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At least 19 recordsLinked to original sources

bioRxiv2023

Diminishing growth of zoological natural history collections threatens future research in the life sciences and beyond

Natural history museums comprise a unique and important component of biological infrastructure worldwide, and underlie diverse research, education, and outreach in the natural sciences. Each museum is built around one or more biological collections that serve as a repository of important materials for study, which have contributed to scientific research in increasingly important areas ranging from understanding global climate change to developing new biotechnological applications. However, despite centuries of existence, global collections sizes have only been recently estimated, and aside from analyses of certain institutions or well-studied clades, little is known about how patterns of collecting activity across institutions, geographic regions, or taxonomic clades, or how these patterns vary across time. To address this important gap in our understanding of critical life sciences infrastructure, I gathered and analyzed zoological records associated with preserved specimens collected between 1900 and 2015 and housed in worldwide natural history collections using data from the Global Biodiversity Information Facility. My analysis indicated that global, museum-associated collecting activity focused on animals has varied greatly over time, peaking around 2000 and declining significantly since. By stratifying data by institution, nation, and taxonomic phylum and class, I also illuminated how individual data series contribute to these global patterns. Institutions and nations had either concentrated or dispersed periods of relatively high collecting activity that occurred over different time periods, although most growth occurred in the second half of the 20th century for both many individual institutions and globally. Certain taxonomic clades comprise the largest proportions of collections records over this time period, namely arthropods (especially insects) and chordates (especially vertebrates), underscoring the taxonomically biased collecting histories of many institutions. Altogether, my analyses provide a critical, early view of historical zoological collecting activity and, to help other museum stakeholders to explore the data and results in more depth, I also describe and release NHMinformatics, an interactive dashboard built using R Shiny. These resources, when combined with recommendations I have made for sustainable collections growth, will be helpful for establishing policy goals, provisioning museum infrastructure, and training curatorial personnel.

zoology↗

bioRxiv2020

Does visitation dictate animal welfare in captivity? A case study of tigers and leopards from National Zoological Park, New Delhi

Zoological Parks serve a salient purpose of entertaining many visitors by housing various exclusive animal species. Big cats like tigers and leopard are among the most visited species in zoos globally. We investigated the behavioral response of the zoo-housed big cats to visitor densities and noise. We also aimed to understand the relationship between stereotypy, animal history, feeding schedules, and enclose design. The behavior of eight big cats housed in the National Zoological Park, New Delhi, was monitored using the focal sampling technique during the May and June 2019 to construct the ethograms. We also recorded the visitor density, ambient noise, for the same duration. Both species were found devoting a significant amount (>50%) of time in displaying inactive behaviors. Tigers and leopards performed stereotypic behaviors for 22% and 28% of their time, respectively. Pearson chi-square analysis revealed a significant variation of stereotypy in association with biological (age, sex, and rearing history) and captive (enclosure design) variables. Big cats stereotypic behaviors were found significantly influenced by the high visitor density. However, ambient noise did not impact the stereotypy of both the felid species. Visitors form an integral part of zoos, and their detrimental impact diminishes the well-being of captive animals. This study revealed that tigers and leopards in NZP display a high proportion of inactive and stereotypic behaviors. Thus, we suggest zoo authorities adopt more enclosure enrichment initiatives.

animal behavior and cognition↗

bioRxiv2021

Neural Regression, Representational Similarity, Model Zoology & Neural Taskonomy at Scale in Rodent Visual Cortex

