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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, R 2  = 0.995, P  < 0.001) . Fat percentage regressed with body mass significantly predicted the DXA fat percentage ( N = 29, R 2 adj.   = 0.862, p < 0.001 ). Live wet mass was significantly correlated with predicted fat mass ( N  = 30, R 2  = 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 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.

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.

Coastal dune habitats have been declining globally over the last several decades due to rapid urbanization. Within remaining dune systems, dune fixation has resulted in further losses of mobile dunes with negative impacts on their associated species. Some studies suggest vegetation removal can initially promote habitat heterogeneity, and increase availability of suitable habitats for psammophile, xeric and endemic mobile dune species, but longer-term responses are generally unknown. We investigated the temporal trends of four taxonomic groups to determine the effect of vegetation removal on dune assemblages over a 12-year period at an LTER site. Three different forms of removal are investigated here—removal in a grid form on fixed dunes, removal of the wind-facing slope vegetation on semi-fixed dunes and opportunistic off-road driving on disturbed dunes. Results were varied across taxa, highlighting the need for multi-taxa monitoring in conservation and restoration management. Overall, fixed dune treatment had very little effect, while a stronger response was found in semi-fixed treatments in particular for mobile dune indicator species, which showed evidence of recolonization within a few years following treatment. Disturbed dunes were most similar to mobile dunes for animal taxa indicating that pulse removal may not be as effective as continuous press disturbance. Nevertheless, a less destructive form of disturbance such as re-introduction of grazing might be preferable and requires further investigation.

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.

Substantial evidence now suggests that a positive diversity–stability relationship exists. Yet few studies examine the facets of biodiversity that contribute to this relationship, and empirical research is predominantly conducted on grassland communities under controlled conditions. We investigate the roles of species richness, environmental condition (vegetation cover), asynchrony, and weighted population stability in driving community stability across multiple taxa. We used data from a Long-term Ecological Research project to investigate temporal stability of annual plants, beetles, reptiles, and rodents in Nizzanim Coastal Sand Dune Nature Reserve in Israel. All four taxa had a strong positive relationship between asynchrony and community stability. Only rodents showed a positive richness–stability relationship. Perennial plant cover had a significant relationship with community stability for three taxa, but the direction of the correlation varied. Asynchrony had a stronger relationship with perennial plant cover than it did with richness for both plants and beetles. We suggest that community stability is driven by asynchrony for flora as well as fauna. Stability appears to be determined by species’ interactions and their responses to the environment, and not always by diversity. This has important consequences for understanding the effects of environmental degradation on ecosystem stability and productivity, which have destabilizing consequences beyond biodiversity loss.

Ontogenetic habitat shifts have been documented in numerous fish and amphibians and in some reptiles. Intraspecific competition together with differential predation, prey size, social interactions, size-related thermal requirements, and morphological constraints on movement are often implicated in this ontogenetic habitat separation. In the current study, we combined field observation with experiments in seminatural arenas to test various hypotheses regarding the ontogenetic habitat shift that we have documented in the common chameleon. Juveniles (mean, 1 g) occupied low grasses and the adults (mean, 35 g) were found on bushes and trees. Overlap in habitat use between these two age classes was minimal. Our field experiments showed that juveniles actively avoid the presence of adults by concealment or flight. Adults readily attacked and consumed juveniles, regardless of their own mass. These results suggest that the risk of cannibalism towards juveniles is an important selective force behind the ontogenetic habitat shift observed in the common chameleon and may be important in other species too.

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.

The effects of predation risk from snakes on microhabitat use of kangaroo rats (Dipodomys deserti and D. merriami) was studied in the Mojave Desert. I concentrated on the effects of the predator on the foraging behavior of the rodents and eliminated effects of prey capture on prey population size. Foraging stations contained three seed trays, one in each of three microhabitats (Open, Bush, Grass). The amount of seed left in each tray after one night of foraging was used to assess the responses to predation risk and other foraging costs; additional data were collected during direct observations and by trapping. To investigate the effect of snakes on foraging and microhabitat use of kangaroo rate I manipulated snake presence at the stations. I studied the interactions between predation risk from snakes and moonlight by conducting experiments near full and new moon nights. Both species of kangaroo rats preferred to forage in the Open and avoided the Bush. The preference is opposite to the preference of the main rodent—eating snake at the study site, the sidewinder (Crotalus cerastes), which prefers the Bush over the Open. At stations with snakes, D. deserti reduced its foraging and avoided the Bush more than in control plots. However, D. merriami foraged more at stations with snakes. D. merriami thus foraged at the trays that were avoided by D. deserti and it reduced the risk of interference from the dominant D. deserti. In contrast to studies by other investigators, moonlight (which is associated with increased risk from owls) did not reduce the foraging or affect the micro habitat use of kangaroo rates in summer; moonlight effect was seen only in the fall, when snakes were not active. Unlike risk from owls, risk from snakes is high under bushes and during dark nights. The activity or rodents in summer is a combined reaction to the different predation risks posed by snakes and by owls.

ContextStudying biodiversity in light of increased fragmentation in agroecosystems requires the understanding of scale-dependent and multi-scale determinants of various community measures.ObjectivesIn a heterogeneous agro-landscape, we aimed to understand whether: (1) Reptile communities are affected by a certain variable that belongs to a particular scale, or, by a combination of variables at different scales, and (2) Reptile community measures are affected differentially by variables related to different scales.MethodsWe sampled reptiles in three 12.6 km2 land units by using 100 × 50 m plots within 27 natural habitat patches. We collected spatial information of different scale-oriented physical and biotic variables and analyzed changes in community measures at four scales—landscape, land unit, patch and plot—by using the model selection approach based on the AICc.ResultsMultiple-scale, rather than single-scale models, best explained all three community measures, indicating that the reptile community structure is highly affected by ecological processes operating at different scales, from the local up to the entire landscape scale. However, abundance, species richness and diversity were affected dissimilarly by different combined determinants and at different scales.ConclusionsReptile biodiversity at our heterogenous agro-landscape is highly influenced by determinants of multiple scales, where each scale has its contribution to the overall obtained pattern. Number of individuals and species richness respond differently to various processes, depending on the scale at which these processes operate. Agro-landscapes retain the complexity of ecological systems and can serve to maintain natural communities through land sharing practices.