Understanding How Science Works

Non-scientists are often understandably frustrated by the conflicting results commonly reported in the media on any one of a myriad of science-related topics. It seems that hardly a day goes by that we don't hear another story about how a previous study showed one thing but the newest study now refutes those results. With all of this conflicting information I can understand when some people throw up their hands and conclude that scientists don't know what the heck they are talking about.

This lack of clarity can be partly attributed to the superficial coverage provided by most media outlets in this sound-bite age of ours. When a relatively complex issue is distilled down to a one minute story there are bound to be lots of important facts lost in the process. However, to a large extent these conflicting results are inherent in how science works. Scientific progress is not a linear path. Instead, it is a process that zigs and zags and over time closes in on something resembling the truth. This non-linear progression may be frustrating but it is an unavoidable consequence of the fact that complex questions have complex answers (and are there any simple questions these days?) and different approaches to these questions will often provide different answers.  

The amphibian decline literature provides some excellent examples of this non-linear scientific progression. For example, starting in the mid-1990s Andrew Blaustein at Oregon State University published a series of papers in high-profile scientific journals showing that ultraviolet (UV) radiation had a range of negative effects on amphibians and that increasing UV radiation could be responsible for global amphibian declines.This hypothesis was compelling because it fit with known increases in UV radiation resulting from thinning of the ozone layer and it potentially explained the global nature of these declines. As a consequence, the UV hypothesis received lots of attention from the media and these many stories had the effect of solidifying in the public's mind that UV radiation was in fact a cause of amphibian declines. In fact, the science to test that hypothesis in different ecosystems and using different methods had just begun.

As with any novel idea Blaustein's hypothesis caught the attention of other scientists and in the following 15 years resulted in a plethora of additional scientific studies focused specifically on testing the idea. That research has provided a much more comprehensive picture of the effects of UV radiation on amphibians. In large part, the current thinking is generally that global UV radiation levels have in fact increased during the last 30 years but these increases have been relatively modest (~5% in North America) and have leveled off since the mid-1990s. For several reasons these increases, although obviously of concern, don't necessarily translate into impacts to amphibians. First, UV radiation has been a selective force on amphibians since amphibians first evolved more than 300 million years ago. As a consequence many amphibians have adaptations that effectively protect them from UV exposure. Second, water is a strong attenuator of UV radiation and can block UV from even reaching amphibian life stages. So, increased UV radiation may be having some effects in localized areas but this hypothesis is no longer seen as providing a general explanation for global amphibian declines. 

So, science worked the way it almost always does: someone puts out an idea and then over subsequent years that idea is subjected to many tests by different groups of people and we eventually arrive at a more complete understanding of the phenomenon in question. To understand the full story you just need to read beyond the splashy headlines.

For more information on UV radiation and its impacts on amphibians check out the following papers (you can find PDFs of most of these by conducting your searches using Google Scholar):

Adams, M. J., B. R. Hossack, R. A. Knapp, P. S. Corn, S. A. Diamond, P. C. Trenham, and D. B. Fagre. 2005. Distribution patterns of lentic-breeding amphibians in relation to ultraviolet radiation exposure in western North America. Ecosystems 8:488-500.

Blaustein, A. R., P. D. Hoffman, D. G. Hokit, J. M. Kiesecker, S. C. Walls, and J. B. Hays. 1994. UV repair and resistance to solar UV-B in amphibian eggs:  a link to population declines? Proceedings of the National Academy of Sciences, USA 91:1791-1795.

Blaustein, A. R. and D. B. Wake. 1995. The puzzle of declining amphibian populations. Scientific American 272:52-57.

Herman, J. R. 2010. Global increase in UV irradiance during the past 30 years (1979–2008) estimated from satellite data. Journal of Geophysical Research 115: D04203.

Kiesecker, J. M., A. R. Blaustein, and L. K. Belden. 2001. Complex causes of amphibian population declines. Nature 410:681-684.

Palen, W. J. and D. E. Schindler. 2010. Water clarity, maternal behavior, and physiology combine to eliminate UV radiation risk to amphibians in a montane landscape. Proceedings of the National Academy of Sciences 107:9701-9706.

Vredenburg, V. T., J. M. Romansic, L. M. Chan, and T. Tunstall. 2010. Does UV-B radiation affect embryos of three high elevation amphibian species in California? Copeia 2010:502-512.

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Frog Recovery - An Emerging Story

I've spent a large portion of the last 10 years describing the spread of the amphibian chytrid fungus (Batrachochytrium dendrobatidis - "Bd") across the Sierra Nevada. Given the hundreds of frog population extinctions that have resulted from the arrival of Bd it is sometimes easy to forget about the other side of this story - that there is also evidence of frog recovery following Bd-caused population crashes. 

To read more about what is happening in the Sierra Nevada and Australia check out this recent story in the New Scientist. The writer somewhat exaggerates the recovery angle but it is a worthwhile read nonetheless. The reality in the Sierra Nevada is that recovery of populations to a pre-Bd population size is very rare and has happened at just a handful of sites. But the fact that it is happening at all is important.

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Pesticide Harmful to Amphibians is Banned in U.S.

Last week the U.S. Environmental Protection Agency announced that it would ban the use of endosulfan. Endosulfan is an organochlorine pesticide that was developed in the 1950s. Although it is an effective compound against many crop pests it comes with serious health risks to humans and wildlife, including acute neurotoxicity and endocrine disruption. As a consequence endosulfan is banned in more than 63 countries, including the European Union.

Several studies indicate that because endosulfan persists in the environment for years it can be transported long distances from application sites. For example, endosulfan is commonly detected in the Sierra Nevada despite the fact that it is not applied anywhere nearby. The idea that endosulfan detected in the Sierra Nevada originates from applications in upwind agricultural areas is supported by the fact that endosulfan concentrations in the Sierra Nevada correspond very closely with application rates in the Central Valley, with a lag time of 1-2 weeks.

The fact that endosulfan can disperse widely and persist in the environment has long raised concerns about its effects on wildlife. Research on its impacts on amphibians in the Sierra Nevada indicates that endosulfan is detectable in Pacific treefrog populations (Pseudacris regilla) throughout the range and is toxic to amphibians at extraordinarily low concentrations. However, a just-published study indicates that concentrations in frog tissues are generally well below levels that would cause direct or indirect impacts. 

