Novel chytrid pathogen variants and the global amphibian pet trade.

Global wildlife trade spreads emerging infectious diseases that threaten biodiversity. The amphibian chytrid pathogen Batrachochytrium dendrobatidis (Bd) has caused population declines and species extinctions worldwide except in Asia. Fire-bellied toads (Bombina orientalis), exported in large numbers from Asia, are tolerant of Bd and carry hypervirulent ancestral chytrid BdAsia-1 variants. We assayed the virulence of a new isolate of BdAsia-1 on the model Australasian frog host Litoria caerulea. Infected individuals (n = 15) all showed rapid disease progression culminating in death, whereas sham-inoculated individuals (n = 10) presented no clinical signs of disease and all survived (log rank test, χ2 = 15.6, df = 1, p < 0.0001). The virulence of the new isolate of BdAsia-1 is comparable to the one we assayed previously (χ2 = 0.0, df = 1, p = 0.91). Internationally traded wildlife, even when they appear healthy, can carry hypervirulent variants of pathogens. Once new pathogen variants escape into the environment, native species that have had no opportunity to evolve resistance to them may perish. Our study suggests that hypervirulent pathogens are being spread by the international pet trade. Notifiable wildlife diseases attributable to locally endemic pathogens often fail to generate conservation concern so are rarely subject to border surveillance or import controls. Because of the danger novel variants pose, national border control agencies need to implement disease screening and quarantine protocols to ensure the safety of their endemic fauna.

Variantes Patógenas Nuevas de Quitridios y el Mercado Mundial de Anfibios Mascota Resumen El mercado mundial de fauna dispersa enfermedades infecciosas emergentes que amenazan a la biodiversidad. El quitridio patógeno de anfibios Batrachochytrium dendrobatidis (Bd) ha causado declinaciones poblacionales y la extinción de especies en todo el mundo excepto Asia. El sapo Bombina orientalis, exportado en grandes cantidades desde Asia, es tolerante al Bd y carga genéticamente las variantes ancestrales hipervirulentas de quitridio BdAsia-1. Analizamos la virulencia de una nueva cepa de BdAsia-1 con el modelo de la rana australo-asiática hospedera Litoria caerulea. Todos los individuos infectados (n = 15) mostraron una progresión acelerada de la enfermedad que culminaba con la muerte, mientras que los individuos con inoculación simulada (n = 10) no presentaron señales clínicas de la enfermedad y todos sobrevivieron (prueba log de rango, χ2 = 15.6, df = 1, p < 0.0001). La virulencia de la nueva cepa de BdAsia-1 es comparable a la que analizamos previamente (χ2 = 0.0, df = 1, p = 0.91). La fauna comercializada internacionalmente, incluso cuando parece estar saludable, puede portar variantes hipervirulentas de los patógenos. Una vez que un patógeno nuevo se introduce al ambiente, pueden perecer las especies nativas que no han tenido la oportunidad de evolucionar la resistencia a estos patógenos. Nuestro estudio sugiere que los patógenos hipervirulentos se están dispersando mediante el mercado internacional de mascotas. Con frecuencia las enfermedades silvestres notificables que pueden atribuirse a los patógenos endémicos no generan interés para la conservación, así que rara vez están sujetas a la vigilancia fronteriza o el control de importación. Debido al riesgo que representan las variantes nuevas, las agencias nacionales de control fronterizo necesitan implementar evaluaciones patológicas y protocolos de cuarentena para asegurar la seguridad de su fauna endémica.

Investigating the Effect of Disturbance on Prey Consumption in Captive Congo Caecilians Herpele squalostoma

Maintaining Gymnophiona in captivity provides opportunities to study the behaviour and life-history of this poorly known Order, and to investigate and provide species-appropriate welfare guidelines, which are currently lacking. This study focuses on the terrestrial caecilian Herpele squalostoma to investigate its sensitivity to disturbances associated with routine husbandry needed for monitoring and maintaining adequate wellbeing in captivity. Fossorial caecilians gradually pollute their environment in captivity with waste products, and substrate must be replaced at intervals;doing so disturbs the animals directly and via destruction of burrow networks. As inappetence is frequently associated with stress in amphibians, the percentage consumption of offered food types, river shrimp (Palaemon varians) and brown crickets (Gryllus assimilis), was measured as an indicator of putative stress following three routine substrate changes up to 297 days post-substrate change. Mean daily variation in substrate temperatures were also recorded in order to account for environmental influences on food consumption, along with nitrogenous waste in tank substrate prior to a substrate change and fresh top soil in order to understand the trade-off between dealing with waste accumulation and disturbing animals. We found a significant negative effect of substrate disturbance on food intake, but no significant effect of prey type. Variations in daily soil temperatures did not have a significant effect on food intake, but mean substrate temperature did. Additionally, substrate nitrogenous waste testing indicated little difference between fresh and tank substrate. In conclusion, this study provides a basis from which to develop further welfare assessment for this and other rarely kept and rarely observed terrestrial caecilian species.