How well do deep neural networks fare as models of mouse visual cortex? A majority of research to date suggests results far more mixed than those produced in the modeling of primate visual cortex. Here, we perform a large-scale benchmarking of dozens of deep neural network models in mouse visual cortex with both representational similarity analysis and neural regression. Using the Allen Brain Observatorys 2-photon calcium-imaging dataset of activity in over 6,000 reliable rodent visual cortical neurons recorded in response to natural scenes, we replicate previous findings and resolve previous discrepancies, ultimately demonstrating that modern neural networks can in fact be used to explain activity in the mouse visual cortex to a more reasonable degree than previously suggested. Using our benchmark as an atlas, we offer preliminary answers to overarching questions about levels of analysis (e.g. do models that better predict the representations of individual neurons also predict representational similarity across neural populations?); questions about the properties of models that best predict the visual system overall (e.g. is convolution or category-supervision necessary to better predict neural activity?); and questions about the mapping between biological and artificial representations (e.g. does the information processing hierarchy in deep nets match the anatomical hierarchy of mouse visual cortex?). Along the way, we catalogue a number of models (including vision transformers, MLP-Mixers, normalization free networks, Taskonomy encoders and self-supervised models) outside the traditional circuit of convolutional object recognition. Taken together, our results provide a reference point for future ventures in the deep neural network modeling of mouse visual cortex, hinting at novel combinations of mapping method, architecture, and task to more fully characterize the computational motifs of visual representation in a species so central to neuroscience, but with a perceptual physiology and ecology markedly different from the ones we study in primates.

neuroscience↗

bioRxiv2025

Exotic and Zoological Birds Resident and Imported into Nigeria harbour Highly Pathogenic Avian Influenza Virus: Threat to Poultry Production, Food security and Public Health.

Influenza is a major infectious disease challenge affecting animal and human health globally, and wild birds are historically the primary reservoirs of all the known Influenza A virus subtypes. Here, we detected the Highly Pathogenic Avian Influenza (HPAI) virus in exotic and aquatic birds in three different locations in Nigeria. On the 8th of February 2021, exotic birds: Yellow Golden Pheasant (Chrysolophus pictus), Sultan chicken (Gallus gallus domesticus), Lakenvelder chicken (Gallus gallus domesticus), and Common pheasant (Phasianus calchicus), imported from Libya and transported across the Niger Republic border to Nigeria, were presented to the National Veterinary Research Institute, Vom, for screening. Also, a family in Lagos State bought some exotic aquatic birds from a live bird market in Sokoto State, Nigeria, where sudden death was recorded with the birds showing few clinical signs. Similarly, the sudden death of some aquatic birds was reported in Mandela Parks and Gardens in Asaba, Delta State, few weeks after some captured wild birds were introduced to the Park and Gardens. Oropharyngeal, cloacal, and tissue samples were all collected from the reported cases. Total viral nucleic acid was extracted and screened for Influenza A viruses using real-time RT-PCR. The HPAI viruses H5N1 and H5N8 were detected in the imported aquatic (geese and ducks) and exotic (yellow golden pheasant) birds. The samples tested negative for low-pathogenic Avian Influenza Virus (H9N2) as well as other avian viruses, viz., Avian avulavirus-1 (Newcastle disease Virus) and infectious bronchitis virus. This highlights the role of these resident and imported exotic birds in the local transmission and spread of the HPAI virus to domestic poultry. The findings call for proper biosecurity and quarantine measures for exotic and wild birds to reduce the potential risk to animal and public health in Nigeria.

microbiology↗

bioRxiv2023

Leveraging whole genome sequencing to promote genetic diversity and population health in zoo-housed western lowland gorillas

The sustainability of zoo populations is dependent on maintaining genetic diversity and controlling heritable disease. Here, we explore the integration of whole genome sequencing data in the management of the international zoological population of western lowland gorillas, focusing on genetic diversity and heritable diseases. By comparing kinship values derived from classical pedigree mapping and whole genome sequencing, we demonstrate that genomic data provides a more sensitive measure of relatedness. Our analysis reveals a decrease in genetic diversity due to closed breeding, emphasizing the potential for genetic intervention to mitigate negative impact on population fitness. We identify contributing factors to the decreasing genetic diversity including breeding within a closed population, unknown kinship among potential mates, and disproportionate genetic contributions from individual founders. Additionally, we highlight idiopathic myocardial fibrosis (IMF), a common cardiovascular pathology observed in zoologically housed gorillas, and identify a novel genetic variant in the TNNI3K gene that appears to be associated with this condition. These findings underscore the importance of incorporating molecular data into ex-situ population management strategies, and advocate for the adoption of advanced genomic techniques to optimize the genetic health and diversity of zoologically housed western lowland gorillas.

zoology↗

bioRxiv2020

Neotype designation and re-description of Forsskal's reticulate whipray Himantura uarnak

