Isolation and characterization of tetramicrosatellite DNA markers in the Eurasian otter (Lutra lutra)

Eight new tetramicrosatellite loci for Eurasian otter (Lutra lutra) were designed. Polymorphism of these eight loci in 29 otter individuals was tested. The results indicated that the allele numbers of each of loci ranged from three to five and the observed heterozygosity from 0.483 to 0.828. These new loci can be useful for population genetic research on otters and help improve the resolution of individual identification using noninvasive method.     

Genetic diversity in the Eurasian otter, Lutra lutra, in Scotland. Evidence from microsatellite polymorphism

The relationship between microsatellite diversity and geographical fragmentation and isolation was studied in Scottish populations of the Eurasian otter, Lutra lutra. The geographic range of the study encompassed isolated archipelagos, islands adjacent to the Scottish mainland and both fragmented and continuous mainland populations. Tissue samples of 496 individuals from across Scotland were assayed for polymorphism at ten microsatellites. The isolation of populations on Shetland, and to a lesser degree on Orkney, was associated with reduced levels of microsatellite diversity. Most of the remaining island and fragmented mainland populations contained levels of microsatellite diversity similar to the high levels observed in die continuous mainland populations. Unexpectedly, both island and continuous mainland populations showed similar rates of departures from mutation-drift equilibrium. Such departures could have arisen from a variety of local demographic processes besides population bottlenecks. Gene flow appeared to be a major factor maintaining microsatellite diversity in all of these populations except the one on Shedand.     

Spatially restricted gene flow and reduced microsatellite polymorphism in the Eurasian otter Lutra lutra in Britain

Although gene flow and population fragmentationwill often have opposed effects on geneticstructure, their actual effects on many elusiveanimal species are unknown. We assessed sucheffects in British populations of the Eurasianotter Lutra lutra by analysis ofgenotypes consisting of 12 microsatellites from618 carcasses representing the period 1982–1998. Spatial patterns of genetic subdivisionand levels of polymorphism in the continuouspopulation in Scotland were estimated. Theseresults were used to infer patterns of geneflow in Scottish otters and assess theinfluence of fragmentation on the geneticstructure of otters in Wales and SW England.The latter showed no higher genetic divergencethan expected given the degree of isolation bydistance found in the Scottish population, andtheir distributions of microsatellite allelesizes provided no evidence for populationbottlenecks. Nonetheless, otters in southernBritain contained significantly lower levels ofmicrosatellite polymorphism than otters inScotland, and the population in the westernpeninsula of SW England was geneticallydistinct. These results suggested that thegenetic structure of the Scottish population isdue more to restricted contemporary gene flowthan to historical fluctuations insubpopulation size, and that the geneticstructure of the southern British populationsis due more to small historical effective sizesthan to recent declines. If spatiallyrestricted gene flow is typical of all Eurasianotter populations then data on dispersal shouldbe taken into account when sitting protectedareas for this species.     

Genetic variability and size estimates of the Eurasian otter (Lutra lutra) population in the Bohemian Forest Ecosystem

Even though recent years have shown a slow recovery of the Eurasian otter (Lutra lutra) populations from their previous lows, the species is still highly endangered in most parts of its European distribution range. Surprisingly, only a few studies have so far assessed the species’ genetic variability and population density, and they have mostly been carried out only in small territories. In Germany, most otter populations live in protected areas whose management urgently needs data on population sizes and densities as well as on genetic variability of the species under their custody. Thus, we analyzed genetic variability and assessed size and density of the otter population in the Bohemian Forest Ecosystem, an area that had not been included in the few previous molecular studies. The study area comprised of 1500 km², divided into fifteen squares of 10 × 10 km², each of which was sampled in two collection periods. Overall we collected 261 fecal samples (spraints), of which 60 (23%) could be genotyped at least at eight microsatellite loci, yielding 38 distinct otter genotypes. The low genotyping success rate was the result of high ambient temperature at the time of sampling rather than that of high humidity. The population did not show signs of a past bottleneck, indicating a small yet stable population size. Population size was estimated to be 118 (CI_95% 64–163) individuals, with a mean density of 1 animal per 8.5 km² or 3.1 km river length. Our results imply that hunting, requested by local fishpond owners, should remain banned to avoid a decline in (effective) population size.     

