The Origin of the Amphibian Chytrid Fungus

The amphibian chytrid fungus (Batrachochytrium dendrobatidis: Bd) is the cause of the most spectacular loss of vertebrate biodiversity in recorded history. To date, at least 200 species have been driven extinct and hundreds more have suffered major declines. Even amphibians within the world's best protected ecosystems have been hard-hit, including California's mountain yellow-legged frog (Rana muscosa, Rana sierrae). This amphibian pathogen appears to have emerged in just the last 50 years, subsequently spreading around the world at lightning speed. 

So, where did Bd come from and what allowed its recent emergence? These are questions that researchers have asked since its description in 1999. Using the best available methods, molecular biologists from around the world have slowly but surely been zeroing in on the answers. In 2003 and 2007, studies by Morehouse et al. and Morgan et al., respectively, used evidence that Bd had little genetic variation to suggest that Bd was a recently emerged clone, not a pathogen with a long evolutionary history with amphibians. Results published in 2009 by James et al. supported these interpretations and suggested that the emergence of Bd may have been caused by a single hybridization event.

A just-published paper by Farrer et al. now advances this story even further. Using sequences of entire Bd genomes, Farrer et al. found evidence of multiple distinct Bd strains with apparently non-overlapping distributions. However, they also found a single lineage that was globally distributed, more virulent than the geographically isolated strains, and associated with worldwide frog die-offs. Based on this evidence, they suggest that contact between two previously isolated strains produced a hypervirulent strain that subsequently spread globally, causing amphibian declines and extinctions in its wake. They further postulate that the global amphibian trade was likely responsible for bringing these genetically isolated strains into contact with each other.

Another research group is using similar methods to provide an even more detailed view of the emergence of Bd as an amphibian pathogen, and will hopefully publish their results in the near future. I suspect that we haven't yet heard the final word of this evolving story. Given the likely role of human commerce in driving the emergence of Bd, there are important lessons here for biodiversity conservation in the Anthropocene. Namely, as our increasingly global economy moves goods around the world we will inevitably also move less desirable things, including invasive animals and plants but also invisible things like pathogens. The spread of introduced pathogens from their new introduction points will often be impossible to control, and decimation of naive animal and plant populations into which they come into contact is all but guaranteed. Bd provides a sobering example of what is to come.  

The citation for the latest paper is as follows: Farrer, R. A., et al. 2011. Multiple emergences of genetically diverse amphibian-infecting chytrids include a globalized hypervirulent recombinant lineage. Proceedings of the National Academy of Sciences, USA 108:18732-18736. [link]

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Do High Elevations Provide Amphibians with a Refuge from Disease?

One of the most puzzling aspects about the impact of the amphibian chytrid fungus (Batrachochytrium dendrobatidis: Bd) on amphibian populations is the diversity of disease outcomes. In some landscapes, the arrival of Bd causes the complete extirpation of all populations, but in others it has little or no negative effect on amphibians. There are lots of reasons for these different disease outcomes, including differences between amphibian species in their susceptibility to Bd and different environmental conditions that change Bd virulence and amphibian susceptibility. The environmental condition that has received the most attention is temperature. Bd grows best at temperatures of 15-25° C and growth is greatly reduced at temperatures above and below this optimum range. Importantly, at temperatures above 30° C Bd is killed within a matter of hours, but no lethal effects are known at the low end of the temperature range (i.e., around 0° C). 

This relationship between temperature and Bd growth likely explains several general patterns related to Bd infection intensities on frogs in hot climates (e.g., tropical and subtropical regions). These include lower Bd infection intensities at low versus high elevation, low versus high latitude, and summer versus winter. However, in temperate climates little is known as to whether similar patterns hold. That is, do colder temperatures limit the growth rates of Bd and impacts to amphibians? If so, then we would expect lower Bd infection intensities at higher elevations. 

During the last several years, my colleagues and I have tested this idea using a series of studies on the Sierra Nevada yellow-legged frog (Rana sierrae) in Yosemite National Park. These studies included a park-wide (i.e., low to high elevation) survey of Bd infection intensities, detailed measurements of infection intensity over the entire ice-free period (from the cold temperatures immediately after ice-out to warm temperatures of mid-summer to cold temperatures of late-fall), and frog reintroductions in which we moved frogs from a single Bd-positive R. sierrae population to five nearby lakes that spanned a wide elevation range.

The results provided no support for the idea that the coldest habitats might provide frogs with a refuge from Bd. In the park-wide survey, Bd infection intensity was unrelated to elevation. In the seasonal study, despite temperatures that ranged from 4° C to 25° C, Bd infection intensities remained remarkably constant. And the reintroduction study indicated no changes in infection intensities related to elevation. As a consequence, in the paper that was recently published describing these results (see below) we concluded that in the temperate zone even the coldest habitats are unlikely to provide amphibians with a refuge from Bd. 

