The effect of ethanol concentration on the morphological and molecular preservation of insects for biodiversity studies

Bilateral asymmetry in craniofacial structures and kinematics of feeding attacks in the scale-eating cichlid fish, Perissodus microlepis

Cichlid fishes are a textbook example for adaptive radiations, since they diversified into several hundred highly specialized species in each of three great East African lakes. Even scale-eating, an extremely specialized feeding mode, evolved independently multiple times in these radiations and in Lake Tanganyika alone, six endemic scale-eating species occupy this extremely specialized ecological niche. Perissodus microlepis went a step further, by evolving bilaterally asymmetrical heads with an intra-specific polymorphism where left- and right-headed morphs predominantly scrape scales from the opposite sides of their prey. While the bilateral asymmetry of scale-eating cichlids has been known, exactly which craniofacial features explain the laterality of the heads remained unclear. Here we aimed, by utilizing micro-computed tomography (μCT), to resolve this issue of how bilateral symmetry in the skeletal structure is broken in scale-eating Perissodus. Our 3D geometric morphometrics analysis clearly separated and identified the two groups of either left- or right-headed fish. In addition, we observed consistent asymmetric volume changes in the premaxilla, maxilla, and mandible of the craniofacial structures, where left-headed fish have larger jaw elements on the right side, and vice versa. The bimodality implies that the effect sizes of environmental factors might be minor while genetics might be responsible to a larger extent for the asymmetry observed in their head morphology. High-speed video analyses of attacks by asymmetrical morphotypes revealed that they utilize their asymmetrical mouth protrusion, as well as lateralized behavior, to re-orientate the gape towards the preferred side of their prey fish to more efficiently scrape scales.

Participatory epidemiological approaches for risk assessment of bed bug (Insecta: Hemiptera: Cimicidae) infestation in public hospitals in the city of Faisalabad, Punjab, Pakistan

This study was to determine risk assessment associated with bed bugs (Insecta: Hemiptera: Cimicidae) using participatory epidemiological tools in the selected public hospitals of district Faisalabad, Punjab, Pakistan. Bed bugs were collected and morphologically identified through a standard taxonomic key. A descriptive cross-sectional survey of patients using a pre-designed questionnaire containing open-ended and closed-ended questions was conducted for six months between January 2023 and June 2023. Of the 384 participants, 113 (29.43%) had experienced itching or skin irritation presumably from the bed bug feeding activity. The study further revealed patients above age 40 (35.43%) and males (30.57%) experienced greater skin irritation responses compared to other participants. Among administrative divisions (tehsils) in the city of Faisalabad, Tehsil Sadar had the highest number of participants with itching or skin irritation (35.48%), while Tehsil Chak Jhumra had the lowest number (24.62%). Most observations of bed bugs by patients were in their beds (10.42%), with chairs (3.91%) being the second most reported location. However, we found bed bugs from only 17 (4.42%) beds and 5 (1.30%) from chairs. A majority of patients (60.9%) reported daily change of bedding; however, a significant proportion (29.9%) reported infrequent changes. About 25.5% of the patients shared beds with others and about 77.1% of patients brought their own bedding or clothing to the hospitals. The current study concluded that the bed bug infestation is a problem in the public hospitals of Faisalabad, Punjab, Pakistan. Risk factors such as sharing a bed, infrequent change of bedding, and bringing personal bedding to hospital while having medical treatment pose a concern.

High genomic connectivity within Anatoma at hydrothermal vents along the Central and Southeast Indian Ridge

Hydrothermal vents are ecosystems inhabited by a highly specialized fauna. To date, more than 30 gastropod species have been recorded from vent fields along the Central and Southeast Indian Ridge and all of them are assumed to be vent-endemic. During the INDEX project, 701 representatives of the genus Anatoma (Mollusca: Vetigastropoda) were sampled from six abyssal hydrothermal vent fields. Traditional morphology and COI barcoding of Hoffman et al. (Eur J Taxon 826:135-162, 2022) were combined with 2b-RAD sequencing to investigate the anatomid community structure and connectivity between the different vent fields. Consequently, 2b-RAD sequencing supported the primary species hypothesis (based on morphology) for 125 individuals of the recently described taxa A. discapex, A. declivis, A. laevapex and A. paucisculpta. We assigned 22 additional specimens to species with 2b-RAD sequencing and updated the community analyses that confirmed the pattern of expanding populations. Population structure and FST values indicated high connectivity along the six sampled vent fields for the three most abundant species. High levels of gene flow are suggested, pointing to high dispersal potential of the target species along the study area. However, low levels of heterozygosity revealed a small gene pool and therefore an increased vulnerability towards environmental change. Our results demonstrate that 2b-RAD sequencing, in combination with other molecular methods, can accurately characterise macrobenthic mollusc communities. Sequencing technology is an essential tool for ongoing monitoring. Furthermore, we highlight that the inferred molecular and ecological patterns provide valuable insights into hydrothermal vent ecosystems, which are crucial for the successful conservation of these ecosystems.

Morphological and Molecular Characterization of Tick Species Infesting Cattle in South Africa

Ticks are a significant threat to livestock globally, with certain species displaying distinct host preferences at various developmental stages. Accurate species-level identification is essential for studying tick populations, implementing control strategies, and understanding disease dynamics. This study evaluated ticks infesting cattle across six provinces in South Africa using morphological and molecular methods. Ticks were preserved, examined morphologically using an Olympus Digital Camera Microscope, and identified using the 16S rRNA gene. The study identified four genera, namely Amblyomma, Hyalomma, Ixodes, and Rhipicephalus, comprising 15 ixodid species. Amblyomma hebraeum was the most prevalent species, with an infestation rate of 54.4%. Molecular analysis revealed genetic relationships among tick species, with genetic distances ranging from 0.00 to 0.13, and phylogenetic analysis clustered species into distinct genera with high bootstrap support. Principal Component Analysis highlighted clear genetic relatedness among species. These findings enhance our understanding of tick diversity, morphology, and distribution in South Africa's cattle populations, emphasizing their economic significance. The study provides critical baseline data for monitoring and developing effective strategies to manage tick-borne diseases, ensuring improved livestock health and productivity.

