Biology subjects

Coloma, L. A.

Publications and source records attributed to Coloma, L. A..

10 recordsLinked to original sources

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↗

bioRxiv2024

Museum insights for conservation: Unraveling the Extinction Factors in the Jambato Harlequin Frog, Atelopus ignescens

Natural history museums harbor invaluable resources for conserving endangered species by providing insights into the mechanism of historical population declines. Here we conducted data synthesis to better understand the extinction factors of the iconic Jambato Harlequin frog, Atelopus ignescens, which was widespread in the Ecuadorian Andes before 1985 but vanished in 1988. The mechanism of extinction remains elusive, as it was uncertain whether Batrachochytrium dendrobatidis (Bd) fungus infection, climate change, or the interaction of the two factors primarily contributed to the rapid population decline. Here we synthesize historical data from natural history museums, the Global Biodiversity Information Facility (GBIF), and mitochondrial DNA sequences to uncover the factors that have potentially contributed to the extinction of the Jambato Harlequin frog. We found excessive rare alleles reflected in the negative Tajimas D estimated from the mitochondrial DNA samples collected in 1984, which indicates a selective sweep or bottleneck in the population shortly before the historical extinction. There was a marginal effect of the time before versus during Bd epizootics on the body sizes of the adult males, which was relatively weaker than the sex effect and geographic effect. The body size of adult males, but not the females form a geographic cline where the individuals in the northeast were larger than the males in the southwest. Species distribution modeling based on temperature and precipitation accurately predicted the occupancy of A. ignescens in 1960-69 (R2 = 0.72, accuracy = 0.9). This model further predicted the rapid decline in species distribution over decades of climate change between 1970-2020, which could have contributed to the rapid population decline in the 1980s. Collectively, our data synthesis revealed a strong climate effect and a weak epizootics effect on A. ignescens extinction, which unravels the mysterious rapid population decline and informs ongoing conservation efforts. This investigation inspires future museum genomic studies to dissect the potential climatic maladaptation behind one of the most dramatic extinction events in modern history.

evolutionary biology↗

bioRxiv2024

A toxic environment selects for specialist microbiome in poison frogs

Shifts in microbiome community composition can have large effects on host health. It is therefore important to understand how perturbations, like those caused by the introduction of exogenous chemicals, modulate microbiome community composition. In poison frogs within the family Dendrobatidae, the skin microbiome is exposed to the alkaloids that the frogs sequester from their diet and use for defense. Given the demonstrated antimicrobial effects of these poison frog alkaloids, these compounds may be structuring the skin microbial community. To test this, we first characterized microbial communities from chemically defended and closely related non-defended frogs from Ecuador. Then we conducted a laboratory experiment to monitor the effect of the alkaloid decahydroquinoline (DHQ) on the microbiome of a single frog species. In both the field and lab experiments, we found that alkaloid-exposed microbiomes are more species rich and phylogenetically diverse, with an increase in rare taxa. To better understand the strain-specific behavior in response to alkaloids, we cultured microbial strains from poison frog skin and found the majority of strains exhibited either enhanced growth or were not impacted by the addition of DHQ. Additionally, stable isotope tracing coupled to nanoSIMS suggests that some of these strains are able to metabolize DHQ. Taken together, these data suggest that poison frog chemical defenses open new niches for skin-associated microbes with specific adaptations, including the likely metabolism of alkaloids, that enable their survival in this toxic environment. This work helps expand our understanding of how exposure to exogenous compounds like alkaloids can impact host microbiomes.

microbiology↗

bioRxiv2022

Binding and sequestration of poison frog alkaloids by a plasma globulin

Alkaloids are important bioactive molecules throughout the natural world, and in many animals they serve as a source of chemical defense against predation. Dendrobatid poison frogs bioaccumulate alkaloids from their diet to make themselves toxic or unpalatable to predators. Despite the proposed roles of plasma proteins as mediators of alkaloid trafficking and bioavailability, the responsible proteins have not been identified. We use chemical approaches to show that a ~50 kDa plasma protein is the principal alkaloid binding molecule in blood from poison frogs. Proteomic and biochemical studies establish this plasma protein to be liver-derived alkaloid-binding globulin (ABG) that is a member of the serine-protease inhibitor (serpin) family. In addition to alkaloid binding activity, ABG sequesters and regulates the bioavailability of "free" plasma alkaloids in vitro. Unexpectedly, ABG is not related to saxiphilin, albumin, or other known vitamin carriers, but instead exhibits sequence and structural homology to mammalian hormone carriers and amphibian biliverdin binding proteins. Alkaloid-binding globulin (ABG) represents a new small molecule binding functionality in serpin proteins, a novel mechanism of plasma alkaloid transport in poison frogs, and more broadly points towards serpins acting as tunable scaffolds for small molecule binding and transport across different organisms.

