Changing U.S. political environment and amphibians

Sorry it has been a long time since I last wrote. Recently I have been trying to understand this last U.S. election results, and why everything that I believed about America has been turned on its head. One of the many questions that has been going through my head is this: what does the new presidency mean for amphibians and the people who study them?

If you live in another country, hopefully you won’t be affected by this transition. If you live in the U.S. or one of its territories, I hope that all of the good work to conserve the environment that was done under previous government administration will endure. Save the Frogs has already said that they will continue their work as usual, no matter what the election results.

Now here are some photos of cute tropical frogs to brighten the mood.

Agalychnis annae at La Selva Biological Station, Costa Rica

Agalychnis saltator at La Selva Biological Station, Costa Rica


Red-eyed treefrog (Agalychnis callidryas) pair in amplexus at La Selva Biological Station, Costa Rica

Red-eyed tree frog (Agalychnis callidryas) revealing nictitating membrane.

Red-eyed tree frog (Agalychnis callidryas) revealing nictitating membrane.

I think this is an asian horned frog from the Georgia Aquarium (not sure on the species)

I think this is an Asian horned frog from the Georgia Aquarium (not sure on the species). He is pretty disgusted with the election results.

Two pairs of túngara frogs whipping up foam nests while on display. As long as they have water, these guys will breed anywhere!

Two pairs of túngara frogs whipping up foam nests to deposit their eggs in.

Fitzinger's Robber Frog (Craugastor fitzingeri) from Panama.

Fitzinger’s Robber Frog (Craugastor fitzingeri) from Panama.

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On salamandrivorans and the importance of salamanders

Batrachochytrium salamandrivorans has been on the news lately in the U.S., where the trade of salamanders is now banned due to the risk of spreading this disease. This video explains what B. sal. is and why salamanders are so important that legislation was passed to protect them in the United States.


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Natural disturbance reduces chytridiomycosis

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Loss of canopy cover due to a hurricane lowered chytrid infection in the Endangered common mist frog (Litoria rheocola) of Australia.

A study published in Nature this year found that after a cyclone hit Australia in 2011, the incidence of Bd infection in frogs dropped in areas where canopy had been reduced by the loss of branches and trees. The reduced canopy due to Cyclone Yasi resulted in more sunlight and higher temperatures, making the area less favorable for the growth of Bd, since the amphibian chytrid fungus prefers cooler temperatures (~20˚C). In Panama, Golden frogs (Atelopus zeteki) were found to use basking to eliminate Bd from their skin [*]. Thus, both behavioral adaptations by frogs and changes in habitat can limit growth of chytrid in a natural environment. Does this mean that we should cut down trees to save frogs? The authors suggest that targeted canopy reduction could be used to provide warm areas that might allow populations to survive infection. Personally, I am a little hesitant because dense canopy cover can be important for other species unaffected by chytrid and although higher temperatures and UV exposure are beneficial for clearing infection, they are typically harmful to frogs. Nevertheless, the role that disturbance plays in disease ecology remains an important field of study on the chytrid front.

Featured literature: Roznik et al. 2015. Natural disturbance reduces disease risk in endangered rainforest frog populations. Nature

Frog: 13, Fungus: 19

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Dominant isolates in amphibian skin bacteria communities can be cultured


Red-spotted newts were swabbed so that their skin bacteria communities could be examined.

A new study in the Applied and Environmental Microbiology journal presents some results from sequencing DNA of amphibian skin bacteria communities. The authors captured spring peepers (Pseudacris crucifer), red-spotted newts (Notophthalmus viridescens viridescens), bullfrogs (Lithobates catesbeianus) and American toads (Anaxyrus americanus), and then swabbed them for their skin bacteria. One swab from each individual was plated onto agar to culture bacteria for inhibitory assays, the cultured bacteria were isolated, and then had DNA extracted from them (culture-dependent) and the other swab had bacterial DNA extracted directly from it (culture-independent).

A comparison of the cultured and un-cultured bacterial communities showed that although there was a considerable amount of bacterial diversity that had not been cultured, most of the dominant OTUs (Operational Taxonomic Units; see definition here) from the culture-independent sequencing were able to be cultured.


Plates of cultured bacterial isolates from the skin of spring peeper frogs.

This finding is exciting because these culturable dominant bacterial species or OTUs may be the most important for preventing infection by the chytrid fungus, and thus are useful as probiotics.

Frog: 12, Fungus: 19

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Aventuras en Costa Rica (2): independent projects

During the six-week OTS Tropical Biology course in Costa Rica, students participated in three different faculty-led projects and worked in groups (or alone) to design two independent projects. The independent projects that I worked on with some friends were in La Selva and Las Cruces. Here are some highlights of those mini-projects.