A "One health" approach to the understanding of mammals, ticks and Rickettsia interactions in the Andes of Colombia

Infectious diseases, especially zoonotic, represent a significant global threat to both human and animal health. Ticks are among the primary vectors of pathogens affecting wild and domestic animals, some of which can also cause severe human diseases. To effectively face zoonotic diseases, the "One Health" approach is being promoted to integrate the health of human, animals, and ecosystems. Here, we identify the associations between ticks, rickettsiae, wild and domestic mammals, and humans in the Andean region of Colombia. A total of 366 ticks of 17 species belonging to the genera Amblyomma, Dermacentor, Ixodes, Ornithodoros, and Rhipicephalus were collected as free-living organisms, or parasitizing humans, wild (22 species) and domestic (3 species) mammals. Infection with Rickettsia parkeri strain NOD, Rickettsia cf. monacensis and 'Candidatus Rickettsia tarasevichiae' was detected in 3.4% of the ticks analyzed (n = 3). This study highlights the diversity of ticks in humans and wild and domestic mammals in Colombia. It also underscores the risk these ectoparasites represent to human and animal health due to the potential transmission of zoonotic pathogens such as Rickettsia spp.

Faecal sample storage without ethanol for up to 24 h followed by freezing performs better than storage with ethanol for shotgun metagenomic microbiome analysis in patients with inflammatory and non-inflammatory intestinal diseases and healthy controls

OBJECTIVE

The influence of different faecal collection methods on metagenomic analyses remains under discussion, and there is no general agreement on which collection method is preferable for gut microbiome research. We compared faecal samples collected in tubes without preservatives with those containing 10 mL of 96% ethanol for gut microbiome research when the timeframe from defecation to freezing at - 80 °C was up to 24 h. We aimed to compare the collection methods on faeces from participants with inflammatory and non-inflammatory gastrointestinal disorders and healthy controls to investigate the most suitable method when considering data yield, human fraction of sequencing reads, and ease of use. We also examined the faecal sample homogeneity.

RESULTS

Faeces collected in tubes without preservatives resulted in more sequencing reads compared to faeces collected in tubes with 96% ethanol and were also easier to handle. The human fraction of total reads in faeces collected in ethanol from participants with inflammatory bowel disease was higher than all other samples. DNA extraction and sequencing from two different locations in the same faecal sample gave similar results and showed sample homogeneity.

Commercial products are not effective at repelling European deer keds, Lipoptena cervi (Diptera: Hippoboscidae) but may increase mortality after exposure

European deer keds, Lipoptena cervi (Linnaeus, 1758), are hematophagous ectoparasitic flies known to bite cervids and noncervids, including humans. To prevent deer keds from landing and biting hosts, 5 commercially available insect repellents (DEET, IR3535, oil of lemon eucalyptus (OLE), picaridin, and permethrin) and water control were evaluated to determine repellency efficacy and postexposure mortality of deer keds. While there was a significant difference between the groups tested, a post hoc analysis revealed that no treatment was significantly different from the water control. Deer ked survival was different amongst the treatments, with deer keds exposed to permethrin dying much sooner than those exposed to other treatments or control (median survival for permethrin = 0.58 h). Post-hoc pairwise comparisons revealed that deer keds exposed to DEET or IR3535 had similar survival rates (4.82 and 5.15 h, respectively). Still, there were significantly lower survival times for DEET compared to OLE (6.33 h) and picaridin (15.00 h). Deer keds exposed to the water control survived the longest (23.12 h). Overall, deer ked repellency was not significantly different from the control, but permethrin-treated clothes can effectively kill deer keds in a short amount of time, thereby protecting those who recreate outdoors or encounter animals carrying deer keds.

Experimental Evolution of a Mammalian Holobiont? Genetic and Maternal Effects on the Cecal Microbiome in Bank Voles Selectively Bred for Herbivorous Capability

AbstractMammalian herbivory represents a complex adaptation requiring evolutionary changes across all levels of biological organization, from molecules to morphology to behavior. Explaining the evolution of such complex traits represents a major challenge in biology, as it is simultaneously muddled and enlightened by a growing awareness of the crucial role of symbiotic associations in shaping organismal adaptations. The concept of hologenomic evolution includes the partnered unit of the holobiont, the host with its microbiome, as a selection unit that may undergo adaptation. Here, we test some of the assumptions underlying the concept of hologenomic evolution using a unique experimental evolution model: lines of the bank vole (Myodes [=Clethrionomys] glareolus) selected for increased ability to cope with a low-quality herbivorous diet and unselected control lines. Results from a complex nature-nurture design, in which we combined cross-fostering between the selected and control lines with dietary treatment, showed that the herbivorous voles harbored a cecal microbiome with altered membership and structure and changed abundances of several phyla and genera regardless of the origin of their foster mothers. Although the differences were small, they were statistically significant and partially robust to changes in diet and housing conditions. Microbial characteristics also correlated with selection-related traits at the level of individual variation. Thus, the results support the hypothesis that selection on a host performance trait leads to genetic changes in the host that promote the maintenance of a beneficial microbiome. Such a result is consistent with some of the assumptions underlying the concept of hologenomic evolution.

