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РИС. 4. Раковины анатомически проверенных особей H. zangezurica с раЗных участков. A. Типовое местонахождение (участок № 1). B. Шикахох (участок № 2). С. СраШен (участок № 4). D. Ваганаванк (участок № 7). МасШтаб 5 мм. in Harmozica zangezurica (Gastropoda, Pulmonata, Hygromiidae) - a cryptic species of land molluscs from southern Armenia
РИС. 4. Раковины анатомически проверенных особей H. zangezurica с раЗных участков. A. Типовое местонахождение (участок № 1). B. Шикахох (участок № 2). С. СраШен (участок № 4). D. Ваганаванк (участок № 7). МасШтаб 5 мм.
Social Context Affects Camouflage in a Cryptic Fish Species
<p>Crypsis, or the ability to avoid detection and/or recognition, is an important and widespread anti-predator strategy across the animal kingdom. Many animals are able to camouflage themselves by adapting their body colour to the local environment. In particular, rapid changes in body colour are often critical to the survival of cryptic prey which rely on evading detection by predators. This is especially pertinent for animals subject to spatiotemporal variability in their environment, as they must adapt to acute changes in their visual surroundings. However, which features of the local environment are most relevant is not well understood. In particular, little is known about how social context interacts with other environmental stimuli to influence crypsis. Here we use a common cryptic prey animal, the goby (Pseudogobius species 2) to examine how the presence and body colour of conspecifics influences the rate and extent to which gobies change colour. We find that solitary gobies change colour to match their background faster and to a greater extent than gobies in pairs. Further, we find that this relationship holds irrespective of the colour of nearby conspecifics. This study demonstrates the importance of social context in mediating colour change in cryptic animals.</p>
Uncovering cryptic pockets in the SARS-CoV-2 spike glycoprotein
<p>The COVID-19 pandemic has prompted a rapid response in vaccine and drug development targeting SARS-CoV-2. Herein, we modelled a complete membrane-embedded SARS-CoV-2 spike (S) protein and used molecular dynamics (MD) simulations in the presence of benzene probes designed to enhance discovery of cryptic, potentially druggable pockets. This approach recapitulated lipid binding sites previously characterized by cryo-electron microscopy, and uncovered a novel cryptic pocket with promising druggable properties located underneath the 617-628 loop, which was shown to be involved in modulating the stability of cleaved S protein trimers a well as the formation of S protein multimers on the viral surface. A multi-conformational behaviour of this loop in simulations was validated using hydrogen-deuterium exchange mass spectrometry (HDX-MS) experiments, supportive of opening and closing dynamics. The pocket is the site of multiple mutations associated with increased transmissibility and severity of infection found in SARS-CoV-2 variants of concern including D614G. Collectively, this work highlights the utility of the benzene mapping approach in uncovering potential druggable sites on the surface of SARS-CoV-2 targets.</p> <p> </p>
Bemisia tabaci cryptic species: supplementary materials
<p>This archive contains supplementary materials relating to the investigation of morphological differences in Bemisia tabcai puparia as rescribed in <span>MacLeod, N., Canty, R.J., and Polazek, A., 2022, Morphology-based identification of Bemisia tabaci cryptic species puparia via embedded group-contrast convolution neural network analysis: Systematic Biology. The materials archived include (1) and inventory of all puparial images, (2) full sets of results files for the image-based t-SNE and embedded, group-contrasts CNN analyses, (3) Wolfram Mathematical™ scripting code lisitngs for the image processing and CNN software used in the analysis.</span></p>
