Thermal conditions determine lizards' response to oil contamination in a desert habitat.

A unique, hyper-arid habitat in southern Israel was polluted by crude oil in 2014. Surveys following the event found that some species of local lizards avoid the oil, while other species were found more frequently in polluted plots. These results raised the question: why do species react differently to oil-polluted soil? We evaluated how soil type, thermal conditions, and food availability interacted to shape habitat preferences of three lizard species. Generally, thermal conditions determined habitat selection and preferences for contaminated or clean soils, while the effects of food availability were weak. The diurnal Acanthodactylus opheodurus avoided artificial heating sources, perhaps to avoid hot soil during warm hours. Both nocturnal Stenodactylus species showed a preference for higher temperature treatments. While crude oil is considered harmful, ectotherms may not recognize it as a danger and may be attracted to it due to its thermal properties, which may create an ecological trap.

Optimal stopover model: A state-dependent habitat selection model for staging passerines.

During their seasonal migration, birds stage in areas comprising stopover sites of varying quality. Given that migrating birds have a limited information about their environment, they may land at a low-quality stopover site in which their fuel deposition rate (FDR) is low. Birds landing at such sites should decide either to extend their stopover duration or to quickly depart in search for a better site. These decisions, however, strongly depend on their body condition upon landing. To understand the decision-making process of passerines within a stopover area, comprising stopover sites of varying quality, prior to the crossing of a large ecological barrier, we constructed a state-dependent habitat selection model. The model assumes that even if migrating birds have an expectation of encountered area quality, they cannot control for their initial landing site. Once landing, movement between low- and high-quality stopover sites will occur only if the body condition of these birds is high to the extent that they can entail the energetic cost of movement. Birds in the model aim to maximize their fuel load at the end of the stopover period, to suffice for successfully crossing a large ecological barrier. The model is based on empirical data on autumn migrating Blackcaps Sylvia atricapilla, collected at two important stopover sites in the Negev desert of Israel. Migrating passerines staging at these two sites differ in their FDR and body condition. The model shows that the optimal behaviour when arriving at a low-quality stopover site is to abandon it quickly. However, as lean individuals cannot entail the costs of searching for an alternative site, they have no other choice but to stay there even if their chances to successfully cross the Sahara Desert ahead are low. Our model can be applied to other ecological systems. Proper use of this model may allow good assessment of stopover site quality, as indicated by the bird's FDR, regardless of specific site characteristics. Hence, it can help applying targeted management decisions regarding the maintenance of stopover sites or establishment of new ones.

Measuring body condition of lizards: a comparison between non-invasive dual-energy X-ray absorptiometry, chemical fat extraction and calculated indices.

BACKGROUND: Condition indices (CIs) are used in ecological studies as a way of measuring an individual animal's health and fitness. Noninvasive CIs are estimations of a relative score of fat content or rely on a ratio of body mass compared to some measure of size, usually a linear dimension such as tarsus or snout-vent length. CIs are generally validated invasively by lethal fat extraction as in a seasonal sample of individuals in a population. Many alternatives to lethal fat extraction are costly or time consuming. As an alternative, dual-energy X-ray absorptiometry (DXA) allows for non-destructive analysis of body composition and enables multiple measurements during an animal's life time. DXA has never been used for ecological studies in a small, free-ranging lizard before, therefore we calibrated this method against a chemical extraction of fat from a sample of 6 geckos (Israeli fan toed gecko Ptyodactylus guttatus) ranging in body mass between 4.2-11.5 g. We then  used this calibrated  DXA measurements to determine the best linear measurement calculated CI for this species. RESULTS: We found that fat mass measured with DXA was significantly correlated with the mass of chemically extracted fat for specimens more than 4.8 g (N = 5, R2 = 0.995, P < 0.001). Fat percentage regressed with body mass significantly predicted the DXA fat percentage (N = 29, R2adj. = 0.862, p < 0.001). Live wet mass was significantly correlated with predicted fat mass (N = 30, R2 = 0.984, P < 0.001) for specimens more than 4.8 g. Among the five calculated non-invasive CIs that we tested, the best was mass/SVL. CONCLUSIONS: We recommend that in situations where DXA cannot be used, that the most accurate of the body condition estimators for  this species is mass/SVL (snout-vent length) for both sexes.

The contextual separation of lateral white line patterns in chameleons.