Overall, the effects of endosulfan on Sierran amphibians is likely relatively minor compared to those caused by trout introductions and the amphibian chytrid fungus (Batrachochytrium dendrobatidis). But given its broad toxicity to wildlife and humans the ban on endosulfan use was nonetheless long overdue. 

The following publications provide additional information on the effects of pesticides on amphibians in the Sierra Nevada:

Bradford, D. F., E. M. Heithmar, N. G. Tallent-Halsell, G.-M. Momplaisir, C. G. Rosal, K. E. Varner, M. S. Nash, and L. A. Riddick. 2010. Temporal patterns and sources of atmospherically deposited pesticides in alpine lakes of the Sierra Nevada, California, U.S.A. Environmental Science and Technology 44:4609-4614.

Bradford, D. F., K. Stanley, L. L. McConnell, N. G. Tallent-Halsell, M. S. Nash, and S. M. Simonich. 2010. Spatial patterns of atmospherically deposited organic contaminants at high elevation in the southern Sierra Nevada mountains, California, USA. Environmental Toxicology and Chemistry 29:1056-1066.

Davidson, C. and R. A. Knapp. 2007. Multiple stressors and amphibian declines:  dual impacts of pesticides and fish on yellow-legged frogs. Ecological Applications 17:587–597.

Davidson, C., H. B. Shaffer, and M. R. Jennings. 2002. Spatial tests of the pesticide drift, habitat destruction, UV-B, and climate-change hypotheses for California amphibian declines. Conservation Biology 16:1588-1601.

McConnell, L. L., J. S. Lenoir, S. Datta, and J. N. Seiber. 1998. Wet deposition of current-use pesticides in the Sierra Nevada mountain range, California, USA. Environmental Toxicology and Chemistry 17:1908-1916.

Sparling, D. W. and G. Fellers. 2009. Toxicity of two insecticides to California, USA, anurans and its relevance to declining amphibian populations. Environmental Toxicology and Chemistry 28:1696–1703.

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Otters and Trout in Sierran Lakes: Which Came First?

Despite having spent the last couple of decades hiking around the Sierra Nevada to conduct my research I'd never seen a river otter nor heard much about their presence in the mountains.That all changed a few years ago when a colleague observed a family of five otters swimming across a lake in northwestern Yosemite National Park. The following winter he observed otter tracks along a stream while doing snow surveys in the Park. And then this past summer I found evidence of otters at a lake in northern Yosemite. My curiosity was definitely piqued and I had to learn more. 

Otters are typically described as feeding mainly on fish, and trout are a favorite prey item. So were river otters found historically in the Sierra despite the absence of fish in most water bodies? Or did they expand their range into the Sierra following the introduction of trout into many lakes and streams starting in the mid-1800s? And if they were found in the mountains prior to fish introductions what did they eat? 

Several of us are still trying to answer these questions but the otter sign I found this past summer and some additional information sources we've turned up have provided some intriguing details. First, otters have been reported in the High Sierra for many decades, suggesting that their presence predated trout introductions. Second, some notes recorded by a Yosemite wilderness ranger in the 1970s suggested that otters were eating Sierra Nevada yellow-legged frogs (Rana sierrae). He reported seeing otters in a lake in the Vogelsang area and also found numerous pairs of discarded frog legs around the lake shore. Given how abundant R. sierrae were historically it certainly seems possible that otters could have subsisted on them. And finally, the otter sign that I found this summer was several otter scats atop a lakeshore boulder. I collected the scats and dissected them back in my lab. What I found amazed me. The scats contained dozens of bones of a size and structure that likely makes them those of Rana sierrae adults and juveniles. But the dominant remains in the scats were from aquatic invertebrates, including giant water bugs (Lethocerus americanus), backswimmers (Notonecta sp.), and dragonfly and damselfly larvae (Aeshna and Enallagma, respectively)! Given the relatively large size of frogs their inclusion in otter diets isn't particularly surprising. But invertebrates?? Notonecta are barely an inch long and yet otters were eating them by the dozens.

To return to the questions I posed at the beginning of this story, I'm guessing that otters utilized Sierran lakes prior to the introduction of trout and subsisted on a diet of amphibians, aquatic reptiles, and invertebrates. With the introduction of trout, otters had another food item on their menu. But did this new food item allow otters to increase in numbers? If so, could their elevated numbers be negatively impacting the few frog populations remaining today? I wish I knew. I'd sure love to be able to radio track some of these guys around Yosemite and figure out what habitats they use and get a more complete picture of their diets. 

If any of you readers have observations of river otters in the Sierra Nevada, I'd love to hear about them.

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Do We Have to Exclude People to Save Frogs?

When species are listed under the Endangered Species Act, potential impacts to those species justifiably receive greater scrutiny. In our crowded world an issue that federal and state agencies frequently have to contend with is direct impacts from human visitation on habitat for a sensitive species. One of the key challenges in making such decisions is to balance the need for species protection with the need to provide the public with opportunities to see the species in question. Public support for a species and the actions necessary to ensure its survival are much more likely when the public actually has the opportunity to see the organism in its natural environment. Those interactions build empathy and fascination and a greater understanding of the threats that organisms face. Decisions to simply exclude people may provide some short-term protection but in the long-term people have to be part of the solution. 

In southern California where millions of people live within a one hour drive of several national forests, human use of those public lands is intense and conflicts with sensitive species are common. In 2002 the dwindling populations of the southern mountain yellow-legged frog (Rana muscosa) in the Transverse and Peninsular Ranges were listed as "endangered" under the federal Endangered Species Act (see In the News > ESA listing page for details). In 2005 the US Fish and Wildlife Service proposed several thousand acres of stream and riparian habitat as "critical habitat" for these R. muscosa populations. In response, in late-2005 the Angeles National Forest opted to close access to 1000 acre area along Little Rock Creek due to the presence of R. muscosa in this section of creek. This resulted in the closure of a popular climbing area, Williamson Rock, because it directly abuts Little Rock Creek. The closure also prevented access to a portion of the Pacific Crest Trail, forcing hikers to use a detour that required walking along a highway for some distance. 

