Genotyping Error Detection and Customised Filtration for SNP Datasets.

A major challenge in analysing single-nucleotide polymorphism (SNP) genotype datasets is detecting and filtering errors that bias analyses and misinterpret ecological and evolutionary processes. Here, we present a comprehensive method to estimate and minimise genotyping error rates (deviations from the 'true' genotype) in any SNP datasets using triplicates (three repeats of the same sample) in a four-step filtration pipeline. The approach involves: (1) SNP filtering by missing data; (2) SNP filtering by error rates; (3) sample filtering by missing data and (4) detection of recaptured individuals by using estimated SNP error rates.

An experimental design for obtaining DNA of a target species and its diet from a single non-invasive genetic protocol.

Next-generation sequencing technology has enabled accurate insights into the diet of wildlife species. The protocols for faecal sample collection and DNA extraction for diet analysis have differed from those focusing on target species, even in most studies combining questions on both aspects. We designed an experiment to evaluate two protocols using 11 parameters and select a single one that will generate both target species (Asiatic wild ass, , in Israel) and diet DNA, as an effective strategy to minimise time, effort, and cost without hampering efficiency.

Positive selection and heat-response transcriptomes reveal adaptive features of the Brassicaceae desert model, Anastatica hierochuntica.

Plant adaptation to a desert environment and its endemic heat stress is poorly understood at the molecular level. The naturally heat-tolerant Brassicaceae species Anastatica hierochuntica is an ideal extremophyte model to identify genetic adaptations that have evolved to allow plants to tolerate heat stress and thrive in deserts. We generated an A.

Subspecies hybridization as a potential conservation tool in species reintroductions.

Reintroductions are a powerful tool for the recovery of endangered species. However, their long-term success is strongly influenced by the genetic diversity of the reintroduced population. The chances of population persistence can be improved by enhancing the population's adaptive ability through the mixing of individuals from different sources.

An appetite for pests: Synanthropic insectivorous bats exploit cotton pest irruptions and consume various deleterious arthropods.

Conservation biological control (CBC) seeks to minimize the deleterious effects of agricultural pests by enhancing the efficiency of natural enemies. Despite the documented potential of insectivorous bats to consume pests, many synanthropic bat species are still underappreciated as beneficial species. We investigated the diet of Kuhl's pipistrelle (Pipistrellus kuhlii), a common synanthropic insectivorous bat that forages in urban and agricultural areas, to determine whether it may function as a natural enemy in CBC.

Long-term reevaluation of spatially explicit models as a means for adaptive wildlife management.

We evaluated a 20-yr-old spatially explicit model (SEM) that predicted the spatial expansion of reintroduced Persian fallow deer in northern Israel. Using the current distribution of the deer and based on multi-model inference we assessed the accuracy of the SEM's prediction and what other factors affected the population's current distribution. If the SEM's projection was still valid, the leading model in the multi-model inference would include only the SEM's projection as an explanatory variable with a good fit.

Detecting hierarchical levels of connectivity in a population of Acacia tortilis at the northern edge of the species' global distribution: Combining classical population genetics and network analyses.

Genetic diversity and structure of populations at the edge of the species' spatial distribution are important for potential adaptation to environmental changes and consequently, for the long-term survival of the species. Here, we combined classical population genetic methods with newly developed network analyses to gain complementary insights into the genetic structure and diversity of Acacia tortilis, a keystone desert tree, at the northern edge of its global distribution, where the population is under threat from climatic, ecological, and anthropogenic changes. We sampled A.

Taming the late Quaternary phylogeography of the Eurasiatic wild ass through ancient and modern DNA.

Taxonomic over-splitting of extinct or endangered taxa, due to an incomplete knowledge of both skeletal morphological variability and the geographical ranges of past populations, continues to confuse the link between isolated extant populations and their ancestors. This is particularly problematic with the genus Equus. To more reliably determine the evolution and phylogeographic history of the endangered Asiatic wild ass, we studied the genetic diversity and inter-relationships of both extinct and extant populations over the last 100,000 years, including samples throughout its previous range from Western Europe to Southwest and East Asia.

Inference and Analysis of Population Structure Using Genetic Data and Network Theory.

Clustering individuals to subpopulations based on genetic data has become commonplace in many genetic studies. Inference about population structure is most often done by applying model-based approaches, aided by visualization using distance-based approaches such as multidimensional scaling. While existing distance-based approaches suffer from a lack of statistical rigor, model-based approaches entail assumptions of prior conditions such as that the subpopulations are at Hardy-Weinberg equilibria.

Space-Use Patterns of the Asiatic Wild Ass (Equus hemionus): Complementary Insights from Displacement, Recursion Movement and Habitat Selection Analyses.

The way in which animals move and use the landscape is influenced by the spatial distribution of resources, and is of importance when considering species conservation. We aimed at exploring how landscape-related factors affect a large herbivore's space-use patterns by using a combined approach, integrating movement (displacement and recursions) and habitat selection analyses. We studied the endangered Asiatic wild ass (Equus hemionus) in the Negev Desert, Israel, using GPS monitoring and direct observation.

Stochastic modelling of shifts in allele frequencies reveals a strongly polygynous mating system in the re-introduced Asiatic wild ass.

Small populations are prone to loss of genetic variation and hence to a reduction in their evolutionary potential. Therefore, studying the mating system of small populations and its potential effects on genetic drift and genetic diversity is of high importance for their viability assessments. The traditional method for studying genetic mating systems is paternity analysis.

Allelic richness following population founding events--a stochastic modeling framework incorporating gene flow and genetic drift.

Allelic richness (number of alleles) is a measure of genetic diversity indicative of a population's long-term potential for adaptability and persistence. It is used less commonly than heterozygosity as a genetic diversity measure, partially because it is more mathematically difficult to take into account the stochastic process of genetic drift for allelic richness. This paper presents a stochastic model for the allelic richness of a newly founded population experiencing genetic drift and gene flow.

A factorial design experiment as a pilot study for noninvasive genetic sampling.

Noninvasive genetic sampling has increasingly been used in ecological and conservation studies during the last decade. A major part of the noninvasive genetic literature is dedicated to the search for optimal protocols, by comparing different methods of collection, preservation and extraction of DNA from noninvasive materials. However, the lack of quantitative comparisons among these studies and the possibility that different methods are optimal for different systems make it difficult to decide which protocol to use.

Effectiveness of multiple release sites in reintroduction of Persian fallow deer.

Releasing animals in more than one location may increase or decrease the probability of success of a reintroduction project, yet the question of how many release sites to use has received little attention. We used empirical data from the reintroduction program of the Persian fallow deer (Dama mesopotamica) (Galilee region in northern Israel) in an individual-based spatially explicit simulation model to assess the effects of releasing deer from multiple sites. We examined whether multiple release sites increase reintroduction success, and if so, whether the optimal number of sites for a given scenario can be determined and whether the outcome differs if animals are released alternately (i.

Methods for assessing movement path recursion with application to African buffalo in South Africa.

Recent developments of automated methods for monitoring animal movement, e.g., global positioning systems (GPS) technology, yield high-resolution spatiotemporal data.

Dynamics and management of infectious disease in colonizing populations.

The introduction of chronic, infectious diseases by colonizing populations (invasive or reintroduced) is a serious hazard in conservation biology, threatening the original host and other spillover species. Most research on spatial invasion of diseases has pertained to established host populations, either at steady state or fluctuating through time. Within a colonizing population, however, the spread of disease may be influenced by the expansion process of the population itself.