Search

Next-Generation sequencing technology has enabled accurate insights into the diet of wildlife species. The protocols for faecal sample collection and extraction of DNA for diet analysis have been different from those focusing on focal species DNA, even in studies combining questions on a focal species and its diet. We designed an experiment to evaluate two protocols and select a single one that will generate both focal species (Asiatic wild ass, Equus hemionus, in Israel) and diet DNA, as an effective strategy to minimize time, efforts, and cost without hampering efficiency. In Protocol A, we swabbed the outer surface of faecal boluses and extracted DNA using a Stool Kit, while for Protocol B, we homogenised faecal matter from inside the bolus followed by extraction using a Powersoil Kit. Protocol A performed significantly better for most of the measures, which included, for the focal species, microsatellite amplification success and the quantity of the GAPDH gene; and for its diet, amplification success of a chloroplast barcoding marker, trnL, number of reads, and plant genus richness and diversity. However, there was no significant difference for the amplification success of a sex-linked marker and plant genus composition. Both protocols yielded results for the focal species and its diet, demonstrating that one single protocol can be used for both purposes; although, a pilot study is recommended to optimise the protocol for specific systems. This strategy may also be useful for studies combining focal species and their gut microbiome and parasitic load.

Translocated animals typically find themselves in a novel environment in which they must establish a home range in a manner that will maximize their fitness. We hypothesized that the initial establishment of a home range is followed by adjustments expressed as home range shifting, and occurs as familiarity with the landscape increases, until the home range is stabilized. We studied the process of home range shifting in 42 female Persian fallow deer (Dama mesopotamica) reintroduced into the Galilee, Israel over a period of 2–5 years. We used changes in the degree of home range overlap between consecutive years as an indicator of stabilization. We then compared how the mean percent cover of the key vegetation types (woodland, scrubland and open pastures) differed between the areas abandoned in the first year's home range and the areas added to the last year's home range relative to the first (using a weighted paired t-test). We also compared the distribution (using χ2 test of independence and Levene's test for homogeneity of variance) of %cover of the 3 vegetation types between the first and last year's home range. The average home range overlap increased over the 5 years following the first release. During the first-year post release, deer avoided open pastures and preferred woodland. In later years deer increase in the % open pastures (weighted t-test: p < 0.001) and decreased the % woodland cover (weighted t-test: p = 0.07) by abandoning areas with little open pasture and steeper terrain and moving into areas with more open pasture and moderate terrain. Variance of the cover types across individuals increased with time. We conclude that the home ranges of the reintroduced deer stabilized with time. The changes in vegetation and slope are driven by time-dependent changing needs reflecting a tradeoff between safety (refuge) and foraging. Our findings suggest that using the initially established home range to determine species preferences can create a misleading picture of what the optimal home range of the species really is. Individual variation in term of preferences can take a few years to be expressed due to the initial high-risk perceived by individuals in a novel environment.

SummaryPlant 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. hierochuntica reference transcriptome and pinpointed extremophyte adaptations by comparing Arabidopsis thaliana and A. hierochuntica transcriptome responses to heat and identifying positively selected genes in A. hierochuntica.The two species exhibit similar transcriptome adjustment in response to heat and the A. hierochuntica transcriptome does not exist in a constitutive heat “stress-ready” state. Furthermore, the A. hierochuntica global transcriptome as well as heat-responsive orthologs, display a lower basal and higher heat-induced expression than in A. thaliana. Genes positively selected in multiple extremophytes are associated with stomatal opening, nutrient acquisition, and UV-B induced DNA repair while those unique to A. hierochuntica are consistent with its photoperiod-insensitive, early-flowering phenotype.We suggest that evolution of a flexible transcriptome confers the ability to quickly react to extreme diurnal temperature fluctuations characteristic of a desert environment while positive selection of genes involved in stress tolerance and early flowering could facilitate an opportunistic desert lifestyle.