The Angeles National Forest recently released a draft Environmental Assessment of the closure that proposes to keep the area closed for at least three more years while the response of the Little Rock Creek frog population to the 2009 Station fire is monitored.This potentially open-ended closure of the area has upset several user groups, in particular the climbing community (e.g., Friends of Williamson Rock). It is clear that user-created trails that access Williamson Rock and the proximity of some climbing routes to Little Rock Creek (some climbing routes actually start in the creek itself) have the potential to impact the frog population. However, many of these impacts would be relatively easy to mitigate. For example, the numerous user-created trails could be replaced by a single maintained trail and those climbing routes closest to the creek could be closed. In addition, climbers could be required to use "wag bags" for the disposal of all human waste. Discussions I recently had with a representative from the climbing community indicated that they are willing to work with the Angeles National Forest to implement these actions. It remains a big question whether the Forest will go along with this, however. 

The easiest action for agencies to take when confronted with conflicts  between human visitation and an endangered species is to simply restrict access. Although complete closures may sometimes be necessary, it is often possible to find creative solutions to conflicts that minimize impacts to sensitive species and in doing so help to build a constituency for conservation of the species. The Williamson Rock issue seems to have all the hallmarks of a situation where a suitable compromise is attainable. I hope the Angeles National Forest and Friends of Williamson Rock don't let this opportunity slip away. 

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A.B. 2376: Opening the Door to Restructuring the Department of Fish and Game

In late September California governor Arnold Schwarzenegger signed A.B. 2376 into law. This bill was supported by numerous fishing groups, including California Trout, Trout Unlimited, and The Sportfishing Conservancy, and was motivated by the recently-released Treanor Report that suggested changes to how the California Department of Fish and Game (DFG) and the California Fish and Game Commission (FGC) are structured (Treanor Report available here). A.B. 2376 requires that the Secretary of Natural Resources convene a committee to "develop and submit to the Governor and Legislature, a strategic vision for the Department of Fish and Game (DFG) and the Fish and Game Commission". Specifically related to the management of fish and game, it requires the following:

"....that the strategic vision address specified matters relating to fish and game management, including but not limited to: biodiversity management and ecosystem functions; permitting and regulatory functions; recreational and commercial harvest; scientific capacity; relations with the public, landowners, nonprofits and other land management agencies; reforms necessary to address challenges of the 21st Century; use of technology and data systems; clarification of the roles of DFG and FGC; and strategies for identifying other stable funding options to reduce DFG's dependence on the General Fund."

That is a pretty broad statement so who knows what will come of it. But the DFG and the FGC both certainly need to be updated to better accomplish their respective missions. One change that would be high on my list of priorities is for the DFG to increase its scientific capacity and to use science (instead of political expediency) to resolve resource-related disputes. An increased capacity to conduct critical resource-related scientific studies would go a long way toward allowing the DFG to anticipate resource problems. This proactive position would provide for far better decision-making than the current DFG model which seems to be to ignore growing issues for as long as possible and then deal with them in crisis mode when forced to by outside pressure. As I've said many times before, science will not provide all of the answers to our resource issues but it can provide a solid foundation upon which rational solutions can be developed.

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Mitigating the Effects of Chytridiomycosis

For the last couple of years our research group has conducted several field experiments aimed at understanding the extent to which we can change the outcome of outbreaks of the amphibian chytrid fungus (Batrachochytrium dendrobatidis - "Bd") from frog population extinction to persistence. This summer and last we treated frogs at die-off sites with anti-fungal drugs, something I never in my wildest nightmares imagined that I'd ever be doing. My field crews and I put everything we had into those experiments but so far success remains elusive. 

Given our attempts at changing disease outcomes I was excited to attend a disease mitigation workshop last week in Zurich, Switzerland and learn what other researchers from around the world have been trying. Over a two day period we learned of each others myriad efforts to confront the Bd plague and were sobered to realize that all of the attempts at changing Bd disease outcomes attempted so far have failed. 

At a Bd-positive site in Mallorca (Spain) Jaime Bosch and his colleagues removed all of the amphibians, treated them in the laboratory with an anti-fungal drug until they were Bd-free, and then completely dried the pond. When winter rains refilled the pond the treated tadpoles were released back into the site. Much to everyone's surprise by spring the tadpoles were once again infected with Bd. Given that Bd apparently does not have a resistant stage that could survive dessication it remains a mystery how Bd survived at the site or reinvaded so quickly (additional details are provided here). 

A graduate student at the University of Zurich, Corina Geiger, recently conducted an experiment in which she established frog populations in large outdoor tanks which she subsequently infected with Bd. Once the frogs showed evidence of chytridiomycosis she treated the entire tanks with antifungal drugs. For six weeks following treatment frogs were uninfected, but then Bd reappeared and reinfected the frogs. These results mirror our own results to date in the Sierra Nevada. 

Other mitigation efforts are currently ongoing, including an experiment using frog skin bacteria that have strong anti-Bd properties (additional details provided here), and another in which amphibian densities are being temporarily reduced to assess the effect on disease dynamics.

The ineffectiveness of the anti-Bd treatments attempted to date is obviously disappointing and illustrates just how incomplete our understanding of Bd still is. If we do stumble across an effective mitigation strategy it seems it will be almost entirely a stroke of luck. And yet, with Bd spreading into new uninfected populations with every passing month, we don't have the luxury of waiting for better information.

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An Unnatural Quiet

This summer I returned again to one of the Sierra's most remote lake basins to resurvey the amphibian populations there. This basin holds a special place in my heart due to its spectacular beauty, isolation, and at one time, an incredible Sierra Nevada yellow-legged frog population. The first time I visited this basin was in 1997 when my assistants and I conducted our initial surveys of its frogs, fish, and invertebrates. Back then, the sheer number of frogs was overwhelming. 

