessment and wildlife management measures. Scat surveys have become the method of choice to monitor species distribution range, abundance and habitat use. Although methodological concerns exist, scat abundance is often used as main indicator for otter population estimates and trends. To evaluate whether scat counts serve as good proxy for otter densities in linear stream habitats, we modelled the relationship between old/fresh scat abundance and otter numbers on two spatial scales, including also seasonal effects. Actual otter densities and marking behaviour were ascertained by genotyping of otter faeces collected at 218 marking sites along 132.6 km of four salmonid streams. Otter densities in our study areas ranged from 0.16 to 0.28 otters per stream kilometre. The age of scats and the level of spatial scale were determining factors when evaluating the suitability of scat abundance as index for otter densities. Covering large parts of an otter’s territory, fresh scat abundance increased with otter density, irrespectively of season. On the spatial scale of single marking sites, the relationship was not well supported, and no relationship could be found when using old scats in the models. Otter marking behaviour and differences in marking site use intensity, as well as seasonal differences in traceability and accumulation of old scats were discussed to bias the relationship between scat abundance and otter numbers.

Performance of detection dogs and visual searches for scat detection and discrimination amongst related species with identical diets

Ecology often faces the problem that many threatened species are highly elusive but also conflict-laden. Thus, proper monitoring data are inevitable for their conservation and management. Indirect monitoring through scats is frequently used for such species, but scats of related species or species with similar diet are often visually indistinguishable. Since genetic methods for species identification are time-consuming and cost-intensive, a verification of the target species beforehand would be extremely beneficial in reducing effort to the analysis of the target species only. Such species discrimination could be provided through species-specific scat detection dogs. Therefore, we evaluated the reliability of species-specific scat detection dogs for two mustelid species feeding on identical diets: the Eurasian otter (Lutra lutra) and the American mink (Neovison vison), both of which are conflict-laden and increasing their populations and distribution ranges in central Europe. Their scats resemble each other in morphology and odour, exacerbating the differentiation even for experts. To evaluate whether detection dogs can reliably discriminate between related species feeding on similar diets and if their use would be beneficial, we tested their abilities against those of humans. We first proved that scat characteristics are not statistically different between species. Likewise, visual species identification through people with different experience levels was only partly successful. Experts showed higher average accuracy (0.89) than non-experts (0.72 and below), but detection dogs (4 dogs) were able to discriminate otter and mink scats under laboratory conditions with an accuracy of 0.95. Moreover, otter scat detection dogs found up to four times more scat samples in the field, were twice as fast as human searchers and found an almost equal number of scats with different characteristics, while humans mostly found older and larger scats placed on hotspots. We conclude that using detection dogs for species identity will allow subsequent laboratory analyses to be species-specific and avoid spending time and money on laboratory work of the wrong species. It also provides more precise and unbiased information about the target species.

Non-invasive genetic censusing and monitoring of primate populations

Knowing the density or abundance of primate populations is essential for their conservation management and contextualizing socio-demographic and behavioral observations. When direct counts of animals are not possible, genetic analysis of non-invasive samples collected from wildlife populations allows estimates of population size with higher accuracy and precision than is possible using indirect signs. Furthermore, in contrast to traditional indirect survey methods, prolonged or periodic genetic sampling across months or years enables inference of group membership, movement, dynamics, and some kin relationships. Data may also be used to estimate sex ratios, sex differences in dispersal distances, and detect gene flow among locations. Recent advances in capture-recapture models have further improved the precision of population estimates derived from non-invasive samples. Simulations using these methods have shown that the confidence interval of point estimates includes the true population size when assumptions of the models are met, and therefore this range of population size minima and maxima should be emphasized in population monitoring studies. Innovations such as the use of sniffer dogs or anti-poaching patrols for sample collection are important to ensure adequate sampling, and the expected development of efficient and cost-effective genotyping by sequencing methods for DNAs derived from non-invasive samples will automate and speed analyses.

Fine-scale population genetic structure of the Bengal tiger (Panthera tigris tigris) in a human-dominated western Terai Arc Landscape, India

Despite massive global conservation strategies, tiger populations continued to decline until recently, mainly due to habitat loss, human-animal conflicts, and poaching. These factors are known to affect the genetic characteristics of tiger populations and decrease local effective population sizes. The Terai Arc Landscape (TAL) at the foothills of the Himalaya is one of the 42 source sites of tigers around the globe. Therefore, information on how landscape features and anthropogenic factors affect the fine-scale spatial genetic structure and variation of tigers in TAL is needed to develop proper management strategies for achieving long-term conservation goals. We document, for the first time, the genetic characteristics of this tiger population by genotyping 71 tiger samples using 13 microsatellite markers from the western region of TAL (WTAL) of 1800 km2. Specifically, we aimed to estimate the genetic variability, population structure, and gene flow. The microsatellite markers indicated that the levels of allelic diversity (MNA = 6.6) and genetic variation (Ho = 0.50, HE = 0.64) were slightly lower than those reported previously in other Bengal tiger populations. We observed moderate gene flow and significant genetic differentiation (FST= 0.060) and identified the presence of cryptic genetic structure using Bayesian and non-Bayesian approaches. There was low and significantly asymmetric migration between the two main subpopulations of the Rajaji Tiger Reserve and the Corbett Tiger Reserve in WTAL. Sibship relationships indicated that the functionality of the corridor between these subpopulations may be retained if the quality of the habitat does not deteriorate. However, we found that gene flow is not adequate in view of changing land use matrices. We discuss the need to maintain connectivity by implementing the measures that have been suggested previously to minimize the level of human disturbance, including relocation of villages and industries, prevention of encroachment, and banning sand and boulder mining in the corridors.