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. However, where source populations are too diverse the reintroduced population could also suffer from outbreeding depression or unsuccessful admixture due to behavioural or genetic barriers. For the reintroduction of Asiatic wild ass Equus hemionus ssp. in Israel, a breeding core was created from individuals of two different subspecies (E. h. onager & E. h. kulan). Today the population comprises approximately 300 individuals and displays no signs of outbreeding depression. The aim of this study was a population genomic evaluation of this conservation reintroduction protocol. We used maximum likelihood methods and genetic clustering analyses to investigate subspecies admixture and test for spatial autocorrelation based on subspecies ancestry. Further, we analysed heterozygosity and effective population sizes in the breeding core prior to release and the current wild population. We discovered high levels of subspecies admixture in the breeding core and wild population, consistent with a significant heterozygote excess in the breeding core. Furthermore, we found no signs of spatial autocorrelation associated with subspecies ancestry in the wild population. Inbreeding and variance effective population size estimates were low. Our results indicate no genetic or behavioural barriers to admixture between the subspecies and suggest that their hybridization has led to greater genetic diversity in the reintroduced population. The study provides rare empirical evidence of the successful application of subspecies hybridization in a reintroduction. It supports use of intraspecific hybridization as a tool to increase genetic diversity in conservation translocations.

The long-term success of species reintroductions is strongly dependent on the availability of large areas of suitable habitat and the genetic make-up of the population. If available habitat is poorly connected this can hinder gene flow and lead to genetic fragmentation of the population, potentially increasing its extinction risk. We employed a conservation genomics approach in which we combined analyses of genetic structure with testing for potential landscape effects on habitat selection and gene flow in reintroduced Asiatic wild ass Equus hemionus ssp. in the Israeli Negev desert. Genetic structure and pairwise relatedness were first investigated followed by examination of landscape effects on individual habitat selection using records of GPS collared individuals. We then built habitat resistance surfaces and used electrical circuit theory to test for landscape effects on genetic relatedness. We detected weak genetic structuring, yet low spatial coherence among individuals from the same genetic cluster. Landscape variables had a significant impact on individual habitat selection, with wild ass avoiding steep slopes and habitats of low suitability as predicted by a species distribution model. However, the landscape genetic analysis revealed no effect of habitat resistance on genetic relatedness. These results suggest that gene flow in the reintroduced population is not impacted by landscape resistance. Indeed, the high mobility of the species may increase its resistance to the genetic effects of habitat fragmentation, at least over a small number of generations. We discuss other potential causes for the observed genetic structure including a behavioural effect. Our study highlights the importance of understanding species-habitat interactions for the long-term success of reintroductions.

In a reintroduced population, the social behavior of the species can strongly affect the long-term viability of the population through its effects on movement, information flow, disease spread and the population's genetic variability. Therefore, information on the social behavior of a reintroduced population can contribute to conservation practices; however, its importance is often underestimated. The initial phase of the Asiatic wild ass's (Equus hemionus) reintroduction in Israel has been considered a success, and the population is currently estimated at more than 250 individuals. However, the current social structure of the population remained unknown. We aimed to study this important population trait and to provide helpful information for efficient conservation and management protocols. The study was based on direct observations that were conducted over four consecutive years, and on the analyses of groups' composition and female groups' stability. Female groups accompanied by males constituted only 5% of the total 659 observations, males were observed to be mainly solitary or in groups of various sizes, and females were organized in non-stable groups, indicating that the reintroduced population exhibits a fission-fusion social structure. Identifying the social structure for the species in the expanding Negev population of the Asiatic wild ass can assist in implementing future reintroductions and can contribute to effective management decisions aimed at protecting the species.

