Collagen IV of basement membranes: II. Emergence of collagen IVα345 enabled the assembly of a compact GBM as an ultrafilter in mammalian kidneys

The collagen IVα345 (Col-IVα345) scaffold, the major constituent of the glomerular basement membrane (GBM), is a critical component of the kidney glomerular filtration barrier. In Alport syndrome, affecting millions of people worldwide, over two thousand genetic variants occur in the COL4A3, COL4A4, and COL4A5 genes that encode the Col-IVα345 scaffold. Variants cause loss of scaffold, a suprastructure that tethers macromolecules, from the GBM or assembly of a defective scaffold, causing hematuria in nearly all cases, proteinuria, and often progressive kidney failure. How these variants cause proteinuria remains an enigma. In a companion paper, we found that the evolutionary emergence of the COL4A3, COL4A4, COL4A5, and COL4A6 genes coincided with kidney emergence in hagfish and shark and that the COL4A3 and COL4A4 were lost in amphibians. These findings opened an experimental window to gain insights into functionality of the Col-IVα345 scaffold. Here, using tissue staining, biochemical analysis and TEM, we characterized the scaffold chain arrangements and the morphology of the GBM of hagfish, shark, frog, and salamander. We found that α4 and α5 chains in shark GBM and α1 and α5 chains in amphibian GBM are spatially separated. Scaffolds are distinct from one another and from the mammalian Col-IVα345 scaffold, and the GBM morphologies are distinct. Our findings revealed that the evolutionary emergence of the Col-IVα345 scaffold enabled the genesis of a compact GBM that functions as an ultrafilter. Findings shed light on the conundrum, defined decades ago, whether the GBM or slit diaphragm is the primary filter.

Metabarcoding of trap nests reveals differential impact of urbanization on cavity-nesting bee and wasp communities

Urbanization is affecting arthropod communities worldwide, for example by changing the availability of food resources. However, the strength and direction of a community's response is species-specific and depends on species' trophic level. Here, we investigated interacting species at different trophic levels in nests of cavity-nesting bees and wasps along two urbanization gradients in four German cities using trap nests. We analysed bee and wasp diversity and their trophic interaction partners by metabarcoding the DNA of bee pollen and preyed arthropods found in wasp nests. We found that the pollen richness increased with increasing distance from city centres and at sites characterized by a high percentage of impervious and developed surface, while the richness of pollinators was unaffected by urbanization. In contrast, species richness of wasps, but not their arthropod prey, was highest at sites with low levels of urbanization. However, the community structure of wasp prey changed with urbanization at both local and regional scales. Throughout the study area, the community of wasps consisted of specialists, while bee species were generalists. Our results suggest that Hymenoptera and their food resources are negatively affected by increasing urbanization. However, to understand distribution patterns of both, wasps and bees in urban settings other factors besides food availability should be considered.

A new species of Ellipsomyxa Køie, 2003 (Bivalvulida) infecting the gall bladder of Pangasius macronema Bleeker (Siluriformes: Pangasiidae) from the Mekong River Delta, Vietnam

During a parasitological survey of freshwater fishes in the Mekong River Delta, Vietnam, disporic plasmodia containing myxospores morphologically consistent with Ellipsomyxa Køie, 2003 (Bivalvulida) were observed infecting the gall bladder of Pangasius macronema Bleeker (Siluriformes: Pangasiidae). Herein, we use morphology and small subunit ribosomal DNA (SSU rDNA, 18S) sequence data to describe Ellipsomyxa intravesica Ksepka & Bullard n. sp. and relate it to other myxozoans. The new species resembles Ellipsomyxa adlardi Whipps & Font, 2013, which infects the naked goby, Gobiosoma bosc (Lacepede) (Gobiiformes: Gobiidae) in Lake Pontchartrain, Louisiana, but differs from it by having a longer myxospore (mean = 13.3; range = 12.0-15.0 vs. 12.4; 11.3-14.4) and shorter polar capsules (3.7; 3.0-4.0 vs. 4.3; 3.9-4.9). The 18S phylogenetic analysis recovered the sequence of the new species sister to those ascribed to Ellipsomyxa ariusi Chandran, Zacharia, Sathianandan & Sanil, 2020 and Ellipsomyxa sp. (MK561979); both of which infect the gall bladder of the threadfin sea catfish, Arius arius (Hamilton) (Siluriformes: Ariidiae) from the southwest coast of India. Consistent with previous phylogenetic analyses of Ellipsomyxa spp., Ellipsomyxa was recovered as monophyletic. The new species is the first species of Ellipsomyxa reported from a freshwater fish in Asia and the first myxozoan reported from P. macronema.

Evolution of neuronal cell classes and types in the vertebrate retina

The basic plan of the retina is conserved across vertebrates, yet species differ profoundly in their visual needs1. Retinal cell types may have evolved to accommodate these varied needs, but this has not been systematically studied. Here we generated and integrated single-cell transcriptomic atlases of the retina from 17 species: humans, two non-human primates, four rodents, three ungulates, opossum, ferret, tree shrew, a bird, a reptile, a teleost fish and a lamprey. We found high molecular conservation of the six retinal cell classes (photoreceptors, horizontal cells, bipolar cells, amacrine cells, retinal ganglion cells (RGCs) and Müller glia), with transcriptomic variation across species related to evolutionary distance. Major subclasses were also conserved, whereas variation among cell types within classes or subclasses was more pronounced. However, an integrative analysis revealed that numerous cell types are shared across species, based on conserved gene expression programmes that are likely to trace back to an early ancestral vertebrate. The degree of variation among cell types increased from the outer retina (photoreceptors) to the inner retina (RGCs), suggesting that evolution acts preferentially to shape the retinal output. Finally, we identified rodent orthologues of midget RGCs, which comprise more than 80% of RGCs in the human retina, subserve high-acuity vision, and were previously believed to be restricted to primates2. By contrast, the mouse orthologues have large receptive fields and comprise around 2% of mouse RGCs. Projections of both primate and mouse orthologous types are overrepresented in the thalamus, which supplies the primary visual cortex. We suggest that midget RGCs are not primate innovations, but are descendants of evolutionarily ancient types that decreased in size and increased in number as primates evolved, thereby facilitating high visual acuity and increased cortical processing of visual information.

TMPRSS2 is a functional receptor for human coronavirus HKU1

Four endemic seasonal human coronaviruses causing common colds circulate worldwide: HKU1, 229E, NL63 and OC43 (ref. 1). After binding to cellular receptors, coronavirus spike proteins are primed for fusion by transmembrane serine protease 2 (TMPRSS2) or endosomal cathepsins2-9. NL63 uses angiotensin-converting enzyme 2 as a receptor10, whereas 229E uses human aminopeptidase-N11. HKU1 and OC43 spikes bind cells through 9-O-acetylated sialic acid, but their protein receptors remain unknown12. Here we show that TMPRSS2 is a functional receptor for HKU1. TMPRSS2 triggers HKU1 spike-mediated cell-cell fusion and pseudovirus infection. Catalytically inactive TMPRSS2 mutants do not cleave HKU1 spike but allow pseudovirus infection. Furthermore, TMPRSS2 binds with high affinity to the HKU1 receptor binding domain (Kd 334 and 137 nM for HKU1A and HKU1B genotypes) but not to SARS-CoV-2. Conserved amino acids in the HKU1 receptor binding domain are essential for binding to TMPRSS2 and pseudovirus infection. Newly designed anti-TMPRSS2 nanobodies potently inhibit HKU1 spike attachment to TMPRSS2, fusion and pseudovirus infection. The nanobodies also reduce infection of primary human bronchial cells by an authentic HKU1 virus. Our findings illustrate the various evolution strategies of coronaviruses, which use TMPRSS2 to either directly bind to target cells or prime their spike for membrane fusion and entry.