1. Microhabitat preference of leaf litter herpetofauna at La Selva

Objective: To determine if herpetofaunal diversity was associated with certain microhabitats and what microclimate conditions might explain patterns of diversity.

Methodology: My friend Peter and I had 4 sites, with three 3 x 3 meter quadrats of each microhabitat (fallen log, tree buttress and leaf litter). Two of the sites were close to a river, and had had mud deposited over the leaf litter in many of the quadrats due to flooding at La Selva. Data was collected for this project over 3 days – on the first day, we set up the quadrats and took environmental measurements (canopy cover, leaf litter layers, mud depth, temperature, etc.), and then on the next two days we surveyed for reptiles and amphibians. Troubles encountered included a bullet ant nest, army ants marching through several of our sites, and torrential rains. My favorite memory of possibly the whole trip is when it was raining cats and dogs, we were at the most muddy site, over our ankles in mud, and trying to look for lizards and frogs in a quadrat that had become a mud pit.


A fallen log quadrat at La Selva. Note how muddy the area is.

The Results: 36 hours after initiating the experiment, we started analyzing data. On the surveys we encountered 8 different species – 4 frogs and 4 lizards. The most frequently encountered species was Craugastor bransfordii. Generalized linear models revealed that only site had any significant interaction with species richness, with richness being higher at two of the sites. One of the sites had significantly fewer leaf litter layers, and mud depth varied by site, but, contrary to our expectations, there were no differences in any of the environmental variables between microhabitats. This may have been because we measured variables for the quadrat, when we should have focused exclusively on the specific microhabitat in question. We also should have included randomized control quadrats.


The moral of the study: There is a lot of variability in leaf litter systems, so more replication is better, and it is important to take into account variation at multiple scales (i.e. variation between sites and between quadrats within a site, temporal variation, etc.).


2. Stream frog and lizard community variation across a land use gradient at Las Cruces

Objective: To investigate how stream amphibian and reptile community composition, species richness and abundance of a common stream lizard (Anolis aquaticus) varies across three different land use areas.

Methodology: My friends Thais, Peter, and I set up six stream transects along one creek – one transect in a garden area, two in selectively-logged primary forest, one in abandoned pasture and two in transitional areas. We did nocturnal surveys on 4 nights, and on the 2nd night, started marking the common stream anole (Anolis aquaticus) with nail polish so that we could get a more accurate estimate of their abundance. During the day, we collected some environmental measurements from the transects. The main obstacles that we encountered during this study were illness and exhaustion, as it was nearing the end of the six-week course and some of us were running on coffee, tequila and fumes.

Stream anole (Anolis aquaticus) marked with red nail polish for abundance surveys.

Stream anole (Anolis aquaticus) marked with red nail polish for abundance surveys.

The Results: We encountered 10 species in our surveys. Anolis aquaticus was the most common species, and the only one found on all six transects. We observed that some A. aquaticus were found sleeping in male-female pairs, but the one pair that we marked on our transect separated after we marked them. The transects in more disturbed habitats (garden and abandoned pasture) had the lowest number of leafy branches crossing the stream, the highest observed herpetofaunal species richness, and were more similar in community composition to each other than to adjacent transects. Anolis aquaticus abundance did not vary significantly by site but was higher in primary forest and transitional transects. However, even on our last night of sampling, we were still catching a lot of unmarked individuals, suggesting that our estimates of A. aquaticus abundance were not terribly accurate.

Total of frog and lizard richness for a 4-night survey at Las Cruces. Transect 1 and 6 are garden and abandoned pasture transects, respectively. 3 and 4 are primary forest, and 2 and 5 are transitional.

Total of frog and lizard richness for a 4-night survey at Las Cruces. Transects 1 and 6 are garden and abandoned pasture transects, respectively. 3 and 4 are primary forest, and 2 and 5 are transitional.

The moral of the study: Species richness of stream reptiles and amphibians was highest in the more disturbed areas, suggesting that disturbance is not always bad for herpetofaunal communities. However this study was only conducted in a single stream during the rainy season, so we can not extrapolate our results to other habitats, seasons or locations.


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“Caecilian cotillions” video

Caecilian Cotillions

For those caecilian lovers out there, the song and video in the above link will warm the cockles of your heart and make you giggle. If you don’t know what a caecilian is, check out this post and then watch the video!

(‘~’| | | | | | | || | )          <– (this is supposed to be a caecilian)

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Aventuras en Costa Rica (1): overview of amphibian declines

The charismatic strawberry poison dart frog (Oophaga pumilio) is highly abundant at La Selva Biological Station.

The charismatic strawberry poison dart frog (Oophaga pumilio) is highly abundant at La Selva Biological Station.

