In the land of the blind: Exceptional subterranean speciation of cryptic troglobitic spiders of the genus Tegenaria (Araneae: Agelenidae) in Israel.

Caves have long been recognized as a window into the mechanisms of diversification and convergent evolution, due to the unique conditions of isolation and life in the dark. These lead to adaptations and reduce dispersal and gene flow, resulting in high levels of speciation and endemism. The Israeli cave arachnofauna remains poorly known, but likely represents a rich assemblage. In a recent survey, we found troglophilic funnel-web spiders of the genus Tegenaria in 26 caves, present mostly at the cave entrance ecological zone. In addition, we identified at least 14 caves inhabited by troglobitic Tegenaria, which are present mostly in the twilight and dark ecological zones. Ten of the caves, located in the north and center of Israel, are inhabited by both troglophilic and troglobitic Tegenaria. These spiders bear superficial phenotypic similarities but differ in the levels of eye reduction and pigmentation. To test whether these taxa constitute separate species, as well as understand their relationships to epigean counterparts, we conducted a broad geographic sampling of cave-dwelling Tegenaria in Israel and Palestine, using morphological and molecular evidence. Counterintuitively, our results show that the troglobitic Tegenaria we studied are distantly related to the troglophilic Tegenaria found at each of the cave entrances we sampled. Moreover, seven new troglobitic species can be identified based on genetic differences, eye reduction level, and features of the female and male genitalia. Our COI analysis suggest that the Israeli troglobitic Tegenaria species are more closely related to eastern-Mediterranean congeners than to the local sympatric troglophile Tegenaria species, suggesting a complex biogeographic history.

Recent speciation and phenotypic plasticity within a parthenogenetic lineage of levantine whip spiders (Chelicerata: Amblypygi: Charinidae).

Caves constitute ideal study systems for investigating adaptation and speciation, as the abiotic conditions shared by aphotic habitats exert a set of environmental filters on their communities. Arachnids constitute an important component of many cave ecosystems worldwide. We investigated the population genomics of two whip spider species: Sarax ioanniticus, a widely distributed parthenogenetic species found across the eastern Mediterranean; and S. israelensis, a recently described troglomorphic species that is endemic to caves in Israel. Here, we show that S. israelensis is completely genetically distinct from S. ioanniticus and most likely also a parthenogen. Counterintuitively, despite the lack of genetic variability within S. ioanniticus and S. israelensis, we discovered considerable variation in the degree of median eye reduction, particularly in the latter species. Natural history data from captive-bred specimens of S. israelensis validated the interpretation of parthenogenesis. Our results are most consistent with a scenario of a sexual ancestral species that underwent speciation, followed by independent transitions to apomictic parthenogenesis in each of the two daughter species. Moreover, the lack of genetic variability suggests that variation in eye morphology in S. israelensis is driven exclusively by epigenetic mechanisms.

Phylogenomics of Scorpions Reveal Contemporaneous Diversification of Scorpion Mammalian Predators and Mammal-Active Sodium Channel Toxins.

Scorpions constitute a charismatic lineage of arthropods and comprise more than 2500 described species. Found throughout various tropical and temperate habitats, these predatory arachnids have a long evolutionary history, with a fossil record that began in the Silurian. While all scorpions are venomous, the asymmetrically diverse family Buthidae harbors nearly half the diversity of extant scorpions, and all but one of the 58 species that are medically significant to humans. However, the lack of a densely sampled scorpion phylogeny has hindered broader inferences of the diversification dynamics of scorpion toxins. To redress this gap, we assembled a phylogenomic data set of 100 scorpion venom gland transcriptomes and genomes, emphasizing the sampling of highly toxic buthid genera. To infer divergence times of venom gene families, we applied a phylogenomic node dating approach for the species tree in tandem with phylostratigraphic bracketing to estimate the minimum ages of mammal-specific toxins. Our analyses establish a robustly supported phylogeny of scorpions, particularly with regard to relationships between medically significant taxa. Analysis of venom gene families shows that mammal-active sodium channel toxins (NaTx) have independently evolved in five lineages within Buthidae. Temporal windows of mammal-targeting toxin origins are correlated with the basal diversification of major scorpion mammal predators such as shrews, bats, and rodents. These results suggest an evolutionary model of relatively recent diversification of buthid NaTx homologs in response to the diversification of scorpion predators. [Adaptation; arachnids; phylogenomic dating; phylostratigraphy; venom.].