A serious impediment to the taxonomy of the reticulate whipray Himantura spp. species complex has been the absence of a type specimen for P. Forssk[a]ls H. uarnak. Here, reticulate whipray specimens were sampled from the Jeddah region, the assumed type locality of H. uarnak, and characterized genetically at the cytochrome-oxidase subunit 1 (CO1) locus. One of these specimens now in the fish collection of the California Academy of Sciences in San Francisco was designated as neotype. A maximum-likelihood phylogeny of all available CO1 gene sequences from the genus Himantura had the following topology: ((H. leoparda, H. uarnak), (H. undulata, (Himantura sp. 2, (H. australis + Himantura sp. 1))), H. tutul), where H. uarnak haplotypes formed a distinct sub-clade sister to H. leoparda. Based on these CO1 gene sequences, the geographic distribution of H. uarnak includes the eastern Mediterranean, the Red Sea, the East African coast, and the Arabian Sea. Two lineages in the reticulate whipray species complex remain to be named. NoticeThe present article in portable document (.pdf) format is a published work in the sense of the International Code of Zoological Nomenclature [International Commission on Zoological Nomenclature (ICZN)1999]. It has been registered in ZooBank (http://zoobank.org/), the online registration system for the ICZN. The ZooBank life science identifier for this publication is urn:lsid:zoobank.org:pub:B2113697-5EBF-4364-B50C-63019A1A076A. The online version of this work is archived and available from the bioRxiv (https://biorxiv.org/) repository.

zoology↗

bioRxiv2021

Four new species of Cichlidogyrus (Platyhelminthes, Monogenea, Dactylogyridae) from Lake Victoria haplochromine cichlid fishes, with the redescription of C. bifurcatus and C. longipenis

African cichlids are model systems for evolutionary studies and for host-parasite interactions, because of their adaptive radiations and because they harbour many species of monogenean parasites with high host-specificity. Here, we sampled five locations in southern Lake Victoria, the youngest of the African Great Lakes. We surveyed gillinfecting monogeneans from 18 cichlid species belonging to the Lake Victoria radiation superflock and two cichlid species representing two older and distantly related lineages. We found one species of Gyrodactylus (Gyrodactylidae, Monogenea), Gyrodactylus sturmbaueri Vanhove, Snoeks, Volckaert & Huyse, 2011, and seven species of Cichlidogyrus (Dactylogyridae, Monogenea). Four species are herein described: Cichlidogyrus pseudodossoui n. sp., C. nyanza n. sp., C. furu n. sp., C. vetusmolendarius n. sp.. Another species is reported but not formally described (because of few specimens and morphological similarity with C. furu n. sp.). Two other species are redescribed: Cichlidogyrus bifurcatus Paperna, 1960 and C. longipenis Paperna & Thurston, 1969. Our results confirm that the monogenean fauna of Victorian littoral cichlids displays lower species richness and lower host-specificity than that of Lake Tanganyika littoral cichlids. In C. furu n. sp., hooks V are clearly longer than the other hooks, highlighting the need to re-evaluate the current classification system of haptoral configurations that considers hook pairs III-VII as rather uniform. Some morphological features of C. bifurcatus, C. longipenis and C. nyanza n. sp. suggest that these are closely related to other congeners that infect haplochromines. We also found morphological indications that representatives of Cichlidogyrus colonised Lake Victoria haplochromines or their ancestors at least twice, which is in line with the Lake Victoria superflock being colonized by two cichlid tribes (Haplochromini and Oreochromini). DisclaimerThis preprint is disclaimed for purposes of Zoological Nomenclature in accordance with the International Code of Zoological Nomenclature, Fourth Edition Articles 8.2 and 8.3 (ICZN 1999). No new names or nomenclatural changes are available from statements in this preprint. Resume - Quatre especes nouvelles de Cichlidogyrus (Platyhelminthes, Monogenea, Dactylogyridae) parasites dhaplochromine (Cichlidae) du lac Victoria, avec la redescription de C. bifurcatus and C. longipenisA cause des radiations adaptatives quils ont subies, les cichlides africain sont des systemes modeles pour etudier levolution, mais aussi les relations hotes/parasites, car ils hebergent de nombreuses especes de Monogenes parasites qui presentent une specificite etroite vis-a-vis de leurs hotes. Dans ce travail, nous avons echantillonne cinq localites dans le Sud du lac Victoria, le plus jeune des grands lacs dAfrique de lEst. Nous avons examine les Monogenes presents sur les branchies de 18 especes de Cichlides appartenant a la radiation adaptative << superflock >> du lac Victoria et de deux especes representant deux lignees anciennes et non etroitement apparentees. Nous avons trouve une espece de Gyrodactylus (Gyrodactylidae, Monogenea), Gyrodactylus sturmbaueri Vanhove, Snoeks, Volckaert & Huyse, 2011 et sept especes de Cichlidogyrus (Dactylogyridae, Monogenea). Quatre especes nouvelles sont decrites dans le present travail : Cichlidogyrus pseudodossoui n. sp., C. nyanza n. sp., C. furu n. sp., C. vetusmolendarius n. sp.. Une est signalee mais non decrite formellement (trop peux dindividus recueillis, morphologiquement proche de C. furu n. sp.). Deux autres sont redecrites : Cichlidogyrus bifurcatus Paperna, 1960 and C. longipenis Paperna & Thurston, 1969. Nos resultats confirment que la faune des Monogenes des Cichlides du lac Victoria fait preuve dune richesse specifique et dune specificite moins importante que celle du lac Tanganyika. Chez C. furu n. sp. la paire de crochet V etant nettement plus longue que les autres, il faudra reconsiderer le systeme de classification actuel des types de hapteurs chez les Cichlidogyrus, qui considere que tous les crochets (III a VII) ont la meme taille. Quelques caracteristiques morphologiques de C. bifurcatus, C. longipenis et C. nyanza n. sp. pourraient etre la preuve dune ascendance commune avec des congeneres presents chez dautres Haplochromines. De meme, certains caracteres indiqueraient que des representants des Cichlidogyrus ont colonise les Haplochromines du lac Victoria, ou leurs ancetres, au moins a deux reprises, ce qui est coherent avec une colonisation du lac par deux lignees de cichlides distinctes (Haplochromini and Oreochromini).