Supplementary material for "Oikopleura dioica, the cosmopolitan appendicularian hides multiple cryptic species around the globe"
<p>18S and ITS sequences used to estimate phylogenetic trees for "Oikopleura dioica, the cosmopolitan appendicularian hides multiple cryptic species around the globe." To identify 18S rDNA genes from genome sequences, we searched genome sequences for the best-hit matches to the Rfam models for the eukaryotic small subunit (SSU; RF01960) and large subunit (LSU; RF02543) using cmsearch of the Infernal package (v.1.1.4). The SSU and LSU models from Rfam were downloaded in April 2021. The internal transcribed spacer (ITS) regions were obtained by extracting the region between SSU and LSU.<strong> </strong>Multiple sequence alignments for the 18S and ITS regions were created with MUSCLE (v5) within Seaview (v.3.2).</p>
Fig. 6 in A new semi-cryptic Filistata from caves in the Levant with comments on the limits of Filistata insidiatrix (Forsskål, 1775) (Arachnida: Araneae: Filistatidae)
Fig. 6. Filistata insidiatrix (Forsskål, 1775), left bulb, prolateral (A, C, E, G) and dorsal (B, D, F, H) views. A–B. France (MACN-Ar 39461, ♂ collected with ♀ IFM-1702). C–D. Spain (CRBA IFM-2196). E–F. Israel, Ornit cave (MACN-Ar 41813, IFM-2175). G–H. Israel, Sharakh cave (MACN-Ar 41218, IFM-2144). Scale bar = 0.1 mm, all figures to scale.
Fig. 10. Filistatid morphology. A in A new semi-cryptic Filistata from caves in the Levant with comments on the limits of Filistata insidiatrix (Forsskål, 1775) (Arachnida: Araneae: Filistatidae)
Fig. 10. Filistatid morphology. A. Filistata insidiatrix (Forsskål, 1775), ♀, leg tarsus, arrow points to macrosetae. B. Pritha nana (Simon, 1968), arrow points to right calamistrum. C. Sahastata aravaensis Ganem et al., 2022, left calamistrum. D. Zaitunia schmitzi Kulczyński, 1911, left calamistrum, arrow points to gap between setae. E. Filistata insidiatrix, left calamistrum. F. Filistata lubinae Zonstein & Marusik, 2019, ♂, tarsus I. G. Sahastata aravaensis, ♀. H. Pritha IFMsp185, ♀. I. Pritha sp., male abdomen, dorsal view. J. Zaitunia schmitzi, ♂. K. Zaitunia schmitzi, spermathecae ventral view. L. Pritha tenuispina (Strand, 1914), ♂, left pedipalp, prolateral view, arrow points to cymbium. M. Filistata lubinae, left copulatory bulb, prolateral view. N. Zaitunia schmitzi, ♂, left pedipalp, prolateral view, arrow points to cymbium. O. Filistata albens Zonstein & Marusik, 2019, left copulatory bulb, prolateral view. P. Zaitunia schmitzi, male clypeus, lateral view, arrow points to stout setae. Q. Filistata insidiatrix, female clypeus, lateral view. Scale bars = 0.2 mm.
Fig. 2 in A new semi-cryptic Filistata from caves in the Levant with comments on the limits of Filistata insidiatrix (Forsskål, 1775) (Arachnida: Araneae: Filistatidae)
Fig. 2. Phylogenetic tree of cytochrome c oxidase subunit I haplotypes of different species of Filistata Latreille, 1810 inferred under maximum likelihood. Numbers below branches are bootstrap supports. The histogram shows the distribution of pairwise Kimura two-parameter genetic distances within and between F. insidiatrix (Forsskål, 1775) and F. betarif sp. nov. (for pairwise distances of other species, see Table 2). Note that some intraspecific genetic distances within F. insidiatrix are larger than interspecific distances between F. insidiatrix and F. betarif sp. nov., denoting a lack of a barcode gap in this group, or cryptic species within F. insidiatrix.