physiology↗

bioRxiv2022

Poison frog diet and chemical defense are influenced by availability and selectivity for ants

The ability to use small molecule alkaloids as defensive chemicals, often acquired via trophic interactions, has evolved in many organisms. Animals with diet-derived defenses must balance food choices to maintain their defense reservoirs along with other physiological needs. Poison frogs accumulate skin alkaloids from their arthropod diet, but whether they show preference for specific prey remains unexplored. Here, we explore the role of leaf litter prey availability and diet preferences in shaping poison frog chemical defenses along a geographic gradient. We examined skin alkaloid composition, stomach contents and leaf litter ants in aposematic diablito frogs (Oophaga sylvatica) at five sites in northwestern Ecuador, and in sympatric, cryptic Chimbo rocket frogs (Hyloxalus infraguttatus) at one site. We found that differential availability of leaf litter ants influenced alkaloid profiles across diablito populations, and low levels of alkaloids were observed in the sympatric, undefended Chimbo rocket frog. Ants were the primary dietary component of the defended species, while undefended species ate other prey categories including beetles and larvae in addition to ants. A prey selection analysis suggested that defended and undefended frogs both feed on a high proportion of specific small ant genera that naturally contain alkaloids, suggesting that selectivity for toxic prey is not restricted to classically aposematic and highly toxic species. These findings suggest that poison frogs use of feeding resources relative to availability may be an understudied and important selection factor in the evolution of acquired defenses. ResumenLa capacidad de usar alcaloides como productos quimicos defensivos ha evolucionado en muchos organismos, a menudo a traves de interacciones troficas. Los animales con defensas que se derivan de la dieta deben balancear la seleccion de los alimentos para mantener sus reservas defensivas junto con otras necesidades fisiologicas. Las ranas venenosas acumulan alcaloides en la piel procedentes de su dieta de artropodos, pero aun no se ha explorado si muestran preferencia por presas especificas. En este estudio, investigamos el papel de la disponibilidad de presas en la hojarasca y las preferencias dietarias en la configuracion de las defensas quimicas de las ranas venenosas a lo largo de un gradiente geografico. Examinamos la composicion de alcaloides en la piel, el contenido estomacal y la presencia de hormigas de la hojarasca en ranas aposematicas diablito (Oophaga sylvatica) en cinco sitios del noroeste de Ecuador, asi como en la especie criptica y simpatrica rana cohete de Chimbo (Hyloxalus infraguttatus) en un sitio. Encontramos que la disponibilidad diferencial de hormigas en la hojarasca influyo en los perfiles de alcaloides en las poblaciones de diablito, y se detectaron niveles bajos de alcaloides en la rana cohete de Chimbo, previamente considerada indefensa. Las hormigas fueron el componente principal de la dieta en la especie defendida, mientras que la especie indefensa consumio otras categorias de presas, incluidos escarabajos y larvas, ademas de hormigas. Un analisis de seleccion de presas indico que tanto las ranas defendidas como las indefensas prefieren ciertos generos de hormigas pequenas que contienen alcaloides de forma natural, lo que sugiere que la preferencia por presas toxicas no esta restringida a especies clasicamente aposematicas y altamente toxicas. Estos hallazgos sugieren que las preferencias de comportamiento pueden ser un factor de seleccion poco estudiado, pero crucial, en la evolucion de las defensas adquiridas.

ecology↗

bioRxiv2022

Contrasting parental roles shape sex differences in poison frog space use but not navigational performance