zoology↗

bioRxiv2019

Genomics reveals the origins of ancient specimens

Centuries of zoological studies amassed billions of specimens in collections worldwide. Genomics of these specimens promises to rejuvenate biodiversity research. The obstacles stem from DNA degradation with specimen age. Overcoming this challenge, we set out to resolve a series of long-standing controversies involving a group of butterflies. We deduced geographical origins of several ancient specimens of uncertain provenance that are at the heart of these debates. Here, genomics tackles one of the greatest problems in zoology: countless old, poorly documented specimens that serve as irreplaceable embodiments of species concepts. The ability to figure out where they were collected will resolve many on-going disputes. More broadly, we show the utility of genomics applied to ancient museum specimens to delineate the boundaries of species and populations, and to hypothesize about genotypic determinants of phenotypic traits.

zoology↗

bioRxiv2023

Uncovering Hidden Data in the AMNH Marine Invertebrate Collections

Average global sea surface temperatures have been consistently higher during the past thirty years than any other time since reliable temperature recordings in 1880. Marine life is sufficiently adaptable to survive in a range of temperatures, but extended periods of temperature extremes can have a profound effect on the biology and behavior of aquatic organisms. Historic baseline data is often critical to understanding these changes in biology, distribution, migration, and population dynamics. Data from museum specimens can provide such baselines, but are often an overlooked resource, in part because museum collection data are not readily available. The American Museum of Natural Historys invertebrate zoology collection is home to an estimated 7.5 million marine specimens dating back to the mid-1800s. Although many of the specimens have been catalogued in a public online database, data from a large number of these specimens are not yet in digital form and are therefore only accessible to staff and researchers visiting or borrowing from the collection. The Museums Crustacea collection contains around 19,400 specimen lots which hold significant historic value, including lots from the New York Zoological Societys Bermuda Oceanographic Expeditions. The Bermuda Oceanographic Expeditions provide a rare opportunity to examine historic abundance and distribution of pelagic crustacea taxa that are currently experiencing extended periods of increased ocean temperatures. We synthesized data from the fluid-preserved specimens and from expedition field logs to compose a depth profile that compared the number of crustacean specimens, identified to family or lower taxonomic level, per depth. The results indicate that crustacean abundance and diversity was highest (4-7 families) between 500-1000 fathoms. Most of the specimens were diel-migratory shrimp from the family Sergestidae. We believe that this study provides a useful basis of historic sergestid distribution data that can be used to contextualize modern research in the warming Sargasso Sea.

ecology↗

bioRxiv2021

Phylogeography of Lanius senator reveals conflicts between alpha taxonomy, subspecies ranges and genetics.