Fig. 8. A–G in A new semi-cryptic Filistata from caves in the Levant with comments on the limits of Filistata insidiatrix (Forsskål, 1775) (Arachnida: Araneae: Filistatidae)
Fig. 8. A–G. Filistata betarif sp. nov., holotype, ♂ (HUJ -INVAr 21058), left pedipalp. A–B, E. Prolateral view. Arrow points to prolateral strong setae in cymbium. C, F–G. Retrolateral view. Arrow points to embolic keel. D. Dorsal view. — H. Filistata insidiatrix (Forsskål, 1775) (MACN-Ar 39461), bulb, retrolateral view. Arrow points to embolic keel. Scale bars: A–F = 0.2 mm; G–H = 0.05 mm.
Fig. 9 in A new semi-cryptic Filistata from caves in the Levant with comments on the limits of Filistata insidiatrix (Forsskål, 1775) (Arachnida: Araneae: Filistatidae)
Fig. 9. Filistata betarif sp. nov., female spermathecae, ventral. A. Oah cave (HUJ-INVAr 21055). B. Tinshemet cave (MACN-Ar 41222). C–D. Tinshemet cave (MACN-Ar 41791). Scale bars: A–C = 0.2 mm; D = 0.05 mm.
Fig. 4. Distribution maps. A in A new semi-cryptic Filistata from caves in the Levant with comments on the limits of Filistata insidiatrix (Forsskål, 1775) (Arachnida: Araneae: Filistatidae)
Fig. 4. Distribution maps. A. Filistata insidiatrix (Forsskål, 1775) in the Mediterranean and Middle East (note the species has been recorded from Angola, Venezuela and the islands of Socotra, Azores and Cabo Verde, but these records seem to be introduced); literature records have been taken from Benoit (1968), Brignoli (1982), Marusik & Zonstein (2014), Marusik & Zamani (2015a) and Zonstein & Marusik (2019). B. Filistata insidiatrix (circles) and F. betarif sp. nov. (star) in Israel and Palestine; only specimens examined by us are included in the map. Darker shades of orange are records that include at least one male specimen. C. Other species of Filistata Latreille, 1810 in Israel (except F. insidiatrix).
Fig. 7 in A new semi-cryptic Filistata from caves in the Levant with comments on the limits of Filistata insidiatrix (Forsskål, 1775) (Arachnida: Araneae: Filistatidae)
Fig. 7. Filistata betarif sp. nov., habitus. A–C. Holotype, ♂, from Tinshemet cave (HUJ -INVAr 21058). A. Dorsal view. B. Lateral view. C. Ventral view. — D–F. Paratype, ♀, from the same locality (MACN-Ar 41222). D. Lateral view. E. Dorsal view. F. Ventral view. Scale bars = 1 mm.
Fig. 5. A, C, E in A new semi-cryptic Filistata from caves in the Levant with comments on the limits of Filistata insidiatrix (Forsskål, 1775) (Arachnida: Araneae: Filistatidae)
Fig. 5. A, C, E. Filistata betarif sp. nov., paratype, ♂, from Israel, Tinshemet cave, (MACN-Ar 41793), left pedipalp. B, D, F. Filistata insidiatrix (Forsskål, 1775), ♂, from Spain, Mallorca (MACN-Ar 42347), right pedipalp, mirrored. A–B. Prolateral view. C–D. Dorsal view. E–F. Retrolateral view. Abbreviations: k = embolic keel; ps = prolateral setae. Scale bars = 0.1 mm.
Fig. 1. A–B in A new semi-cryptic Filistata from caves in the Levant with comments on the limits of Filistata insidiatrix (Forsskål, 1775) (Arachnida: Araneae: Filistatidae)
Fig. 1. A–B. Habitat and webs of Filistata betarif sp. nov. in Tinshemet cave. C. Paratype male in life (MACN-Ar 41793). D. Surroundings of Tinshemet cave. Note the entrance to the cave at the right side of the picture. Photos A–B by Shlomi Aharon and C–D by Ivan L.F. Magalhaes.