Five-Year Monitoring of a Desert Burrow-Dwelling Spider Following an Environmental Disaster Indicates Long-Term Impacts.

Deserts are characterized by unpredictable precipitation and extreme temperatures. Their fauna and flora are sensitive to anthropogenic environmental changes, and often recover slowly from environmental disasters. The effects of oil spills on the biota of desert regions, however, have scarcely been studied. We predicted that terrestrial invertebrates suffer long-term negative effects from an oil spill, due to their close association with the substrate. Thus, we investigated the effects of two oil spills that occurred in 1975 and 2014 in the hyper-arid 'Arava desert (Israel), on a spider that constructs silk-lined nests in burrows in compact, sandy soil in this extreme desert habitat. The spider, Sahastata aravaensis sp. nov. (Filistatidae), is described herein. We assessed spider burrow abundance in plots located in oil-contaminated and nearby uncontaminated clean soil (control) areas over five consecutive years and measured habitat characteristics in these plots. In the laboratory, we determined the preference of individuals for clean vs. oil-contaminated soil as a resting substrate. Finally, as this species was previously undescribed, we added a new species description. The abundance of Sahastata was significantly lower in oil-contaminated plots, and this was the case in the 40-year-old oil spill (1975) as well as in the recent one (2014). In laboratory tests, spiders showed a significant preference for the clean soil substrate over the oil-contaminated substrate. In the field, soil crust hardness and vegetation density did not differ significantly between oil-contaminated and control plots, but these measures were highly variable. The burrows were significantly clustered, suggesting that the young disperse only short distances. In the laboratory adult spiders did not dig burrows, perhaps indicating that adults remain permanently in their natal burrows and that in the field they may use vacant burrows. We conclude that Sahastata populations were affected negatively by the oil spills and these effects were long-lasting. We propose that by monitoring their spatial distribution, burrow-dwelling spiders such as Sahastata can be used as effective bioindicators of soil pollution in desert habitats.

Taxonomic Sampling and Rare Genomic Changes Overcome Long-Branch Attraction in the Phylogenetic Placement of Pseudoscorpions.

Long-branch attraction is a systematic artifact that results in erroneous groupings of fast-evolving taxa. The combination of short, deep internodes in tandem with long-branch attraction artifacts has produced empirically intractable parts of the Tree of Life. One such group is the arthropod subphylum Chelicerata, whose backbone phylogeny has remained unstable despite improvements in phylogenetic methods and genome-scale data sets. Pseudoscorpion placement is particularly variable across data sets and analytical frameworks, with this group either clustering with other long-branch orders or with Arachnopulmonata (scorpions and tetrapulmonates). To surmount long-branch attraction, we investigated the effect of taxonomic sampling via sequential deletion of basally branching pseudoscorpion superfamilies, as well as varying gene occupancy thresholds in supermatrices. We show that concatenated supermatrices and coalescent-based summary species tree approaches support a sister group relationship of pseudoscorpions and scorpions, when more of the basally branching taxa are sampled. Matrix completeness had demonstrably less influence on tree topology. As an external arbiter of phylogenetic placement, we leveraged the recent discovery of an ancient genome duplication in the common ancestor of Arachnopulmonata as a litmus test for competing hypotheses of pseudoscorpion relationships. We generated a high-quality developmental transcriptome and the first genome for pseudoscorpions to assess the incidence of arachnopulmonate-specific duplications (e.g., homeobox genes and miRNAs). Our results support the inclusion of pseudoscorpions in Arachnopulmonata (new definition), as the sister group of scorpions. Panscorpiones (new name) is proposed for the clade uniting Scorpiones and Pseudoscorpiones.

Genetic improvement of wheat early vigor promote weed-competitiveness under Mediterranean climate.