Implementing the effort in understanding biogeographic distribution patterns and taxonomic limits within animal groups is crucial for addressing several challenges of modern zoology. Although avian phylogeography has been deeply investigated within Western Palearctic, several families, such as shrikes, still display complicated or neglected biogeographic patterns both between and within species, thus requiring further investigations. The Woodchat Shrike (Lanius senator) is a long-distance migratory species that exhibits three morphologically well-recognizable subspecies, whose boundaries have never been molecularly investigated. Here, we aimed to define the phylogeographic structure of Lanius senator throughout its breeding range and assess the genetic coherence with the phenotypically described subspecies. We assembled a collection of 34 samples mainly from breeding populations of each subspecies and analyzed them at four mtDNA and two nuDNA markers. We did not find a clear phylogenetic structure with nuclear Ornithine Decarboxylase (ODC) and myoglobin intron 2 (MYO), while all the four mtDNA loci (i.e., ND2, COI, cytb and Control Region) highlighted two main haplogroups, one including both the nominate subspecies L. s. senator and L. s. badius and the second consistent with L. s. niloticus only from the easternmost part of the range. Surprisingly, individuals phenotypically assigned to L. s. niloticus from Israel were genetically assigned to the senator/badius haplogroup. Moreover, genetic distances showed intermediate values between inter-intraspecies diversity usually found in Passerines. We estimated a divergence time among the two haplogroups around 800 kya (549 - 1.259 kya HPD). Our findings showed a mismatch in subspecies assignment using morphology and genetic information and a marked differentiation between the eastern L.s. niloticus and all the other L. senator populations.

zoology↗

bioRxiv2022

Contribution of private game ranching and captive bred operations in South Africa to white rhino Ceratotherium simum species survival conservation

The southern white rhinoceros (SWR) Ceratotherium simum simum, like all extant rhinoceros species, is under global threat of extinction, due to their dwindling wild population numbers in protected areas and state-owned parks as a result of poaching. The Kruger National Park (KNP), the renowned state-owned stronghold for SWR, has suffered an estimated decline of over 75.0% of its population since 2011, with the highest annual poaching rates over the past decade and a remaining population estimated at only 2,607 animals by the end of 2020, which is an average annual population decline of -10.2% from 2008 to 2020, and 2,458 animals left by the end of June 2022. On the contrary, SWR under private custodianship and management on rewilded agro-sustainable biodiversity game ranches in South Africa (estimated currently at >8,000 animals, some of which are registered Captive Breeding Operations [CBO]; assessed CBOs contained 2,882 rhinos at the time of this study (Sep 2021), have increased in population numbers and survival rates, sustaining average annual population growth performances of 9.0%. This increase has been attributed to effective security, provision of additional habitat, dispersal, and frequent genetic exchange of rhinos between breeding subpopulations by the private sector. The conservation success of the private sector has largely been overlooked and disregarded by world conservation bodies and organizations, mostly due to misguided and prejudiced media publicity and the lack of scientific analytical assessment. Private rhino custodians and their biological/ conservation breeding practices, with private agro-sustainable biodiversity wildlife management and/ or captive breeding, generally being perceived and branded as either "canned" or equated to "captive zoological-gardens". Since the commencement of the International Convention on Biodiversity, global controversy exists whereby most of mankind today perceive bio-conservation of a species to be assigned in principle solely to protected areas and state-owned parks. The unique and advantageous roles of rewilded bio-conservation and sustainable-use conservation CBOs, being a key to green-economy and natural capital in a post-Covid-19 struggle, are mostly ignored. This study serves to assess and quantify the impact of private wildlife ranching in South Africa with specific focus on its potential contribution to rhino conservation specifically for that of the SWR C.s. simum. Data Availability StatementThe data belong to third parties, six different private owners respectively, and cannot be shared publicly. Interested, qualified researchers can request the data by contacting the author, subject to owners permission. The authors confirm that they did not have any special access privileges to the data and data will be made available to other researchers in the same manner that the authors accessed it.