Fig. 3. A–G. Endogynes Filistata Latreille, 1810, ventral view. A in A new semi-cryptic Filistata from caves in the Levant with comments on the limits of Filistata insidiatrix (Forsskål, 1775) (Arachnida: Araneae: Filistatidae)
Fig. 3. A–G. Endogynes Filistata Latreille, 1810, ventral view. A. Filistata wunderlichi Zonstein & Marusik, 2019 from Spain, Boca de los Frailes (CRBA IFM-2197). B. Filistata IFMsp191 from Israel, Odem (MACN-Ar 41262). C. Filistata insidiatrix (Forsskål, 1775) from France, Gonfaron (MACN-Ar 39461). D. Filistata insidiatrix from Israel, Beriniki (HUJ-INVAr 21052). E. Filistata betarif sp. nov. from Israel, Oah cave (HUJ-INVAr 21055). F. Filistata betarif sp. nov. from Israel, Tinshemet cave (MACN-Ar 41222). G. Filistata IFMsp99 (subadult ♀?) from Palestine, En Fashkha (HUJ-INVAr 20277). — H–I. ♂♂, left pedipalp, prolateral. H. Filistata betarif sp. nov., holotype from Israel, Tinshemet cave (HUJ -INVAr 21058). I. Filistata insidiatrix from Spain, Mallorca (MACN-Ar 42346). Scale bar = 0.1 mm, all figures to scale. Colours correspond to clades in Fig. 2.
Figure 4 in Integrative taxonomy reveals cryptic diversity in North American Lasius ants, and an overlooked introduced species
Figure 4. Average thorax profile of Lasius ponderosae sp. nov. (a) and members of the Palearctic L. nigercomplex (b). Figures were created by image averaging (L. ponderosae sp. nov n = 35; Palearctic L. niger-complex n = 30 specimens). Frontal view of head and detail of clypeus of the Holotype worker of L. ponderosae sp. nov. (c) and a non-type worker of L. niger (d).
Figure 5. Principal component plot for the 4 in Integrative taxonomy reveals cryptic diversity in North American Lasius ants, and an overlooked introduced species
Figure 5. Principal component plot for the 4 most diagnostic morphometric variables (GUHL, dCLAN, MP6 and nSt) to distinguish individual specimens of Lasius ponderosae sp. nov. (n = 39) from those belonging to morphologically similar-looking Palearctic species (n = 49). For a definition of variables see Supplementary Table S3 and Fig. S1.
Figure 6 in Integrative taxonomy reveals cryptic diversity in North American Lasius ants, and an overlooked introduced species
Figure 6. Projected occurrence probability from ecological niche modeling for the Palearctic ant Lasius niger which has been introduced to Canada, based on 19 climatic and one land use variable. The intensity of blue colour indicates the probability of occurrence on a 0–1 scale based on 180 presences (black circles) and 182 absences (white circles) in the native range in the Old World (a). The model was then projected to North America to estimate areas of suitable habitat for this introduced species (b). These maps have been created using the free R-package "ggplot2" v3.3.5 (https://ggplot2.tidyverse.org) in R v4.1.1.
Figure 2. Mitotype tree and distribution maps for 98 in Integrative taxonomy reveals cryptic diversity in North American Lasius ants, and an overlooked introduced species
Figure 2. Mitotype tree and distribution maps for 98 DNA-barcodes belonging to 7 mitotypes of the ant Lasius niger (blue, n = 70) and 15 mitotypes of L. ponderosae sp. nov. (red, n = 28). The red dashed line delimits the expected natural range of L. ponderosae sp. nov.53 Maps have been created using the free R-package "ggmap" v3.0.0 (https://github.com/dkahle/ggmap) in R v4.1.1. Map tiles by Stamen Design, under CC BY 3.0.
Figure 3 in Integrative taxonomy reveals cryptic diversity in North American Lasius ants, and an overlooked introduced species
Figure 3. Frontal, lateral and dorsal view of the holotype worker (a–c), a paratype gyne (d–f) and a paratype male of Lasius ponderosae sp. nov. (g–i).
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