Chemical weed-control is the most effective practice for wheat, however, rapid evolution of herbicide-resistant weeds threat food-security and calls for integration of non-chemical practices. We hypothesis that integration of alternative GA-responsive dwarfing genes into elite wheat cultivars can promote early vigor and weed-competitiveness under Mediterranean climate. We develop near-isogenic lines of bread wheat cultivars with GAR dwarfing genes and evaluate them for early vigor and weed-competitiveness under various environmental and management conditions to identify promising NIL for weed-competitiveness and grain yield. While all seven NILs responded to external gibberellic acid application, they exhibited differences in early vigor. Greenhouse and field evaluations highlighted NIL OC1 (Rht8andRht12) as a promising line, with significant advantage in canopy early vigor over its parental. To facilitate accurate and continuous early vigor data collection, we applied non-destructive image-based phenotyping approaches which offers non-expensive and end-user friendly solution for selection. NIL OC1 was tested under different weed density level, infestation waves, and temperatures and highlight the complex genotypic × environmental × management interactions. Our findings demonstrate the potential of genetic modification of dwarfing genes as promising approach to improve weed-competitiveness, and serve as basis for future breeding efforts to support sustainable wheat production under semi-arid Mediterranean climate.

Systemic paralogy and function of retinal determination network homologs in arachnids.

BACKGROUND: Arachnids are important components of cave ecosystems and display many examples of troglomorphisms, such as blindness, depigmentation, and elongate appendages. Little is known about how the eyes of arachnids are specified genetically, let alone the mechanisms for eye reduction and loss in troglomorphic arachnids. Additionally, duplication of Retinal Determination Gene Network (RDGN) homologs in spiders has convoluted functional inferences extrapolated from single-copy homologs in pancrustacean models. RESULTS: We investigated a sister species pair of Israeli cave whip spiders, Charinus ioanniticus and C. israelensis (Arachnopulmonata, Amblypygi), of which one species has reduced eyes. We generated embryonic transcriptomes for both Amblypygi species, and discovered that several RDGN homologs exhibit duplications. We show that duplication of RDGN homologs is systemic across arachnopulmonates (arachnid orders that bear book lungs), rather than being a spider-specific phenomenon. A differential gene expression (DGE) analysis comparing the expression of RDGN genes in field-collected embryos of both species identified candidate RDGN genes involved in the formation and reduction of eyes in whip spiders. To ground bioinformatic inference of expression patterns with functional experiments, we interrogated the function of three candidate RDGN genes identified from DGE using RNAi in the spider Parasteatoda tepidariorum. We provide functional evidence that one of these paralogs, sine oculis/Six1 A (soA), is necessary for the development of all arachnid eye types. CONCLUSIONS: Our work establishes a foundation to investigate the genetics of troglomorphic adaptations in cave arachnids, and links differential gene expression to an arthropod eye phenotype for the first time outside of Pancrustacea. Our results support the conservation of at least one RDGN component across Arthropoda and provide a framework for identifying the role of gene duplications in generating arachnid eye diversity.

Good reasons to leave home: proximate dispersal cues in a social spider.

Natal dispersal is a successful tactic under a range of conditions in spite of significant costs. Habitat quality is a frequent proximate cause of dispersal, and studies have shown that dispersal increases both when natal habitat quality is good or poor. In social species kin competition, favouring dispersal may be balanced by the benefits of group living, favouring philopatry. We investigated the effect of changes in the local environment on natal dispersal of adult females in a social spider species, Stegodyphus dumicola (Araneae, Eresidae), with a flexible breeding system, where females can breed either within the colony or individually following dispersal. We manipulated foraging opportunities in colonies by either removing the capture webs or by adding prey and recorded the number of dispersing females around each focal colony, and their survival and reproductive success. We predicted that increasing kin competition should increase dispersal of less-competitive individuals, while reducing competition could cause either less dispersal (less competition) or more dispersal (a cue indicating better chances to establish a new colony). Dispersal occurred earlier and at a higher rate in both food-augmented and web-removal colonies than in control colonies. Fewer dispersing females survived and reproduced in the web-removal group than in the control or food-augmented groups. The results support our prediction that worsening conditions in web-removal colonies favour dispersal, whereby increased kin competition and increased energy expenditure on web renewal cause females to leave the natal colony. By contrast, prey augmentation may serve as a habitat-quality cue; when the surrounding habitat is expected to be of high quality, females assess the potential benefit of establishing a new colony to be greater than the costs of dispersal.