Using DNA barcoding to identify high-priority taxa (Hymenoptera: Ichneumonidae) from Great Smoky Mountains National Park

The All Taxa Biodiversity Inventory (ATBI) in Great Smoky Mountains National Park (GSMNP) seeks to document every species of living thing in the park. The ATBI is decades in progress, yet some taxa remain virtually untouched by taxonomists. Such "high priority" taxa include the hyper-diverse parasitoid wasp family Ichneumonidae. Despite the positive and multifaceted effects ichneumonids have on their environment, only a small percentage of those collected in the park have been identified as species, mostly to their complex morphology and overwhelming diversity. Recently, DNA barcoding has transformed biodiversity inventories, streamlining the process to be more rapid and efficient. To test the effectiveness of barcoding 20 + year-old specimens of Ichneumonidae and catalog new records for GSMNP, COI was amplified from 95 ichneumonid morphospecies collected from Andrew's Bald, NC. Species identifications were confirmed morphologically. Eighty-one ichneumonids generated sequence data, representing 16 subfamilies and 44 genera. The subfamily Oxytorinae is newly recorded from GSMNP, along with 10 newly recorded genera and 23 newly recorded species across Ichneumonidae. These results contribute significantly to the ATBI by adding new park records for a high-priority taxon and demonstrate the effectiveness of applying DNA barcoding to samples in long-term storage or those lacking immediate taxonomic expertise.

Pathogens associated with ticks (Acari: Ixodidae) and mammals in the Orinoquia region of Colombia: An approach to understanding vector-pathogen-host interactions

The hard tick clade (Ixodidae) currently comprises 762 species worldwide (266 Prostriata and 496 Metastriata). A quarter of hard ticks are found in the Neotropical region, and 42 species have been documented in Colombia. Ixodidae species are important vectors of pathogens such as bacteria, helminths, protozoa, and viruses. In tick-borne diseases, vertebrate hosts perform an important role in the transmission, maintenance, and spread of pathogens. Colombia ranks sixth among countries with the highest mammal biodiversity, with a total of 548 species, where some of these species may be involved in pathogen transmission cycles with ticks as vectors. This research evaluated the presence of two genera of bacteria (Borrelia and Rickettsia) and the protozoan (Babesia) in ticks and mammals in the Orinoquia region of Colombia, establishing interaction networks. The information comes from 734 mammals (655 wild and 79 domestic), belonging to 59 species. Tick infestation (n = 1,805) was found with 14.85 % (n = 109) of the examined mammals and corresponds to nine tick species confirmed morphologically and molecularly. To detect pathogens 272 ticks were collected while feeding on 96 mammals; samples from 93 mammals were analyzed. The presence of borreliae from the relapsing fever group (RFG) and the Lyme disease group (LDG) were detected. Rickettsia spp. was detected in ticks and mammals, while Babesia bigemina was only detected in ticks. This research is the first to address the prevalence of zoonotic pathogens in domestic and wild mammals infested with hard ticks in the Department of Arauca, Colombia. Considering that reporting cases of infections with Babesia, Borrelia, and Rickettsia in Colombia is not mandatory, their impact on public health cannot be estimated. This highlights the importance of continuously detecting, confirming, and identifying these and other important pathogens within the "One Health" framework, as they have a significant economic and medical-veterinary impact globally.

Three steps towards comparability and standardization among molecular methods for characterizing insect communities

Molecular methods are currently some of the best-suited technologies for implementation in insect monitoring. However, the field is developing rapidly and lacks agreement on methodology or community standards. To apply DNA-based methods in large-scale monitoring, and to gain insight across commensurate data, we need easy-to-implement standards that improve data comparability. Here, we provide three recommendations for how to improve and harmonize efforts in biodiversity assessment and monitoring via metabarcoding: (i) we should adopt the use of synthetic spike-ins, which will act as positive controls and internal standards; (ii) we should consider using several markers through a multiplex polymerase chain reaction (PCR) approach; and (iii) we should commit to the publication and transparency of all protocol-associated metadata in a standardized fashion. For (i), we provide a ready-to-use recipe for synthetic cytochrome c oxidase spike-ins, which enable between-sample comparisons. For (ii), we propose two gene regions for the implementation of multiplex PCR approaches, thereby achieving a more comprehensive community description. For (iii), we offer guidelines for transparent and unified reporting of field, wet-laboratory and dry-laboratory procedures, as a key to making comparisons between studies. Together, we feel that these three advances will result in joint quality and calibration standards rather than the current laboratory-specific proof of concepts. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.

New insights into the DNA extraction and PCR amplification of minute ascomycetes in the genus Laboulbenia (Pezizomycotina, Laboulbeniales)

Molecular studies of fungi within the order Laboulbeniales (Ascomycota, Pezizomycotina) have been hampered for years because of their minute size, inability to grow in axenic culture, and lack of reliable and cost-efficient DNA extraction protocols. In particular, the genus Laboulbenia is notorious for low success with DNA extraction and polymerase chain reaction (PCR) amplification. This is attributed to the presence of melanin, a molecule known to inhibit PCR, in the cells. We evaluated the efficacy of a standard single cell-based DNA extraction protocol by halving the recommended amount of reagents to reduce the cost per extraction and adding bovine serum albumin (BSA) during the multiple displacement amplification step to reverse the effect of melanin. A total of 196 extractions were made, 111 of which were successful. We found that halving the reagents used in the single cell-based extraction kit did not significantly affect the probability of successful DNA extraction. Using the halved protocol reduces cost and resource consumption. Moreover, there was no significant difference in the probability of successfully extracting DNA based on whether BSA was added or not, suggesting that the amount of melanin present in cells of the thallus has no major inhibitory effect on PCR. We generated 277 sequences from five loci, but amplification of the internal transcribed spacer region, the mitochondrial small subunit rDNA, and protein-coding genes remains challenging. The probability of successfully extracting DNA from Laboulbeniales was also impacted by specimen storage methods, with material preserved in > 95% ethanol yielding higher success rates compared to material stored in 70% ethanol and dried material. We emphasize the importance of proper preservation of material and propose the design of Laboulbeniales-specific primers to overcome the problems of primer mismatches and contaminants. Our new insights apply not only to the genus Laboulbenia; Laboulbeniales generally are understudied, and the vast majority of species remain unsequenced. New and approachable molecular developments will benefit the study of Laboulbeniales, helping to elucidate the true diversity and evolutionary relationships of these peculiar microfungi.