While many animals display different colour patterns that signal different messages, some species use various tactics to separate between colour and pattern displays. The common chameleon (Chamaeleo chamaeleon) is capable of rapidly changing and separating among displays of colour patterns and ornaments. We used chameleons to study the contextual role of separation among colour and pattern displays. Specifically, we studied the predominant white badge, which is composed of multiple parts, during different seasons and in different social contexts. We hypothesized that the badge contains important information about the sender and, therefore, would be present during important social contexts. We carried out a series of trials to document the presence/absence of the badge and found that the badge is individually specific and reflects body size. We also revealed that the badge remained fixed throughout other body colour changes, but was replaced by other colour patterns during mating behaviour. During social encounters, additional dark patches delineating the badge appeared, presumably amplifying its signal. Thus, we suggest that the badge constitutes an important feature in intraspecific communication, and is possibly employed to display quality. However, the replacement of the badge by other displays during courtship suggests that during important social events like mating, chameleons transmit exclusive information that is not broadcast by the badge. Our findings demonstrate the importance of separation between colour patterns, and the alternative use of intraspecific colour patterns for specific social contexts in chameleons.

Revealing life-history traits by contrasting genetic estimations with predictions of effective population size.

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.

Alternative Mating Tactics in Male Chameleons (Chamaeleo chamaeleon) Are Evident in Both Long-Term Body Color and Short-Term Courtship Pattern.

Alternative mating tactics in males of various taxa are associated with body color, body size, and social status. Chameleons are known for their ability to change body color following immediate environmental or social stimuli. In this study, we examined whether the differential appearance of male common chameleon during the breeding season is indeed an expression of alternative mating tactics. We documented body color of males and used computer vision techniques to classify images of individuals into discrete color patterns associated with seasons, individual characteristics, and social contexts. Our findings revealed no differences in body color and color patterns among males during the non-breeding season. However, during the breeding season males appeared in several color displays, which reflected body size, social status, and behavioral patterns. Furthermore, smaller and younger males resembled the appearance of small females. Consequently, we suggest that long-term color change in males during the breeding season reflects male alternative mating tactics. Upon encounter with a receptive female, males rapidly alter their appearance to that of a specific brief courtship display, which reflects their social status. The females, however, copulated indiscriminately in respect to male color patterns. Thus, we suggest that the differential color patterns displayed by males during the breeding season are largely aimed at inter-male signaling.

Combined effects of climatic gradient and domestic livestock grazing on reptile community structure in a heterogeneous agroecosystem.

Grazing plays an important role in shaping ecological communities in human-related ecosystems. Although myriad studies have explored the joint effect of grazing and climate on plant communities, this interactive effect has rarely been studied in animals. We hypothesized that the effect of grazing on the reptile community varies along a climatic gradient in relation to the effect of grazing on habitat characteristics, and that grazing differentially affects reptiles of different biogeographic regions. We tested our hypotheses by collecting data on environmental characteristics and by trapping reptiles in four heterogeneous landscapes experiencing differing grazing intensities and distributed along a sharp climatic gradient. We found that while reptile diversity increased with grazing intensity at the mesic end of the gradient, it decreased with grazing intensity at the arid end. Moreover, the proportion of reptile species of differing biogeographic origins varied with the interactive effect of climate and grazing. The representation of species originating in arid biogeographic zones was highest at the arid end of the climatic gradient, and representation increased with grazing intensity within this area. Regardless of the climatic context, increased grazing pressure results in a reduction in vegetation cover and thus in changes in habitat characteristics. By reducing vegetation cover, grazing increased habitat heterogeneity in the dense mesic sites and decreased habitat heterogeneity in the arid sites. Thus, our results suggest that the same direction of habitat alteration caused by grazing may have opposite effects on biodiversity and community composition in different climatic contexts.

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. We found that the main landscape-related factors affecting the species' space-use patterns, on a daily and seasonal basis, were vegetation cover, water sources and topography. Two main habitat types were selected: high-elevation sites during the day (specific microclimate: windy on warm summer days) and streambed surroundings during the night (coupled with high vegetation when the animals were active in summer). Distribution of recursion times (duration between visits) revealed a 24-hour periodicity, a pattern that could be widespread among large herbivores. Characterizing frequently revisited sites suggested that recursion movements were mainly driven by a few landscape features (water sources, vegetation patches, high-elevation points), but also by social factors, such as territoriality, which should be further explored. This study provided complementary insights into the space-use patterns of E. hemionus. Understanding of the species' space-use patterns, at both large and fine spatial scale, is required for developing appropriate conservation protocols. Our approach could be further applied for studying the space-use patterns of other species in heterogeneous landscapes.