Mitochondrial genetic diversity and structure of the European otter (Lutra lutra) in Britain

The European otter (Lutra lutra) is a focus for conservation efforts throughout Europe due to a population decline in recent decades and because of its importance as a biological indicator of the health of rivers and waterways. The aim of this study was to aid the conservation of this species by adding genetic information from samples originating in the United Kingdom (UK), to help build up a picture of the phylogeographic structure of the European otter throughout Europe. This was done by a comparison of 299 base pairs of the mitochondrial DNA control region. Four haplotypes were identified in the UK, one of which has not been found outside the west of the UK in the wild, and one of which was unique. Populations in the UK, and in particular the west were shown to have a higher haplotype diversity than previously found for the European otter in Europe (h = 0.7338 for the 58 UK otters sampled in this study) and an overall nucleotide diversity of π = 0.003. The western UK population was shown to have a high level of genetic distinctiveness. We discuss possible contributory population processes, the importance of the western UK population for the future conservation of the species and comment on future conservation strategies.     

Individual identification and sex determination of Eurasian otters (Lutra lutra) in Daegu city based on genetic analysis of otter spraint

The Eurasian otter, Lutra lutra, is a well known endangered species in South Korea that experienced rapid population decreases through poaching and industrialization until the 1980’s. To evaluate the genetic diversity and the existing number of otters recently found in Daegu City, 81 fecal samples collected from the Gumho River and Shincheon stream were subjected to DNA extraction for sex determination and genetic analysis using nuclear genetic markers. Individual identification and relatedness between individuals were detemined by genotypic data using twelve microsatellite loci, and sex identification was also determined based on sequence variation of the zinc finger protein gene on sex chromosomes. Our results showed that at least seven otter individuals were identified and the kinship relationships of seven individual pairs were determined. It was concluded that otters distributed widely in Daegu City have moderate levels of genetic diversity, and close monitoring of the small-sized otter population is necessary to promote successful settlement of the otters in the area.     

Development of novel real‐time TaqMan® PCR assays for the species and sex identification of otter (Lutra lutra) and their application to noninvasive genetic monitoring

Developing strategies to maintain biodiversity requires baseline information on the current status of each individual species. The development of genetic techniques and their application to noninvasively collected samples have the potential to yield information on the structure of elusive animal populations and so are important tools in conservation management. Using DNA isolated from faecal samples can be challenging owing to low quantity and quality. This study, however, presents the development of novel real‐time polymerase chain reaction assays using fluorescently labelled TaqMan^® MGB probes enabling species and sex identification of Eurasian otter (Lutra lutra) spraints (faeces). These assays can also be used in determining an optimum microsatellite panel and can be employed as cost‐saving screening tools for downstream genetic testing including microsatellite genotyping and haplotype analysis. The techniques are shown to work efficiently with L. lutra DNA isolated from tissue, hair, spraint, blood and anal jelly samples.     

A method for estimating population sex ratio for sage‐grouse using noninvasive genetic samples

Population sex ratio is an important metric for wildlife management and conservation, but estimates can be difficult to obtain, particularly for sexually monomorphic species or for species that differ in detection probability between the sexes. Noninvasive genetic sampling (NGS) using polymerase chain reaction (PCR) has become a common method for identifying sex from sources such as hair, feathers or faeces, and is a potential source for estimating sex ratio. If, however, PCR success is sex‐biased, naively using NGS could lead to a biased sex ratio estimator. We measured PCR success rates and error rates for amplifying the W and Z chromosomes from greater sage‐grouse (Centrocercus urophasianus) faecal samples, examined how success and error rates for sex identification changed in response to faecal sample exposure time, and used simulation models to evaluate precision and bias of three sex assignment criteria for estimating population sex ratio with variable sample sizes and levels of PCR replication. We found PCR success rates were higher for females than males and that choice of sex assignment criteria influenced the bias and precision of corresponding sex ratio estimates. Our simulations demonstrate the importance of considering the interplay between the sex bias of PCR success, number of genotyping replicates, sample size, true population sex ratio and accuracy of assignment rules for designing future studies. Our results suggest that using faecal DNA for estimating the sex ratio of sage‐grouse populations has great potential and, with minor adaptations and similar marker evaluations, should be applicable to numerous species.     

Genetic structure of Eurasian otter (Lutra lutra,Carnivora: Mustelidae) populations from the western Baltic sea region and its implications for the recolonization of north‐western Germany

We analysed 229 Eurasian otters from eastern and north‐western Germany, Denmark and southern Sweden based on sequences of the mtDNA control region and genotypes at 12 polymorphic nuclear microsatellite loci. The main focus of the study lay on the north‐west German otters from Schleswig‐Holstein, which represent a newly established and expanding population recolonizing a formerly inhabited region, thereby closing the distributional gap between the large eastern population and the long‐isolated and genetically depleted Danish population. As found before in this species, mtDNA variability was very low but we identified a hitherto unknown haplotype in Sweden. Expected heterozygosities were between 0.46 and 0.69 and thus within the range known from the literature. There were only weak signs of a founder effect in the Schleswig‐Holstein otters with respect to allelic diversity (but not heterozygosity). Nevertheless, there was a statistically significant bottleneck signal based on deviations from mutation‐drift equilibrium in Schleswig‐Holstein. All statistical approaches (amova s, factorial correspondence analysis, assignment tests and Bayesian structure analysis) unequivocally showed that north‐western Germany has so far been predominantly recolonized by otters of east German origin, but we also found evidence of admixture through immigration from Denmark. Both the Danish and the north‐west German otter population will benefit from further exchange in the wake of the ongoing range expansion.     