Description of a new species, Pseudodiscocotyla mikiae n. sp. (Monogenea: Discocotylidae) parasitic on gills of Pristipomoides filamentosus from off Okinawa-jima island in Japan, with redescription of Pseudodiscocotyla opakapaka

Two species of Pseudodiscocotyla Yamaguti, 1965 (Monogenea: Discocotylidae) were collected from crimson jobfish Pristipomoides filamentosus (Valenciennes) (Perciformes: Lutjanidae) off Okinawa-jima island, southern Japan. Pseudodiscocotyla opakapaka is redescribed and represents the first Japanese record. A new species, Pseudodiscocotyla mikiae n. sp., differs from Ps. opakapaka in the absence of spines around the male genital pore, the shape of the vaginal pore, the presence of spines inside the vaginal pore, and the shape of the clamp. The locations of the male genital atrium and the vaginal pore in both species were similar, and the observed armament differences of the male copulatory organ are therefore presumed to establish reproductive isolation. The phylogenetic trees for the Mazocraeidea based on the partial 28S rDNA sequences were created using new sequences of Pseudodiscocotyla mikiae n. sp., and Discocotylidae formed a sister group with the species Diclidophoridae, Macrovalvitrematidae, and Plectanocotylidae. Pristipomoides filamentosus is widely distributed across the Indo-Pacific, and Pseudodiscocotyla mikiae n. sp. could share the distribution of the host.

Description and molecular data for a new acanthocephalan parasite, Polymorphus circi n. sp. (Polymorphidae) from the Australasian harrier (Circus approximans Peale) in New Zealand

Species of genus Polymorphus Lühe, 1911 (Polymorphidae) are acanthocephalans found in fish-eating birds and waterfowl. Although found in many parts of the world, including Australia, no records exist from New Zealand. Because of the largely aquatic intermediate host, Polymorphus species are rarely found in terrestrial birds of prey. During a study of the helminths of the Australasian harrier Circus approximans Peale specimens of Polymorphus were recovered that were found to be new to science. Polymorphus circi n. sp. is formally described and genetic sequence data presented. Specimens were distinguished from all other species by a combination of characters, including their proboscis hook arrangement (20-22 rows of 11-13 hooks), as well as absence of sexual dimorphism, trunk size, proboscis shape and egg size. These acanthocephalans were found in birds from areas with the potential to support freshwater, brackish or marine amphipods, but as yet the actual intermediate hosts are unknown.

Waynella nom. nov. (Siphonaptera: Ceratophyllidae), a new replacement name for Rowleyella Lewis, 1971, a junior homonym of Rowleyella Weller, 1911 (Brachiopoda: Meristidae)

Rowleyella Lewis, 1971, established for a genus of fleas, was found to be a junior homonym of the brachiopod genus Rowleyella Weller, 1911 and is therefore replaced by Waynella nom. nov., a substitute that preserves the meaning of the original name. The four previously included nominal species, viz., Rowleyella arborea Lewis, 1971 (type-species), R. gongshanensis Gong and Duan, 1989, R. nujiangensis Lin and Xie, 1990 and R. fugongensis Gong and Li, 2020, are accordingly now to be called Waynella arborea (Lewis, 1971) n. comb., W. gongshanensis (Gong and Duan, 1989) n. comb., W. nujiangensis (Lin and Xie, 1990) n. comb. and W. fugongensis (Gong and Li, 2020) n. comb., respectively.

New species of Foleyellides (Nematoda: Onchocercidae: Waltonellinae), parasite of Lithobates brownorum (Amphibia: Ranidae) from South-eastern Mexico and genetic barcodes of the Mexican species of the genus

Specimens of Foleyellides were collected from the body cavity of frogs in different regions of Mexico; Lithobates brownorum from Yucatán, Quintana Roo and Campeche; L. megapoda from Jalisco and Rhinella marina, from Guerrero. Foleyellides calakmulesis n. sp. is described based on specimens found parasitizing L. brownorum. The new species is distinguished from the other members of the genus by the combination of the following male characters: four pairs of caudal papillae different in size and the presence of a preanal plaque. Partial DNA sequences of the mitochondrial Cytochrome Oxidase C, subunit I of the four known Mexican species of Foleyellides and two potentially new species collected in this study were generated and compared, validating the erection of the new species.

A new species of Eutrombicula Ewing, 1938 (Trombidiformes: Trombiculidae) from the Galápagos Islands, with a checklist of Ecuadorian chiggers

Few studies have been carried out on the Ecuadorian chigger fauna. In this study, we are describing a new species of Eutrombicula from the Galápagos Islands. Also, we provide an updated checklist of Ecuadorian and Galápagos Islands chiggers, including a new host association and locality record for Eutrombicula nerudai Stekolnikov and González-Acuña.

Cataphryxus zapoteca sp. nov. (Isopoda, Bopyridae) and new hosts and records of bopyrid isopods from the Mexican Eastern Pacific

Based on the examination of diverse crustacean taxa collected along the Mexican Pacific and deposited in the Colección Nacional de Crustáceos of the Instituto de Biología, UNAM, six species of bopyrid isopods were detected. New hosts and localities are reported for Munidion pleuroncodis Markham, 1975, Probopyrus pacificensis Román-Contreras, 1993, Probopyrus markhami Román-Contreras, 1996, Progebiophilus bruscai Salazar-Vallejo & Leija-Tristán, 1990 and Schizobopyrina striata (Nierstrasz & Brender à Brandis, 1929). Cataphryxus zapoteca sp. nov., is described as abdominal parasite of the shrimp Lysmata galapagensis Schmitt; this bopyrid is the second species described in the genus Cataphryxus Shiino, 1936 and the first registered on the American continent. Taxonomic characters, distribution and some reproductive data for five of the six species examined are provided in order to update the knowledge of this parasite group in this Eastern Pacific region.

Two new species of Dichelyne Jägerskiöld, 1902 (Nematoda: Cucullanidae) parasitising marine fishes in Iraq

Recent examinations of some marine fishes from off the southern coast of Iraq revealed the presence of two new species of Dichelyne (Dichelyne) Jägerskiöld, 1902 (Nematoda: Cucullanidae), both intestinal parasites, namely: D. (D.) lethrini n. sp. from the smalltooth emperor Lethrinus microdon Valenciennes (Lethrinidae, Acanthuriformes) and D. (D.) iraqiensis n. sp. from the humphead snapper Lutjanus sanguineus (Cuvier) (Lutjanidae, Acanthuriformes). Specimens are described and illustrated based on light and scanning electron microscopical examinations. Dichelyne (D.) lethrini n. sp. is mainly characterised by the length of spicules (522 µm), presence of a dorsal caecum, location of deirids at the level of the posterior end of oesophagus and the post-oesophageal position of the excretory pore, number (10 pairs) and distribution of caudal papillae in the male, and the presence of two minute terminal spines on the female tail tip. Dichelyne (D.) iraqiensis n. sp. differs from the species of the subgenus Dichelyne mainly based on the absence of caudal spines, the presence of a dorsal caecum, the length of spicules (789-884 µm), the location of deirids and the excretory pore approximately at the same level, and the size of eggs (72-78 × 42-51 µm). These new species infecting marine fishes in Iraq represent new geographic records of cucullanids of the subgenus Dichelyne from fishes in marine waters off Iraq.

Bacterial diversity in arboreal ant nesting spaces is linked to colony developmental stage

The omnipresence of ants is commonly attributed to their eusocial organization and division of labor, however, bacteria in their nests may facilitate their success. Like many other arboreal ants living in plant-provided cavities, Azteca ants form dark-colored "patches" in their nesting space inside Cecropia host plants. These patches are inhabited by bacteria, fungi and nematodes and appear to be essential for ant colony development. Yet, detailed knowledge of the microbial community composition and its consistency throughout the life cycle of ant colonies was lacking. Amplicon sequencing of the microbial 16S rRNA genes in patches from established ant colonies reveals a highly diverse, ant species-specific bacterial community and little variation within an individual ant colony, with Burkholderiales, Rhizobiales and Chitinophagales being most abundant. In contrast, bacterial communities of early ant colony stages show low alpha diversity and no ant species-specific community composition. We suggest a substrate-caused bottleneck after vertical transmission of the bacterial patch community from mother to daughter colonies. The subsequent ecological succession is driven by environmental parameters and influenced by ant behavior. Our study provides key information for future investigations determining the functions of these bacteria, which is essential to understand the ubiquity of such patches among arboreal ants.