I remember counting 10,000 tadpoles in a single lake. The frantic swimming of these tadpole masses at my approach turned the tranquil water surface to a muddy froth. Adult frogs seemed to occupy every possible bit of water; nearly every lake, pond, stream, and puddle was full of them. As I walked along one lake shore, a frog dove off of a damp ledge ten feet above my head and with legs splayed wide splashed into the water at my feet. The abundant bears in this basin seemed just as fond of the frogs as I was. In several spots where tadpoles aggregated by the thousands, I saw where bears had waded out into the water to catch them. One evening I watched a Clark's Nutcracker land at the waters edge and spear a tadpole. With the tadpole in its beak it flew to a nearby snag, snipped off the tadpole's tail, and fed the body to a begging fledgling. Transfixed, I sat down and watched the show repeat itself several more times. When the adult and fledgling had flown away I walked to the snag and saw that the branch the fledgling had been perched on was covered with 50 or more tadpole tails, some dry and shriveled, some still wet. What an incredible web of life these frogs were a part of!

Back then the world was unaware of the amphibian chytrid fungus (Batrachochytrium dendrobatidis - "Bd") and its devastating effects on amphibians around the globe. I took it for granted that given the paucity of trout in this basin the frogs would always be there, for the bears, for me. A few years later Bd arrived in the basin, causing the collapse of one frog population after another. Within five years the frog numbers had decreased by 95% but I still held out the hope that maybe a few would survive to repopulate the lakes. 

Our resurveys this summer showed that even that modest hope was too optimistic. Most water bodies were now entirely frogless. A few contained only a single adult frog. We found some tadpoles, but too few to give us much hope that the population would still be there the next time we did our resurveys. 

Sitting on a lakeside boulder eating my lunch in the summer sun, I couldn't help notice how quiet the basin had become. No more frothing masses of tadpoles. No frogs jumping into the water by the 10s and 100s in front of me as I walked along the shoreline. Bear sign, once so common, was far less in evidence, although I did see one set of bear tracks that went into the lake where a few tadpoles still basked in the warm shallows, but the paucity of animals would hardly have made a snack much less a meal. No Clark's Nutcrackers eating tadpoles. The mayflies, caddisflies, and beetles were still there, but the once-dominant frogs and the web of life they once supported were gone.

When I first happened upon this place it was defined by the frogs, frogs as predators, frogs as prey, frogs as inhabitants. Now it was different. In the span of less than a decade, a shangri la had become a place of ghosts.


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Back from a Summer in the Mountains

It has been months since I've added any posts. My only excuse is that I've been in the mountains almost continuously since mid-June conducting research. I've been impressed at the number of people who emailed me during my absence from the blogosphere to make sure I hadn't abandoned my practice of regular posts related to the mountain yellow-legged frog. Rest assured that I have not. Now that my field season is over I'll do my best to again provide updates on a more regular basis. 

Of the many frog-related happenings that occurred this summer, perhaps the most important was a decision on September 15 by the California Fish and Game Commission to designate the mountain yellow-legged frog (both Rana sierrae and Rana muscosa) as a "candidate" species under the California Endangered Species Act (CESA). This action was taken in response to a petition submitted earlier this year by the Center for Biological Diversity. The California Department of Fish and Game now has one year to develop a formal status review that will recommend whether or not the mountain yellow-legged frog should be listed. 


During the one-year review period, the CESA requires that candidate species be treated as if they were already listed. This is an important difference between the Federal and California Endangered Species Acts. Under the Federal ESA, a candidate species has no formal status until it is actually listed. Because of the potential for the new "candidate" status of the mountain yellow-legged frog to immediately impact a wide variety of ongoing activities the Commission adopted a series of "take" exemptions (i.e., exemptions for actions that could potentially result in harassment or mortality of mountain yellow-legged frogs). 

Exempted actions include those for the Department's ongoing fish stocking programs (no surprise there), timber harvest, reservoir operations, and scientific research. Although some have expressed their displeasure with these exemptions, I support them because they will provide individuals and agencies with some breathing room to continue already-permitted activities during the one-year review period. The negatively publicity that could result from an immediate shutting down of these existing projects (especially fish stocking) would likely have more long-lasting negative effects on frog conservation efforts than these projects would. 


So, by next October we'll get an up-or-down vote by the Commission on the listing status of the mountain yellow-legged frog. If the frog is listed under CESA I suspect that efforts to conserve and restore populations of this imperiled species will ramp up to a level not yet seen.


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Captive-bred Frogs Released into the Wild for the First Time

The southern mountain yellow-legged frog (Rana muscosa) inhabits lakes, ponds, and streams in the southern Sierra Nevada and southern California. The southern California Distinct Population Segment (DPS) was listed as "endangered" under the federal Endangered Species Act in 2002. This DPS currently contains fewer than 200 adult frogs and these remaining populations are at extreme risk of extinction due to a myriad of threats.

In response to the perilous status of this southern California DPS, scientists from the U.S. Geological Survey and San Diego Zoo have been working to develop an indoor captive breeding population the could eventually produce sufficient offspring for release into the wild. In an effort to stimulate frog breeding, this spring captive adult frogs were refrigerated for several weeks to simulate winter conditions. Once temperatures were increased frogs quickly began breeding, resulting in the production of numerous egg masses. 

In mid-April several of these egg masses were moved to a creek within the James San Jacinto Mountains Reserve, a reserve managed by the University of California. This is the first time that captive-bred mountain yellow-legged frogs have been released into the wild, and represents an important milestone in the recovery of frogs in this DPS. Time will tell how well the released animals survive. 

In addition to aiding the conservation of mountain yellow-legged frogs in southern California, these efforts have also produced a wealth of information regarding the breeding of these frogs in captivity. Whether we'll ever need these techniques for restoring mountain yellow-legged frogs in the Sierra Nevada remains to be seen but it is nice to have these methods already worked out. I continue to believe that one of the highest conservation priorities for Sierra Nevada frogs is to develop several outdoor captive populations of frogs in artificial ponds at an accessible location. Such populations are much less expensive to maintain than indoor captive populations (frogs don't need to be fed, water doesn't need to be changed, etc.) and would provide lots of offspring for use in research and conservation. All we need is a few ponds. Efforts to identify suitable ponds are ongoing.


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Two New Papers Detail Impact of Disease on Sierran Frogs

Two papers by our research group were published today in the journal, Proceedings of the National Academy of Sciences (PNAS). Both papers are open access and can be downloaded from the PNAS web site (Vredenburg et al. paper; Briggs et al. paper). These papers represent more than a decade of research by our group on the role of the amphibian chytrid fungus (Batrachochytrium dendrobatidis - Bd) in driving the decline of mountain yellow-legged frogs in the Sierra Nevada.

