SEARCH · Search bioRxiv

Results for “zoology”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Systematic revision of the suborder Astrophorina (Porifera: Demospongiae) in the temperate Northeast Pacific

This study presents a systematic revision of the suborder Astrophorina for the temperate Pacific coast of the United States and Canada. Major findings include a reduction in the number of species previously thought to range into the region from Japan; validation of most Geodia species erected by Lendenfeld (1910), which were later synonymized by de Laubenfels (1932); the formal description of 10 new species (Poecillastra alaskensis sp. nov., Vulcanella explorata sp. nov., Vulcanella rupta sp. nov., Stelletta cardenasi sp. nov., Stelletta nicolenya sp. nov., Stelletta limuwensis sp. nov., Dercitus (Stoeba) giveni sp. nov., Penares anyapax sp. nov., Penares foxi sp. nov., and Thenea diastra sp. nov.); and one new combination, Penares orientalis comb. nov. Extensive SCUBA-based collection efforts yielded new samples for 11 of the 26 species identified in the region, which enabled an integrative taxonomic approach that combined field photography, fresh material for DNA sequencing, and improved characterization of species ranges and morphological variability in previously described taxa. Illumina sequencing generated complete nuclear ribosomal haplotypes for five species, while Sanger sequencing of the 28S and cox1 loci placed 20 of the 26 species within molecular phylogenies. The use of very short "mini-barcode" amplicons also enabled sequence recovery from historic type specimens up to 137 years old. This study additionally reports the discovery of sponge grounds of abundant, large Geodia at diving depths in Southern California. Together, these results substantially advance our understanding of global astrophorid diversity and systematics, and the biogeography of sponge diversity in the Northeast Pacific. Note about species names: this pre-print is not intended to be a publication of the associated species names for the purposes of zoological nomenclature.

zoology↗

bioRxiv2026

Griphus Software for Multi Panel Figure Composition and Experimentation with Emphasis on Taxonomy

The preparation of multi panel figures remains a labor intensive step in scientific publication. Albeit there are specific tools available to solve this problem, they are often highly specialized, difficult to install, or time consuming to learn. Griphus is a standalone graphical application designed for rapid composition and experimentation with multi panel figures, developed by and for zoological taxonomists. Functions specifically designed for multi panel composition include automatic figure numbering and placement, aspect ratio operations, spacers, layout rotation, layout suggestions, and automatic generation of figure legends, including scale bar descriptions. The software can perform both spatial interpretation of images on the canvas and work with a simple, editable layout formula. It also enables instant multi panel composition, with numbered images and automatic contrast selection for the numbers, obtained simply by loading images. User defined parameters such as target printable dimensions, resolution, spacing, and color mode are preserved throughout the work. The program produces coordinated outputs consisting of the final composite figure, a readable file describing the layout structure, and a .gri file storing images, transformations, and parameters for exact regeneration. Griphus is intended as a complementary tool to professional image software, providing a simple and efficient environment for constructing high quality multi panel figures.

zoology↗

bioRxiv2026

Dietary macronutrients influence the gut microbiome and FA1PI, a non-invasive marker for GI health, in zoo-managed maned wolves (Chrysocyon brachyurus)