Excised leaves show limited and species-specific effects on photosynthetic parameters across crop functional types

Photosynthesis is increasingly becoming a recognized target for crop improvement. Phenotyping photosynthesis-related traits on field-grown material is a key bottleneck to progress here due to logistical barriers and short measurement days. Many studies attempt to overcome these challenges by phenotyping excised leaf material in the laboratory. To date there are no demonstrated examples of the representative nature of photosynthesis measurements performed on excised leaves relative to attached leaves in crops. Here, we tested whether standardized leaf excision on the day prior to phenotyping affected a range of common photosynthesis-related traits across crop functional types using tomato (C3 dicot), barley (C3 monocot), and maize (C4 monocot). Potentially constraining aspects of leaf physiology that could be predicted to impair photosynthesis in excised leaves, namely leaf water potential and abscisic acid accumulation, were not different between attached and excised leaves. We also observed non-significant differences in spectral reflectance and chlorophyll fluorescence traits between the treatments across the three species. However, we did observe some significant differences between traits associated with gas exchange and photosynthetic capacity across all three species. This study represents a useful reference for those who perform measurements of this nature and the differences reported should be considered in associated experimental design and statistical analyses.

Using geometric wing morphometrics to distinguish Aedes japonicus japonicus and Aedes koreicus

BACKGROUND

Aedes japonicus japonicus (Theobald, 1901) and Aedes koreicus (Edwards, 1917) have rapidly spread in Europe over the last decades. Both species are very closely related and occur in sympatry. Females and males are difficult to distinguish. However, the accurate species discrimination is important as both species may differ in their vectorial capacity and spreading behaviour. In this study, we assessed the potential of geometric wing morphometrics as alternative to distinguish the two species.

METHODS

A total of 147 Ae. j. japonicus specimens (77 females and 70 males) and 124 Ae. koreicus specimens (67 females and 57 males) were collected in southwest Germany. The left wing of each specimen was removed, mounted and photographed. The coordinates of 18 landmarks on the vein crosses were digitalised by a single observer. The resulting two-dimensional dataset was used to analyse the differences in the wing size (i.e. centroid size) and wing shape between Ae. j. japonicus and Ae. koreicus using geometric morphometrics. To analyse the reproducibility of the analysis, the landmark collection was repeated for 20 specimens per sex and species by two additional observers.

RESULTS

The wing size in female Ae. koreicus was significantly greater than in Ae. j. japonicus but did not differ significantly for males. However, the strong overlap in wing size also for the females would not allow to discriminate the two species. In contrast, the wing shape clustering was species specific and a leave-one-out validation resulted in a reclassification accuracy of 96.5% for the females and 91.3% for the males. The data collected by different observers resulted in a similar accuracy, indicating a low observer bias for the landmark collection.

CONCLUSIONS

Geometric wing morphometrics provide a reliable and robust tool to distinguish female and male specimens of Ae. j. japonicus and Ae. koreicus.

Species differences in hormonally mediated gene expression underlie the evolutionary loss of sexually dimorphic coloration in Sceloporus lizards

Phenotypic sexual dimorphism often involves the hormonal regulation of sex-biased expression for underlying genes. However, it is generally unknown whether the evolution of hormonally mediated sexual dimorphism occurs through upstream changes in tissue sensitivity to hormone signals, downstream changes in responsiveness of target genes, or both. Here, we use comparative transcriptomics to explore these possibilities in 2 species of Sceloporus lizards exhibiting different patterns of sexual dichromatism. Sexually dimorphic S. undulatus develops blue and black ventral coloration in response to testosterone, while sexually monomorphic S. virgatus does not, despite exhibiting similar sex differences in circulating testosterone levels. We administered testosterone implants to juveniles of each species and used RNAseq to quantify gene expression in ventral skin. Transcriptome-wide responses to testosterone were stronger in S. undulatus than in S. virgatus, suggesting species differences in tissue sensitivity to this hormone signal. Species differences in the expression of genes for androgen metabolism and sex hormone-binding globulin were consistent with this idea, but expression of the androgen receptor gene was higher in S. virgatus, complicating this interpretation. Downstream of androgen signaling, we found clear species differences in hormonal responsiveness of genes related to melanin synthesis, which were upregulated by testosterone in S. undulatus, but not in S. virgatus. Collectively, our results indicate that hormonal regulation of melanin synthesis pathways contributes to the development of sexual dimorphism in S. undulatus, and that changes in the hormonal responsiveness of these genes in S. virgatus contribute to the evolutionary loss of ventral coloration.

Species-specific traits affect bird species' susceptibility to global change

The current ecological crisis has risen extinction rates to similar levels of ancient mass extinctions. However, it seems to not be acting uniformly across all species but affecting species differentially. This suggests that species' susceptibility to the extinction process is mediated by specific traits. Since understanding this response mechanism at large scales will benefit conservation effort around the world, we used the IUCN global threat status and population trends of 8281 extant bird species as proxies of the extinction risk to identify the species-specific traits affecting their susceptibility to extinction within the biogeographic regions and at the global scale. Using linear mixed effect models and multinomial models, we related the global threat status and the population trends with the following traits: migratory strategy, habitat and diet specialization, body size, and generation length. According to our results and independently of the proxy used, more vulnerable species are sedentary and have larger body size, longer generation time, and higher degree of habitat specialization. These relationships apply globally and show little variation across biogeographic regions. We suggest that such concordant patterns might be caused either by a widespread occurrence of the same threats such as habitat modification or by a uniform capacity of some traits to reflect the impact of different local threats. Regardless of the cause of this pattern, our study identified the traits that affect species' response capability to the current ecological crisis. Conservation effort should focus on the species with trait values indicating the limited response capacity to overcome this crisis.

Meeting Ferret Enrichment Needs in Infectious Disease Laboratory Settings

Environmental enrichment is a necessary component of all research vivarium settings. However, appropriate enrichment decisions vary greatly depending on the species involved and the research use of the animals. The increasing use of ferrets in research settings-notably for modeling the pathogenicity and transmissibility of viral pathogens that require containment in ABSL-2 to -4 environments-presents a particular challenge for veterinary and research staff to ensure that enrichment needs for these animals are met consistently. Here, we discuss the species-specific enrichment needs of ferrets, enrichment considerations for ferrets housed in research settings, and the challenges and importance of providing appropriate enrichment during experimentation, including when ferrets are housed in high-containment facilities. This article is organized to support the easy availability of information that will facilitate the design and implementation of optimal environmental enrichment for ferrets used in diverse research efforts in vivarium settings.

Broad spectrum and species specificity of plant allelochemicals 1,2-benzenediol and 3-indoleacrylic acid against marine and freshwater harmful algae

Allelochemicals derived from plants have shown great potential in mitigating harmful algal blooms (HABs), although different algal species can respond differently to these chemicals. Therefore, we first investigated the allelopathic effects of two newly identified plant-derived allelochemicals, 1,2-benzenediol (1,2-BD) and 3-indoleacrylic acid (3-IDC), on six algal species. Then we further evaluated the allelopathic responses of two bloom-forming species, Microcystis aeruginosa FACHB-905 and Heterosigma akashiwo to 1,2-BD. Results showed that 1,2-BD had a broader antialgal spectrum than 3-IDC. Allelopathic response analysis indicated that 1,2-BD consistently and stably inhibit the growth of M. aeruginosa FACHB-905, with inhibitory mechanism being disruption of photosynthetic activity, overwhelming of the antioxidant system and activation of programmed cell death (PCD). H. akashiwo displayed resistance to 1,2-BD during exposure, and the growth inhibition was mainly attributed to PCD. Therefore, the species-specific allelopathic responses provide new insights for controlling HABs using 1,2-BD and 3-IDC.

Sensitivity of habitat network models to changes in maximum dispersal distance

Predicting the presence or absence (occurrence-state) of species in a certain area is highly important for conservation. Occurrence-state can be assessed by network models that take suitable habitat patches as nodes, connected by potential dispersal of species. To determine connections, a connectivity threshold is set at the species' maximum dispersal distance. However, this requires field observations prone to underestimation, so for most animal species there are no trustable maximum dispersal distance estimations. This limits the development of accurate network models to predict species occurrence-state. In this study, we performed a sensitivity analysis of the performance of network models to different settings of maximum dispersal distance. Our approach, applied on six amphibian species in Switzerland, used habitat suitability modelling to define habitat patches, which were linked within a dispersal distance threshold to form habitat networks. We used network topological measures, patch suitability, and patch size to explain species occurrence-state in habitat patches through boosted regression trees. These modelling steps were repeated on each species for different maximum dispersal distances, including a species-specific value from literature. We evaluated mainly the predictive performance and predictor importance among the network models. We found that predictive performance had a positive relation with the distance threshold, and that almost none of the species-specific values from literature yielded the best performance across tested thresholds. With increasing dispersal distance, the importance of the habitat-quality-related variable decreased, whereas that of the topology-related predictors increased. We conclude that the sensitivity of these models to the dispersal distance parameter stems from the very different topologies formed with different movement assumptions. Most reported maximum dispersal distances are underestimated, presumably due to leptokurtic dispersal distribution. Our results imply that caution should be taken when selecting a dispersal distance threshold, considering higher values than those derived from field reports, to account for long-distance dispersers.