Despite this discouraging finding, we did significantly advance our understanding of Bd-frog dynamics and learned a lot about frog reintroductions as a method of reestablishing R. sierrae populations in Bd-positive landscapes. Although three of the five reintroduced populations quickly declined and never showed evidence of reproduction, the remaining two populations did produce tadpoles in the years following reintroduction and at least one of these  populations shows evidence of becoming a self-sustaining population despite ongoing Bd infections. Future reintroductions are planned to allow us to learn more about how best to conduct these reintroductions to maximize the chances of success. 

The citation for the paper described above is as follows: 

Knapp, R. A., C. J. Briggs, T. C. Smith, and J. R. Maurer. 2011. Nowhere to hide: impact of a temperature-sensitive amphibian pathogen along an elevation gradient in the temperate zone. Ecosphere 2:art93.

The paper is available here: http://vesr.ucnrs.org/pages/knapp/publications/publications.html.

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The Amazing Disappearing Frogs

This summer we focused much of our research effort on resurveying known mountain yellow-legged frog populations in Sequoia and Kings Canyon National Parks. We first surveyed these areas for amphibians and fish 11-14 years ago and found mountain yellow-legged frogs to be pretty common. Since then, on multiple occasions we've resurveyed the subset of sites that had contained mountain yellow-legged frogs during the original surveys, but no resurveys have been conducted since 2007. So this year, as soon as the snow and ice of winter were gone, we started at the southern border of Sequoia National Park and made our way north, resurveying every site at which mountain yellow-legged frogs were found during the original surveys. By summer's end, we'd covered all of the sites in Sequoia and most of those in southern Kings Canyon National Park. 

Results from this year's resurveys painted a pretty grim picture. Seventy-five percent of the revisited sites were now without any mountain yellow-legged frogs, and in some cases frogs had been extirpated from entire basins. Where frogs were still present, populations were generally much smaller than they had been 11-14 years ago. Many of these remnant populations appear to be spiraling toward extinction, and most of these will likely be gone in another five or so years. For the most part, the resurvey results were as we had expected. The amphibian chytrid fungus (Batrachochytrium dendrobatidis: "Bd") has spread through this region during the past decade, and the outcome of Bd arrival is invariably the collapse of mountain yellow-legged frog populations. What previously had been a reasonably "froggy" landscape was now one in which remaining populations were small and widely scattered. This summer, it was common to go several consecutive days and not find even a single mountain yellow-legged frog. 

But there were a few welcome surprises. In a couple of spots, mountain yellow-legged frog populations had rebounded to levels that far exceeded what we'd seen at these sites in recent years. And this had occurred despite the fact that frogs in these populations remained infected with Bd. Plans are now underway to use small numbers of frogs from these "persistent" populations to reestablish frogs at nearby sites from which they were extirpated following Bd arrival. I'm under no illusions that this will be easy, but we've got to try. The realization that mountain yellow-legged frogs are now gone from vast expanses of Sequoia and Kings Canyon National Parks, and that their disappearance is having far-reaching consequences for these ecosystems provides all the motivation I need to keep on trying.

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Another Field Season......

Well, the field season is over for another year. I've been doing amphibian-related field work in the High Sierra for almost 20 years now, and I can't remember a summer as weird as this one was. In mid-July, high elevation lakes were still frozen solid. Summer finally arrived at the beginning of August, but in early September I found myself in a backcountry snow storm. As I hiked through a blizzard of swirling white, all I could think was, "What?! Already? Summer has just started!". And for the past couple of weeks, the blue skies typical of early fall in the Sierra have instead been leaden skies portending of thunderstorms. What the heck? 

In my absence from the front country, lots has happened in the world of frog conservation. Most importantly, perhaps, was the die-off of more than 100 mountain yellow-legged frogs being housed at Fresno's Chaffee zoo. The cause of death remains a mystery. These frogs were collected in southern California as part of an effort to establish another captive breeding colony, the progeny of which could eventually be released back into the wild. This incident should serve as an important reminder of how difficult it is to maintain healthy frog populations in captivity. Whenever possible, I'd like to instead see concerted efforts to establish frog populations in suitable natural habitats across the range of the frog. Populations of the mountain yellow-legged frog have tremendous reproductive potential, and under the right conditions could produce lots of offspring for reintroduction to additional sites. And those offspring would come at a fraction of the cost of those from captive rearing facilities. The fact that fewer than 200 adult mountain yellow-legged frogs exist in southern California limits the options available, but I worry that the current focus on captive breeding has distracted us from a broader approach that includes trying to establish additional wild populations. 