A protocol and training guidelines for mosquito sampling in remote areas with limited power supply

Mosquito-borne diseases pose a significant threat in many Southeast Asian countries, particularly through the sylvatic cycle, which has a wildlife reservoir in forests and rural areas. Studying the composition and diversity of vectors and pathogen transmission is especially challenging in forests and rural areas due to their remoteness, limited accessibility, lack of power, and underdeveloped infrastructure. This study is based on the WHO mosquito sampling protocol, modifies technical details to support mosquito collection in difficult-to-access and resource-limited areas. Specifically, we describe the procedure for using rechargeable lithium batteries and solar panels to power the mosquito traps, demonstrate a workflow for processing and storing the mosquitoes in a -20 °C freezer, data management tools including microclimate data, and quality assurance processes to ensure the validity and reliability of the results. A pre- and post-test was utilized to measure participant knowledge levels. Additional research is needed to validate this protocol for monitoring vector-borne diseases in hard-to-reach areas within other countries and settings.

Arctos: Community-driven innovations for managing natural and cultural history collections

More than tools for managing physical and digital objects, museum collection management systems (CMS) serve as platforms for structuring, integrating, and making accessible the rich data embodied by natural history collections. Here we describe Arctos, a scalable community solution for managing and publishing global biological, geological, and cultural collections data for research and education. Specific goals are to: (1) Describe the core features and implementation of Arctos for a broad audience with respect to the biodiversity informatics principles that enable high quality research; (2) Highlight the unique aspects of Arctos; (3) Illustrate Arctos as a model for supporting and enhancing the Digital Extended Specimen concept; and (4) Emphasize the role of the Arctos community for improving data discovery and enabling cross-disciplinary, integrative studies within a sustainable governance model. In addition to detailing Arctos as both a community of museum professionals and a collection database platform, we discuss how Arctos achieves its richly annotated data by creating a web of knowledge with deep connections between catalog records and derived or associated data. We also highlight the value of Arctos as an educational resource. Finally, we present the financial model of fiscal sponsorship by a nonprofit organization, implemented in 2022, to ensure the long-term success and sustainability of Arctos.

Facilitating taxonomy and phylogenetics: An informative and cost-effective protocol integrating long amplicon PCRs and third-generation sequencing

Phylogenetic inference has become a standard technique in integrative taxonomy and systematics, as well as in biogeography and ecology. DNA barcodes are often used for phylogenetic inference, despite being strongly limited due to their low number of informative sites. Also, because current DNA barcodes are based on a fraction of a single, fast-evolving gene, they are highly unsuitable for resolving deeper phylogenetic relationships due to saturation. In recent years, methods that analyse hundreds and thousands of loci at once have improved the resolution of the Tree of Life, but these methods require resources, experience and molecular laboratories that most taxonomists do not have. This paper introduces a PCR-based protocol that produces long amplicons of both slow- and fast-evolving unlinked mitochondrial and nuclear gene regions, which can be sequenced by the affordable and portable ONT MinION platform with low infrastructure or funding requirements. As a proof of concept, we inferred a phylogeny of a sample of 63 spider species from 20 families using our proposed protocol. The results were overall consistent with the results from approaches based on hundreds and thousands of loci, while requiring just a fraction of the cost and labour of such approaches, making our protocol accessible to taxonomists worldwide.

Assessing morphological preservation of gastrointestinal parasites from fecal samples of wild capuchin monkeys (Cebus imitator) stored in ethanol versus formalin

The copromicroscopic identification of gastrointestinal parasites is a common, cost-effective method vital to understanding host-parasite interactions. However, its efficacy depends on effective preservation of the samples. In this study, we compare the preservation of ethanol and formalin preserved gastrointestinal parasites collected from a wild population of Costa Rican capuchin monkeys (Cebus imitator). Fecal samples were collected, halved, and stored in either 10% formalin or 96% ethanol at ambient temperature, then microscopically screened for the presence of parasites. Parasites were morphologically identified and rated based on their preservation using a newly developed rubric. We identified more parasitic morphotypes in formalin-preserved samples but found no difference in the number of parasites per fecal gram (PFG) between mediums. There was no difference in the PFG of two most prevalent parasite morphotypes, Filariopsis barretoi larvae and Strongyle-type eggs, and while Filariopsis larvae were better preserved in formalin, strongyle eggs showed no preservation difference between mediums. Our results support the suitability of both ethanol and formalin for morphological parasite identification in samples stored over 1 year, describe the morphological changes and challenges associated with parasite degradation, and highlight the potential for future studies to use both morphological and molecular methods in non-invasively collected samples.