Mycorrhizal specificity differences in epiphytic habitat: three epiphytic orchids harbor distinct ecological and physiological specificity

Orchidaceae has diversified in tree canopies and accounts for 68% of vascular epiphytes. Differences in mycorrhizal communities among epiphytic orchids can reduce species competition for mycorrhizal fungi and contribute to niche partitioning, which may be a crucial driver of the unusual species diversification among orchids. Mycorrhizal specificity-the range of fungi allowing mycorrhizal partnerships-was evaluated by assessment of mycorrhizal communities in the field (ecological specificity) and symbiotic cultures in the laboratory (physiological specificity) for three epiphytic orchids inhabiting Japan. Mycorrhizal communities were assessed with co-existing individuals growing within 10 cm of each other, revealing that ecological specificity varied widely among the three species, ranging from dominance by a single Ceratobasidiaceae fungus to diverse mycobionts across the Ceratobasidiaceae and Tulasnellaceae. In vitro seed germination tests revealed clear differences in physiological specificity among the three orchids, and that the primary mycorrhizal partners contributed to seed germination. In vitro compatibility ranges of three orchids strongly reflect the mycorrhizal community composition of wild populations. This suggests that differences in in situ mycorrhizal communities are not strongly driven by environmental factors, but are primarily due to physiological differences among orchid species. This study shows that the symbiotic strategy among the epiphytic orchid species varies from specialized to generalized association, which may contribute to biotic niche partitioning.

Sex differences in avoidance behavior and cued threat memory dynamics in mice: Interactions between estrous cycle and genetic background

Anxiety disorders are the most prevalent mental illnesses worldwide, exhibit high heritability, and affect twice as many women as men. To evaluate potential interactions between genetic background and cycling ovarian hormones on sex differences in susceptibility to negative valence behaviors relevant to anxiety disorders, we assayed avoidance behavior and cued threat memory dynamics in gonadally-intact adult male and female mice across four common inbred mouse strains: C57Bl/6J, 129S1/SVlmJ, DBA/2J, and BALB/cJ. Independent of sex, C57Bl/6J mice exhibited low avoidance but high threat memory, 129S1/SvlmJ mice high avoidance and high threat memory, DBA/2J mice low avoidance and low threat memory, and BALB/cJ mice high avoidance but low threat memory. Within-strain comparisons revealed reduced avoidance behavior in the high hormone phase of the estrous cycle (proestrus) compared to all other estrous phases in all strains except DBA/2J, which did not exhibit cycle-dependent behavioral fluctuations. Robust and opposing sex differences in threat conditioning and extinction training were found in the C57Bl/6J and 129S1/SvlmJ lines, whereas no sex differences were observed in the DBA/2J or BALB/cJ lines. C57Bl/6J males exhibited enhanced acute threat memory, whereas 129S1/SvlmJ females exhibited enhanced sustained threat memory, compared to their sex-matched littermates. These effects were not mediated by estrous cycle stage or sex differences in active versus passive defensive behavioral responses. Our data demonstrate that core features of behavioral endophenotypes relevant to anxiety disorders, such as avoidance and threat memory, are genetically driven yet dissociable and can be influenced further by cycling ovarian hormones.

Phenotypic molecular features of long-lived animal species

One of the challenges facing science/biology today is uncovering the molecular bases that support and determine animal and human longevity. Nature, in offering a diversity of animal species that differ in longevity by more than 5 orders of magnitude, is the best 'experimental laboratory' to achieve this aim. Mammals, in particular, can differ by more than 200-fold in longevity. For this reason, most of the available evidence on this topic derives from comparative physiology studies. But why can human beings, for instance, reach 120 years whereas rats only last at best 4 years? How does nature change the longevity of species? Longevity is a species-specific feature resulting from an evolutionary process. Long-lived animal species, including humans, show adaptations at all levels of biological organization, from metabolites to genome, supported by signaling and regulatory networks. The structural and functional features that define a long-lived species may suggest that longevity is a programmed biological property.

Global Analysis of 2-Hydroxy Fatty Acids by Gas Chromatography-Tandem Mass Spectrometry Reveals Species-Specific Enrichment in Echinoderms

Abnormal levels of 2-hydroxy fatty acids (2-OH FAs) are characterized in multiple diseases, and their quantification in foodstuffs is critical to identify the sources of supplementation for potential treatment. However, due to the structural complexity and limited available standards, the comprehensive profiling of 2-OH FAs remains an ongoing challenge. Herein, an innovative approach based on gas chromatography-tandem mass spectrometry (GC-MS/MS) was developed to determine the full profile of these FA metabolites. MS and MS/MS spectra of the trimethylsilyl (TMS) derivatives of 2-OH fatty acid methyl esters (FAMEs) were collected for peak annotation by their signature fragmentation patterns. The structures were further confirmed by validated structure-dependent retention time (RT) prediction models, taking advantage of the correlation between the RT, carbon chain length, and double bond number from commercial standards and pseudostandards identified in the whole-brain samples from mice. An in-house database containing 50 saturated and monounsaturated 2-OH FAs was established, which is expandible when additional molecular species with different chain lengths and backbone structures are identified in the future. A quantitation method was then developed by scheduled multiple reaction monitoring (MRM) and applied to investigate the profiling of 2-OH FAs in echinoderms. Our results revealed that the levels of total 2-OH FAs in sea cucumber Apostichopus japonicas (8.40 ± 0.28 mg/g dry weight) and starfish Asterias amurensis (7.51 ± 0.18 mg/g dry weight) are much higher than that in sea urchin Mesocentrotus nudus (531 ± 108 μg/g dry weight). Moreover, 2-OH C24:1 is the predominant molecular species accounting for 67.9% of the total 2-OH FA in sea cucumber, while 2-OH C16:0 is the major molecular species in starfish. In conclusion, the current innovative GC-MS approach has successfully characterized distinct molecular species of 2-OH FAs that are highly present in sea cucumbers and starfish. Thus, these findings suggest the possibility of developing future feeding strategies for preventing and treating diseases associated with 2-OH FA deficiency.

Fluid and particle retention in a small New World and a small Old World cervid, the southern pudu (Pudu puda) and Reeves's muntjac (Muntiacus reevesi)

Ruminants differ in the pattern how small particles and liquids pass through their gastrointestinal tract, and in particular their reticulorumen (RR). Based on that they may be classified into 'moose-type' and 'cattle-type' species (smaller and larger differences between particle and liquid passage, respectively). The ratio between the retention of particles and fluids is called the 'selectivity factor' (SF) and is a species-specific characteristic, studied in tragulids, giraffids and bovids, but not in many cervid species. Recently, it has been suggested that a high SF might also serve to wash digesta clean of external abrasives prior to regurgitation for rumination. In this study, we measured SF and passage kinetics (using a liquid marker and markers of different particle size, fed with the diet) in a capreoline deer, the southern pudu (Pudu puda, n = 5, 10.3 ± 2.9 kg, kept at two zoos) and a cervine deer, the Reeves's muntjac (Muntiacus reevesi, n = 6, 11.0 ± 1.7 kg, kept at a research facility). The relative daily dry matter intake (38 ± 3 g/kg0.75 for pudu and 76 ± 5 g/kg0.75 for muntjac) was higher, and the mean retention times (MRT) correspondingly shorter (e.g., MRT small particles in the total digestive tract 39 ± 8 h for pudu and 15 ± 2 h for muntjac), in the muntjac. The SF for small particles/liquid in the reticulorumen were, however, similar for both species, at 1.47 ± 0.21 for pudu and 1.66 ± 0.20 for muntjac, indicating a 'moose-type' physiology for both, irrespective of their different phylogenetic origin. To date, SF recorded in bovids attain distinctively higher values than the few reported for cervids. This situation reflects the degree of hypsodonty (tooth crown height) attained by these taxa, which is higher in bovids than in cervids. Together, constraints in hypsodonty as well as SF might limit cervids to more mesic habitats without distinct loads of external abrasives (such as dust or grit) on their food. In both species, some animals showed the typical ruminant pattern of a longer MRT for large than for small particle markers, but in some animals, this difference was not evident. This may be due to variable degrees of marker chewing during ingestion.

