ChiroVox: a public library of bat calls

Recordings of bat echolocation and social calls are used for many research purposes from ecological studies to taxonomy. Effective use of these relies on identification of species from the recordings, but comparative recordings or detailed call descriptions to support identification are often lacking for areas with high biodiversity. The ChiroVox website (www.chirovox.org) was created to facilitate the sharing of bat sound recordings together with their metadata, including biodiversity data and recording circumstances. To date, more than 30 researchers have contributed over 3,900 recordings of nearly 200 species, making ChiroVox the largest open-access bat call library currently available. Each recording has a unique identifier that can be cited in publications; hence the acoustic analyses are repeatable. Most of the recordings available through the website are from bats whose species identities are confirmed, so they can be used to determine species in recordings where the bats were not captured or could not be identified. We hope that with the help of the bat researcher community, the website will grow rapidly and will serve as a solid source for bat acoustic research and monitoring.

A physiological profile approach to animal temperament: How to understand the functional significance of individual differences in behaviour

Animal behaviour research has experienced a renewed interest in consistent individual differences (i.e. animal personality or temperament). Recent ecological studies have identified environmental conditions that give rise to the development and evolution of temperaments and to fitness-related outcomes of temperament. Additional literature has also described relationships between temperaments and physiological regulation. However, one-to-one relationships between one behavioural trait and one physiological system do not account for co-selection of behavioural and physiological traits, nor the complex signalling among physiological systems. In the current paper, we review the literature on multiple physiological processes associated with temperament, propose temperament-specific physiological profiles, and focus on next steps to understand the functional significance, evolution and maintenance of temperaments. We propose that to understand causes and consequences of temperament we need to characterize integrative physiological profiles associated with different temperaments.

Bee diversity in fragmented areas of Volcano Etna (Sicily, Italy) at different degrees of anthropic disturbance (Hymenoptera: Apoidea, Anthophila)

The present three-year study traces the diversity of four bee communities in fragmented pedemontane areas of Volcano Etna (Catania province, Sicily) near the Metropolitan City of Catania, under different land management regimes. The selected areas comprise two different urban parks within Catania (Parco Gioeni and Parco degli Ulivi), a Nature Reserve (Complesso Immacolatelle e Micio Conti, San Gregorio di Catania), and an agroecosystem (a citrus orchard, Aci Catena). Previous data obtained from a well-investigated area (Leucatia, north of Catania) have been used as a control for bee diversity for this study. The results include an outline of bee species richness, data on the composition of bee communities, and seasonal patterns, using several diversity indexes. The study of bee diversity shows a total of 163 species, arranged in five families. The four investigated locations include 104 species arranged in four families: Andrenidae (20 species), Halictidae (15 species), Megachilidae (31 species), and Apidae (38 species); with a similar number of species (102) recorded in the control site (Leucatia). The study highlights strong seasonal variations of bee communities in all investigated sites, with differentiated seasonal patterns, whose compositions are affected mainly by forage sources, suitable nesting sites, as well as human activities. The data obtained provide a rough but basilar framework to assess management strategies to maintain adequate levels of bee diversity, especially for those areas with moderate to high environmental fragmentation. Our findings highlight the importance of season-long sampling of bee population factors if used as indicators in ecological studies.

Seed Dormancy Class and Ecophysiological Features of Veronicastrum sibiricum (L.) Pennell (Scrophulariaceae) Native to the Korea Peninsula

Veronicastrum sibiricum is a perennial species distributed in Korea, Japan, Manchuria, China, and Siberia. This study aimed to determine the requirements for germination and dormancy break of V. sibiricum seeds and to classify the kind of seed dormancy. Additionally, its class of dormancy was compared with other Veronicastrum and Veronica species. V. sibiricum seeds were permeable to water and had a mature embryo during seed dispersal. In field conditions, germination was prevented by physiological dormancy, which was, however, relieved by March of the next year, allowing the start of germination when suitable environmental conditions occurred. In laboratory experiments, the seeds treated with 0, 2, 4, 8, and 12 weeks of cold stratification (4 °C) germinated to 0, 79, 75, 72, and 66%, respectively. After the GA3 treatment (2.887 mM), ≥90% of the seeds germinated during the four incubation weeks at 20/10 °C. Thus, 2.887 mM GA3 and at least two weeks at 4 °C were effective in breaking physiological dormancy and initiating germination. Therefore, the V. sibiricum seeds showed non-deep physiological dormancy (PD). Previous research, which determined seed dormancy classes, revealed that Veronica taxa have PD, morphological (MD), or morphophysiological seed dormancy (MPD). The differences in the seed dormancy classes in the Veronicastrum-Veronica clade suggested that seed dormancy traits had diverged. The results provide important data for the evolutionary ecological studies of seed dormancy and seed-based mass propagation of V. sibiricum.