LEMONS - A Tool for the Identification of Splice Junctions in Transcriptomes of Organisms Lacking Reference Genomes.

RNA-seq is becoming a preferred tool for genomics studies of model and non-model organisms. However, DNA-based analysis of organisms lacking sequenced genomes cannot rely on RNA-seq data alone to isolate most genes of interest, as DNA codes both exons and introns. With this in mind, we designed a novel tool, LEMONS, that exploits the evolutionary conservation of both exon/intron boundary positions and splice junction recognition signals to produce high throughput splice-junction predictions in the absence of a reference genome. When tested on multiple annotated vertebrate mRNA data, LEMONS accurately identified 87% (average) of the splice-junctions. LEMONS was then applied to our updated Mediterranean chameleon transcriptome, which lacks a reference genome, and predicted a total of 90,820 exon-exon junctions. We experimentally verified these splice-junction predictions by amplifying and sequencing twenty randomly selected genes from chameleon DNA templates. Exons and introns were detected in 19 of 20 of the positions predicted by LEMONS. To the best of our knowledge, LEMONS is currently the only experimentally verified tool that can accurately predict splice-junctions in organisms that lack a reference genome.

Mitochondrial Involvement in Vertebrate Speciation? The Case of Mito-nuclear Genetic Divergence in Chameleons.

Compatibility between the nuclear (nDNA) and mitochondrial (mtDNA) genomes is important for organismal health. However, its significance for major evolutionary processes such as speciation is unclear, especially in vertebrates. We previously identified a sharp mtDNA-specific sequence divergence between morphologically indistinguishable chameleon populations (Chamaeleo chamaeleon recticrista) across an ancient Israeli marine barrier (Jezreel Valley). Because mtDNA introgression and gender-based dispersal were ruled out, we hypothesized that mtDNA spatial division was maintained by mito-nuclear functional compensation. Here, we studied RNA-seq generated from each of ten chameleons representing the north and south populations and identified candidate nonsynonymous substitutions (NSSs) matching the mtDNA spatial distribution. The most prominent NSS occurred in 14 nDNA-encoded mitochondrial proteins. Increased chameleon sample size (N = 70) confirmed the geographic differentiation in POLRMT, NDUFA5, ACO1, LYRM4, MARS2, and ACAD9. Structural and functionality evaluation of these NSSs revealed high functionality. Mathematical modeling suggested that this mito-nuclear spatial divergence is consistent with hybrid breakdown. We conclude that our presented evidence and mathematical model underline mito-nuclear interactions as a likely role player in incipient speciation in vertebrates.

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. Yet, as small populations are often rare and elusive, the genetic data required for paternity analysis are frequently unavailable. The endangered Asiatic wild ass (Equus hemionus), like all equids, displays a behaviourally polygynous mating system; however, the level of polygyny has never been measured genetically in wild equids. Combining noninvasive genetic data with stochastic modelling of shifts in allele frequencies, we developed an alternative approach to paternity analysis for studying the genetic mating system of the re-introduced Asiatic wild ass in the Negev Desert, Israel. We compared the shifts in allele frequencies (as a measure of genetic drift) that have occurred in the wild ass population since re-introduction onset to simulated scenarios under different proportions of mating males. We revealed a strongly polygynous mating system in which less than 25% of all males participate in the mating process each generation. This strongly polygynous mating system and its potential effect on the re-introduced population's genetic diversity could have significant consequences for the long-term persistence of the population in the Negev. The stochastic modelling approach and the use of allele-frequency shifts can be further applied to systems that are affected by genetic drift and for which genetic data are limited.

The first Chameleon transcriptome: comparative genomic analysis of the OXPHOS system reveals loss of COX8 in Iguanian lizards.