This summer I spent six weeks in Costa Rica for a Tropical Biology field course with the Organization for Tropical Studies/Organización para Estudios Tropicales (OTS/OET). During the field course, the class visited several different biological stations across different habitats in Costa Rica, including Palo Verde (season dry forest/wetland), Monteverde (cloud forest), La Selva (lowland rain forest), and Las Cruces (botanical garden/mid-elevation rain forest). I also went on a post-course trip to the Smithsonian Tropical Research Institute‘s station at Barro Colorado Island (BCI) in Panamá. At each of these sites, we heard stories about how amphibians were being affected by global changes. In Palo Verde, densities of burrowing frogs had declined over the years, in Monteverde several species had gone extinct, in La Selva there have been long-term declines of both reptiles and amphibians, and at Las Cruces some rare species were believed to be recovering from declines.

A female yellow toad (Incilius luetkenii) at Palo Verde Biological Station.

A female yellow toad (Incilius luetkenii) at Palo Verde Biological Station.

Costa Rica was one of the first places in the Neotropics where amphibian declines due to the amphibian chytrid fungus were recorded. Now it is thought that most of the remaining amphibians are resistant to the chytrid fungus. However, long-term amphibian declines have been reported from Costa Rica, continuing into the present. Some scientists (i.e. Alan Pounds) have suggested that these amphibian declines, starting with the extinction of the Costa Rican Golden Toad (Incilius periglenes), are the result of climate change. Temperatures in tropical regions are usually fairly stable so many tropical organisms have a relatively low range of temperatures they can tolerate, meaning that they are particularly sensitive to global warming. In addition to temperature changes, there have also been changes in precipitation and in severity of climatic events such as El Niño/La Niña. With the El Niño this year (“Godzilla“), we observed an extended dry season in Palo Verde and at BCI in Panamá, but flooding at La Selva, on the Atlantic side of Costa Rica.

Carpenter's anole (Anolis carpenteri) at La Selva. Leaf litter lizards and frogs have both been declining over the past 30 years in La Selva.

Carpenter’s anole (Anolis carpenteri) at La Selva. Leaf litter lizards and frogs have both been declining over the past 30+ years in La Selva.

Amphibian and reptile declines at La Selva are particularly interesting because there are likely a variety of factors contributing to the long-term declines in abundance of leaf litter reptiles and amphibians. The area surrounding the biological station has been developed for pineapple plantations, where pesticides are often applied that may be traveling to the forest and affecting reptiles and amphibians in as yet undiscovered ways. Diseases such as the amphibian chytrid fungus (Batrachochytrium dendrobatidis) and Ranavirus are likely present at the reserve (if interested in learning more, see this paper on temporal variation of Bd infection at La Selva). In conclusion, there is a lot of research occurring in Costa Rica right now on amphibian and reptile declines, living up to Costa Rica’s reputation as one of the more well-studied neotropical countries.

Bransford's leaf litter frog (Craugastor bransfordi), one of the most common terrestrial frogs at La Selva.

Bransford’s leaf litter frog (Craugastor bransfordi), one of the most common terrestrial frogs at La Selva.

Stay tuned: In part (2) of my “Aventuras”, I will talk about the two independent mini-projects on reptiles and amphibians that I and some friends designed and carried out at La Selva and Las Cruces as part of the OTS course.

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Chytrid now officially present in Madagascar

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Golden Mantella (Mantella aurentiaca), a critically endangered Malagasy species, and arguably the most poisonous frog in the world. Is the golden mantella now in danger from the amphibian chytrid fungus?

The unthinkable but inevitable has finally occurred.  Chytrid (Batrachochytrium dendrobatidis) is established in Madagascar. A number of surveys occurring from 2010-2014 have documented the incidence of Bd at locations throughout the country (see this Scientific Report). Based on the article published just this year, Bd has been sporadically found throughout Madagascar for the past few years. There is also evidence that the Bd in Madagascar could be related to the BdGPL lineage – BdGPL refers to the strain of chytrid that has been responsible for worldwide amphibian declines.

Although thus far no amphibian declines due to chytridiomycosis have been recorded from Madagascar, it may be only a matter of time. Alternatively, Malagasy frogs might have some sort of innate immunity to the chytrid fungus, or the strain of Bd present there is not dangerous at this time. In any case, as the authors state in the report, “researchers must adopt strict hygiene protocols.” This means that whether you are doing research or planning on a pleasure trip to Madagascar, please make sure to bleach your boots and other field gear between sites so as not to spread Bd. Until scientists learn more about the amphibian chytrid fungus in Madagascar, it is imperative that measures are taken to try to control its spread.