Fluid preservation in brain banking: a review

Fluid preservation is nearly universally used in brain banking to store fixed tissue specimens for future research applications. However, the effects of long-term immersion on neural circuitry and biomolecules are not well characterized. As a result, there is a need to synthesize studies investigating fluid preservation of brain tissue. We searched PubMed and other databases to identify studies measuring the effects of fluid preservation in nervous system tissue. We categorized studies based on the fluid preservative used: formaldehyde solutions, buffer solutions, alcohol solutions, storage after tissue clearing, and cryoprotectant solutions. We identified 91 studies containing 197 independent observations of the effects of long-term storage on cellular morphology. Most studies did not report any significant alterations due to long-term storage. When present, the most frequent alteration was decreased antigenicity, commonly attributed to progressive crosslinking by aldehydes that renders biomolecules increasingly inaccessible over time. To build a mechanistic understanding, we discuss biochemical aspects of long-term fluid preservation. A subset of lipids appears to be chemical altered or extracted over time due to incomplete retention in the crosslinked gel. Alternative storage fluids mitigate the problem of antigen masking but have not been extensively characterized and may have other downsides. We also compare fluid preservation to cryopreservation, paraffin embedding, and resin embedding. Overall, existing evidence suggests that fluid preservation provides maintenance of neural architecture for decades, including precise structural details. However, to avoid the well-established problem of overfixation caused by storage in high concentration formaldehyde solutions, fluid preservation procedures can use an initial fixation step followed by an alternative long-term storage fluid. Further research is warranted on optimizing protocols and characterizing the generalizability of the storage artifacts that have been identified.

Scanning electron microscopy study of Lars Silns cheilostome bryozoan type specimens in the historical collections of natural history museums in Sweden

The type specimens of 42 cheilostome bryozoan species introduced by Lars Siln between 1938 and 1954 and housed at three different Swedish institutions (the Swedish Museum of Natural History in Stockholm, the Biological Museum in Lund and the Museum of Evolution in Uppsala) are here revised using scanning electron microscopy, with two exceptions, for the first time. As a result of this revision, new morphological observations were made for some species, such as ooecia in Antropora erecta, a costal pseudopore in Jullienula hippocrepis, intracolonial variation in the number of intracostal windows in Costaticella gisleni, and oral spines in Triphyllozoon mauritzoni. Some other observations confirmed the presence of structures/polymorphs in type material that had previously only been noted in non-type specimens, such as spinose interzooidal kenozooids in Retevirgula triangulata and putative brooding zooids in Bugulina kiuschiuensis. Structures originally interpreted as hydroid tube openings on the dorsal side of Triphyllozoon microstigmatum were confirmed to be avicularia, while the supposed kenozooidal attachment rootlet of Fedora nodosa might be the polypide tube of a coronate scyphozoan. In addition, the original combination Heliodoma goesi is here reinstated after Lagaaij assigned the species to Setosellina in 1963. The following new combinations are also proposed: Labioporella aviculifera for Siphonoporella aviculifera; Mangana canui and Mangana incrustata for Callopora canui and Tegella incrustata, respectively; Sphaerulobryozoon ovum for Fedora ovum. Lectotypes were selected when appropriate. This work clarifies the exact identity of some species that have never been recorded after their first description, such as Stylopoma magnovicellata and three species of Triphyllozoon, and contributes to the current increasing effort to digitize historical key specimens in natural history museum collections.

A practical approach to the sampling, fixation, softening, and sectioning of whole honey bees for histologic evaluation

The Western honey bee (Apis mellifera) is economically important as the primary managed pollinator of many agricultural crops and for the production of various hive-related commodities. Honey bees are not classically or thoroughly covered in veterinary pathology training programs. Given their unique anatomic and biological differences from the other species more traditionally evaluated by veterinary pathologists, establishing routine and consistent methods for processing samples for histology ensures accurate diagnostic and research conclusions. We developed and tested several field protocols for the sampling of honey bees. We compared the tissue-quality outcomes for worker bees fixed, collected, and/or softened under the following protocols: 1) routine formalin fixation; 2) softening chitin via exposure to Nair for 2 d or 3) 5 d; 4) shortened times between formalin submersion and trimming of body segments to enhance penetration of formalin into internal tissues; 5) ethanol submersion of specimen prior to formalin fixation; 6) indirect dry ice exposure; and 7) prolonged -80°C storage. Routine formalin fixation, exposure to Nair for 2 d, indirect dry ice exposure, and trimming body segments within 2 h of formalin submersion resulted in the highest quality histologic tissue sections. The poorest quality sections resulted from softening of chitin by exposure to Nair for 5 d, submersion in ethanol for 3 d before formalin fixation, and prolonged storage at -80°C. Our results indicate that routine formalin fixation is adequate, and that immobilizing bees with indirect dry ice exposure aids in sample collection without negatively impacting the quality of histologic sections.

Procedure for Handling and Storage of Onchocerca volvulus Microfilariae Obtained from Skin Snips for Downstream Genetic Work

WHO and endemic countries target elimination of transmission of Onchocerca volvulus, the parasite causing onchocerciasis. Population genetic analysis of O. volvulus may provide data to improve the evidence base for decisions on when, where, and for how long to deploy which interventions and post-intervention surveillance to achieve elimination. Development of necessary methods and tools requires parasites suitable for genetic analysis. Based on our experience with microfilariae obtained from different collaborators, we developed a microfilariae transfer procedure for large-scale studies in the Democratic Republic of Congo (DRC) comparing safety and efficacy of ivermectin, the mainstay of current onchocerciasis elimination strategies, and moxidectin, a new drug. This procedure is designed to increase the percentage of microfilariae in skin snips suitable for genetic analysis, improve assignment to metadata, and minimize time and materials needed by the researchers collecting the microfilariae. Among 664 microfilariae from South Sudan, 35.7% and 39.5% failed the mitochondrial and nuclear qPCR assay. Among the 576 microfilariae from DRC, 16.0% and 16.7% failed these assays, respectively. This difference may not only be related to the microfilariae transfer procedure but also to other factors, notably the ethanol concentration in the tubes in which microfilariae were stored (64% vs. ≥75%).