Recently, we found dramatic mitochondrial DNA divergence of Israeli Chamaeleo chamaeleon populations into two geographically distinct groups. We aimed to examine whether the same pattern of divergence could be found in nuclear genes. However, no genomic resource is available for any chameleon species. Here we present the first chameleon transcriptome, obtained using deep sequencing (SOLiD). Our analysis identified 164,000 sequence contigs of which 19,000 yielded unique BlastX hits. To test the efficacy of our sequencing effort, we examined whether the chameleon and other available reptilian transcriptomes harbored complete sets of genes comprising known biochemical pathways, focusing on the nDNA-encoded oxidative phosphorylation (OXPHOS) genes as a model. As a reference for the screen, we used the human 86 (including isoforms) known structural nDNA-encoded OXPHOS subunits. Analysis of 34 publicly available vertebrate transcriptomes revealed orthologs for most human OXPHOS genes. However, OXPHOS subunit COX8 (Cytochrome C oxidase subunit 8), including all its known isoforms, was consistently absent in transcriptomes of iguanian lizards, implying loss of this subunit during the radiation of this suborder. The lack of COX8 in the suborder Iguania is intriguing, since it is important for cellular respiration and ATP production. Our sequencing effort added a new resource for comparative genomic studies, and shed new light on the evolutionary dynamics of the OXPHOS system.

Mitochondrial DNA variation, but not nuclear DNA, sharply divides morphologically identical chameleons along an ancient geographic barrier.

The Levant is an important migration bridge, harboring border-zones between Afrotropical and palearctic species. Accordingly, Chameleo chameleon, a common species throughout the Mediterranean basin, is morphologically divided in the southern Levant (Israel) into two subspecies, Chamaeleo chamaeleon recticrista (CCR) and C. c. musae (CCM). CCR mostly inhabits the Mediterranean climate (northern Israel), while CCM inhabits the sands of the north-western Negev Desert (southern Israel). AFLP analysis of 94 geographically well dispersed specimens indicated moderate genetic differentiation (PhiPT = 0.097), consistent with the classical division into the two subspecies, CCR and CCM. In contrast, sequence analysis of a 637 bp coding mitochondrial DNA (mtDNA) fragment revealed two distinct phylogenetic clusters which were not consistent with the morphological division: one mtDNA cluster consisted of CCR specimens collected in regions northern of the Jezreel Valley and another mtDNA cluster harboring specimens pertaining to both the CCR and CCM subspecies but collected southern of the Jezreel Valley. AMOVA indicated clear mtDNA differentiation between specimens collected northern and southern to the Jezreel Valley (PhiPT = 0.79), which was further supported by a very low coalescent-based estimate of effective migration rates. Whole chameleon mtDNA sequencing (∼17,400 bp) generated from 11 well dispersed geographic locations revealed 325 mutations sharply differentiating the two mtDNA clusters, suggesting a long allopatric history further supported by BEAST. This separation correlated temporally with the existence of an at least 1 million year old marine barrier at the Jezreel Valley exactly where the mtDNA clusters meet. We discuss possible involvement of gender-dependent life history differences in maintaining such mtDNA genetic differentiation and suggest that it reflects (ancient) local adaptation to mitochondrial-related traits.

Ecological trap for desert lizards caused by anthropogenic changes in habitat structure that favor predator activity.

Anthropogenic habitat perturbation is a major cause of population decline. A standard practice managers use to protect populations is to leave portions of natural habitat intact. We describe a case study in which, despite the use of this practice, the critically endangered lizard Acanthodactylus beershebensis was locally extirpated from both manipulated and natural patches within a mosaic landscape of an afforestation project. We hypothesized that increased structural complexity in planted patches favors avian predator activity and makes these patches less suitable for lizards due to a heightened risk of predation. Spatial rarity of natural perches (e.g., trees) in arid scrublands may hinder the ability of desert lizards to associate perches with low-quality habitat, turning planted patches into ecological traps for such species. We erected artificial trees in a structurally simple arid habitat (similar to the way trees were planted in the afforestation project) and compared lizard population dynamics in plots with these structures and without. Survival of lizards in the plots with artificial trees was lower than survival in plots without artificial trees. Hatchlings dispersed into plots with artificial trees in a manner that indicated they perceived the quality of these plots as similar to the surrounding, unmanipulated landscape. Our results showed that local anthropogenic changes in habitat structure that seem relatively harmless may have a considerable negative effect beyond the immediate area of the perturbation because the disturbed habitat may become an ecological trap.

Moonlight avoidance in gerbils reveals a sophisticated interplay among time allocation, vigilance and state-dependent foraging.