zoology↗

bioRxiv2022

One Health Approach for the sampling of different bat species living in a sympatric colony

Bats are important contributors to the global ecosystems; at the same time, they are known to be a natural reservoir host for a number of human pathogenic viruses. These and many other unique features make them an interdisciplinary research object in the context of One Health, comprising zoology, ecology, virology, microbiology, molecular biology, immunology and public health issues. Performing field studies for bat research often aims to cover several of these topics and requires the combination of specific expertise in different fields. We carried out three individual field studies in Wavul Galge cave (Koslanda, Sri Lanka), where several bat species roost sympatrically. The main goals were to study the bat colony for ecological aspects and to sample bats for virological and molecular biological analyses. In the course of the field studies, we optimized the sampling procedure regarding safety aspects, a preferably low impact on the captured bats and an improved output of high-quality samples for further analysis. Different sampling methods and procedures were compared in order to establish a suitable strategy for frequent sampling and monitoring of these bats. In the present case study, we report on this process of optimizing our field work and provide suggestions for bat sampling methods that cause comparably less stress for the captured animals. We also report on constraints and obstacles encountered during the practical implementation and possible measures to overcome these. With these practical experiences, we hope to give support to other interdisciplinary research teams preparing for bat field work. Furthermore, we emphasize the need for the respectful treatment of the animals and minimized disturbance of their natural habitat when carrying out sustainable bat research.

zoology↗

bioRxiv2024

Expanding the use of reindeer foetal bone measurements for zooarchaeological applications

When foetal bones are preserved in archaeological sites, they are often used to identify the seasonality of prey acquisition by past human populations and, subsequently, to discuss their lifestyle, their management of food resources, nomadic cycles, etc. To do so, zooarchaeologists use charts to estimate foetal age based on the growth of their bones. For reindeer (Rangifer tarandus), a species that was widely exploited since the Palaeolithic throughout Eurasia, existing reference data are limited and require the measurement of complete bones, a procedure that is rarely applicable to archaeological contexts in which bones are often fragmented. In this study we present a wide range of measurements (9-10 measurements per bone) taken on the humerus, radius, metacarpal, femur, tibia and metatarsal of 31 individuals housed at the Zoological Museum of the University of Oulu (Finland). With this large data set, a more accurate estimation of the time of death of reindeer foetus can be achieved using skeletal measurements, even in the case of fragmented bones. To facilitate the use of this referential, an open-access web interface (foetusmeteR) was designed in RShiny. This interface allows for the direct estimation of foetal age and season of death by entering a single skeletal measurement, as well as the possibility of estimating if two bones might correspond to the same individual using two different measurements. This new tool should help to discuss in more detail the condition of reindeer herds hunted in the past, the hunting techniques and strategies that may have been used by human groups, and allow for a more detailed reconstruction of the seasonal nomadic cycle of past societies that focused their subsistence on Rangifer populations.

zoology↗

bioRxiv2024

Sexual dimorphism in the tardigrade Paramacrobiotus metropolitanus transcriptome

BackgroundIn gonochoristic animals, the sex determination pathway induces different morphological and behavioral features that can be observed between sexes, a condition known as sexual dimorphism. While many components of this sex differentiation cascade shows high levels of diversity, factors such as the Doublesex-Mab-3-related transcription factor (DMRT) are highly conserved throughout animals. Species of the phylum Tardigrada exhibits remarkable diversity in morphology and behavior between sexes, suggesting a pathway regulating such dimorphism. Despite the wealth of genomic and zoological knowledge accumulated in recent studies, the sexual differences in tardigrades genomes have not been identified. In this study, we focused on the gonochoristic species Paramacrobiotus metropolitanus and employed omics analyses to unravel the molecular basis of sexual dimorphism. ResultsTranscriptome analysis between sex identified numerous differentially expressed genes, of which approximately 2,000 male-biased genes were focused on 29 non-male-specific genomic loci. From these regions, we identified two Macrobiotidae family specific DMRT paralogs, which were significantly upregulated in males and lacked sex specific splicing variants. Furthermore, phylogenetic analysis indicated all tardigrade genomes lacks the doublesex ortholog, suggesting doublesex emerged after the divergence of Tardigrada. In contrast to sex-specific expression, no evidence of genomic difference between the sexes were found. We also identified several anhydrobiosis genes exhibiting sex-biased expression, possibly suggesting a mechanism for protection of sex specific tissues against extreme stress. ConclusionsThis study provides a comprehensive analysis for analyzing the genetic differences between sexes in tardigrades. The existence of male-biased, but not male-specific, genomic loci and identification of the family specific male-biased DMRT subfamily would provide the foundation for understanding the sex determination cascade. In addition, sex-biased expression of several tardigrade-specific genes which are involved their stress tolerance suggests a potential role in protecting sex-specific tissue and gametes.