The first paper (by Vredenburg, Knapp, Tunstall, and Briggs) describes the frog-Bd dynamics in detail for the first time and provides a critical insight into how Bd outbreaks might be controlled. Bd was absent from the three study basins at the inception of the research but invaded the basins in 2004-2005. Following its initial arrival Bd spread through the basins at 0.6 km per year, eventually infecting all mountain yellow-legged frog populations. 

Within 1-2 years of its first detection in a frog population, the population began to show evidence of severe chytridiomycosis (the disease caused by Bd). Frog die-offs and population crashes occurred when infection intensities (amount of Bd on a frog's skin) reached a critical threshold. The fact that a disease threshold exists is important because it provides a target for intervention strategies, strategies designed to prevent infection intensities from surpassing this threshold. One strategy, clearing frogs of Bd using an anti-fungal drug, was tested in two of the study basins in 2009 and preliminary results are promising. We'll be conducting additional tests in 2010, one designed to investigate whether clearing frogs of Bd early in an epidemic can actually prevent the epidemic from occurring.


Although most frog populations are extirpated following Bd epidemics, a few persist despite ongoing chytridiomycosis. Scientists have suggested that this persistence could be a consequence of selection for reduced susceptibility of frogs or reduced virulence of Bd. In the Briggs et al. paper, we use a mathematical model to demonstrate that neither of these changes are necessary to explain the long-term persistence of infected frog populations in the presence of Bd. Instead, this outcome could be solely the result of density-dependent host-pathogen dynamics. Under this scenario, epidemics are the result of Bd invading naive frog populations existing at their naturally high densities. This allows the production of vast numbers of zoospores (the infective stage of Bd) that overwhelm any frog defenses and causes massive frog die-offs. Most populations are extirpated but frogs in a few populations survive by chance alone. In these populations, zoospore density is kept low by low frog numbers, and frogs are able to tolerate the resulting low Bd infection intensities. As a consequence frog populations persist at low densities with Bd over the long term. 


This model assumes no role for an adaptive immune response by frogs against Bd. Although this is consistent with our current knowledge of the frog-Bd interaction, a series of experiments we are currently conducting will provide clearer insights into the existence of any such response. 


For the first time in several years I feel like we are making substantial progress toward understanding and potentially controlling chytridiomycosis. Let's hope our advances haven't come too late.

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Impacts of Fish Stocking on Willow Flycatchers - Really?

As opening day for trout fishing season approaches, stories in the local papers often dwell on impending issues that might affect the number of fish stocked and stocking locations. Last year the stories focused primarily on issues surrounding the court order that mandated that the California Department of Fish and Game (DFG) prepare an environmental impact report detailing the effects of its fish stocking program. This year the stories have focused almost exclusively on the concern that the presence of willow flycatchers could preclude fish stocking. All of the media stories that I've read on this issue have failed to provide much context for this issue, focusing instead on how outside environmental groups are to blame for the current "crisis". The following is my attempt at clarifying how the willow flycatcher got wrapped up in the fish stocking issue and what the current DFG plans are related to this species. 

When I read the DFG fish stocking EIR-EIS I was quite surprised to see the willow flycatcher listed as a "decision species" ("decision species" were defined as those species potentially affected by hatchery and stocking programs). My surprise stemmed from the fact that there were no published studies suggesting such impacts on willow flycatchers. Furthermore, the interim court order that was developed jointly by the Center for Biological Diversity, Pacific Rivers Council, and the DFG (the intent of which was to prevent harm to sensitive species while the EIR-EIS was being written) focused only on fish and amphibians (13 and 11 species, respectively). So, how did the willow flycatcher end up in the EIR-EIS as a decision species? 

It turns out that it was the DFG that added the willow flycatcher to the decision species list, and without any prompting from environmental groups or the public at large. The rationale was basically that trout and willow flycatchers both depend on insect prey for a large proportion of their diets. Because the introduction of trout into mountain lakes dramatically reduces the biomass of aquatic insect larvae and the subsequent emergence of adult forms of these aquatic insects, the DFG reasoned that this reduction in adult aquatic insects could reduce prey availability for willow flycatchers. The willow flycatcher was on the DFG "radar screen" because it is listed as "endangered" under the California Endangered Species Act. 

The possibility that trout stocked into aquatic ecosystems could affect adjacent terrestrial ecosystems is a fascinating area of ecological study, and recent research in the Sierra Nevada shows that stocked trout have in fact altered the distribution and foraging habits of the Gray-crowned Rosy-Finch, one of the few species that nests in the alpine zone. This soon-to-be-published study provides evidence that trout-containing lakes had 98% fewer mayflies than did neighboring fishless lakes, and that Rosy-Finches were six times more abundant at fishless lakes than at fish-containing lakes as a result (mayflies make up a significant fraction of Rosy-Finch diets during the emergence period). However, it is a stretch to extend these Rosy-Finch findings to willow flycatchers, but that is exactly what the DFG did. 

In the EIR-EIS the DFG suggested that impacts of trout on willow flycatchers were possible, and proposed to mitigate these impacts by conducting a "pre-stocking evaluation" at each mountain lake that receives hatchery trout and that lies within the range of the willow flycatcher. As stated in the EIR-EIS (page 4-100), "Under the protocol, each stocking location shall be evaluated in a stepwise fashion to determine whether interactions between stocked trout and willow flycatchers may occur and to evaluate the potential for trout stocking to result in an (sic) substantial effect on willow flycatchers. If such an impact is determined likely, then DFG shall either cease stocking at that location or develop and implement, prior to stocking at that location, an ABMP". (ABMP = Aquatic Biodiversity Management Plan).

With the EIR-EIS finalized in January of this year, the upcoming opening of the trout fishing season is the first in which all fish stocking is required to meet the guidelines specified in the EIR-EIS. The range of the willow flycatcher includes the eastern Sierra Nevada so technically no lakes can be stocked in preparation for the season opener unless a pre-stocking evaluation for willow flycatchers has been conducted, and until a few weeks ago no such evaluations had been conducted for stocked waters anywhere in California. And how can evaluations be conducted when most mountain lakes are still surrounded by snow and it will be weeks before willow flycatchers arrive to breed? The DFG has been scrambling to figure this out and the ensuing confusion has generated a slew of rumors, including how the Center for Biological Diversity forced the DFG to include the willow flycatcher in the EIR-EIS and how the willow flycatcher is being used as an excuse by bureaucrats in Sacramento (including DFG bureaucrats, in some version of the rumors) to shut down the fish stocking program. That these rumors have little basis in fact has not stopped the local media from reporting and elaborating on the rumors and innuendo. 