Foraging animals have several tools for managing the risk of predation, and the foraging games between them and their predators. Among these, time allocation is foremost, followed by vigilance and apprehension. Together, their use influences a forager's time allocation and giving-up density (GUD) in depletable resource patches. We examined Allenby's gerbils (Gerbilus andersoni allenbyi) exploiting seed resource patches in a large vivarium under varying moon phases in the presence of a red fox (Vulpes vulpes). We measured time allocated to foraging patches electronically and GUDs from seeds left behind in resource patches. From these, we estimated handling times, attack rates and quitting harvest rates (QHRs). Gerbils displayed greater vigilance (lower attack rates) at brighter moon phases (full < wane < wax < new). Similarly, they displayed higher GUDs at brighter moon phases (wax > full > new > wane). Finally, gerbils displayed higher QHRs at new and waxing moon phases. Differences across moon phases not only reflect changing time allocation and vigilance, but changes in the state of the foragers and their marginal value of energy. Early in the lunar cycle, gerbils rely on vigilance and sacrifice state to avoid risk; later they defend state at the cost of increased time allocation; finally their state can recover as safe opportunities expand. In the predator-prey foraging game, foxes may contribute to these patterns of behaviours by modulating their own activity in response to the opportunities presented in each moon phase.

Developmental patterns in the polyembryonic parasitoid wasp Copidosoma koehleri.

Polyembryony is a unique mode of development in which multiple genetically identical embryos develop from a single egg. In some polyembryonic species a proportion of the embryos develop into soldier larvae, which attack competitors in the host. We studied the development of the polyembryonic wasp Copidosoma koehleri in its host Phthorimaea opercullela. We dissected hosts parasitized by either virgin or mated female wasps at 2day intervals from hatching to the final instars. We documented host mass and head width, the number and size of developing wasps and the presence of a soldier larva. Additionally, we kept a sample of parasitized hosts until emergence of wasps and measured the head width of emerging adults. We characterized wasp development in relation to host development. One half of the broods produced by mated wasps contained one soldier larva throughout development. This suggests that in C. koehleri each female brood produces a single soldier larva, and that the soldier probably survives and grows gradually during host development. Additionally, we found that female broods were larger than male broods during development and also upon emergence. Accordingly, body size was larger for males during development as well as upon emergence. These findings may extend the existing knowledge on polyembryonic development in general, and serve as a baseline for further experiments.

Analysis of the locomotor activity of a nocturnal desert lizard (Reptilia: Gekkonidae: Teratoscincus scincus) under varying moonlight.

1. This project seeks to identify determinants of the variation observed in the foraging behavior of predatory animals, especially in moonlight, using a lizard as a model. 2. Moonlight generally enhances the foraging efficiency of nocturnal visual predators and often depresses the locomotor activity of prey animals. Previous evidence has indicated for three different nocturnal species of smallish gecko lizards that they respond to moonlight by increasing their activity. 3. In this study some aspects of the foraging activity of the somewhat larger nocturnal psammophilous Teratoscincus scincus, observed near Repetek and Ashgabat, Turkmenistan, were significantly depressed by moonlight, while several confounding factors (sex, maturity, size, sand temperature, hour, prior handling and observer effect) were taken into account. 4. This behavioral difference may relate to the eye size of the various species. 5. Additionally, a novel method of analyzing foraging behavior shows that in this species the duration of moves increases the duration of subsequent stationary pauses. Measurement of locomotor speed, yielding an average speed of 220% of the maximum aerobic speed, indicates a need for these pauses. Secondarily, pause duration decreases the duration of subsequent moves, precluding escalation of move duration. 6. The results of this and related projects advocate the taking into account of physiological and environmental factors that may affect an animal's foraging behavior.

Efficiency evaluation of two competing foraging modes under different conditions.

Various foraging modes are employed by predators in nature, ranging from ambush to active predation. Although the foraging mode may be limited by physiological constraints, other factors, such as prey behavior and distribution, may come into play. Using a simulation model, we tested to what extent the relative success of an ambush and an active predator changes as a function of the relative velocity and movement directionality of prey and active predator. In accordance with previous studies, we found that when both active predator and prey use nondirectional movement, the active mode is advantageous. However, as movement becomes more directional, this advantage diminishes gradually to 0. Previous theoretical studies assumed that animal movement is nondirectional; however, recent field observations show that in fact animal movement usually has some component of directionality. We therefore suggest that our simulation is a better predictor of encounter rates than previous studies. Furthermore, we show that as long as the active predator cannot move faster than its prey, it has little or no advantage over the ambush predator. However, as the active predator's velocity increases, its advantage increases sharply.