The maned wolf (Chrysocyon brachyurus) is a near-threatened canid species that suffers from gastrointestinal (GI) disease under human care. While the cause remains poorly understood, recent studies report that altered gut microbiota is linked to GI disease in the domestic dog. The goal of this study was to describe the relationship between gut bacteria and environmental factors, GI health, short chain fatty acid (SCFA) peaks, and genetic relatedness in maned wolves. Fresh fecal samples were collected twice from wolves (first collection n = 29; second collection n = 25) housed in six facilities in the United States. Fecal alpha-1 proteinase inhibitor (FA1PI), a biomarker for GI health in canids, and SCFA peaks were quantified. Information on diet, housing group and history of GI disease or inflammation was provided by the zoological facility for each wolf. We characterized gut microbiota using 16S rRNA gene amplicon sequencing with qPCR abundance corrections. We found that dietary fiber gross energy (GE), protein GE, and number of daily produce items influenced gut microbiota. Additionally, there was a negative relationship between dietary fiber GE and Fusobacterium sp. abundance, corroborating previous findings linking fiber to altered gut microbiome composition in canids. Lastly, fiber GE was negatively correlated with FA1PI, connecting fiber to GI health in the maned wolf. Findings from this study suggest that increasing dietary fiber GE changes the gut microbiome and may improve GI health in the maned wolf, highlighting important management decisions that can be considered to maintain a healthy zoo-managed maned wolf population. IMPORTANCEFindings from this study are important because gastrointestinal disease is a common health concern for maned wolves under human care, and the causes are not well understood. The current study found that diet, especially the amount of fiber gross energy, can affect gut bacteria and may support better gastrointestinal health. Diet alterations could be a practical tool for zoos to support management of gastrointestinal health issues in maned wolves. These findings also show the importance of carefully managing diets for a near-threatened species, since better gastrointestinal health may improve overall health and well-being and support reproduction. More research is needed to determine the best amount and type of fiber, but our results provide foundational information for improving care and supporting healthy zoo-managed maned wolf populations.

zoology↗

bioRxiv2016

A logic approach to modeling nomenclatural change

We utilize an Answer Set Programming (ASP) approach to show that the principles of nomenclature are tractable in computational logic. To this end we design a hypothetical, 20 nomenclatural taxon use case with starting conditions that embody several overarching principles of the International Code of Zoological Nomenclature; including Binomial Nomenclature, Priority, Coordination, Homonymy, Typification, and the structural requirement of Gender Agreement. The use case ending conditions are triggered by the reinterpretation of the diagnostic features of one of 12 type specimens anchoring the corresponding species-level names. Permutations of this child-to-parent reassignment action lead to 36 alternative scenarios, where each scenario requires 1-14 logically contingent nomenclatural emendations. We show that an ASP transition system approach can correctly infer the Code-mandated changes for each scenario, and visually output the ending conditions. The results provide a foundation for further developing logic-based nomenclatural change optimization and compliance verification services, which could be applied in globally coordinated nomenclatural registries. More generally, logic explorations of nomenclatural and taxonomic change scenarios provide a novel means of assessing design biases inherent in the principles of nomenclature, and thus may inform the design of future, big data-compatible identifier systems for systematic products that recognize and mitigate these constraints.

Evolutionary Biology↗

bioRxiv2016

Are foundation species effects different than those of dominant species? A case study of ant assemblages in northeastern North American forests

Foundation species uniquely control associated biodiversity through non-trophic effects, whereas dominant species are locally abundant but are replaceable in ecological systems. Long-term data on ant assemblages at the Harvard Forest Hemlock Removal Experiment (HF-HeRE) and the Black Rock Future of Oak Forests Experiment (BRF-FOFE) provide insights into how ant assemblages change and reassemble following the loss of a foundation species (Tsuga canadensis) or a dominant genus (Quercus). At HF-HeRE, removal of T. canadensis trees resulted in taxonomic and functional shifts in ant assemblages relative to control stands. In contrast, ant assemblages at BRF-FOFE varied little regardless of whether oaks or non-oaks were removed from the canopy. Non-trophic effects of foundation species were stronger than indirect trophic effects on taxonomic and functional diversity of ant assemblages. In contrast, non-trophic effects of dominant species were weaker than indirect trophic effects on ant taxonomic diversity and some measures of ant functional diversity.\n\nStatement of authorshipA.M. Ellison and S. Record conceived the study. A.M. Ellison, T. 17 McCabe, and S. Record collected field data. T. McCabe and S. Record did the taxonomic diversity analyses. B. Baiser and S. Record did the functional diversity analyses. All authors contributed to drafts of the manuscript.\n\nData accessibilityAll data (i.e., ant and trait) and R code are available from the Harvard Forest Data Archive (http://harvardforest.fas.harvard.edu/data-archive), datasets HF-118 (HF-HeRE) and HF-097 (BRF-FOFE). Nomenclature follows Bolton (2016); voucher specimens are stored at the Harvard Forest and at the Museum of Comparative Zoology.