Individual identification of Eurasian otters (Lutra lutra) in South Korea (Sincheon River, Daegu) by microsatellite markers

The objective of this study was to determine the number of Eurasian otters (Lutra lutra) that occupied the Sincheon River in Daegu, South Korea. Twenty-seven spraints collected from February to May 2016 at four sites (Jangam Bridge approximately 6.1 km from the Gachang Dam, Docheong Bridge approximately 13.5 km, Chimsan Bridge approximately 15.1 km and Nogoek Bridge approximately 18 km) along the Sincheon River (approximately 27.06 km) were analyzed using 12 microsatellite markers. The analyses resulted in the identification of 16 (59.3%) individual Eurasian otters in the Sincheon River based on the 27 spraints. Of the 16 individual Eurasian otters, seven were male, and nine were female. Groups were centered at the Jangam Bridge (3 males and 2 females), Chimsan Bridge (2 males and 3 females) and Docheong Bridge (2 males and 4 females). Thus, the 16 Eurasian otters formed three genetically related groups in each sampling area. The number of alleles per locus varied from three to seven, with a mean value of 5.08 alleles.

Non-Invasive Genetic Mark-Recapture as a Means to Study Population Sizes and Marking Behaviour of the Elusive Eurasian Otter (Lutra lutra)

Quantifying population status is a key objective in many ecological studies, but is often difficult to achieve for cryptic or elusive species. Here, non-invasive genetic capture-mark-recapture (CMR) methods have become a very important tool to estimate population parameters, such as population size and sex ratio. The Eurasian otter (Lutra lutra) is such an elusive species of management concern and is increasingly studied using faecal-based genetic sampling. For unbiased sex ratios or population size estimates, the marking behaviour of otters has to be taken into account. Using 2132 otter faeces of a wild otter population in Upper Lusatia (Saxony, Germany) collected over six years (2006-2012), we studied the marking behaviour and applied closed population CMR models accounting for genetic misidentification to estimate population sizes and sex ratios. We detected a sex difference in the marking behaviour of otters with jelly samples being more often defecated by males and placed actively exposed on frequently used marking sites. Since jelly samples are of higher DNA quality, it is important to not only concentrate on this kind of samples or marking sites and to invest in sufficiently high numbers of repetitions of non-jelly samples to ensure an unbiased sex ratio. Furthermore, otters seemed to increase marking intensity due to the handling of their spraints, hence accounting for this behavioural response could be important. We provided the first precise population size estimate with confidence intervals for Upper Lusatia (for 2012: N = 20 ± 2.1, 95% CI = 16-25) and showed that spraint densities are not a reliable index for abundances. We further demonstrated that when minks live in sympatry with otters and have comparably high densities, a non-negligible number of supposed otter samples are actually of mink origin. This could severely bias results of otter monitoring if samples are not genetically identified.

Genome-wide survey and analysis of microsatellites in giant panda (Ailuropoda melanoleuca), with a focus on the applications of a novel microsatellite marker system

Background

The giant panda (Ailuropoda melanoleuca) is a critically endangered species endemic to China. Microsatellites have been preferred as the most popular molecular markers and proven effective in estimating population size, paternity test, genetic diversity for the critically endangered species. The availability of the giant panda complete genome sequences provided the opportunity to carry out genome-wide scans for all types of microsatellites markers, which now opens the way for the analysis and development of microsatellites in giant panda.

Results

By screening the whole genome sequence of giant panda in silico mining, we identified microsatellites in the genome of giant panda and analyzed their frequency and distribution in different genomic regions. Based on our search criteria, a repertoire of 855,058 SSRs was detected, with mono-nucleotides being the most abundant. SSRs were found in all genomic regions and were more abundant in non-coding regions than coding regions. A total of 160 primer pairs were designed to screen for polymorphic microsatellites using the selected tetranucleotide microsatellite sequences. The 51 novel polymorphic tetranucleotide microsatellite loci were discovered based on genotyping blood DNA from 22 captive giant pandas in this study. Finally, a total of 15 markers, which showed good polymorphism, stability, and repetition in faecal samples, were used to establish the novel microsatellite marker system for giant panda. Meanwhile, a genotyping database for Chengdu captive giant pandas (n = 57) were set up using this standardized system. What’s more, a universal individual identification method was established and the genetic diversity were analysed in this study as the applications of this marker system.