Automated detection of frog calls and choruses by pulse repetition rate.

Anurans (frogs and toads) are among the most globally threatened taxonomic groups. Successful conservation of anurans will rely on improved data on the status and changes in local populations, particularly for rare and threatened species. Automated sensors, such as acoustic recorders, have the potential to provide such data by massively increasing the spatial and temporal scale of population sampling efforts. Analyzing such data sets will require robust and efficient tools that can automatically identify the presence of a species in audio recordings. Like bats and birds, many anuran species produce distinct vocalizations that can be captured by autonomous acoustic recorders and represent excellent candidates for automated recognition. However, in contrast to birds and bats, effective automated acoustic recognition tools for anurans are not yet widely available. An effective automated call-recognition method for anurans must be robust to the challenges of real-world field data and should not require extensive labeled data sets. We devised a vocalization identification tool that classifies anuran vocalizations in audio recordings based on their periodic structure: the repeat interval-based bioacoustic identification tool (RIBBIT). We applied RIBBIT to field recordings to study the boreal chorus frog (Pseudacris maculata) of temperate North American grasslands and the critically endangered variable harlequin frog (Atelopus varius) of tropical Central American rainforests. The tool accurately identified boreal chorus frogs, even when they vocalized in heavily overlapping choruses and identified variable harlequin frog vocalizations at a field site where it had been very rarely encountered in visual surveys. Using a few simple parameters, RIBBIT can detect any vocalization with a periodic structure, including those of many anurans, insects, birds, and mammals. We provide open-source implementations of RIBBIT in Python and R to support its use for other taxa and communities.

Los anuros (ranas y sapos) se encuentran dentro de los grupos taxonómicos más amenazados a nivel mundial. La conservación exitosa de los anuros dependerá de información mejorada sobre el estado y los cambios en las poblaciones locales, particularmente para las especies raras y amenazadas. Los sensores automatizados, como las grabadoras acústicas, tienen el potencial para proporcionar dicha información al incrementar masivamente la escala espacial y temporal de los esfuerzos de muestreo poblacional. El análisis de dicha información requerirá herramientas robustas y eficientes que puedan identificar automáticamente la presencia de una especie en las grabaciones de audio. Como las aves y los murciélagos, muchas especies de anuros producen vocalizaciones distintivas que pueden ser capturadas por las grabadoras acústicas autónomas y también son excelentes candidatas para el reconocimiento automatizado. Sin embargo, a diferencia de las aves y los murciélagos, todavía no se cuenta con una disponibilidad extensa de herramientas para el reconocimiento acústico automatizado de los anuros. Un método efectivo para el reconocimiento automatizado del canto de los anuros debe ser firme ante los retos de los datos reales de campo y no debería requerir conjuntos extensos de datos etiquetados. Diseñamos una herramienta de identificación de las vocalizaciones: la herramienta de identificación bioacústica basada en el intervalo de repetición (RIBBIT), el cual clasifica las vocalizaciones de los anuros en las grabaciones de audio con base en su estructura periódica. Aplicamos la RIBBIT a las grabaciones de campo para estudiar a dos especies: la rana coral boreal (Pseudacris maculata) de los pastizales templados de América del Norte y la rana arlequín variable (Atelopus varius), críticamente en peligro de extinción, de las selvas tropicales de América Central. Mostramos que RIBBIT puede identificar correctamente a las ranas corales boreales, incluso cuando vocalizan en coros con mucha superposición, y puede identificar las vocalizaciones de la rana arlequín variable en un sitio de campo en donde rara vez se le ha visto durante censos visuales. Mediante relativamente unos cuantos parámetros simples, RIBBIT puede detectar cualquier vocalización con una estructura periódica, incluyendo aquellas de muchos anuros, insectos, aves y mamíferos. Proporcionamos implementaciones de fuente abierta de RIBBIT en Python y en R para fomentar su uso para otros taxones y comunidades.