zoology↗

bioRxiv2024

Sperm quality metrics exhibit annual fluctuations in a critically endangered amphibian managed under human care

The Puerto Rican crested toad (PRCT) is Puerto Ricos only endemic toad and has undergone rapid population decline within the last 40 years. As a hedge against extinction, captive assurance colonies have been established at several zoological institutions for breeding and reintroduction. However, reproductive output has remained low, despite the use of hormone therapies to attempt to bypass missing abiotic cues and stimulate reproductive behaviors. This low output necessitates a better understanding of natural fluctuations in gamete, specifically sperm, quality in captive individuals. To generate an understanding of natural gametic cycles in captive PRCTs, we administered male PRCTs (n = 86) housed under natural temperature and photoperiod cycles with exogenous hormones monthly for one year. Samples were analyzed for motility and concentration to assess variations in sperm quality by month. Spermiation was successfully stimulated every month, but quality fluctuated; sperm motility was highest in June and July, while sperm concentration was highest in December, January, and March. These results indicate that, while hormones can be utilized to stimulate gamete production in PRCTs year-round, sperm quality is not consistent. Furthermore, the seasonal occurrence of peak sperm production of captive males differed from natural peaks reported for wild PRCTs. Our results illustrate the need for more biologically informed strategies for breeding of at-risk anuran populations.

zoology↗

bioRxiv2019

Parachute geckos free fall into synonymy: Gekko phylogeny, and a new subgeneric classification, inferred from thousands of ultraconserved elements

Recent phylogenetic studies of gekkonid lizards have revealed unexpected, widespread paraphyly and polyphyly among genera, unclear generic boundaries, and a tendency towards the nesting of taxa exhibiting specialized, apomorphic morphologies within geographically widespread \"generalist\" clades. This is especially true in the Australasia, where the monophyly of Gekko proper has been questioned with respect to phenotypically ornate flap-legged geckos of the genus Luperosaurus, the Philippine false geckos of the genus Pseudogekko, and even the elaborately \"derived\" parachute geckos of the genus Ptychozoon. Here we employ sequence capture targeting 5060 ultraconserved elements to infer phylogenomic relationships among 42 representative ingroup gekkonine lizard taxa. We analyzed multiple datasets of varying degrees of completeness (10, 50, 75, 95, and 100 percent complete with 4715, 4051, 3376, 2366, and 772 UCEs, respectively) using concatenated maximum likelihood and multispecies coalescent methods. Our sampling scheme was designed to address four persistent systematic questions in this group: (1) Are Luperosaurus and Ptychozoon monophyletic and are any of these named species truly nested within Gekko? (2) Are prior phylogenetic estimates of Sulawesis L. iskandari as sister to Melanesian G. vittatus supported by our genome-scale dataset? (3) Is the high elevation L. gulat of Palawan Island correctly placed within Gekko? (4) And, finally, where do the enigmatic taxa P. rhacophorus and L. browni fall in a higher-level gekkonid phylogeny? We resolve these issues; confirm with strong support some previously inferred findings (placement of Ptychozoon taxa within Gekko; the sister relationship between L. iskandari and G. vittatus); resolve the systematic position of unplaced taxa (L. gulat, and L. browni); and transfer L. iskandari, L. gulat, L. browni, and all members of the genus Ptychozoon to the genus Gekko. Our unexpected and novel systematic inference of the placement of Ptychozoon rhacophorus suggests that this species is not related to Ptychozoon or even Luperosaurus (as previously expected) but may, in fact, be most closely related to several Indochinese species of Gekko. With our final, well-supported topologies, we recognize seven newly defined subgenera to accommodate [~]60 species within the more broadly defined and maximally-inclusive Australasian genus Gekko. The newly defined subgenera will aide taxonomists and systematists in species descriptions by allowing them to only diagnose putatively new species from the most relevant members of the same subgenus, not necessarily the phenotypically variable genus Gekko as a whole, and we argue that it appropriately recognizes geographically circumscribed units (e.g., a new subgenus for a novel clade, entirely endemic to the Philippines) while simultaneously recognizing several of the most systematically controversial, phenotypically distinct, and phylogenetically unique lineages. An added benefit of recognizing the most inclusive definition of Gekko, containing multiple phylogenetically-defined subgenera, is that this practice has the potential to alleviate taxonomic vandalism, if widely adopted, by creating formally available, supraspecific taxa, accompanied by character-based diagnoses and properly assigned type species, such that future, more atomized classifications would necessarily be required to adopt todays subgenera as tomorrows genera under the guidelines of The Code of Zoological Nomenclature. Not only does this simple practice effectively eliminate the nefarious motivation behind taxonomic vandalism, but it also ensures that supraspecific names are created only when accompanied by data, that they are coined with reference to a phylogenetic estimate, and that they explicitly involve appropriate specifiers in the form of type species and, ultimately, type specimens.