Effective population size, a central concept in conservation biology, is now routinely estimated from genetic surveys and can also be theoretically predicted from demographic, life-history, and mating-system data. By evaluating the consistency of theoretical predictions with empirically estimated effective size, insights can be gained regarding life-history characteristics and the relative impact of different life-history traits on genetic drift. These insights can be used to design and inform management strategies aimed at increasing effective population size. We demonstrated this approach by addressing the conservation of a reintroduced population of Asiatic wild ass (Equus hemionus). We estimated the variance effective size (Nev ) from genetic data (N ev =24.3) and formulated predictions for the impacts on Nev of demography, polygyny, female variance in lifetime reproductive success (RS), and heritability of female RS. By contrasting the genetic estimation with theoretical predictions, we found that polygyny was the strongest factor affecting genetic drift because only when accounting for polygyny were predictions consistent with the genetically measured Nev . The comparison of effective-size estimation and predictions indicated that 10.6% of the males mated per generation when heritability of female RS was unaccounted for (polygyny responsible for 81% decrease in Nev ) and 19.5% mated when female RS was accounted for (polygyny responsible for 67% decrease in Nev ). Heritability of female RS also affected Nev ; hf2=0.91 (heritability responsible for 41% decrease in Nev ). The low effective size is of concern, and we suggest that management actions focus on factors identified as strongly affecting Nev, namely, increasing the availability of artificial water sources to increase number of dominant males contributing to the gene pool. This approach, evaluating life-history hypotheses in light of their impact on effective population size, and contrasting predictions with genetic measurements, is a general, applicable strategy that can be used to inform conservation practice.

The Near Eastern fire salamander, Salamandra infraimmaculata , is considered an endangered species in Israel and is near-threatened regionally. For 25 years, our laboratory has sought ethical sampling methods to protect individuals and populations of Salamandra . To “mark” individuals for estimating dispersal and population size, we use non-invasive individual-specific markings from photographs of larvae and adults. We demonstrated through mesocosm experiments (which are less mortality-driven than in nature) that exotic Gambusia affinis have extreme negative mortality effects on Salamandra larvae. From a compassionate conservation aspect, G. affinis should not be killed and placed in habitats where amphibians are not in danger and mosquitoes can be controlled. We identified breeding-site characteristics demonstrating that permanent breeding sites support larger adult populations than temporary breeding sites. For population genetics studies, we take minimal sized tail tips from adults (which have no adverse effects) for microsatellite data. For gene expression studies, rather than sacrifice entire bodies, we demonstrated that by taking only small larval tail tips, we could follow gene expression. We additionally demonstrated that tail tip removal does not affect survival, time to or size at metamorphosis. We documented high road kill rates at a specific breeding site. To prevent potential disease spread, we sterilize boots and sampling gear. We use results for implementing or recommending conservation of individuals and populations – e.g., identifying: movement corridors for breeding site dispersal; roadkill hotspots for under-road tunnels; suitable habitat for pool construction for more effective conservation; utilizing population genetics for recommending management units; information on demography and genetic diversity to identify hotspots for conservation; removal of Gambusia for amphibian protection.

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. Faecal samples of P. kuhlii were collected throughout the cotton-growing season from five roost sites near cotton fields located in a Mediterranean agroecosystem, Israel, and analyzed using DNA metabarcoding. Additionally, data on estimated abundance of major cotton pests were collected. We found that the diet of P. kuhlii significantly varied according to sites and dates and comprised 27 species of agricultural pests that were found in 77.2% of the samples, including pests of key economic concern. The dominant prey was the widespread cotton pest, the pink bollworm, Pectinophora gossypiella, found in 31% of the samples and in all the roosts. Pink bollworm abundance was positively correlated with its occurrence in the bat diet. Furthermore, the bats' dietary breadth narrowed, while temporal dietary overlap increased, in relation to increasing frequencies of pink bollworms in the diet. This suggests that P. kuhlii exploits pink bollworm irruptions by opportunistic feeding. We suggest that synanthropic bats provide important pest suppression services, may function as CBC agents of cotton pests and potentially contribute to suppress additional deleterious arthropods found in their diet in high frequencies.

