Navarrete Mendez, M. J. | Search bioRxiv

bioRxiv2026

Dorsal skin biopsies: A non-lethal sampling method for studying amphibians, including the highly endangered Harlequin frogs (Bufonidae: Atelopus)

Non-lethal sampling methods are increasingly essential for amphibian research as global declines intensify and many species persist in small, vulnerable populations. Skin biopsies offer a promising alternative to whole-animal collection and other minimally invasive approaches; however, systematic evaluations of recovery and impacts on body condition remain limited. Here, we assess the effects of small (2-mm) dorsal skin biopsies in four frog species, including three highly endangered Harlequin frogs (Atelopus bomolochos, A. balios, A. longirostris) and the Gualataco marsupial frog (Gastrotheca riobambae). Under controlled laboratory conditions and in semi-natural enclosures, we monitored wound healing, survival, and body mass trajectories in biopsied and control individuals over a one-month period. Across all species, biopsy sites fully healed within approximately three weeks, following consistent stages of re-epithelialization and subsequent repigmentation. No biopsy-related mortality was observed, and body mass did not differ between biopsied and control individuals, indicating no detectable effects of skin biopsies on body condition during the wound-healing period. Occasional minor post-biopsy reactions resolved without intervention within the observation period. We additionally report anecdotal field recovery observations for three other species (A. coynei, A. laetissimus, and A. sp. aff. longirostris), indicating survival and visible wound closure following release. Together, these results indicate that small dorsal skin biopsies represent a safe, non-lethal sampling method for amphibians, including highly endangered taxa. By providing sufficient tissue for diverse downstream applications--such as chemical analyses, genomics, transcriptomics, microbiome characterization, and disease detection--this approach expands the range of questions that can be addressed while minimizing harm to threatened species.

zoology↗

bioRxiv2025

Caecilians maintain a functional long-wavelength-sensitive cone opsin gene despite signatures of relaxed selection and more than 200 million years of fossoriality

Vision is tuned to animals ecologies, evolving in response to specific light environments and visual needs. Transitions to fossorial lifestyles impose strong selective pressures favoring adaptations for underground life, such as increased skull ossification and reduced eye protrusion. Fossoriality may simultaneously relax constraints on vision leading to diminished visual capabilities. Caecilians (Gymnophiona)--specialized, fossorial amphibians--possess reduced eyes covered by skin or bone. For years, these traits, along with the presence of a single photoreceptor expressing one functional opsin gene, have been interpreted as evidence of limited vision, including an inability to focus or perceive color. Our results challenge these assumptions: we identified the long-wavelength-sensitive (LWS) opsin gene in 13 species of caecilians spanning 8 of 10 recognized families. Molecular evidence indicates that LWS is intact and transcribed in the eye of at least one species (Caecilia orientalis). However, the specific photoreceptor type expressing LWS remains uncertain, as our survey of cone phototransduction genes revealed a mosaic of losses, and anatomical observations from five families did not conclusively identify cone-like cells, though they revealed highly organized retinae even in families with vestigial eyes. Altogether, our results suggest that vision in caecilians may be underestimated and the role of light perception in their ecology is possible. TEASER TEXTThe colonization of low-light environments exerts selective pressure to enhance non-visual senses while relaxing selection on vision, often leading to opsin gene loss. We present compelling evidence for the retention of a cone opsin gene (LWS) in caecilians--a fossorial amphibian lineage with a 200-million-year history of burrowing and reduced eyes. Despite signs of relaxed selection, LWS appears functional, echoing patterns in other low-light-adapted vertebrates. Additionally, the loss of key cone phototransduction genes and absence of clear cone cells raises the possibility of LWS expression in rods or a functional change in its use. Our study provides an evolutionary framework for investigating LWS retention in fossorial vertebrates.

evolutionary biology↗