Modeling and comparing the distributions and associations of two co-occurring catshark species off South Africa

Holohalaelurus regani and Scyliorhinus capensis are relatively small catsharks, which both occur off the continental shelf around South Africa and are often caught together as by-catch in demersal trawls. The present study used data collected during annual demersal research surveys conducted between 2009 and 2015 and is a first attempt at modeling the potential intra- and interspecific associations, by maturity stage and depth, of H. regani and S. capensis to elucidate species-specific patterns in their distributions in South African waters. Intraspecifically, both species displayed a wide overlap in distribution between maturity stages, but only H. regani displayed marked changes in distribution with maturity stage, with mature individuals found further eastwards and occupying deeper waters than immature individuals. Interspecifically, the two catsharks displayed an inverse relationship in their distribution, with an increase in the abundance of H. regani and a decrease in the abundance of S. capensis when moving from the south coast to the west coast. Some localized patches of co-occurrence were, however, evident between species and maturity stages, especially in offshore areas. Overall, our results indicated a stronger co-occurrence of mature and immature stages within each species and a rather weak co-occurrence of maturity stages between the two species. The spatial information provided in the present study provides useful information on how sharks with similar morphologies and lifestyles may partition their habitat as a mechanism for potentially reducing competition between them.

A single polymorphic residue in humans underlies species-specific restriction of HSV-1 by the antiviral protein MxB

IMPORTANCE

Herpesviruses present a major global disease burden. Understanding the host cell mechanisms that block viral infections, as well as how viruses can evolve to counteract these host defenses, is critically important for understanding viral disease pathogenesis. This study reveals that the major human variant of the antiviral protein myxovirus resistance protein B (MxB) inhibits the human pathogen herpes simplex virus (HSV-1), whereas a minor human variant and orthologous MxB genes from even closely related primates do not. Thus, in contrast to the many antagonistic virus-host interactions in which the virus is successful in thwarting the host's defense systems, here the human gene appears to be at least temporarily winning at this interface of the primate-herpesvirus evolutionary arms race. Our findings further show that a polymorphism at amino acid 83 in a small fraction of the human population is sufficient to abrogate MxB's ability to inhibit HSV-1, which could have important implications for human susceptibility to HSV-1 pathogenesis.

A systems approach reveals species differences in hepatic stress response capacity

To minimize the occurrence of unexpected toxicities in early phase preclinical studies of new drugs, it is vital to understand fundamental similarities and differences between preclinical species and humans. Species differences in sensitivity to acetaminophen (APAP) liver injury have been related to differences in the fraction of the drug that is bioactivated to the reactive metabolite N-acetyl-p-benzoquinoneimine (NAPQI). We have used physiologically based pharmacokinetic modeling to identify oral doses of APAP (300 and 1000 mg/kg in mice and rats, respectively) yielding similar hepatic burdens of NAPQI to enable the comparison of temporal liver tissue responses under conditions of equivalent chemical insult. Despite pharmacokinetic and biochemical verification of the equivalent NAPQI insult, serum biomarker and tissue histopathology analyses revealed that mice still exhibited a greater degree of liver injury than rats. Transcriptomic and proteomic analyses highlighted the stronger activation of stress response pathways (including the Nrf2 oxidative stress response and autophagy) in the livers of rats, indicative of a more robust transcriptional adaptation to the equivalent insult. Components of these pathways were also found to be expressed at a higher basal level in the livers of rats compared with both mice and humans. Our findings exemplify a systems approach to understanding differential species sensitivity to hepatotoxicity. Multiomics analysis indicated that rats possess a greater basal and adaptive capacity for hepatic stress responses than mice and humans, with important implications for species selection and human translation in the safety testing of new drug candidates associated with reactive metabolite formation.

GLV reveal species differences and responses to environment in alpine shrub Rosa sericea complex

Plant Volatile components are an ecological adaptation mechanism of plants that can reflect species differences and environment information where it is located. The alpine shrub Rosa sericea complex consists of several allied species, which are morphologically similar and difficult to distinguish, they are typical distribution along the elevation in the Himalayas and the Transverse Ranges. We selected two typical areas to find that the different species could be distinguished by their "green leaf volatile components" (GLV) composition as well as their geographical location, and it was evident that species with glands had higher sesquiterpene content. Correlation analysis revealed the relation between volatile components and ecology factors (climate factors, soil factors, phyllospheric microorganisms). Our study adds a new perspective and basis for the environmental adaptations of different species in the alpine shrub Rosa sericea complex from a chemical ecology perspective.

Wing Interferential Patterns (WIPs) and machine learning for the classification of some Aedes species of medical interest

Hematophagous insects belonging to the Aedes genus are proven vectors of viral and filarial pathogens of medical interest. Aedes albopictus is an increasingly important vector because of its rapid worldwide expansion. In the context of global climate change and the emergence of zoonotic infectious diseases, identification tools with field application are required to strengthen efforts in the entomological survey of arthropods with medical interest. Large scales and proactive entomological surveys of Aedes mosquitoes need skilled technicians and/or costly technical equipment, further puzzled by the vast amount of named species. In this study, we developed an automatic classification system of Aedes species by taking advantage of the species-specific marker displayed by Wing Interferential Patterns. A database holding 494 photomicrographs of 24 Aedes spp. from which those documented with more than ten pictures have undergone a deep learning methodology to train a convolutional neural network and test its accuracy to classify samples at the genus, subgenus, and species taxonomic levels. We recorded an accuracy of 95% at the genus level and > 85% for two (Ochlerotatus and Stegomyia) out of three subgenera tested. Lastly, eight were accurately classified among the 10 Aedes sp. that have undergone a training process with an overall accuracy of > 70%. Altogether, these results demonstrate the potential of this methodology for Aedes species identification and will represent a tool for the future implementation of large-scale entomological surveys.

Comparative transcriptomics reveals human-specific cortical features

The cognitive abilities of humans are distinctive among primates, but their molecular and cellular substrates are poorly understood. We used comparative single-nucleus transcriptomics to analyze samples of the middle temporal gyrus (MTG) from adult humans, chimpanzees, gorillas, rhesus macaques, and common marmosets to understand human-specific features of the neocortex. Human, chimpanzee, and gorilla MTG showed highly similar cell-type composition and laminar organization as well as a large shift in proportions of deep-layer intratelencephalic-projecting neurons compared with macaque and marmoset MTG. Microglia, astrocytes, and oligodendrocytes had more-divergent expression across species compared with neurons or oligodendrocyte precursor cells, and neuronal expression diverged more rapidly on the human lineage. Only a few hundred genes showed human-specific patterning, suggesting that relatively few cellular and molecular changes distinctively define adult human cortical structure.

Distribution of Scirtothrips dorsalis (Thysanoptera: Thripidae) cryptic species complex in the United States and reproductive host assessment of its dominant member

Chilli thrips, Scirtothrips dorsalis Hood, is a cryptic species complex of at least 9 species, 2 of which (South Asia 1 and East Asia 1) have been confirmed damaging >50 plant taxa in the United States. To develop a knowledge-based management program for this pest in the United States, the objectives of the study were to (i) survey for S. dorsalis species complex in the suspected regions and (ii) assess the reproductive hosts of the predominant member available. Thrips samples received from collaborators were subjected to morpholo-molecular characterization. Of the 101 thrips populations received across the United States between 2015 and 2021, 71 populations were confirmed as S. dorsalis, with ~25% further identified as East Asia 1, compared with ~41% identified as South Asia 1, suggesting the latter species is more prevalent in the US. East Asia 1 was primarily found in samples collected from Hydrangea sp. (95%) in Massachusetts, New York, and Pennsylvania, indicating geographic range expansion in the Northeast and successful overwintering in areas with hard freezes. While assessing the host range of South Asia 1 (dominant species), 62 plant taxa were evaluated under greenhouse conditions. Among these, 40 feeding and reproductive hosts were confirmed in Florida. We also found 18 new reproductive hosts and 3 feeding hosts of S. dorsalis, which were not previously reported in the literature. The results provide insight into the increasing host range and expanded geographical distribution of S. dorsalis species and will enable the development of a species-specific monitoring and management program.