Madagascar is home to a diverse group of unique and endemic frogs, including species well-known from the pet trade, such as tomato frogs and mantellas. Several Malagasy species tentatively have shown suceptibility to Bd infection outside of Madagascar (for instance, Plethodontohyla tuberata in Tokyo). Although the situation in Madagascar may seem grim for these amazing frogs, fortunately, research groups such as Frog Probiotics are already on the ground in the country and working to develop methods of protection for Malagasy frogs. It is my hope that through research and conservation efforts, we will be able to avoid another mass frog extinction event.

Frog: 11, Fungus: 19

{Don’t let the fungus win! Donate to Frog Probiotics or other amphibian conservation projects today!}

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B. salamandrivorans: Are salamanders and newts facing the next global amphibian epidemic?

First, many apologies for not posting in a long time. Over Christmas break I completely zoned out and did almost nothing productive, and before then I was nose-to-the-grindstone on final assignments and grading for the Biology labs that I teach. When your advisers and older friends tell you that graduate school is a lot of work, more work than when you are an undergraduate… they are not exaggerating. The nice thing is that you do have a little more freedom in your schedule since you will probably take less classes.

European fire salamander (Salamandra salamandra) exhibiting signs of infection by B. salamandrivorans. Photo by Frank Pasmans.

Anyway, enough about graduate school. In between the craziness, I did select out an article from last year to talk about on this blog. A previous post in this blog briefly mentioned the new chytrid fungus, Batrachochytrium salamandrivorans, but did not go into detail. In October of last year, an article was published in Science by authors who conducted surveys of European amphibians and found that B. salamandrivorans (let’s just call it Bs from now on) was found only on salamanders and newts. The authors suggested that Bs may have originated from Asia, where amphibians were resistant to it, but was accidentally transported to Europe, where the salamanders and newts had never been exposed to it before. As a result, populations of the European fire salamander (Salamandra salamandra), the species on which Bs was first discovered, have been devastated by the disease.

Will Bs cause another global amphibian epidemiconly with salamanders and newts? That remains to be seen. For now, it is probably only a matter of time before this fungus is transported to the U.S. through captive animals or field equipment that has not been properly sanitized. Since the southeastern U.S. is widely considered to be a global hotspot of salamander diversity, the spread of a fungus specialized in infecting salamanders and newts could be devastating in this country. Many salamanders in the U.S. are endemic, meaning that their ranges are restricted to small areas, so they are particularly likely to face extinction in the event of a massive breakout of Bs. All of us can help to prevent the spread of infectious diseases like salamandrivorans by bleaching and properly sanitizing boots or nets that were used in the field, never releasing captive animals, and carefully sanitizing any materials that may have come into contact with infected captive or wild animamls before disposal. If your pet fire salamander dies, you may be tempted by sentimentality to bury it in the backyard, but if that salamander was a carrier of Bs, the best thing to do might be to burn it, boil it, or soak its body in bleach or alcohol for several days before disposing of it to eliminate any possibility of transmitting the chytrid fungus to U.S. soil.

Rich Mountain salamander (Plethodon ouachitae)

Rich Mountain salamander (Plethodon ouachitae), a species endemic to the Ouachita Mountains in Arkansas

Frog: 11, Fungus: 18

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Spectacular Autumn migrants: ringed salamanders


A gravid female ringed salamander (Ambystoma annulatum) en route to her breeding pond.

It’s that time of year again. The wind starts to get a certain chill, pumpkin lattes are being sold at every coffee shop, and the leaves are beginning to change color. This is also the time of year that an Ozark native salamander, the ringed salamander (Ambystoma annulatum) migrates to breed. Like the spotted salamanders (Ambystoma maculatum) and jefferson salamanders (Ambystoma jeffersonianum) mentioned in an earlier post, ringed salamanders are members of the family Ambystomatidae (the lunged salamanders) and they breed in ephemeral ponds. However, ringed salamanders breed in the fall, so their migrations take place mostly on rainy nights during the month of October. Like other Ambystomatid salamanders, they spend most of their time hidden and are difficult to see when they are not migrating.

A male ringed salamander (Ambystoma annulatum) with complete rings almost all the way down his body.

A male ringed salamander (Ambystoma annulatum) with complete rings almost all the way down his body.

Photos do not do ringed salamanders justice, as they are rather large and impressive salamanders, longer in body than spotted salamanders but still not nearly as large as their relatives, the tiger salamanders. The yellow rings on their body give them an almost exotic look and on top of that, they have adorable little faces with pop-out eyes. Yet, like many other amphibians, they are highly vulnerable to road mortalities during their migration. One gravid female hit by a passing vehicle represents the loss of an entire clutch of eggs as well as her future reproductive potential. So please, if you live in ringed salamander territory, watch the roads carefully for salamanders this month and help across any that you find!


My new favorite North American salamander, the ringed salamander (Ambystoma annulatum)

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