Ecology↗

bioRxiv2017

Chromosome Number of the Monarch Butterfly, Danaus plexippus (Linnaeus 1758) and the Danainae

The monarch butterfly, Danaus plexippus (Linnaeus 1758) is a charismatic butterfly known for its multi-generational migration in Eastern North America, and is emerging as an important system in the study of evolutionary genetics. Assigning genes or genetic elements to chromosomes is an important step when considering how genomes evolved. The monarch butterfly has a reported haploid chromosome number of 30. The specimens that this count is based on are from Madras, India where D. plexippus does not occur. As a consequence the reported haplotype for the D. plexippus is incorrect. A literature review revealed that the specimens this count was based on were most likely Danaus genutia (Cramer 1779), which Linnaeus and others conflated with D. plexippus. In a 1954 Opinion (#282) the International Code of Zoological Nomenclature decided that the name D. genutia refers to specimens originating from the Orient and D. plexippus to those from North America. To clarify the haplotype number of D. plexippus from North America I conducted chromosome squashes of male 5th instar larvae. All specimens examined had a haploid chromosome count of n = 28. Following these new data, I then reconstructed the evolution of haplotypes throughout the Danainae subfamily to provide a testable hypothesis on the evolution of chromosome number for this group.

evolutionary biology↗

bioRxiv2017

Enterovirus-A76 of South-East Asian ancestry in a Captive Chimpanzee (Pan troglodytes) in Jos, Nigeria

We recently detected EV-A119 and EV-B111 (previously shown to co-circulate between nonhuman primates (NHPs) and humans) in Nigerian children diagnosed with acute flaccid paralysis (AFP). This study was designed to investigate and catalogue EVs present in captive NHPs in Nigeria.\n\nTwenty-seven fecal samples collected from captive NHPs in a Wild Life Park and Zoological garden at Jos, Nigeria in April 2016 were analyzed in this study. Samples were resuspended in a phosphate buffered saline (PBS)/chloroform mixture, and the clarified supernatant was subjected to RNA extraction, cDNA synthesis, a Panenterovirus 5I-UTR assay, and three different enterovirus VP1 snPCR assays. All amplicons from the snPCR assays were sequenced, and enteroviruses identified using the enterovirus genotyping tool and phylogenetic analysis.\n\nEight (29.63%) (two each from Chimpanzees, Patas Monkey, Mona Monkey and Baboon) of the 27 samples were positive for the 5I-UTR assay. One (3.70%) of the 27 samples was positive for the enterovirus VP1 snPCR assays in addition to its positivity by 5I-UTR assay. The same sample happens to be one of the two samples from Chimpanzees that tested positive for the 5I-UTR assay, and it was subsequently identified as EV-A76 of South-East Asia ancestry.\n\nThis study documents the first recorded attempt to detect and identify enteroviruses in NHPs in Nigeria. It also reports the first detection and identification of EV-A76 in Nigeria and particularly in a NHP. It is of utmost importance that the enterovirus VP1 assays be improved to enable detection of EVs that have been detected in NHPs but yet to be described in humans.

microbiology↗

bioRxiv2019

The open bar is closed: restructuration of a native parasitoid community following successful control of an invasive pest.