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. Different leading models would reveal key variables overlooked when the SEM was constructed or changes in the landscape unforeseen at the time, thus assisting adaptive management and decision-making. We assessed deer presence from camera trap encounter counts analyzed using N-mixture models. Models included various combinations of seven predictors: the 20-yr predictions of an SEM developed during the initial phases of the reintroduction, three key landscape characteristics on which the SEM was originally based but updated to reflect current conditions, distance from the release site, elevation, and the distribution of gray wolves (a predator that was absent from the area when the SEM was developed). Competing models were ranked by Akaike information criterion (AIC). Wolf distribution was the key predictor explaining the current deer distribution, appearing in all three leading models (∆AIC

Species distribution models (SDMs) are often limited by the use of coarse-resolution environmental variables and by the number of observations required for their calibration. This is particularly true in the case of elusive animals. Here, we developed a SDM by combining three elements: a database of explanatory variables, mapped at a fine resolution; a systematic sampling scheme; and an intensive survey of indirect observations. Using MaxEnt, we developed the SDM for the population of the Asiatic wild ass (Equus hemionus), a rare and elusive species, at three spatial scales: 10, 100, and 1000 m per pixel. We used indirect observations of feces mounds. We constructed 14 layers of explanatory variables, in five categories: water, topography, biotic conditions, climatic variables and anthropogenic variables. Woody vegetation cover and slopes were found to have the strongest effect on the distribution of wild ass and were included as the main predictors in the SDM. Model validation revealed that an intensive survey of feces mounds and high-resolution predictor layers resulted in a highly accurate and informative SDM. Fine-grain (10 and 100 m) SDMs can be utilized to: (1) characterize the variables influencing species distribution at high resolution and local scale, including anthropogenic effects and geomorphologic features; (2) detect potential population activity centers; (3) locate potential corridors of movement and possible isolated habitat patches. Such information may be useful for the conservation efforts of the Asiatic wild ass. This approach could be applied to other elusive species, particularly large mammals.

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. tortilis from 14 sites along the Dead Sea region and the Arava Valley in Israel and in Jordan. In addition, we obtained samples from Egypt and Sudan, the hypothesized origin of the species. Samples from all sites were genotyped using six polymorphic microsatellite loci.Our results indicate a significant genetic structure in A. tortilis along the Arava Valley. This was detected at different hierarchical levels-from the basic unit of the subpopulation, corresponding to groups of trees within ephemeral rivers (wadis), to groups of subpopulations (communities) that are genetically more connected relative to others. The latter structure mostly corresponds to the partition of the major drainage basins in the area. Network analyses, combined with classical methods, allowed for the identification of key A. tortilis subpopulations in this region, characterized by their relatively high level of genetic diversity and centrality in maintaining gene flow in the population. Characterizing such key subpopulations may enable conservation managers to focus their efforts on certain subpopulations that might be particularly important for the population's long-term persistence, thus contributing to species conservation within its peripheral range.

Noninvasive genetic methods enable the sampling of natural populations while minimizing detrimental effects on them. However, noninvasive methods are marred by DNA extraction and amplification difficulties that can be mitigated by improved methodology. Past studies have shown that noninvasive genetic protocols are system specific and highlighted the importance of pilot studies in the establishment of genetic monitoring programs. We tested, using a factorial design experiment, the effect of different methods for the collection-preservation and extraction on the amplification of DNA from Nubian ibex (Capra nubiana) fecal samples. We found collection-preservation using paper bags and extraction with QIAamp® fast DNA stool mini kit to significantly enhance success rate compared to collection-preservation in ethanol and extraction with QIAamp® DNA mini kit. Our results will contribute to the studies of natural populations of the vulnerable C. nubiana.