Evaluating differences in density estimation for central Iowa butterflies using two methodologies

The Pollard-Yates transect is a widely used method for sampling butterflies. Data from these traditional transects are analyzed to produce density estimates, which are then used to make inferences about population status or trends. A key assumption of the Pollard-Yates transect is that detection probability is 1.0, or constant but unknown, out to a fixed distance (generally 2.5 m on either side of a transect line). However, species-specific estimates of detection probability would allow for sampling at farther distances, resulting in more detections of individuals. Our objectives were to (1) evaluate butterfly density estimates derived from Pollard-Yates line transects and distance sampling, (2) estimate how detection probabilities for butterflies vary across sampling distances and butterfly wing lengths, and (3) offer advice on future butterfly sampling techniques to estimate population density. We conducted Pollard-Yates transects and distance-sampling transects in central Iowa in 2014. For comparison to densities derived from Pollard-Yates transects, we used Program DISTANCE to model detection probability (p) and estimate density (D) for eight butterfly species representing a range of morphological characteristics. We found that detection probability among species varied beyond 2.5 m, with variation apparent even within 5 m of the line. Such variation correlated with wing size, where species with larger wing size generally had higher detection probabilities. Distance sampling estimated higher densities at the 5-m truncation for five of the eight species tested. At this truncation, detection probability was <0.8 for all species, and ranged from 0.53 to 0.79. With the exception of the little yellow (Pyrisitia lisa), species with median wing length <5.0 mm had the lowest detection probabilities. We recommend that researchers integrate distance sampling into butterfly sampling and monitoring, particularly for studies utilizing survey transects >5 m wide and when smaller species are targeted.

Identification of Myxobolus distalisensis n. sp. (Cnidaria: Myxozoa) infecting yellow catfish Tachysurus fulvidraco (Richardson), with a supplement description of M. voremkhai (Akhmerov, 1960) Landsberg and Lom, 1991

With growing scale of intensive fish cultivation, the risk of parasite infection in commercial fish is increased. Precisely identifying and characterizing the parasites that infect the farmed fish is critical to understanding the dynamics of their communities. Here, two species of Myxobolus were identified in farmed yellow catfish Tachysurus fulvidraco (Richardson) in China. Myxobolus distalisensis n. sp. developed plasmodia in the gill filaments, with oval to elliptical myxospores measuring 11.3 ± 0.6 (10.4-12.6) × 8.1 ± 0.3 (7.5-8.6) × 5.5 ± 0.2 (5.2-5.8) μm. Two pyriform polar capsules of equal size were measured 5.3 ± 0.4 (4.5-6.3) × 2.7 ± 0.1 (2.3-3) μm. Myxobolus voremkhai (Akhmerov, 1960) Landsberg and Lom, 1991 developed plasmodia in the gill arch and had a myxospore morphology similar to the conspecific isolates described in previous studies. The consensus sequences of M. distalisensis was remarkably distinct from those deposited in the GenBank, with exception of whereas M. voremkhai showing 99.84% identity. The genetic data on both isolates differed considerably from each other, revealing only 86.96% molecular identity. Histologically, M. distalisensis resided in the filament cartilage, and the aggressive proliferation of the sporogenic stages led to lytic cartilage corrosion. In contrast, plasmodia of M. voremkhai grossly observed at the base of the gill filament were embedded by the connective tissue in the gills arch. Phylogenetically, both isolates were separately placed in different subclades, indicating difference in their evolutionary history. Besides, the taxon under the family Myxobolidae was demonstrated non-monophyletic origins, and parasite radiation largely followed their host affinity.

Morphological and molecular description of Dictyocaulus xanthopygus sp. nov. (Nematoda: Trichostrongyloidea) from the Manchurian wapiti Cervus elaphus xanthopygus

Dictyocaulus xanthopygus sp. nov. (Nematoda: Trichostrongyloidea) was isolated from the lungs of the Manchurian wapiti in Primorsky kray, Russia. The newly described species exhibits morphological characteristics of Dictyocaulus but is distinct from congeneric species based on morphological (lengths of body and esophagus, distances from the anterior end to nerve ring and to excretory pore, the thickness of the buccal capsule, etc.) and molecular features. High levels of genetic divergence as well as Bayesian phylogenetic analyses based on 18S rRNA nuclear and cox1 mitochondrial genes supported the independence of Dictyocaulus xanthopygus sp. nov. Secondary structures of helix 39 of 18S rRNA were identical, while ES9 adjacent to the helix has a unique conformation for newly described worms. Energy-efficient conformational rearrangements of rRNA secondary structures can be applicable in studies on the pathogenesis, epidemiology, taxonomy and evolutionary biology of parasites. Additionally, bracketed dichotomous keys to six valid species of Dictyocaulus were prepared.

Oncoceratium amphidactylum n. gen. n. sp. (Monogenoidea: Gyrodactylidae) from Hoplosternum littorale (Hancock) (Siluriformes, Callichthyidae) from southeastern Brazil

Oncoceratium n. gen. is proposed to accommodate Oncoceratium amphidactylum n. gen. n. sp. (Monogenoidea, Gyrodactylidae). Although the proposed genus is monotypic, the differences presented in the diagnosis clearly establish it as distinct from species from other genera, such as Gyrodactylus von Nordmann, 1832 and especially those that occur exclusively in the Neotropical region. The new genus is diagnosed by the presence of a bulbous male copulatory organ, with one row of spinelets of similar sizes and shapes, while the only spine usually found in the gyrodactylids is absent or not differentiated; a haptor with anchors presenting points folded outwards, and superficial and deep roots continuous and indistinguishable; the absence of a deep bar; and hooks in two bilateral clusters of eight hooks. Oncoceratium amphidactylum n. gen. n. sp. is described from the tamboatá fish, Hoplosternum littorale (Hancock) (Callichthyidae), and is characterized by the presence of a pair of horn-shaped anchors with the point turned outwards, a superficial bar shield and absent deep bar, hooks disposed in bilateral lobes, and a MCO with no spine or with a row with large spinelets visible in place of the spine. In addition to the morphological features, distance analysis and Bayesian inference, based on 5.8s and partial ITS2, support placing the new species in a new genus, and not including it in a cluster of species of Gyrodactylus and near to Gyrodactyloides bychowskii Albova, 1948, Ieredactylus rivuli Schelkle et al., 2011 and Laminiscus gussevi (Bychowsky & Polyansky, 1953) Pálsson & Beverely-Burton, 1983.

A redescription of Hedruris moniezi Ibáñez & Córdova, 1976 (Nematoda: Hedruridae), an endoparasite of the Titicaca water frog Telmatobius culeus (Garman, 1876) (Anura: Telmatobiidae), with comments on all other known Hedruris species in Peru

Hedruris moniezi Ibáñez & Córdova, 1976 (Nematoda: Hedruridae) was described using light and scanning electron microscopy (SEM) based on specimens collected from the stomach of Telmatobius culeus (Anura: Telmatobiidae) in Peru. We observed some characteristics not reported previously, including sessile and pedunculated papillae and amphid on the pseudolabia, bifid deirids, morphology of the retractable chitinous hook, morphology and arrangement of the plates on ventral surface of the posterior end of the males, and arrangement of caudal papillae. Telmatobius culeus represents a new host of H. moniezi. In addition, H. basilichtensis Mateo, 1971 is considered to be a junior synonym of H. oriestae Moniez, 1889. A key to valid species of Hedruris in Peru is provided.