So, here is my take on all of this. While I applaud the DFG for acknowledging that fish stocking impacts likely extend beyond the water's edge and can in some cases impact songbirds and other terrestrial predators, it is ill-advised to change fish stocking management without a scientific rationale. There are no data suggesting that willow flycatchers are negatively impacted by fish stocking. The current lack of evidence certainly does not indicate that no such impacts are occurring, but the lack of any scientific evidence makes designing effective mitigation essentially impossible. I would have much preferred a more cautious approach in which the DFG acknowledged the potential for impacts of fish stocking on willow flycatchers and committed to studying the issue over the next year. Subsequent management actions and mitigation could then have been designed based on the results of the accumulated evidence.


I never thought I would criticize the DFG for being overly aggressive in developing mitigation strategies to reduce impacts of fish stocking. Go figure.

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A Busy Week in the Media for California Amphibians and Fish

The media was abuzz this week with frog and fish-related stories. First came the news that the California Fish and Game Commission voted 3-2 to support the listing of the California tiger salamander as "threatened" under the California Endangered Species Act (Santa Rosa Press-Democrat story). Because this species is already federally-listed I don't think this will change the existing management significantly.

And then last Tuesday there was an excellent discussion about nonnative fish impacts on NPRs Diane Rehm show (archive available here). This show topic was prompted by the publication of the book, "An Entirely Synthetic Fish: How Rainbow Trout Beguiled America and Overran the World", by Anders Halverson. This is a must-read book that provides an exploration of the history, biology, and sociology of trout aquaculture and stocking. Anders was joined on the show by Curtis Milliron from the California Department of Fish and Game and Gerald Smith from the University of Michigan, and the three of them contributed to a lively discussion. 

And finally, we had the publication of a new study by Tyrone Hayes (UC Berkeley), this one showing that exposure of frogs to low doses of the herbicide atrazine can result in complete feminization of males. The authors state, "Ten percent of the exposed genetic males developed into functional females that copulated with unexposed males and produced viable eggs." These results are remarkable and scary. If atrazine causes these bizarre effects in frogs, what effects does this stuff have on humans?

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Lawsuit Update and Other Legal Intrigue

In my last post I mentioned that in addition to the fish stocking lawsuits recently filed by the Center for Biological Diversity and the Owens Valley Committee I'd heard rumor of a third lawsuit. That rumor has now been substantiated. It was filed by Californians for Alternatives to Toxics, the Environmental Protection Information Center, Wilderness Watch, and Public Employees for Environmental Responsibility. Their petition focuses on many of the same issues covered by the other two petitions, including use of an improper objective, improper baseline against which impacts were evaluated, inadequate range of alternatives, and failure to adequately mitigate impacts of fish stocking. In addition, the petitioners argue that the practice of stocking fish into designated wilderness areas violates provisions of numerous laws related to wilderness.

On a somewhat different topic, on March 3 the California Fish and Game Commission is scheduled to vote on a petition to list the California Tiger Salamander as "threatened" under the state Endangered Species Act. This will be an interesting vote given its potential to put into place additional protections for this species, and also for what it will tell us about the likelihood that the Commission will vote to list the mountain yellow-legged frog under the California Endangered Species Act. The effort to list the California Tiger Salamander under the state Endangered Species Act is quite a twisted tale, with the Commission rejecting the original 2001 petition, rejecting a subsequent 2004 petition, this decision being overturned by the Sacramento Superior Court, the Commission appealing the court's decision, and the 2008 decision by the Third District of the California Court of Appeals upholding the original Superior Court decision. Now, almost 10 years after the original petition was filed, the Department of Fish and Game is recommending to the Commission that the species be listed as "threatened". For more information on this issue, click here.

The information upon which the latest petition is based is essentially unchanged over the decade since the original petition was filed, so why all of the legal contortions to prevent the listing? Delaying the inevitable seems to be the name of the game. It doesn't make for good policy, but it does make for good politics for those whose sympathies lie more with unbridled economic development than with the fate of this inconspicuous salamander that spends its life in and around vernal pools in California's grasslands. 

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Déjà Vu - Lawsuits Filed Against DFG Over Fish Stocking Document

The California Department of Fish and Game (DFG) released their court-mandated fish stocking EIR-EIS on January 11, 2010. In response, at least two groups (and I've heard rumor of a third) have filed separate court petitions against the DFG. The Center for Biological Diversity petition focuses broadly on a wide variety of deficiencies in the EIR-EIS, including a flawed baseline against which environmental impacts were judged, failure to include an adequate range of alternatives, and the failure to adopt reasonable mitigation measures. The Owens Valley Committee petition focuses more specifically on groundwater withdrawals that supply two fish hatcheries in the Owens Valley and the failure of the EIR-EIS to adequately mitigate the associated impacts.

And so the legal wrangling begins anew. The DFGs strategy on fish stocking -related CEQA issues has always been to frame the issue as narrowly as possible. For years, that meant denying that fish stocking was subject to CEQA. They got away with that for 35 years. When an environmental group with sufficient guts (Center for Biological Diversity) finally called the DFG bluff and sued them in court, the DFG arguments were finally revealed for what they were - a house of cards. But unable to abandon their tired strategy, the EIR-EIS was written as a defense of the current fish stocking program instead as a thorough evaluation of the environmental impacts the program has caused. This failure reeks of a DFG leadership unwilling to take the inevitable political and public flak and lead. 

The DFG public response to the petitions so far has been a predictable plaintive whimper of "but we've already spent so much money on the EIR-EIS". Instead of complaining about how much money the EIR-EIS process is costing, the DFG should realize for once and for all that hijacking the CEQA process to justify a pre-ordained conclusion will not fly. Perhaps someone within the DFG will raise the obvious point that many of the complaints raised in the recently-filed court petitions were also raised by the DFG-appointed EIR-EIS Scientific Advisory Team. Those concerns were summarily dismissed by the DFG but are now coming back to haunt them.