Effective population size, a central concept in conservation biology, is now routinely estimated from genetic surveys and can also be theoretically predicted from demographic, life-history, and mating-system data. By evaluating the consistency of theoretical predictions with empirically estimated effective size, insights can be gained regarding life-history characteristics and the relative impact of different life-history traits on genetic drift. These insights can be used to design and inform management strategies aimed at increasing effective population size. We demonstrated this approach by addressing the conservation of a reintroduced population of Asiatic wild ass (Equus hemionus). We estimated the variance effective size (N(ev)) from genetic data (N(ev) = 24.3) and formulated predictions for the impacts on N(ev) of demography, polygyny, female variance in lifetime reproductive success (RS), and heritability of female RS. By contrasting the genetic estimation with theoretical predictions, we found that polygyny was the strongest factor affecting genetic drift because only when accounting for polygyny were predictions consistent with the genetically measured N(ev). The comparison of effective-size estimation and predictions indicated that 10.6% of the males mated per generation when heritability of female RS was unaccounted for (polygyny responsible for 81% decrease in N(ev)) and 19.5% mated when female RS was accounted for (polygyny responsible for 67% decrease in N(ev)). Heritability of female RS also affected N(ev); [Formula: see text] (heritability responsible for 41% decrease in N(ev)). The low effective size is of concern, and we suggest that management actions focus on factors identified as strongly affecting N(ev), namely, increasing the availability of artificial water sources to increase number of dominant males contributing to the gene pool. This approach, evaluating life-history hypotheses in light of their impact on effective population size, and contrasting predictions with genetic measurements, is a general, applicable strategy that can be used to inform conservation practice.

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 genusEquus.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. Using 229 bp of the mitochondrial hypervariable region, an approach which allowed the inclusion of information from extremely poorly preserved ancient samples, we classify all non-African wild asses into nine clades that show a clear phylogeographic structure revealing their phylogenetic history. This study places the extinct European wild ass,E. hydruntinus, the phylogeny of which has been debated since the end of the 19thcentury, into its phylogenetic context within the Asiatic wild asses and reveals recent gene flow events between populations currently regarded as separate species. The phylogeographic organization of clades resulting from these efforts can be used not only to improve future taxonomic determination of a poorly characterized group of equids, but also to identify historic ranges, interbreeding events between various populations, and the impact of ancient climatic changes. In addition, appropriately placing extant relict populations into a broader phylogeographic and genetic context can better inform ongoing conservation strategies for this highly endangered species.

Recursive movement—returns to previously visited areas—is a widespread phenomenon exhibited by a large range of species from bees and birds to primates and large felines, at different spatial scales. Nevertheless, the wide scope and generality of this phenomenon remain underestimated by the scientific community. This limited appreciation for the pervasiveness of recursive movement can be attributed to its study by parallel lines of research, with different methodologies and nomenclature, and almost no cross referencing among them. Among these lines of studies are traplining behavior in foraging ecology, path recursions in movement ecology and the ecology of fear in predator–prey studies. We synthesize these three lines of research, to underline the mechanisms driving these patterns and create a conceptual model for recursive movement behavior across species and spatio-temporal scales. The emergence and complexity of recursive movement patterns are determined by the rate of resource recovery, environmental...

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. The model follows the dynamics of alleles lost during the founder event and simulates the effect of gene flow on maintenance and recovery of allelic richness. The probability of an allele's presence in the population was identified as the relevant statistical property for a meaningful interpretation of allelic richness. A method is discussed that combines the probability of allele presence with a population's allele frequency spectrum to provide predictions for allele recovery. The model's analysis provides insights into the dynamics of allelic richness following a founder event, taking into account gene flow and the allele frequency spectrum. Furthermore, the model indicates that the “One Migrant per Generation” rule, a commonly used conservation guideline related to heterozygosity, may be inadequate for addressing preservation of diversity at the allelic level. This highlights the importance of distinguishing between heterozygosity and allelic richness as measures of genetic diversity, since focusing merely on the preservation of heterozygosity might not be enough to adequately preserve allelic richness, which is crucial for species persistence and evolution.