Conclusion

The microsatellite abundance and diversity were characterized in giant panda genomes. A total of 154,677 tetranucleotide microsatellites were identified and 15 of them were discovered as the polymorphic and stable loci. The individual identification method and the genetic diversity analysis method in this study provided adequate material for the future study of giant panda.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1268-z) contains supplementary material, which is available to authorized users.

The risks of learning: confounding detection and demographic trend when using count-based indices for population monitoring

Theory recognizes that a treatment of the detection process is required to avoid producing biased estimates of population rate of change. Still, one of three monitoring programmes on animal or plant populations is focused on simply counting individuals or other fixed visible structures, such as natal dens, nests, tree cavities. This type of monitoring design poses concerns about the possibility to respect the assumption of constant detection, as the information acquired in a given year about the spatial distribution of reproductive sites can provide a higher chance to detect the species in subsequent years. We developed an individual-based simulation model, which evaluates how the accumulation of knowledge about the spatial distribution of a population process can affect the accuracy of population growth rate estimates, when using simple count-based indices. Then, we assessed the relative importance of each parameter in affecting monitoring performance. We also present the case of wolverines (Gulo gulo) in southern Scandinavia as an example of a monitoring system with an intrinsic tendency to accumulate knowledge and increase detectability. When the occupation of a nest or den is temporally autocorrelated, the monitoring system is prone to increase its knowledge with time. This happens also when there is no intensification in monitoring effort and no change in the monitoring conditions. Such accumulated knowledge is likely to increase detection probability with time and can produce severe bias in the estimation of the rate and direction of population change over time. We recommend that a systematic sampling of the population process under study and an explicit treatment of the underlying detection process should be implemented whenever economic and logistical constraints permit, as failure to include detection probability in the estimation of population growth rate can lead to serious bias and severe consequences for management and conservation.

Successful carnivore identification with faecal DNA across a fragmented Amazonian landscape

The use of scat surveys to obtain DNA has been well documented in temperate areas, where DNA preservation may be more effective than in tropical forests. Samples obtained in the tropics are often exposed to high humidity, warm temperatures, frequent rain and intense sunlight, all of which can rapidly degrade DNA. Despite these potential problems, we demonstrate successful mtDNA amplification and sequencing for faeces of carnivores collected in tropical conditions and quantify how sample condition and environmental variables influence the success of PCR amplification and species identification. Additionally, the feasibility of genotyping nuclear microsatellites from jaguar (Panthera onca) faeces was investigated. From October 2007 to December 2008, 93 faecal samples were collected in the southern Brazilian Amazon. A total of eight carnivore species was successfully identified from 71% of all samples obtained. Information theoretic analysis revealed that the number of PCR attempts before a successful sequence was an important negative predictor across all three responses (success of species identification, success of species identification from the first sequence and PCR amplification success), whereas the relative importance of the other three predictors (sample condition, season and distance from forest edge) varied between the three responses. Nuclear microsatellite amplification from jaguar faeces had lower success rates (15-44%) compared with those of the mtDNA marker. Our results show that DNA obtained from faecal samples works efficiently for carnivore species identification in the Amazon forest and also shows potential for nuclear DNA analysis, thus providing a valuable tool for genetic, ecological and conservation studies.

Non-invasive genetic monitoring of wild central chimpanzees

BACKGROUND

An assessment of population size and structure is an important first step in devising conservation and management plans for endangered species. Many threatened animals are elusive, rare and live in habitats that prohibit directly counting individuals. For example, a well-founded estimate of the number of great apes currently living in the wild is lacking. Developing methods to obtain accurate population estimates for these species is a priority for their conservation management. Genotyping non-invasively collected faecal samples is an effective way of evaluating a species' population size without disruption, and can also reveal details concerning population structure.

METHODOLOGY/PRINCIPAL FINDINGS

We opportunistically collected wild chimpanzee faecal samples for genetic capture-recapture analyses over a four-year period in a 132 km(2) area of Loango National Park, Gabon. Of the 444 samples, 46% yielded sufficient quantities of DNA for genotyping analysis and the consequent identification of 121 individuals. Using genetic capture-recapture, we estimate that 283 chimpanzees (range: 208-316) inhabited the research area between February 2005 and July 2008. Since chimpanzee males are patrilocal and territorial, we genotyped samples from males using variable Y-chromosome microsatellite markers and could infer that seven chimpanzee groups are present in the area. Genetic information, in combination with field data, also suggested the occurrence of repeated cases of intergroup violence and a probable group extinction.

CONCLUSIONS/SIGNIFICANCE

The poor amplification success rate resulted in a limited number of recaptures and hence only moderate precision (38%, measured as the entire width of the 95% confidence interval), but this was still similar to the best results obtained using intensive nest count surveys of apes (40% to 63%). Genetic capture-recapture methods applied to apes can provide a considerable amount of novel information on chimpanzee population size and structure with minimal disturbance to the animals and represent a powerful complement to traditional field-based methods.