AO_SCPLOWBSTRACTC_SCPLOWThe rise of the Asian chestnut gall wasp Dryocosmus kuriphilus in France has benefited the native community of parasitoids originally associated with oak gall wasps by becoming an additional trophic subsidy and therefore perturbing population dynamics of local parasitoids. However, the successful biological control of this pest has then led to significant decreases in its population densities. Here we investigate how the invasion of the Asian chestnut gall wasp Dryocosmus kuriphilus in France and its subsequent control by the exotic parasitoid Torymus sinensis has impacted the local community of native parasitoids. We explored 5 years of native community dynamics within 26 locations during the rise and fall of the invasive pest. In an attempt to understand how mechanisms such as local extinction or competition come into play, we analyzed how the patterns of co-occurrence between the different native parasitoid species changed through time. Our results demonstrate that native parasitoid communities experienced increased competition as the D. kuriphilus levels of infestation decreased. During the last year of the survey, two alternative patterns were observed depending on the sampled location: either native parasitoid communities were represented by an extremely limited number of species occurring at low densities, in some cases no native parasitoid species at all, or they were dominated by one main parasitoid: Mesopolobus sericeus. These two patterns seemed to correlate with the habitat type, M. sericeus being more abundant in semi-natural habitats compared to agricultural lands, the former known to be natural reservoirs for native parasitoids. These results highlight how the "boom-and-bust" dynamics of an invasive pest followed by successful biological control can deeply alter the structure of native communities of natural enemies. This article has been peer-reviewed and recommended by Peer Community in Zoology https://doi.org/10.24072/pci.zool.100004

ecology↗

bioRxiv2020

High throughput micro-CT scanning of small fossils: preparation, packing, parameters and post-processing

High-resolution X-ray microcomputed tomography, or microCT (CT), enables the digital imaging of whole objects in three dimensions. The power of CT to visualise internal features without disarticulation makes it particularly valuable for the study of museum collections, which house millions of physical specimens documenting the spatio-temporal patterns of life. Despite its potential for comparative analyses, most CT studies include limited numbers of museum specimens, due to the challenges of digitising numerous individuals within a project scope. Here we describe a method for high-throughput CT scanning of hundreds of small (< 2 cm) specimens in a single container, followed by individual labelling and archival storage. We also explore the effects of various packing materials and multiple specimens per capsule to minimize sample movement that can degrade image quality, and hence CT investment. We demonstrate this protocol on vertebrate fossils from Queensland Museum, Australia, as part of an effort to track community responses to climate change over evolutionary time. This system can be easily modified for other types of wet and dry material amenable to X-ray attenuation, including geological, botanical and zoological samples, providing greater access to large-scale phenotypic data and adding value to global collections.

evolutionary biology↗

bioRxiv2020

QuoVidi : a open-source web application for the organisation of large scale biological treasure hunts

Learning biology, and in particular systematics, requires learning a substantial amount of specific vocabulary, both for botanical and zoological studies. While crucial, the precise identification of structures serving as evolutionary traits and systematic criteria is not per se a highly motivating task for students. Teaching this in a traditional teaching setting is quite challenging especially with a large crowd of students to be kept engaged. This is even more difficult if, as during the COVID-19 crisis, students are not allowed to access laboratories for hands-on observation on fresh specimens and sometimes restricted to short-range movements outside their home. Here we present QuoVidi, a new open-source web platform for the organisation of large scale treasure hunts. The platform works as follows: students, organised in teams, receive a list of quests that contain morphologic, ecologic or systematic terms. They have to first understand the meaning of the quests, then go and find them in the environment. Once they find the organism corresponding to a quest, they upload a geotagged picture of their finding and submit this on the platform. The correctness of each submission is evaluated by the staff. During the COVID-19 lockdown, previously validated pictures were also submitted for evaluation to students that were locked in low-biodiversity areas. From a research perspective, the system enables the creation of large image databases by the students, similar to citizen-science projects. Beside the enhanced motivation of students to learn the vocabulary and perform observations on self-found specimens, this system allows faculties to remotely follow and assess the work performed by large numbers of students. The interface is freely available, open-source and customizable. It can be used in other disciplines with adapted quests and we expect it to be of interest in many classroom settings.

scientific communication and education↗

bioRxiv2020

The morphology and evolution of chondrichthyan cranial muscles: a digital dissection of the elephantfish Callorhinchus milii and the catshark Scyliorhinus canicula.