Parallel And Divergent Morphological Adaptations Underlying The Evolution of Jumping Ability in Ants

Jumping is a rapid locomotory mode widespread in terrestrial organisms. However, it is a rare specialization in ants. Forward jumping has been reported within four distantly related ant genera: Gigantiops, Harpegnathos, Myrmecia, and Odontomachus. The temporal engagement of legs/body parts during jump, however, varies across these genera. It is unknown what morphological adaptations underlie such behaviors and whether jumping in ants is solely driven directly by muscle contraction or additionally relies on elastic recoil mechanism. We investigated the morphological adaptations for jumping behavior by comparing differences in the locomotory musculature between jumping and non-jumping relatives using X-ray micro-CT and 3D morphometrics. We found that the size-specific volumes of the trochanter depressor muscle (scm6) of the middle and hind legs are 3-5 times larger in jumping ants, and that one coxal remotor muscle (scm2) is reduced in volume in the middle and/or hind legs. Notably, the enlargement in the volume of other muscle groups is directly linked to the legs or body parts engaged during the jump. Furthermore, a direct comparison of the muscle architecture revealed two significant differences between jumping vs. non-jumping ants: First, the relative Physiological Cross-Sectional Area (PCSA) of the trochanter depressor muscles of all three legs were larger in jumping ants, except in the front legs of Odontomachus rixosus and Myrmecia nigrocincta; second, the relative muscle fiber length was shorter in jumping ants compared to non-jumping counterparts, except in the front legs of O. rixosus and M. nigrocincta. These results suggest that the difference in relative muscle volume in jumping ants is largely invested in the area (PCSA), and not in fiber length. There was no clear difference in the pennation angle between jumping and non-jumping ants. Additionally, we report that the hind leg length relative to body length was longer in jumping ants. Based on direct comparison of the observed vs. possible work and power output during jumps, we surmise that direct muscle contractions suffice to explain jumping performance in three species, except for O. rixosus, where the lack of data on jumping performance prevents us from drawing definitive conclusions for this particular species. We suggest that increased investment in jumping-relevant musculature is a primary morphological adaptation that separates jumping from non-jumping ants. These results elucidate the common and idiosyncratic morphological changes underlying this rare adaptation in ants. まとぅみ (Okinawan language-Uchinaaguchi) (Japanese) РЕЗЮМЕ (Kazakh) ZUSAMMENFASSUNG (German).

Aquatic environmental DNA: A review of the macro-organismal biomonitoring revolution

Environmental DNA (eDNA) is the fastest growing biomonitoring tool fuelled by two key features: time efficiency and sensitivity. Technological advancements allow rapid biodiversity detection at both species and community levels with increasing accuracy. Concurrently, there has been a global demand to standardise eDNA methods, but this is only possible with an in-depth overview of the technological advancements and a discussion of the pros and cons of available methods. We therefore conducted a systematic literature review of 407 peer-reviewed papers on aquatic eDNA published between 2012 and 2021. We observed a gradual increase in the annual number of publications from four (2012) to 28 (2018), followed by a rapid growth to 124 publications in 2021. This was mirrored by a tremendous diversification of methods in all aspects of the eDNA workflow. For example, in 2012 only freezing was applied to preserve filter samples, whereas we recorded 12 different preservation methods in the 2021 literature. Despite an ongoing standardisation debate in the eDNA community, the field is seemingly moving fast in the opposite direction and we discuss the reasons and implications. Moreover, by compiling the largest PCR-primer database to date, we provide information on 522 and 141 published species-specific and metabarcoding primers targeting a wide range of aquatic organisms. This works as a user-friendly 'distillation' of primer information that was hitherto scattered across hundreds of papers, but the list also reflects which taxa are commonly studied with eDNA technology in aquatic environments such as fish and amphibians, and reveals that groups such as corals, plankton and algae are under-studied. Efforts to improve sampling and extraction methods, primer specificity and reference databases are crucial to capture these ecologically important taxa in future eDNA biomonitoring surveys. In a rapidly diversifying field, this review synthetises aquatic eDNA procedures and can guide eDNA users towards best practice.

Optimizing insect metabarcoding using replicated mock communities

1: Metabarcoding (high-throughput sequencing of marker gene amplicons) has emerged as a promising and cost-effective method for characterizing insect community samples. Yet, the methodology varies greatly among studies and its performance has not been systematically evaluated to date. In particular, it is unclear how accurately metabarcoding can resolve species communities in terms of presence-absence, abundances, and biomass. 2: Here we use mock community experiments and a simple probabilistic model to evaluate the effect of different DNA extraction protocols on metabarcoding performance. Specifically, we ask four questions: (Q1) How consistent are the recovered community profiles across replicate mock communities?; (Q2) How does the choice of lysis buffer affect the recovery of the original community?; (Q3) How are community estimates affected by differing lysis times and homogenization?; and (Q4) Is it possible to obtain adequate species abundance estimates through the use of biological spike-ins? 3: We show that estimates are quite variable across community replicates. In general, a mild lysis protocol is better at reconstructing species lists and approximate counts, while homogenization is better at retrieving biomass composition. Small insects are more likely to be detected in lysates, while some tough species require homogenization to be detected. Results are less consistent across biological replicates for lysates than for homogenates. Some species are associated with strong PCR amplification bias, which complicates the reconstruction of species counts. Yet, with adequate spike-in data, species abundance can be determined with roughly 40% standard error for homogenates, and with roughly 50% standard error for lysates, under ideal conditions. In the latter case, however, this often requires species-specific reference data, while spike-in data generalizes better across species for homogenates. 4: We conclude that a non-destructive, mild lysis approach shows the highest promise for presence/absence description of the community, while also allowing future morphological or molecular work on the material. However, homogenization protocols perform better for characterizing community composition, in particular in terms of biomass.