A cross-species proteomic map reveals neoteny of human synapse development

The molecular mechanisms and evolutionary changes accompanying synapse development are still poorly understood1,2. Here we generate a cross-species proteomic map of synapse development in the human, macaque and mouse neocortex. By tracking the changes of more than 1,000 postsynaptic density (PSD) proteins from midgestation to young adulthood, we find that PSD maturation in humans separates into three major phases that are dominated by distinct pathways. Cross-species comparisons reveal that human PSDs mature about two to three times slower than those of other species and contain higher levels of Rho guanine nucleotide exchange factors (RhoGEFs) in the perinatal period. Enhancement of RhoGEF signalling in human neurons delays morphological maturation of dendritic spines and functional maturation of synapses, potentially contributing to the neotenic traits of human brain development. In addition, PSD proteins can be divided into four modules that exert stage- and cell-type-specific functions, possibly explaining their differential associations with cognitive functions and diseases. Our proteomic map of synapse development provides a blueprint for studying the molecular basis and evolutionary changes of synapse maturation.

A molecular and ecological study of Macracanthorhynchus ingens (von Linstow, 1879) (Acanthocephala: Archiacanthocephala), in its paratenic and definitive hosts in southeastern Mexico and the Eastern USA

The acanthocephalan Macracanthorhynchus ingens (von Linstow 1879) (Acanthocephala: Archiacanthocephala) is a parasite that infects the gut of carnivores (racoons, coyotes, wolves, foxes, badgers, skunks, opossum, mink and bears) as an adult and the body cavity of lizards, snakes, and frogs as a cystacanth in the Americas. In this study, adults and cystacanths of M. ingens from southeastern Mexico and southern Florida, USA, were identified morphologically by having a cylindrical proboscis armed with 6 rows of hooks each with 6 hooks. Hologenophores were used to sequence the small (SSU) and large (LSU) subunits of ribosomal DNA and cytochrome c oxidase subunit 1 (cox 1) from mitochondrial DNA. Phylogenetic analysis of the new SSU and LSU sequences of M. ingens placed them in a clade with other sequences available in GenBank identified as M. ingens. The cox 1 tree showed that the nine new sequences and six previously published sequences of M. ingens from the USA form a clade with other sequences previously identified as M. ingens from GenBank. The intraspecific genetic divergence among isolates from the Americas ranged from 0 to 2%, and in combination with the phylogenetic trees confirmed that the isolates belonged to the same species. The cox 1 haplotype network inferred with 15 sequences revealed 10 haplotypes separated from each other by a few substitutions. Rio Grande Leopard Frogs and Vaillant´s Frogs harbored cystacanths with low prevalence, 28% and 37% respectively, in Mexico. Brown Basilisks, an invasive lizard in Florida, USA, had high values of prevalence, 92% and 93% in males and females, respectively. Females harbored more cystacanths than males (0-39 vs 0-21) for unknown reasons that may, however, be related to ecological differences.

Caligid sea lice (Copepoda: Caligidae) from golden snapper Lutjanus johnii (Bloch) in Australian waters, with the recognition of Sinocaligus Shen, 1957 as a junior synonym of Caligus Müller, 1785

Two species of sea lice are reported from the golden snapper Lutjanus johnii (Bloch) in Australian waters. One was represented by chalimus larvae, adult males and extremely slender females in which the genital complex is scarcely wider than the fourth pedigerous somite. These females are adult as they carry paired spermatophores and are identified as Caligus dussumieri Rangnekar, 1957 on the details of their appendages. Caligus dussumieri was formerly placed in the genus Sinocaligus Shen, 1957 but the characters supporting the validity of this genus are not robust, so it is here proposed to treat it as a junior subjective synonym of Caligus and transfer its species as: Caligus formicoides Redkar, Rangnekar & Murti, 1949, Caligus dussumieri Shen, 1957, Caligus caudatus (Gnanamuthu, 1950) new combination and Caligus timorensis (Izawa, 1995) new combination. All these species can be placed in the C. bonito-species group within Caligus. Caligus rivulatus Pilla, Vankara & Chikkam, 2012 is recognized as a junior subjective synonym of C. dussumieri. A new species, C. auriolus n. sp. is also described and this is placed in the C. diaphanus species-group. A key to species of this species-group is provided which indicates that C. auriolus n. sp. is most closely related to C. stromatei Krøyer, 1863 but the latter can be distinguished by the slender abdomen of the female and by the more complex myxal process on the maxilliped in the male.

Molecular phylogeny of two Rhinoxenus species (Monogenea: Dactylogyridae) from the nasal cavities of serrasalmids (Characiformes: Serrasalmidae) from Brazil

The dactylogyrid genus Rhinoxenus (Monogenea: Dactylogyridae) is composed of specialized monogeneans infecting the nasal cavities of freshwater fishes from the Neotropical region. This taxon currently comprises 11 species and is easily distinguished from other monogeneans by the absence of the dorsal bar, ventral anchor with inconspicuous roots covered by a sclerotized cap, dorsal anchor greatly modified into a needle-like shape, and hook pair 2 located into bilateral lobes of the trunk. Specimens of Rhinoxenus euryxenus and Rhinoxenus paranaensis were found infecting the nasal cavities of Serrasalmus marginatus and Serrasalmus maculatus, respectively, from the Paraná River basin in Brazil. For the first time, molecular data of Rhinoxenus spp. were obtained and used as a basis for phylogenetic analyses of the genus. Furthermore, our findings represent the first record of R. paranaensis in Brazil.

Bioacoustics supports genus identification in piranhasa)

In different teleost species, sound production can utilize specific coding schemes to avoid confusion between species during communication. Piranhas are vocal Neotropical fishes, and both Pygocentrus and Serrasalmus produce similar pulsed sounds using the same sound-producing mechanism. In this study, we analysed the sounds of three Pygocentrus and nine Serrasalmus species to determine whether sounds can be used to discriminate piranha species at both the species and genus levels. Our analysis of temporal and frequency data supports the idea that the sounds of Serrasalmus and Pygocentrus species are species specific, and that different acoustic features can be used to differentiate taxa at the genus level. Specifically, the sounds of Serrasalmus species are shorter, louder, and have a shorter pulse period (as determined after correction for standard length). This suggests that sounds can be used to support taxonomy at the genus level as well as the species level.

Comprehensive analysis of the composition of the major phospholipids during the asexual life cycle of the filamentous fungus Aspergillus nidulans

Filamentous fungi undergo significant cellular morphological changes during their life cycle. It has recently been reported that deletions of genes that are involved in phospholipid synthesis led to abnormal hyphal morphology and differentiation in filamentous fungi. Although these results suggest the importance of phospholipid balance in their life cycle, comprehensive analyses of cellular phospholipids are limited. Here, we performed lipidomic analysis of A. nidulans during morphological changes in a liquid medium and of colonies on a solid medium. We observed that the phospholipid composition and transcription of the genes involved in phospholipid synthesis changed dynamically during the life cycle. Specifically, the levels of phosphatidylethanolamine, and highly unsaturated phospholipids increased during the establishment of polarity. Furthermore, we demonstrated that the phospholipid composition in the hyphae at colony margins is similar to that during conidial germination. Furthermore, we demonstrated that common and characteristic phospholipid changes occurred during germination in A. nidulans and A. oryzae, and that species-specific changes also occurred. These results suggest that the exquisite regulation of phospholipid composition is crucial for the growth and differentiation of filamentous fungi.

Clustering predicted structures at the scale of the known protein universe

Proteins are key to all cellular processes and their structure is important in understanding their function and evolution. Sequence-based predictions of protein structures have increased in accuracy1, and over 214 million predicted structures are available in the AlphaFold database2. However, studying protein structures at this scale requires highly efficient methods. Here, we developed a structural-alignment-based clustering algorithm-Foldseek cluster-that can cluster hundreds of millions of structures. Using this method, we have clustered all of the structures in the AlphaFold database, identifying 2.30 million non-singleton structural clusters, of which 31% lack annotations representing probable previously undescribed structures. Clusters without annotation tend to have few representatives covering only 4% of all proteins in the AlphaFold database. Evolutionary analysis suggests that most clusters are ancient in origin but 4% seem to be species specific, representing lower-quality predictions or examples of de novo gene birth. We also show how structural comparisons can be used to predict domain families and their relationships, identifying examples of remote structural similarity. On the basis of these analyses, we identify several examples of human immune-related proteins with putative remote homology in prokaryotic species, illustrating the value of this resource for studying protein function and evolution across the tree of life.