The anatomy of sharks, rays, and chimaeras (chondrichthyans) is crucial to understanding the evolution of the cranial system in vertebrates, due to their position as the sister group to bony fishes (osteichthyans). Strikingly different arrangements of the head in the two constituent chondrichthyan groups - holocephalans and elasmobranchs - have played a pivotal role in the formation of evolutionary hypotheses targeting major cranial structures such as the jaws and pharynx. However, despite the advent of digital dissections as a means of easily visualizing and sharing the results of anatomical studies in three dimensions, information on the musculoskeletal systems of the chondrichthyan head remains largely limited to traditional accounts, many of which are at least a century old. Here we use synchrotron tomography acquire 3D data which we used to carry out a digital dissection of a holocephalan and an elasmobranch widely used as model species: the elephantfish, Callorhinchus milii, and the small-spotted catshark, Scyliorhinus canicula. We describe and figure the skeletal anatomy of the head, labial, mandibular, hyoid, and branchial cartilages in both taxa as well as the muscles of the head and pharynx. We make new observations, particularly regarding the branchial musculature of Callorhinchus, revealing several previously unreported or previously ambiguous structures. Finally, we review what is known about the evolution of chondrichthyan cranial muscles from their fossil record and discuss the implications for muscle homology and evolution, broadly concluding that the holocephalan pharynx is likely derived from a more elasmobranch-like form. This dataset has great potential as a resource, particularly for researchers using these model species for zoological research, functional morphologists requiring models of musculature and skeletons, as well as for palaeontologists seeking comparative models for extinct taxa.

evolutionary biology↗

bioRxiv2020

Does participation in acoustic experiments provide enrichment to animals under human care? A case study of three grey seals (Halichoerus grypus)

Both mental and physiological conditions determine the well-being state in an animal. Enrichment is a way to increase an animals well-being and may require problem solving through thinking, tolerance of ambiguity, openness, and intrinsic motivation. It is unclear if it is enriching when an animal participates in different types of research. Therefore, it is important to answer the question of whether research can be used as an enrichment tool in zoological facilities. Here, we examine if participation in psychophysical research affected the mental stimulation of three grey seals under human care. The effects varied amongst the three individuals that took part in the research, and indicated that their participation in the research task was dependent on their individual personalities and life history. Two seals indicated that their involvement in the research was positive and motivating, and therefore can be considered enriching. In comparison, the third seal displayed a tendency for frustration and low motivation. Our results indicate that research can be a powerful enrichment tool with animals that find research motivating.

animal behavior and cognition↗

bioRxiv2020

Effects of a combined enrichment intervention on the behavioural and physiological welfare of captive Asiatic lions (Panthera leo persica)

The endangered Asiatic lion (Panthera leo persica) is currently distributed as a single wild population of 670 individuals and [~]400 captive animals globally. Although the captive lions are major hope for the species long-term conservation through repatriation, their welfare status and management practises need research attention. To this end, we tested the efficacy of feeding, sensory and manipulable enrichment interventions on the welfare of Asiatic lions at the conservation breeding centre of Sakkarbaug Zoological Garden, Gujarat. We adopted a holistic approach by measuring physiological and behavioural responses of 35 captive Asiatic lions, divided into control (n=16) and test (n=19) groups. The test subjects approached feeding devices first and manipulable devices for a longer duration. Manipulable devices were used homogenously with two significant time peaks, but sensory devices were used sporadically throughout the day with no discernible peak usage. The control subjects remained unchanged in all welfare parameters compared to their pre-treatment levels. However, post-enrichment behavioural assessments showed higher behaviour diversity (95% increase from the baseline period), reduced enclosure zone bias (40.25% reduction) and aberrant repetitive behaviours (80.68%) in test samples. Similarly, faecal corticosterone measures showed lower stress levels in test samples (58% decrease), confirming significant improvement in all welfare indices than control groups. These results have universal applicability to assess welfare indices of other captive species in Indian zoos. We hope that the results will encourage zoo managers and regulatory agencies to improve animal welfare practices.