Sampling and curation of rove beetles (Insecta, Coleoptera, Staphylinidae) for comprehensive and DNA-grade collections to enhance biodiversity exploration in Northern Eurasia

Staphylinidae beetles form a major portion of terrestrial biodiversity globally and, in particular, in Northern Eurasia, a large area with a historically better known north temperate, subarctic and arctic biota. However, even here, rove beetles remain amongst the so-called "dark taxa" with a high fraction of taxonomically unknown lineage diversity. The propagation of DNA-based technologies in systematic entomology in recent decades has brought new opportunities for biodiversity exploration, true also for Staphylinidae. Simultaneously, new methods have revealed limitations of specimens sampled and curated by traditional practices, as existing legacy collections, whether institutional or private, unfortunately do not always qualify as a source of DNA-grade material. In addition, both legacy and newly-collected DNA-grade material of Staphylinidae remain highly biased towards Central Europe, a region with a traditionally well-developed scientific infrastructure and long-established culture for the maintenance of entomological collections. To increase the degree of biodiversity knowledge for our target organismal group across the globe, efficient sampling of DNA-grade material and, in particular, the development of comprehensive local collections in under-studied regions is highly desirable. To facilitate that, here we provide a practical guide for collecting and curation of Staphylinidae with a focus on capacity building for DNA-grade collections in Siberia and elsewhere in Northern Eurasia.

Toward global integration of biodiversity big data: a harmonized metabarcode data generation module for terrestrial arthropods

Metazoan metabarcoding is emerging as an essential strategy for inventorying biodiversity, with diverse projects currently generating massive quantities of community-level data. The potential for integrating across such data sets offers new opportunities to better understand biodiversity and how it might respond to global change. However, large-scale syntheses may be compromised if metabarcoding workflows differ from each other. There are ongoing efforts to improve standardization for the reporting of inventory data. However, harmonization at the stage of generating metabarcode data has yet to be addressed. A modular framework for harmonized data generation offers a pathway to navigate the complex structure of terrestrial metazoan biodiversity. Here, through our collective expertise as practitioners, method developers, and researchers leading metabarcoding initiatives to inventory terrestrial biodiversity, we seek to initiate a harmonized framework for metabarcode data generation, with a terrestrial arthropod module. We develop an initial set of submodules covering the 5 main steps of metabarcode data generation: (i) sample acquisition; (ii) sample processing; (iii) DNA extraction; (iv) polymerase chain reaction amplification, library preparation, and sequencing; and (v) DNA sequence and metadata deposition, providing a backbone for a terrestrial arthropod module. To achieve this, we (i) identified key points for harmonization, (ii) reviewed the current state of the art, and (iii) distilled existing knowledge within submodules, thus promoting best practice by providing guidelines and recommendations to reduce the universe of methodological options. We advocate the adoption and further development of the terrestrial arthropod module. We further encourage the development of modules for other biodiversity fractions as an essential step toward large-scale biodiversity synthesis through harmonization.

Intersexuality in a natural population of the terrestrial isopod Porcellioscaber

Intersex phenotypes are rarely observed in natural isopod populations and their expression is typically associated with infection of Wolbachia, a reproductive parasite that manipulates arthropod reproduction. During an intensive sampling effort of a natural population of the isopod Porcellioscaber, an adult individual was isolated that expressed both male and female traits. The intersex individual exhibited clearly developed external male genitalia and carried multiple eggs in its brood pouch. No Wolbachia infection could be identified in this individual, a result that needs to be approached with caution due to suboptimal DNA preservation for diagnostic PCR assays. Wolbachia were, however, detected in two adult females of the same population, and appear closely related to isolates that infect other terrestrial isopod species. This is the first demonstration that intersex phenotypes can arise under natural conditions in P.scaber.

Effect of different fixatives on yield of DNA from human fecal samples

Fixation and transportation of human fecal samples is often difficult in geographically remote locations due to unavailability of options for immediate freezing. In this study effectiveness of five different chemical fixatives were evaluated on human fecal samples including for supernatant using RNAprotect Bacteria Reagent (Qiagen), 95% ethanol, acetone, TRIzol and a mixture of all these fixatives, in addition to immediate freezing. DNA was extracted from the fecal samples using QIAamp Fast Stool DNA Minikit as well as quality and yield of extracted DNA was monitored for a period of 30 days. It was found that except TRIzol, all other preservatives showed good DNA quality and yield for a period of one month based on agarose gel electrophoresis, Nanodrop and Qubit measurements. It was also found that supernatant of fecal sample fixed with RNAprotect Bacteria Reagent gave reliable DNA yield in comparison to other various fixatives. The study also revealed that quality and yield of DNA from fecal samples fixed in acetone were very promising since it is a cost-effective fixative. Overall, the study shows future applicability for downstream DNA analyses of the RNAprotect Bacteria Reagent, 95% ethanol, acetone, and a mixture of all these fixatives for fixing human fecal samples to be collected from geographically remote locations or in regions where available resources are largely limited.

Tiny wasps, huge diversity - A review of German Pteromalidae with new generic and species records (Hymenoptera: Chalcidoidea)

Background

Despite their ecological and economic importance, hymenopteran parasitoids are severely understudied. Even in countries with a long taxonomic history such as Germany, dating back to the 18th century and including prolific figures like Christian Gottfired Nees von Esenbeck and Otto Schmiedeknecht, those species-rich groups are seldom the subject of comprehensive research efforts, leaving their true diversity unknown. This is often due to their small size of a few millimetres on average, leading to difficulties in their identification and examination. The chalcidoid family Pteromalidae is no exception to this neglect. So far, 735 species have been reported from Germany. Estimating the diversity of this group is not possible, but it has to be assumed that many more species are still to be discovered in Germany.