Lessons from the use of non-invasive genetic sampling as a way to estimate Eurasian otter population size and sex ratio

Given the difficulties in establishing population parameters of elusive animals in the wild by traditional methods, such as trapping, much attention has been given in recent years to non-invasive genetic sampling. Our work compared estimates of population size and sex ratio derived from genetic sampling with the known number and sex of animals released during an otter reintroduction and reports on the pitfalls and opportunities that may be encountered in studies of this kind. This study makes use of 121 samples of otter spraints (faeces) collected over 7 months during a reintroduction in the Upper Thames (UK) where a total of 17 otters was released in two consecutive phases. Spraints were processed with a multiple tubes approach and seven microsatellites were used. Of all collected samples, 19 % were complete for at least five loci, the minimum required for discrimination between individuals. Six out of nine of the otters that were released in the first phase were detected, four males and two females, while none of the otters released in the second phase was detected probably due to a combination of sampling pitfalls and otter behaviour. In particular, the specific sex (mostly females) and dominance composition (lower) of the individuals in the second release group may explain our failure to detect individuals in this group. Taken together, our results add further evidence that genetic sampling approaches represent a potentially accurate and non-invasive route to census populations of otters but that the sampling design should take into account factors like the sex ratio and dominance composition of the population in order to maximise detection and minimise error.     

Diet composition of the Eurasian otter Lutra lutra in different freshwater habitats of temperate Europe: a review and meta‐analysis

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Factors affecting the amount of genomic DNA extracted from ape faeces and the identification of an improved sample storage method

Abstract Genetic analysis using noninvasively collected samples such as faeces continues to pose a formidable challenge because of unpredictable variation in the extent to which usable DNA is obtained. We investigated the influence of multiple variables on the quantity of DNA extracted from faecal samples from wild mountain gorillas and chimpanzees. There was a small negative correlation between temperature at time of collection and the amount of DNA obtained. Storage of samples either in RNAlater solution or dried using silica gel beads produced similar results, but significantly higher amounts of DNA were obtained using a novel protocol that combines a short period of storage in ethanol with subsequent desiccation using silica.     

Mating frequency, genetic structure, and sex ratio in the intermorphic female producing ant species Myrmecina nipponica

1. Myrmecina nipponica has two types of colonies: a queen colony type, in which the reproductive females are queens and new colonies are made by independent founding, and an intermorphic female colony type, in which reproductive females belong to a wingless intermediate morphology between queen and worker, and where colonies multiply through colonial budding. 2. The mating frequencies of reproductive females in both types indicate monoandry. The relatedness among nestmates in both types was almost 0.75, however relatedness between mother and daughter in intermorphic female colonies was slightly higher than that of queen colonies. 3. The sex ratio (corrected investment female ratio) was 0.70 at the population level, suggesting that the sex ratio is controlled by workers in this species, however the ratio differed greatly between the two types of colonies. Queen colonies (n = 37) had a female‐biased sex ratio of 0.77 while intermorphic female colonies (n = 33) had a ratio of 0.56. 4. Each reproductive intermorphic female was accompanied by an average of 2.9 workers (including virgin intermorphic females) in the colonial budding, and when the investment to those workers was added to the female investment, the sex ratio reached 0.81. 5. The frequency distribution of sex ratio was bimodal, with many colonies producing exclusively males or females, however mean estimated relatedness within colonies was almost 0.75. These data are inconsistent with the genetic variation hypothesis, which is one of the predominant hypotheses accounting for the between‐colony variation in sex ratio.     

Craniometrical variability and developmental stability. Two useful tools for assessing the population viability of Eurasian otter (Lutra lutra) populations in Europe.

Morphometrical univariate analyses of otter skulls collected over the past hundred years in European countries from presumed healthy populations were compared with skulls from presumed endangered populations. The average degree of sexual dimorphism of die European populations was found to be directly correlated to die skull size of die male otters. Fluctuating asymmetry (FA) in metric skull traits was analysed as an estimator of developmental stability. There was evidence for increased FA in different traits over time in some of the presumed endangered populations, and for a reduction in size of skull traits. In contrast, the healthy populations did not show any significant changes in the same traits during the same period. The reduced sexual dimorphism of the endangered populations is suggested to be a product of relaxed sexual selection and deteriorated habitat conditions. Environmental and genetic forces that may have shaped these patterns are discussed.