animal behavior and cognition↗

bioRxiv2020

Effects of faecal inorganic contents in accurate measures of stress and nutrition hormone in large felines: implications for physiological assessments in free-ranging animals

Non-invasive stress and nutritional hormones and their interactions are increasingly being used to monitor psychological and nutritional physiology in free-ranging animals at different ecological scales. However, a number of extrinsic and intrinsic factors including hormone-inert dietary materials, inorganic matters etc. are known to affect accurate hormone measures. Here we addressed the impacts of inorganic matter (IOM) on corticosterone and T3 measures in wild tiger (n=193 from Terai Arc landscape, India) and captive lion (n=120 from Sakkarbaug Zoological Garden, Gujarat, India) faeces and evaluated possible corrective measures. The wild tiger samples contained highly variable IOM content (9-98%, mostly with >40% IOM) compared to captive Asiatic lion (17-57%, majority with <40% IOM). We observed significant negative correlation between IOM content and tiger GC (r=-0.48, p=0.000) and T3 (r=-0.60, p=0.000) measures but not in captive lions (r=-0.05, p=0.579). Two corrective measures viz. removing samples with [≥]80% IOM and subsequently expressing concentrations as per gram of organic dry matter (instead of total dry matter) reduced IOM influence on tiger GC and T3 measures without affecting lion GC results. The corrective measures bring out alterations in the tiger T3 results but no changes in GC results. As faecal IOM content is associated with specific behaviours of many carnivore species, our results emphasize the need to reduce IOM-driven hormone data variation for ecologically relevant interpretations for species conservation.

physiology↗

bioRxiv2020

Design, construction, and advantages of 100% online laboratories in an upper division undergraduate biology course

For centuries, students have been taught by passively listening to lectures, usually in large groups. In many fields, this type of course delivery is not ideal. In addition, students that have grown up with online access and/or have been forced to take online course during the recent pandemic, are seeking improved online educational experiences. As providers of education, Universities must adapt to this rapidly changing environment. The emergence of exciting, "disruptive" technologies has provided the tools needed for educators to revolutionize the delivery of higher education. The University of Florida, through UF Online, provides students the opportunity to enroll in fully online four-year undergraduate degrees. In this report, we describe the development of fully online laboratories for the upper-division course Evolutionary Developmental Biology, which fulfill the University of Floridas laboratory requirement. This course is taken by Biology, Zoology, and related majors, including majors in the 100% online Biology degree. The experiments in the virtual laboratories would have been impossible to teach in a residential setting due to time constraints, cost, student safety issues, and regulatory/certification requirements. The ability to perform these experiments online provided University of Florida undergraduates located throughout the world access to unique, one-of-a-kind laboratory experiences. The virtual laboratories allowed students to undertake in-depth exploration and application of course content that is not possible in a residential setting. Completion of the Evolutionary Developmental Biology course provided undergraduate students the opportunity to obtain a science degree without ever visiting the universitys residential campus. During the Fall 2020 term, this course was made available to residential students, thus allowing this cohort of students to continue to make progress, 100% online, towards their undergraduate degree during the COVID19 pandemic.

developmental biology↗

bioRxiv2021

Computational analysis of vertebrate myoglobins reveals aggregation resistance in aquatic birds and higher surface hydrophobicity in fish