zoology↗

bioRxiv2026

Unravelling historical, taxonomic, and cultural influences on the etymology of scientific names across Animalia

Animal naming is fundamental to scientific communication, yet it also reflects the historical and cultural contexts in which names are bestowed. Scientific names function as taxonomic labels and enduring records of human engagement with nature. Owing to this dual role, species names have recently attracted increasing attention from historical and humanities perspectives, both for their informative value and for the biases they may encode. To objectively assess these patterns at a large scale, we investigated etymological trends across Animalia using a comprehensive dataset of species names. Our analyses reveal that naming practices are shaped by a combination of historical events, taxonomic traditions, and cultural influences. Major global disturbances coincided with marked declines in species descriptions, whereas advances in biological techniques were associated with shifts in naming practices. Furthermore, etymological trends differed among phyla, indicating that taxonomic communities vary in their naming conventions. These differences suggest that taxonomists preferences, shared aesthetics, available knowledge, and cultural biases are differentially preserved in scientific names. Together, our results demonstrate that zoological nomenclature constitutes a valuable archive for understanding the historical and cultural dimensions of taxonomy.

zoology↗

bioRxiv2026

Reassessing display behavior from Bels et al. (2025) given the complexity of anthropogenic hybridization and intraspecific diversity in Iguana iguana

Understanding behavioral differences between non-native and closely related endangered species could be important to aid conservation management. In volume 169 of Zoology, Bels et al. (2025) reported on their comparison of display-action-patterns (DAP) between native Iguana delicatissima and non-native iguanas present on islands of the Guadeloupe Archipelago in the Caribbean Lesser Antilles. Here, we address conceptual and methodological concerns about their work and reanalyze their data given our proposed corrections, primarily a literature-informed adjustment of their "species" category. We additionally utilize online videos from South American mainland I. iguana populations, from where the non-native iguanas in the Guadeloupe Archipelago originate, to better understand the different DAPs between native and non-native iguanas in the Guadeloupe Archipelago. Significant differences in DAP characteristics among "species" categories (native I. delicatissima, non-native iguanas, and hybrids) show that Bels et al. (2025) oversimplified their data analyses by merging all non-native populations into one group. This result indicates the presence of behavioral variation among subpopulations within widely hybridizing iguanid populations, which has been poorly studied. Additionally, videos from mainland populations across two major mitochondrial clades of Iguana iguana show that non-native iguanas on Guadeloupe retained DAP characteristics of those populations from which they originate. We discuss these findings in light of the proposed hypotheses put forward by Bels et al. (2025), of which two can be excluded. Overall, our reanalysis shows that studies focusing on characteristics within settings of complex hybridization in diverse species should acknowledge this complexity.

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