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California Endangered Species Act Petition is Filed

On January 11, 2010, the California Department of Fish and Game (DFG) released their badly flawed fish stocking EIR-EIS. In response to the failure of the EIR-EIS to put into place provisions to adequately protect the imperiled mountain yellow-legged frog from impacts caused by hatchery trout, on January 25 the Center for Biological Diversity petitioned the California Fish and Game Commission ("Commission") to list the mountain yellow-legged frog as "endangered" under the California Endangered Species Act (CESA).

The CESA is similar to the federal Endangered Species Act in most regards but the CESA is administered by the DFG. The DFG now has 90 days to recommend to the Commission whether the petitioned action may be warranted. If so, the DFG has 12 months to prepare a report for the Commission, based on the best scientific information available, which indicates whether the petitioned action is in fact warranted. The Commission then makes it final decision soon thereafter. So, it will be more than a year before the petition makes its way through the process, a process that I suspect will be full of twists and turns. This could get interesting. 

Additional details on the petition process are provided in Fish and Game Code Section 2070-2090. The mountain yellow-legged frog CESA petition is available on the Center for Biological Diversity web site.

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"Ignorance is Bliss": Really?

In my view of the world, science has a central role to play in resource management decisions. Scientific information, if obtained from well-designed studies, can serve as a foundation for such decisions, providing a description of the problem and of potential solutions. To be sure, scientific information is only part of the equation, and social, legal, and financial considerations are also critical to the development of sound management practices. Ideally, all of these information sources are used to develop proposed actions that are presented to the public and then amended as necessary. For this process to be effective, scientists and managers need to be clear about their intent and unbiased in their description of the problem and proposed solutions. Similarly, for public input to be useful the public must educate themselves on the issue. Problems in any of these areas can derail the process of developing sound decisions, and there are ample examples of such derailments. 

I've made a concerted effort to help members of the public educate themselves on the fish-frog issue (in part by writing this blog and maintaining the Mountain Yellow-legged Frog Web Site), and perhaps that is why I find it frustrating to see members of the public refusing to avail themselves of readily available information and instead advocating strongly-held opinions based only on hearsay. The recently released fish stocking EIR-EIS contains a summary of all comments submitted in response to the draft document (Appendix M), and one letter in particular provides a telling example of the dangers of being uninformed. This letter was submitted by the Backcountry Horsemen of California and it states (in part) that "there has been no conclusive scientific evidence to prove that frogs and fish cannot coexist", and that for mountain yellow-legged and Cascades frogs "it has not been determined beyond a shadow of a doubt the absolute specific cause of the decline". Based on this, the letter-writer argues for the "continued management and support of hatcheries to produce adequate number of fingerlings to accommodate the high levels of stocking to provide for high quality recreational fishing in all the high mountain lakes of the Sierras, Cascades and Klamath mountain ranges of California". 

Based on these comments, I'd be willing to bet that the letter-writer has not read a single one of the scientific papers that describe the impacts of introduced trout on amphibians in California's montane habitats. These studies were conducted by different research groups (including the California Department of Fish and Game) and include detailed surveys of amphibians and fish at more than 15,000 lakes and streams. The various studies are unanimous in their conclusion that trout introductions can cause negative impacts to mountain yellow-legged and Cascades frogs, and also demonstrate that trout removal can result in their rapid recovery. These studies have also clearly shown that the amphibian chytrid fungus is a major cause of the mountain yellow-legged frog's decline. Finally, these studies have identified pesticides as a possible additional cause of declines, although evidence in support of pesticides remains relatively weak (including my own paper on this topic). By any analysis, there is ample evidence that ongoing trout stocking has serious consequences for mountain yellow-legged and Cascades frogs. 

The letter-writer also ignores the evidence that the majority of mountain lakes in the Sierra Nevada (and elsewhere) actually harbor self-sustaining trout populations that would likely be negatively impacted by supplemental stocking of hatchery trout. So, in arguing that all mountain lakes in California be stocked with hatchery trout, the letter-writer is unwittingly arguing for policies that would decrease the quality of California's backcountry fisheries. That is hardly a reasonable position to advocate. 

To be productive partners in resolving the "fish-frog" debate, the public needs to make the effort to inform themselves. The best-available science on this issue isn't perfect, but it is by far the most detailed information source collected on the impacts of hatchery trout anywhere in the world. This literature provides a solid foundation for asking the critical questions that all of us interested in this issue should be asking. For example, given that angling is an important activity in California's mountain lakes but that fishless habitat is essential for several amphibian species, (1) what is the appropriate balance between fish and fishless habitat? Assuming that such a balance exists (and I believe that it does), (2) how should that distribution of fish and fishless habitats be achieved? Is a halt to the stocking of critical lakes sufficient? Should gill netting be employed to remove trout from critical habitats? If so, which ones? Should rotenone be used to remove trout from some entire basins? And (3) what role should fish stocking play in the management of California's montane lakes? Which lakes are self-sustaining and do not need to be stocked and which are which ones need to be stocked to maintain important fisheries?

Finding creative solutions to the fish-frog issue will require the informed, open-minded involvement of managers, scientists, and the public. Assertions that trout do not impact amphibians are not supported by the available evidence and hinder any attempts to find those solutions.


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"Final" Fish Stocking EIR/EIS Is Even Worse Than Feared

The final fish stocking EIR/EIS is now available on the California Department of Fish and Game (DFG) web site. A reading of the pertinent sections has left me, well, dejected. With this document, the DFG had an unprecedented opportunity to develop future fish stocking practices that would benefit both native species and anglers. Instead, they've done everything in their power to maintain the status quo and that status quo will benefit neither native species nor anglers. With a few exceptions, the document is substantively unchanged from the draft version. The objective statement ("...continue the rearing and stocking of fish from its existing facilities...") remains the same, the analyses still use the same flawed baseline (2004-2008 stocking program), and the three narrowly-defined alternatives are unchanged. 