Myoglobin is the major oxygen carrying protein of vertebrate muscle, and high myoglobin net charge is known to hold evolutionary significance as a molecular signature of secondarily aquatic diving capacity in mammals. However, the evolution of myoglobins electrostatic properties in non-mammalian vertebrates, such as birds, has not been investigated. Here, we used a new deep learning-based protein folding algorithm to model the tertiary structures of myoglobin from 302 vertebrate species and performed a comparative analysis of their net charge, positively charged solvent-accessible surface area, and negatively charged solvent-accessible surface area. For avian myoglobins, we also calculated selection pressure ({omega}). The results suggest that the myoglobins of diving avians, specifically those of the penguins (Sphenisciformes) and diving ducks (Aythyini), have highly positively charged electrostatic surfaces, which evolved via positive selection to reduce aggregation propensity and allow greater storage of oxygen for extended underwater foraging. In contrast, galliform myoglobins are under high purifying selection. Distribution of charged atoms on myoglobin surface was more indicative of high myoglobin content than net charge. We also found inter-class differences in net charge; bird myoglobins are the most positively charged and reptile and amphibian myoglobins are the most negatively charged, and net charge seems to be negatively associated with herbivory within mammals. Finally, we propose an equation that describes the relationship between myoglobin net charge and concentration better than the previously suggested logarithmic function. Our findings offer novel insights into the diversification of myoglobin in vertebrate clades and highlight the power of computational structural approaches for zoological and evolutionary research.

bioinformatics↗

bioRxiv2021

Up and to the light: intra- and interspecific variability of photo- and geo-tactic oviposition preferences in genus Trichogramma

AO_SCPLOWBSTRACTC_SCPLOWTrichogramma are parasitic microwasps much used as biological control agents. The genus is known to harbor tremendous diversity, at both inter- and intra-specific levels. The successful selection of Trichogramma strains for biocontrol depends on characterizing the existing diversity in this group, especially regarding oviposition performance and behavior. Oviposition preferences in relation to environmental cues such as light and gravity have received little attention so far, although they are suspected to play an important role in microhabitat selection and parasitism patterns. The extent of their variability, and their potential correlated variations, is virtually unknown. Here we use a novel experimental approach relying on automatic image analysis to characterize the oviposition preferences in relation to light and gravity, as well as their interaction, in 25 populations of Trichogramma from five species. We show that most Trichogramma populations and species harbour preferences for light and preferences for elevated parts. However, the two traits harbor significant inter and intraspecific variation. The effects of light and gravity on oviposition patterns were found to be almost perfectly additive overall, with two exceptions. Oviposition preference patterns were not static but very plastic in time: preferences tended to relax over consecutive days, and the strongest preferences relaxed the fastest, presumably because of the density-dependent effect of resource depletion. A correlation of oviposition patterns with the vegetation stratum at which populations were sampled suggests that different species/populations may be associated with different strata with corresponding differentiation in light- and gravity-related oviposition preferences. This article has been peer-reviewed and recommended by Peer Community in Zoology doi: https://doi.org/10.24072/pci.zool.100008

ecology↗

bioRxiv2021

Quantitative analysis of spore shapes improves identification of fungi

Morphology of organisms is an important source of evidence for biodiversity assessment, taxonomic decisions, and understanding of evolution. Shape information about zoological and botanical objects is often treated quantitatively and in this form improves species identification. In studies of fungi, quantitative shape analysis was almost ignored. The disseminated propagules of fungi, the spores, are crucial for their taxonomy - currently in the form of linear measurements or subjectively defined shape categories. It remains unclear how much quantifying spore shape information can improve species identification. In this study, we tested the hypothesis that shape, as a richer source of information, overperforms size when performing automated identification of fungal species. We used the fungi of the genus Subulicystidium (Agaricomycetes, Basidiomycota) as a study object. We analysed 2D spore shape data via elliptic Fourier and Principal Component analyses. With flexible discriminant analysis, we achieved a slightly higher species identification success rate for shape predictors (61.5%) than for size predictors (59.1%). However, we achieved the highest rate for a combination of both (64.7%). We conclude that quantifying fungal spore shapes is worth the effort. We provide an open access protocol which, we hope, will stimulate a broader use of quantitative shape analysis in fungal taxonomy. We also discuss the challenges of such analyses that are specific to fungal spores.

plant biology↗