Bold Frogs or Shy Toads? How Did the COVID-19 Closure of Zoological Organisations Affect Amphibian Activity?

Amphibians are an understudied group in the zoo-focussed literature. Whilst commonly housed in specialist exhibits and of real conservation value due to the global extinction crisis, amphibian welfare is not often investigated empirically in zoo settings. The limited research that is available suggests that enclosure design (structure, planting and naturalistic theming) has a positive impact on the time that amphibians will be on show to visitors. However, the categorisation of any "visitor effect" (i.e., influences of visitor presence on amphibian activity and time on display) is hard to find. The COVID-19 pandemic forced the closure of zoological organisations in the UK for several months from March 2020, with gradual re-openings from the summer into autumn and winter. This event provided a unique opportunity to study the effect of the lack of visitors, the presence of essential zoo staff only, the wider return of organisational staff, and then the return of visitors over a prolonged period. This project at WWT Slimbridge Wetlands Centre assessed the number of individuals of six species of amphibian-common toad (Bufo bufo), common frog (Rana temporaria), smooth newt (Lissotriton vulgaris), pool frog (Pelophylax lessonae), golden mantella (Mantella aurantiaca) and golden poison dart frog (Phyllobates terribilis)-visible to observers under different conditions. All amphibians were housed in a purpose-built indoor exhibit of individual enclosures and were recorded when visible (as a proportion of the total population of the enclosure) during closure, the return of extra centre staff and visitor periods. The results showed species-specific differences in visibility, with some species of amphibian being more likely to be on view when the presence of people at their enclosure was less likely or in smaller numbers. Such differences are likely related to the specific camouflage or anti-predation tactics in these focal species. Further study to quantify amphibian sensitivity to, and perception of, environmental change caused by public presence (e.g., light levels and sound) would be useful welfare-themed research extensions. Our results can help inform husbandry, collection planning and amphibian enclosure design to reduce any noticeable visitor effects, and provide a useful benchmark for further, more complex, welfare assessment measures.

Using the 2020 global pandemic as a springboard to highlight the need for amphibian conservation in eastern Asia.

Emerging infectious diseases are on the rise in many different taxa, including, among others, the amphibian batrachochytrids, the snake fungal disease and the Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) virus, responsible for Coronavirus disease 2019 (COVID-19) in mammals. Following the onset of the pandemic linked to COVID-19, eastern Asia has shown strong leadership, taking actions to regulate the trade of potential vector species in several regions. These actions were taken in response to an increase in public awareness, and the need for a quick reaction to mitigate against further pandemics. However, trade restrictions rarely affect amphibians, despite the risk of pathogen transmission, directly, or indirectly through habitat destruction and the loss of vector consumption. Thus, species that help alleviate the risk of zoonoses or provide biological control are not protected. Hence, in view of the global amphibian decline and the risk of zoonoses, we support the current wildlife trade regulations and support measures to safeguard wildlife from overexploitation. The current period of regulation overhaul should be used as a springboard for amphibian conservation. To mitigate risks, we suggest the following stipulations specifically for amphibians. I) Restrictions to amphibian farming in eastern Asia, in relation to pathogen transmission and the establishment of invasive species. II) Regulation of the amphibian pet trade, with a focus on potential vector species. III) Expansion of the wildlife trade ban, to limit the wildlife-human-pet interface. The resulting actions will benefit both human and wildlife populations, as they will lead to a decrease in the risk of zoonoses and better protection of the environment. SIGNIFICANCE STATEMENT: There is an increasing number of emerging infectious diseases impacting all species, including amphibians, reptiles and mammals. The latest threat to humans is the virus responsible for COVID-19, and the resulting pandemic. Countries in eastern Asia have taken steps to regulate wildlife trade and prevent further zoonoses thereby decreasing the risk of pathogens arising from wild species. However, as amphibians are generally excluded from regulations we support specific trade restrictions: I) Restrictions to amphibian farming; II) regulation of the amphibian pet trade; III) expansion of the wildlife trade ban. These restrictions will benefit both human and wildlife populations by decreasing the risks of zoonoses and better protecting the environment.