The U.S. Fish and Wildlife Service (USFWS)-led effort to develop a Conservation Strategy for Sierra Nevada populations of the mountain yellow-legged frog continues apace. This effort is still in the information-gathering phase and I expect that a draft strategy won't be released until sometime in 2012, perhaps around the time that the USFWS begins the process of deciding whether these Sierra Nevada populations should be listed under the federal Endangered Species Act. In addition, the California Fish and Game Commission will soon be meeting to decide whether to list mountain yellow-legged frogs across their range under the California Endangered Species Act. And then, both Yosemite and Sequoia-Kings Canyon National Parks continue to work on their respective park-wide aquatic restoration plans, plans that will likely propose multi-decade efforts to remove nonnative trout from key frog habitats within these jurisictions. I expect that both parks will release draft plans in 2012. 

So, 2012 looks to be a busy year. Stay tuned for updates....

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Always Something New to See

One of the greatest things about my job as a field biologist is the chance to see amazing things happen in the natural world. I see fascinating stuff every day while out in the mountains, but some happenings are truly memorable. In the past, that has included seeing bears swimming in Sierran lakes, Clark's Nutcrackers eating tadpoles of the mountain yellow-legged frog, water shrews diving for food in alpine lakes, and a deer swimming in a lake to escape two coyotes intent on a late October meal. That strategy by deer of jumping into water to escape predators seems to be one that they use fairly regularly, but I've never seen other animals do the same. Until this week. 

I was in the southern Sierra Nevada doing my usual things, this time paddling around a lake to measure its maximum water depth. On this spectacular day in the mountains, I was staring at the world around me while paddling to what looked to be the deepest spot. I slowly became aware of a squeaking sound coming from somewhere in the surrounding foxtail pine forest. As the sound got louder I looked more carefully into the forest's shade. Suddenly, out of nowhere came a pika running at full speed parallel to the lake shore, with a weasel close behind. The weasel was closing fast on its prey when the pika suddenly turned toward the lake and to my amazement dove in. It then swam furiously out into the lake but the weasel stayed on shore, staring at the pika and at me. Apparently realizing that the weasel was no longer in pursuit, the pika turned to swim parallel to shore and after a minute or so of that, headed to shore in earnest. I was sure the weasel would run along the shore and grab the pika as it approached land, but instead the weasel turned and ran off into the woods. As soon as it hit the shore, the pika did the same but in the opposite direction. 

Swimming pikas?! Who knew?

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Out in the Field Again, Finally!

It has been a long winter here in the Sierra Nevada. This "spring" was one of the coldest and wettest on record, and as a consequence the higher portions of the mountains are still blanketed in snow. But now that the melt has finally begun in earnest, my field season is fast approaching. Last week I hiked into the Golden Trout Wilderness to have a look at a particularly important population of the southern mountain yellow-legged frog (Rana muscosa). This population is the furthest south R. muscosa population left in the Sierra Nevada. Populations historically occurred as far south as Breckenridge Mountain in Kern County, and included large populations in the montane and subalpine meadows along the South Fork Kern River and Golden Trout Creek. As far as we know, those are all gone now, and this population that I visited is the last hold-out in this southern portion of the historic range. 

The fact that this population is still extant is remarkable. Most of the meadows in the Golden Trout Wilderness have been badly degraded by intensive sheep and cattle grazing in the late 1800s and early 1900s that resulted in channel incision and lowered water tables. As a consequence, many of the ponds and other amphibian habitats disappeared. In addition, California golden trout (that were native to much of the South Fork Kern River watershed) were moved into the few naturally fishless lakes and streams that existed in the area, further reducing habitat for R. muscosa. And then probably sometime in the 1970s or 1980s, the amphibian chytrid fungus (Batrachochytrium dendrobatidis) swept across the region, further decimating R. muscosa populations. 

Despite all of these changes, this population of frogs somehow hung on. But for how much longer into the future they will remain is an open question. This R. muscosa population is centered on a single small breeding habitat, an abandoned stream channel filled with sedges and fed by seepage from the adjacent stream. When the stream someday moves back into this channel (as it inevitably will), the only breeding site will be gone and so too will be the frogs. As such, it is imperative that frogs from this population be used to reestablish populations in suitable habitats elsewhere in the vicinity. Based on the low success rate of developing new mountain yellow-legged frog populations, this won't be an easy task. But without such an effort, the range of R. muscosa will continue to contract until this once abundant species is all but gone from its former haunts.

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Captive Breeding Yields Another Round of Eggs

The Los Angeles Zoo is reporting that their technique of holding frogs at cold temperatures over the winter followed by a gradual warm-up in the spring  resulted in another batch of egg masses being laid in March. These egg masses subsequently hatched into hundreds of tadpoles that will be released into the wilds of southern California later this summer. For more information, check out this story. 



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