Sex differences in vertebrate spatial abilities are typically interpreted under the adaptive specialization hypothesis, which posits that male reproductive success is linked to larger home ranges and better navigational skills. The androgen spillover hypothesis counters that enhanced male spatial performance may be a byproduct of higher androgen levels. Animal groups that include species where females are expected to outperform males based on life-history traits are key for disentangling these hypotheses. We investigated the association between sex differences in reproductive strategies, spatial behavior, and androgen levels in three species of poison frogs. We tracked individuals in natural environments to show that contrasting parental sex roles shape sex differences in space use, where the sex performing parental duties shows wider-ranging movements. We then translocated frogs from their home areas to test their navigational performance and found that the caring sex outperformed the non-caring sex only in one out of three species. In addition, males across species displayed more explorative behavior than females. Furthermore, androgen levels correlated with explorative behavior and homing accuracy. Our findings suggest that poison frog reproductive strategies shape space use patterns but not navigational performance, providing counterevidence to the prevailing view of adaptive sex differences in spatial abilities.

animal behavior and cognition↗

bioRxiv2019

Land use impacts poison frog chemical defenses through changes in leaf litter ant communities

Much of the worlds biodiversity is held within tropical rainforests, which are increasingly fragmented by agricultural practices. In these threatened landscapes, there are many organisms that acquire chemical defenses from their diet and are therefore intimately connected with their local food webs. Poison frogs (Family Dendrobatidae) are one such example, as they acquire alkaloid-based chemical defenses from their diet of leaf litter ants and mites. It is currently unknown how habitat fragmentation impacts chemical defense across trophic levels, from arthropods to frogs. We examined the chemical defenses and diets of the Diablito poison frog (Oophaga sylvatica), and the diversity of their leaf litter ant communities in secondary forest and reclaimed cattle pasture. Notably, this research was performed in collaboration with two high school science classrooms. We found that the leaf litter of forest and pasture frog habitats differed significantly in ant community structure. We also found that forest and pasture frogs differed significantly in diet and alkaloid profiles, where forest frogs contained more of specific alkaloids and ate more ants in both number and volume. Finally, ant species composition of frog diets resembled the surrounding leaf litter, but diets were less variable. This suggests that frogs tend to consume particular ant species within each habitat. To better understand how ants contribute to the alkaloid chemical profiles of frogs, we chemically profiled several ant species and found some alkaloids to be common across many ant species while others are restricted to a few species. At least one alkaloid (223H) found in ants from disturbed sites was also found in skins from pasture. Our experiments are the first to link anthropogenic land use changes to dendrobatid poison frog chemical defenses through variation in leaf litter communities, which has implications for conservation management of these threatened amphibians.

ecology↗

bioRxiv2019

Mechanisms of convergent egg-provisioning in poison frogs

Parental provisioning of offspring with physiological products occurs in many animals. Within amphibians, maternal provisioning has evolved multiple times, including in South American dendrobatid and Malagasy mantellid poison frogs. In some of these species, mothers feed unfertilized eggs to their developing tadpoles for several months until tadpoles complete metamorphosis. We conducted field studies in Ecuador and Madagascar to ask whether convergence at the behavioral level provides similar benefits to offspring and whether nursing behavior relies on shared neural mechanisms across frogs and vertebrates more broadly. At an ecological level, we found that nursing allows poison frog mothers to provide chemical defenses to their tadpoles in both species. At the level of brain regions, nursing behavior was associated with increased neural activity in the lateral septum and preoptic area in both species, demonstrating recruitment of shared brain regions in the convergent evolution of maternal care within frogs and across vertebrates. In contrast at a molecular level, only mantellids showed increased oxytocin neuron activity akin to that in nursing mammals. Taken together, our findings demonstrate that convergently evolved maternal provisioning behavior provides similar benefits to offspring and relies on similar brain regions. However, the molecular mechanisms underlying the convergence in nursing behavior may be different, suggesting evolutionary versatility in the mechanisms promoting maternal behavior.