The only significant change that I've found is one that makes the document even worse. In the draft EIR/EIS, the DFG acknowledged that the annual pumping of more than 12,000 acre-feet of groundwater to supply the Black Rock fish hatchery has caused significant impacts to springs and riparian areas due to groundwater draw-down. To mitigate this impact, the draft EIR/EIS proposed reducing groundwater extraction to 8,000 acre-feet per year, an action that was applauded by the California Native Plant Society and others. The Los Angeles Department of Water and Power, which sends the 12,000 acre-feet to L.A. after its use in the hatchery, complained mightily about this mitigation, and it is absent from the final EIR/EIS. 

In reading over the Responses to Comments (Appendix M), I often couldn't believe my eyes. For example, in my comment letter I stated, "It is paradoxical that the DFG's primary objective is to "continue the rearing and stocking of fish from its existing facilities" before impacts of those activities are analyzed, disclosed, and mitigated". The DFG response to this comment states, "It is difficult to understand why the commenter considers this objective paradoxical; DFG is required by law and Fish and Game Commission guidance to provide hatchery-reared fish for recreational fishing in California.... The commenter seems to suggest that DFG should consider an alternative that eliminates hatcheries...". Actually, I said nothing of the kind. I was simply noting that the stated objective of continuing the current stocking program would make it difficult to propose any substantive changes to that program. With their stated objective, the DFG is in effect preordaining a conclusion that fish stocking has minimal effects and no serious changes to the program are necessary. And, lo and behold, that is exactly what we got. 

My comments on the draft EIR/EIS also argued that the document failed to analyze stocking impacts on recreational trout fisheries. In response, the DFG stated (in part) that the management of recreational trout fisheries is specified by the 2004 Strategic Plan For Trout Management and is therefore outside of the purview of the EIR/EIS. This is absurd for a couple of reasons. First, the court required the DFG to analyze the environmental impacts of its current trout stocking program on the environment. That, in my mind, includes analyzing impacts on existing trout fisheries. Second, the Strategic Plan for Trout Management is not a CEQA document. Instead, it is a brief plan that outlines some vague goals for the hatchery trout program and does not even discuss the impacts of hatchery trout on resident trout populations. I can only conclude that the DFG will do anything in its power to avoid dealing with this important issue. 

I guess I've learned one important lesson from all of this. Over the years, I've heard lots of complaints about how agencies are sometimes prone to advocating positions that serve only the agency itself. The lengths to which the DFG went in the EIR/EIS to advocate for the status quo drove this home for me. The DFG is always quick to tout how its stocking program is largely responsible for California's many fishing opportunities. And yet the available evidence makes it abundantly clear that fish stocking often has negative impacts on resident trout populations and that as a consequence the current fish stocking program could actually be making fishing worse. The EIR/EIS objective statement promoting the status quo and the DFG's refusal to acknowledge impacts on resident trout fisheries (much less propose any mitigation measures) indicates to me that the DFG's interest lies not with producing high quality fishing opportunities. Instead, its interest is simply in continuing the current trout stocking program (and associated budget) regardless of whether this program benefits California's anglers. That is unacceptable.


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"Final" Fish Stocking EIR/EIS Released

On November 7, 2008, Judge Marlette of the Sacramento Superior Court ordered the California Department of Fish and Game (CDFG) to prepare an Environmental Impact Report on the impacts of its fish stocking program. This document was to be submitted "no later than January 11, 2010". That would be today. Rumor has it that the document will be submitted today but no information has yet been posted on the DFG Hatchery EIR-EIS web page. I'm assuming that the document will be available to the public in the next few days. 

As I've detailed in previous posts, this document will guide the CDFG fish stocking program for decades to come. So, it is incredibly important that the EIR-EIS be thorough in the development of measures to mitigate the impact of fish stocking on California's aquatic ecosystems. The draft document was badly flawed in this regard and I'm not expecting that the "final" document will be much better. This just doesn't seem to be the way the CDFG operates. Instead, I suspect that this "final" document will be similarly lacking and that these failings will precipitate further litigation to force the CDFG to get it right. That sure is a screwy way to make policy decisions but for the CDFG it seems more the rule than the exception. My blog posts for the next few weeks will describe the changes that the CDFG made to the earlier draft document in response to input from the public. Stay tuned.


In other news, acting CDFG Director John McCamman has been appointed as Director. Don't expect this to change agency politics. As always seems to be the case, science will generally only be used to guide management decisions when the scientific results are convenient. When it comes to fish stocking impacts, you can bet that the "best available science" is far from convenient.


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The Origin of the Amphibian Chytrid Fungus

One of the most pressing questions related to the amphibian chytrid fungus (Batrachochytrium dendrobatidis - "Bd") is where this pathogen originated from. Unfortunately, we still don't know, but a recently published paper adds an interesting wrinkle to what we do know. Until recently, the available data suggested an African origin. The "Out of Africa" hypothesis was based on the fact that the earliest known record of Bd was from South African amphibians collected in 1938. Under this hypothesis, Bd was spread around the world as a consequence of the large-scale export of African clawed frogs (infected with Bd) from Africa for medical research starting in the 1940s.


Now Goka and colleagues present detailed information on the distribution and genetic structure of Bd in Japan, the first such study for any Asian country. In addition to showing that Bd is widespread in amphibian populations across Japan, the authors also state that Bd was detected on amphibian specimens collected as early as 1902. Furthermore, one of the species infected with Bd is the Japanese giant salamander (Andrias japonicus - shown in photograph), an ancient species that reaches a length of more than 1 m (39") and is apparently not negatively affected by Bd infection. This species was infected with unique Bd strains that were not found on any other Japanese amphibians, suggesting that the Bd-Andrias relationship is the result of a long-term coevolution between pathogen and host. These findings led Goka et al. to suggest that Bd originated in Japan, not Africa.

Additional research will be necessary to validate this conclusion, but the possibility that Bd originated in Asia certainly has shaken up our current thinking on the origin of this pathogen. For now, all we can say with some certainty is that Bd originated somewhere in the world and was subsequently moved around the globe by human activities. 

For details on the Japanese study: Goka, K., J. Yokoyama, Y. Une, T. Kuroki, K. Suzuki, M. Nakahara, A. Kobayashi, S. Inaba, T. Mizutani, and A. D. Hyatt. 2009. Amphibian chytridiomycosis in Japan: distribution, haplotypes and possible route of entry into Japan. Molecular Ecology 18:4757-4774.


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