New information

With this study, we improve the knowledge on pteromalid diversity and present new records of 17 genera and 41 species, previously unknown to occur in Germany. We also match and describe previously unknown sexes of two species, based on DNA barcode data. The results of this study were generated as part of the German Barcode of Life Project. The newly-recorded species are illustrated and notes on the biology and distribution are given. The ecological significance of Pteromalidae and potential value as indicators for nature conservation efforts are briefly discussed.

Old Brains in Alcohol: The Usability of Legacy Collection Material to Study the Spider Neuroarchitecture

Natural history collections include rare and significant taxa that might otherwise be unavailable for comparative studies. However, curators must balance the needs of current and long-term research. Methods of data extraction that minimize the impact on specimens are therefore favored. Micro-CT has the potential to expose new character systems based on internal anatomy to taxonomic and phylogenetic analysis without dissection or thin sectioning for histology. However, commonly applied micro-CT protocols involve critical point drying, which permanently changes the specimen. Here, we apply a minimally destructive method of specimen preparation for micro-CT investigation of spider neuroanatomy suitable for application to legacy specimens in natural history collections. We used two groups of female spiders of the common species Araneus diadematus—freshly captured (n = 11) vs. legacy material between 70 and 90 years old (n = 10)—to qualitatively and quantitatively assess the viability of micro-CT scanning and the impact of aging on their neuroarchitecture. We statistically compared the volumes of the supraesophageal ganglion (syncerebrum) and used 2D geometric morphometrics to analyze variations in the gross shape of the brain. We found no significant differences in the brain shape or the brain volume relative to the cephalothorax size. Nonetheless, a significant difference was observed in the spider size. We considered such differences to be explained by environmental factors rather than preservation artifacts. Comparison between legacy and freshly collected specimens indicates that museum specimens do not degrade over time in a way that might bias the study results, as long as the basic preservation conditions are consistently maintained, and where lapses in preservation have occurred, these can be identified. This, together with the relatively low-impact nature of the micro-CT protocol applied here, could facilitate the use of old, rare, and valuable material from collections in studies of internal morphology.

Relationship of insect biomass and richness with land use along a climate gradient

Recently reported insect declines have raised both political and social concern. Although the declines have been attributed to land use and climate change, supporting evidence suffers from low taxonomic resolution, short time series, a focus on local scales, and the collinearity of the identified drivers. In this study, we conducted a systematic assessment of insect populations in southern Germany, which showed that differences in insect biomass and richness are highly context dependent. We found the largest difference in biomass between semi-natural and urban environments (-42%), whereas differences in total richness (-29%) and the richness of threatened species (-56%) were largest from semi-natural to agricultural environments. These results point to urbanization and agriculture as major drivers of decline. We also found that richness and biomass increase monotonously with increasing temperature, independent of habitat. The contrasting patterns of insect biomass and richness question the use of these indicators as mutual surrogates. Our study provides support for the implementation of more comprehensive measures aimed at habitat restoration in order to halt insect declines.

Morphometric Analysis of Coptotermes spp. Soldier Caste (Blattodea: Rhinotermitidae) in Indonesia and Evidence of Coptotermes gestroi Extreme Head-Capsule Shapes

Linear and geometric morphometrics approaches were conducted to analyze the head capsule (HC) shape of collected soldier caste specimens of Coptotermes from various locations in Indonesia. The soldiers' morphology was observed and measured. The results of the principal component analysis of the group of all species showed two important groups of variables, i.e., the body size and setae characteristics of the pronotum and head. The multicollinearity of the morphometric variables showed the importance of body measurements as well as important alternative characteristics such as the pronotum setae (PrS) and HC setae. Four trends of HC shape were observed across the species. Interestingly, three extreme shapes were depicted by geometric morphometrics of the C. gestroi HC. The phylogenetic tree inferred from 12S and 16S mitochondrial gene fragments showed high confidence for C. gestroi populations. The lateral expansion of the posterior part of the HC across the species was in accordance with the increasing of the number of hairlike setae on the pronotum and HC. These differences among species might be associated with mandible-force-related defensive labor and sensitivity to environmental stressors.

Opportunities and challenges for high-quality biodiversity tissue archives in the age of long-read sequencing

The technological ability to characterize genetic variation at a genome-wide scale provides an unprecedented opportunity to study the genetic underpinnings and evolutionary mechanisms that promote and sustain biodiversity. The transition from short- to long-read sequencing is particularly promising and allows a more holistic view on any changes in genetic diversity across time and space. Long-read sequencing has tremendous potential but sequencing success strongly depends on the long-range integrity of DNA molecules and therefore on the availability of high-quality tissue samples. With the scope of genomic experiments expanding and wild populations simultaneously disappearing at an unprecedented rate, access to high-quality samples may soon be a major concern for many projects. The need for high-quality biodiversity tissue archives is therefore urgent but sampling and preserving high-quality samples is not a trivial exercise. In this review, I will briefly outline how long-read sequencing can benefit the study of molecular ecology, how this will substantially increase the demand for high-quality tissues and why it is challenging to preserve DNA integrity. I will then provide an overview of preservation approaches and end with a call for support to acknowledge the efforts needed to assemble high-quality tissue archives. In doing so, I hope to simultaneously motivate field biologists to expand sampling practices and molecular biologists to develop (cost) efficient guidelines for the sampling and long-term storage of tissues. A concerted, interdisciplinary, effort is needed to catalogue the genetic variation underlying contemporary biodiversity and will eventually provide a critical resource for future studies.