Four new species of Anenterotrema Stunkard, 1938 (Digenea: Dicrocoellidae) infecting phyllostomid bats in the Peruvian Amazon

During a research of digeneans (Platyhelminthes: Trematoda) infecting leaf-nosed bats (Chiroptera: Phyllostomidae) from the Kawsay Biological Station in Madre de Dios, southeastern Peru, four new species were described based on light and scanning electron microscopy (SEM): Anenterotrema paramegacetabulum n. sp. from the seba's short-tailed bat Carollia perspicillata Linnaeus, A. hastati n. sp., A. kawsayense n. sp., and A. peruense n. sp. from the greater spear-nosed bat Phyllostomus hastatus (Pallas). Anenterotrema paramegacetabulum n. sp. differs from all congeners by having a terminal oral sucker, a transversely elongated ventral sucker without clamp-shaped, and by having the testes located immediately posterior to ventral sucker. Anenterotrema hastati n. sp. is easily differentiated from the other congeneric species by having an almost clamp-shaped oral sucker, well-developed cirrus sac, a bilobulated seminal receptacle, and a group of well-developed unicellular glands located anterolateral to cirrus sac. Anenterotrema kawsayense n. sp. is characterized by possessing protuberances on the anterior margin of the oral sucker. Anenterotrema peruense n. sp. is mainly characterized by having the testes located principally anterior to ventral sucker and the cirrus sac located perpendicular to midline of the body. The present finding brings to 12, the number of known species of Anenterotrema. A key to the species of Anenterotrema Stunkard, 1938 is provided.

Planting design influences green infrastructure performance: Plant species identity and complementarity in rain gardens

Green infrastructure's capacity to mitigate urban environmental problems, like heat island effects and excessive stormwater runoff, is partially governed by its plant community. Traditionally, green infrastructure design has focused on engineered aspects, such as substrate and drainage, rather than on the properties of its living components. Since the functioning of these plant assemblages is controlled by ecophysiological processes that differ by species, the identity and relative abundance of the species used will influence green infrastructure performance. We used trait-based modeling to derive principles for the effective composition of green infrastructure plant assemblages, parameterizing our model using the vegetation and ecophysiological traits of the species within New York City rain gardens. Focusing on two plant traits that influence rain garden performance, leaf surface temperature and stomatal conductance, we simulated the cumulative temperature and transpiration for plant communities of differing species composition and diversity. The outcomes of the model demonstrate that plant species composition, species identity, selection effects, and interspecific complementarity increase green infrastructure performance in much the way biodiversity affects ecosystem functioning in natural systems. More diverse assemblages resulted in more consistent transpiration and surface temperatures, with the former showing a positive, saturating curve as diversity increased. While the dominant factors governing individual species leaf temperature were abiotic, transpiration was more influential at the community level, suggesting that plants within diverse communities may be cooler in aggregate than any individual species on its own. This implies green infrastructure should employ a variety of vegetation; particularly plants with different statures and physical attributes, such as low-growing ground covers, erect herbaceous perennials, and shrubs.

Isospora speciosae n. sp. (Apicomplexa: Eimeriidae) from the black-polled yellowthroat Geothlypis speciosa Sclater, 1859 (Passeriformes: Parulidae) in Ciénegas del Lerma, Mexico

A new coccidian species, Isospora speciosae n. sp. (Apicomplexa: Eimeriidae) collected from the black-polled yellowthroat Geothlypis speciosa Sclater, is reported from the marsh Ciénegas del Lerma Natural Protected Area, Mexico. Sporulated oöcysts of the new species are subespherical to ovoidal, 24-26 × 21-23 (25.7 × 22.2) μm, with a length/width (L/W) ratio of 1.1; one or two polar granules are present, but micropyle and oöcyst residuum are absent. Sporocyts are ovoidal, 17-19 × 9-11 (18.7 × 10.2) μm, with a L/W ratio of 1.8; Stieda and sub-Stieda bodies are both present, but para-Stieda body is absent; sporocyst residuum compact. The new species is the sixth species of Isospora recorded in a bird of the family Parulidae in the New World.

LIMITATION OF PRIMERS USED IN PCR FOR THE CHARACTERIZATION OF LEISHMANIA INFANTUM

Conventional PCR provides Leishmania species characterization with even a small amount of biological material. Species-specific primers have been a widely used alternative; however, nonspecific amplifications are a reality, interfering with PCR efficiency. In endemic areas with multiple etiological agents for leishmaniasis, there is a requirement for higher specificity of primers. This study evaluates 3 pairs of primers described for the identification and characterization of Leishmania infantum. Primers RV1/RV2, LEISH1/LEISH2, and FLC2/RLC2 were used with the DNA of L. infantum, Leishmania amazonensis, and Leishmania braziliensis. An initial temperature curve was performed (52-62 C) to determine the optimal annealing temperature, followed by a dilution curve of Leishmania DNA (500 pg/μl, 50 pg/μl, 5 pg/μl, 500 fg/μl, 50 fg/μl, 5 fg/μl, and 0.5 fg/μl) to be used for analytical sensitivity. RV1/RV2 PCR amplified L. infantum and L. amazonensis at all analyzed temperatures; LEISH1/LEISH2 PCR amplified all 3 species of Leishmania, although at some temperatures L. infantum was specifically amplified, and, finally, FLC2/RLC2 PCR amplified only L. infantum at all temperatures analyzed. In terms of sensitivity, RV1/RV2 PCR detected 1 fg of L. infantum DNA and 100 pg of L. amazonensis DNA; LEISH1/LEISH2 PCR detected 1 fg of L. infantum DNA, 100 fg of L. amazonensis DNA, and 10 fg of L. braziliensis DNA; and FLC2/RLC2 PCR detected 10 fg of L. infantum DNA. Thus, PCR with FLC2/RLC2 primers is best suited for the molecular characterization of L. infantum, especially in areas where there is an incidence of more than 1 Leishmania species, such as South America.

Characterization of the fragmented mitochondrial genome of domestic pig louse Haematopinus suis (Insecta: Haematopinidae) from China

The domestic pig louse Haematopinus suis (Linnaeus, 1758) (Phthiraptera: Anoplura) is a common ectoparasite of domestic pigs, which can act as a vector of various infectious disease agents. Despite its significance, the molecular genetics, biology and systematics of H. suis from China have not been studied in detail. In the present study, the entire mitochondrial (mt) genome of H. suis isolate from China was sequenced and compared with that of H. suis isolate from Australia. We identified 37 mt genes located on nine circular mt minichromosomes, 2.9 kb-4.2 kb in size, each containing 2-8 genes and one large non-coding region (NCR) (1,957 bp-2,226 bp). The number of minichromosomes, gene content, and gene order in H. suis isolates from China and Australia are identical. Total sequence identity across coding regions was 96.3% between H. suis isolates from China and Australia. For the 13 protein-coding genes, sequence differences ranged from 2.8%-6.5% consistent nucleotides with amino acids. Our result is H. suis isolates from China and Australia being the same H. suis species. The present study determined the entire mt genome of H. suis from China, providing additional genetic markers for studying the molecular genetics, biology and systematics of domestic pig louse.

Exploring spatiotemporal dynamics of flower visitor association pattern on two Avicennia mangroves: a network approach

Plant-flower visitor interaction is one of the most important relationships regarding the co-existence of the floral and faunal communities. The implication of network approaches is an efficient way to understand the impact of community structure on ecosystem functionality. To understand the association pattern of flower visitors, we performed this study on Avicennia officinalis and Avicennia marina mangroves from the islands of Indian Sundarban over three consecutive years. We found that visiting time and sites (islands) influenced the abundance of visitors. The bipartite networks showed a significant generalized structure for both site-visitor and visiting time-visitor networks where the strength and specialization of visitor species showed a highly and moderately significant positive correlation between both networks respectively. All the site-wise visiting time-visitor networks and year-wise site-visitor networks were significantly modular in structure. For both the plants, most of the visitors showed a generalized association pattern among islands and also among visiting times. Additionally, the study of the foraging behavior of dominant visitors showed Apis dorsata and Apis mellifera as the potential visitors for these plants. Our results showed that flower visitor networks are spatiotemporally dynamic. The interactions of visitors with flowers at different times influence their contribution to the network for becoming a generalist or peripheral species in the context of their visiting time, which may subsequently change over islands. This approach will help to devise more precise plant species-specific conservation strategies by understanding the contribution of visitors through the spatiotemporal context.