neuroscience↗

bioRxiv2019

Molecular physiology of chemical defenses in a poison frog

Poison frogs sequester small molecule lipophilic alkaloids from their diet of leaf litter arthropods for use as chemical defenses against predation. Although the dietary acquisition of chemical defenses in poison frogs is well-documented, the physiological mechanisms of alkaloid sequestration has not been investigated. Here, we used RNA sequencing and proteomics to determine how alkaloids impact mRNA or protein abundance in the Little Devil Frog (Oophaga sylvatica) and compared wild caught chemically defended frogs to laboratory frogs raised on an alkaloid-free diet. To understand how poison frogs move alkaloids from their diet to their skin granular glands, we focused on measuring gene expression in the intestines, skin, and liver. Across these tissues, we found many differentially expressed transcripts involved in small molecule transport and metabolism, as well as sodium channels and other ion pumps. We then used proteomic approaches to quantify plasma proteins, where we found several protein abundance differences between wild and laboratory frogs, including the amphibian neurotoxin binding protein saxiphilin. Finally, because many blood proteins are synthesized in the liver, we used thermal proteome profiling as an untargeted screen for soluble proteins that bind the alkaloid decahydroquinoline. Using this approach, we identified several candidate proteins that interact with this alkaloid, including saxiphilin. These transcript and protein abundance patterns suggest the presence of alkaloids influences frog physiology and that small molecule transport proteins may be involved in toxin bioaccumulation in dendrobatid poison frogs.\n\nResumenLas ranas venenosas obtienen moleculas lipofilicas a partir de su dieta de artropodos que luego usan como una defensa quimica contra depredadores. Mientras que la acumulacion de toxinas dieteticas ha sido bien documentada, el mecanismo fisiologico de obtencion de alcaloides no ha sido investigado. En este estudio usamos secuenciacion de RNA y proteomica para determinar como la presencia de alcaloides afecta la abundancia de mRNA y proteinas en ranas diablito (Oophaga sylvatica) silvestres con defensas quimicas en comparacion a ranas diablito criadas en laboratorio con una dieta sin alcaloides. Para entender como las ranas venenosas mueven los alcaloides de su dieta a las glandulas granulares en su piel, nos enfocamos en medir la expresion de genes en tres tejidos: intestinos, piel e higado. En estos tejidos, encontramos varios transcriptomas regulados diferencialmente que tienen actividades involucradas con el transporte y metabolismo de pequenas moleculas, ademas de canales de sodio y bombas de iones. Luego usamos metodos proteomicos para cuantificar proteinas en plasma, donde encontramos varias diferencias en abundancia de proteinas entre las ranas silvestres y de laboratorio, incluyendo la proteina anfibia de fijacion de toxinas, saxifilina. Finalmente, debido a que muchas proteinas encontradas en la sangre se sintetizan en el higado, usamos la tecnica de perfilacion proteomica termal para seleccionar imparcialmente las proteinas solubles que fijan el alcaloide decahydroquinolina. Usando este metodo, identificamos varias posibles proteinas que interactuan con este alcaloide, incluyendo saxifilina. Estos patrones de cambios en abundancia de transcriptomas y proteinas en ranas con y sin defensas quimicas sugieren que la presencia de alcaloides influye en la fisiologia de las ranas y que moleculas proteicas pequenas de transporte podrian estar involucradas en la bioacumulacion de toxinas en ranas venenosas dendrobatidos.\n\nSummary StatementChemically defended wild poison frogs have gene expression and protein abundance differences across several tissue systems compared to poison frogs reared on an alkaloid-free diet.

physiology↗

bioRxiv2017

Real-time DNA barcoding in a remote rainforest using nanopore sequencing

Advancements in portable scientific instruments provide promising avenues to expedite field work in order to understand the diverse array of organisms that inhabit our planet. Here we tested the feasibility for in situ molecular analyses of endemic fauna using a portable laboratory fitting within a single backpack, in one of the worlds most imperiled biodiversity hotspots: the Ecuadorian Choco rainforest. We utilized portable equipment, including the MinION DNA sequencer (Oxford Nanopore Technologies) and miniPCR (miniPCR), to perform DNA extraction, PCR amplification and real-time DNA barcode sequencing of reptile specimens in the field. We demonstrate that nanopore sequencing can be implemented in a remote tropical forest to quickly and accurately identify species using DNA barcoding, as we generated consensus sequences for species resolution with an accuracy of >99% in less than 24 hours after collecting specimens. In addition, we generated sequence information at Universidad Tecnologica Indoamerica in Quito for the recently re-discovered Jambato toad Atelopus ignescens, which was thought to be extinct for 28 years, a rare species of blind snake Trilepida guayaquilensis, and two undescribed species of Dipsas snakes. In this study we establish how mobile laboratories and nanopore sequencing can help to accelerate species identification in remote areas (especially for species that are difficult to diagnose based on characters of external morphology), be applied to local research facilities in developing countries, and rapidly generate information for species that are rare, endangered and undescribed, which can potentially aid in conservation efforts.

evolutionary biology↗