Phylogenomic and mitogenomic data can accelerate inventorying of tropical beetles during the current biodiversity crisis

Conservation efforts must be evidence-based, so rapid and economically feasible methods should be used to quantify diversity and distribution patterns. We have attempted to overcome current impediments to the gathering of biodiversity data by using integrative phylogenomic and three mtDNA fragment analyses. As a model, we sequenced the Metriorrhynchini beetle fauna, sampled from ~700 localities in three continents. The species-rich dataset included ~6,500 terminals, ~1,850 putative species delimited at 5% uncorrected pairwise threshold, possibly ~1,000 of them unknown to science. Neither type of data could alone answer our questions on biodiversity and phylogeny. The phylogenomic backbone enabled the integrative delimitation of robustly defined natural genus-group units that will inform future research. Using constrained mtDNA analysis, we identified the spatial structure of species diversity, very high species-level endemism, and a biodiversity hotspot in New Guinea. We suggest that focused field research and subsequent laboratory and bioinformatic workflow steps would substantially accelerate the inventorying of any hyperdiverse tropical group with several thousand species. The outcome would be a scaffold for the incorporation of further data from environmental sequencing and ecological studies. The database of sequences could set a benchmark for the spatiotemporal evaluation of biodiversity, would support evidence-based conservation planning, and would provide a robust framework for systematic, biogeographic, and evolutionary studies.

Wanted not, wasted not: Searching for non-target taxa in environmental DNA metabarcoding by-catch

Metabarcoding of environmental DNA is based on primers that are specific to the target taxa (e.g. bacteria, zooplankton, fishes). However, due to the nature of the commonly used protocols, regardless of the chosen primers, several sequences of non-target species will inevitably be generated, but are usually discarded in commonly used bioinformatics pipelines. These non-target sequences might contain important biological information about the presence of other species in the studied habitats and its potential for ecological studies is still poorly understood. Here, we analyzed the presence of mammal and bird species in aquatic environmental samples that were originally amplified targeting teleost fish species. After all cleaning and checking steps, we kept 21 amplicon sequence variants (ASVs) belonging to mammals and ten to birds. Most ASVs were taxonomic assigned to farm/domestic animals, such as cats, cows, and ducks. Yet, we were able to identify a native semi-aquatic mammal, the capybara, in the samples. Four native bird species and a non-native potentially invasive bird (Corvus sp.) were also detected. Although the data derived from these samples for mammals and birds are of limited use for diversity analyses, our results demonstrate the potential of aquatic samples to characterize non-aquatic birds and highlight the presence of a potentially invasive species that had not been recorded before in the region.

Counting using deep learning regression gives value to ecological surveys

Many ecological studies rely on count data and involve manual counting of objects of interest, which is time-consuming and especially disadvantageous when time in the field or lab is limited. However, an increasing number of works uses digital imagery, which opens opportunities to automatise counting tasks. In this study, we use machine learning to automate counting objects of interest without the need to label individual objects. By leveraging already existing image-level annotations, this approach can also give value to historical data that were collected and annotated over longer time series (typical for many ecological studies), without the aim of deep learning applications. We demonstrate deep learning regression on two fundamentally different counting tasks: (i) daily growth rings from microscopic images of fish otolith (i.e., hearing stone) and (ii) hauled out seals from highly variable aerial imagery. In the otolith images, our deep learning-based regressor yields an RMSE of 3.40 day-rings and an $$R^2$$ R 2 of 0.92. Initial performance in the seal images is lower (RMSE of 23.46 seals and $$R^2$$ R 2 of 0.72), which can be attributed to a lack of images with a high number of seals in the initial training set, compared to the test set. We then show how to improve performance substantially (RMSE of 19.03 seals and $$R^2$$ R 2 of 0.77) by carefully selecting and relabelling just 100 additional training images based on initial model prediction discrepancy. The regression-based approach used here returns accurate counts ($$R^2$$ R 2 of 0.92 and 0.77 for the rings and seals, respectively), directly usable in ecological research.

Coupling between Ribotypic and Phenotypic Traits of Protists across Life Cycle Stages and Temperatures

Based on phenotypic traits, traditional surveys usually characterize organismal richness, abundance, biomass, and growth potential to describe diversity, organization, and function of protistan populations and communities. The rRNA gene (rDNA) and its transcripts have been widely used as molecular markers in ecological studies of protists.

Bionomy of Mosquitoes in Bamboo Internodes in an Atlantic Forest Remnant of the State of Rio De Janeiro, Brazil

ABSTRACT Living bamboo stalks are one of the most specialized habitats for mosquito oviposition and immature development. Most of the mosquito species that breed in these habitats are sylvatic, and some are of importance for public health as possible vectors of pathogens. Perforated internodes are a very specialized environment due to the difficulty of access. Furthermore, due to their relatively simple fauna, they represent a valuable model for ecological studies that may be applicable to more complex environments. This study aims to assess the mosquito bionomics of species raised in bamboo internodes. Therefore, the diversity of mosquito species and the influence of abiotic variables (pH and temperature) on the distribution of mosquitoes that breed in this habitat were analyzed. The study area is a fragment of Atlantic Forest within the Association of da Armada (ATA) in Nova Iguaçu, state of Rio de Janeiro, Brazil. Immature mosquitoes were sampled with suction tubes (mouth aspirators) between August 2017 and July 2018. A total of 3,170 larvae were collected in 5 bamboo plants, each with 8 stalks perforated. Of these, 688 larvae reached the adult stage, representing 10 genera and 19 species. The most common species were Culex neglectus (43%), Trichoprosopon digitatum (22%), Culex iridescens (8%), Sabethes identicus (7%), and Orthopodomyia albicosta (7%). The richness of the immatures collected in the ATA was 19 species, with a diversity of 1.10 and Shannon evenness of 0.57. A diverse composition of Culicidae in bamboo stalks was found, although dominance was low.