Scott Bar salamander. Photo © Richard S. Nauman
Genetic diversity among species can be a dry subject, a study pursued in labs by biologists seeking to reconstruct history using the four-letter DNA code hidden in the cells of animals and plants. But in the spring of 1996, when U.S. Forest Service biologists Dave Clayton and Sam Cuenca flipped over a rock and found something unexpected underneath, the esoteric study of genes, principally the realm of university researchers, became part of their daily work.
Under the rock was a small woodland salamander. In many ways it looked like the Siskiyou Mountains salamander (Plethodon stormi) found to the north or the Del Norte salamander (P. elongatus) found to the west and south, but Clayton and Cuenca noticed that this salamander was different. It shared the general form and color of neighboring populations, but it appeared a little more full-bodied, with a wider head, shorter body and longer legs than other salamanders. Though they didnœt realize it at the time, the pair had discovered a species new to science, a salamander that may have been living for millions of years along the dry hillsides above the Klamath River in the rain shadow of the Marble Mountains.
Named Plethodon asupak, after the Shasta Indian name for the area near the confluence of the Scott and Klamath Rivers, the Scott Bar salamander—its common name—reminds us that there are still scientific discoveries to be made, even in well-known regions. For many biologists, the discovery of a new species is the highlight of their career. It usually follows years of detailed and sometimes tedious work with no guaranteed outcomes, but the payoff is huge in terms of the knowledge a new species can offer. Gaining a clear understanding of biological systems can be like looking at a puzzle, one with lots of missing pieces. Each new discovery helps complete the picture and offers greater insight into the workings of ecosystems and the processes of evolution that create them.
Although scientists have named more than thirty new species of salamander in the United States since 1990, most of these newly named species were the result of differentiating between what researchers formerly considered a single species. The Scott Bar salamander stands out because it was undetected by scientists until Clayton and Cuencaœs discovery.
The discovery of the Scott Bar salamander provided a unique opportunity for cooperation between Forest Service field biologists, staff from the Forest Service Research Station and university researchers. District biologists are kept busy with the day-to-day business of running a national forest: reviewing land management proposals, coordinating with other agencies and conducting monitoring. Itœs rare that they have the opportunity to play such an instrumental role in the discovery and description of new species, usually the realm of specialists in universities and museums. At the Forest Service research labs, funding for basic single-species research is often limited or non-existent. The agencyœs research programs tend to focus on larger-scale multi-species studies of ecosystems and wildlife habitats.
Clayton and Cuenca knew the area and the Siskiyou Mountains salamander. Clayton, then working as a term biologist, had convinced the Rogue River National Forest to provide a small amount of funding to conduct a basic population genetic study on Siskiyou Mountains salamanders. “We wanted to see if there was gene flow between populations,” he said. “We were in the infancy of conservation planning and wanted to see if we needed to provide connectivity between populations.” Because the forested rocky soils and talus that provide habitat for woodland salamanders occur in small pockets and patches across the landscape, understanding how animals move between habitats is critical to conservation planning. Clayton and Cuenca were collecting genetic data to provide insight into basic questions regarding salamandersœ ability to recolonize habitats after disturbance. Collecting samples while working on other projects and on their own time, they set out to cover the known range of the species.
“Sam and I had collected on Grider Ridge and were headed back towards Yreka,” recalls Dave. “We stopped beside the road east of Seiad Valley—Iœm not sure why—and saw some good-looking habitat and found several animals.” While they were excited to have found salamanders outside the range of known populations, they didnœt realize the significance of their discovery. They collected several tissue samples and sent them off to the laboratory at the University of Oregon. Because they were near the boundary between the ranges of the Siskiyou Mountains and Del Norte salamanders, they expected that their samples were going to be one species or the other. Instead, the results showed that they had found a distant cousin to both, and potentially a new species altogether.
While Clayton and Cuenca were making their discovery, the Klamath National Forest was gearing up to conduct salamander surveys. The Northwest Forest Plan, which was put into effect in 1994, required a survey-and-manage strategy for species thought to be associated with older forests and poorly protected by the system of older-forest reserves established by the plan. Many species were included on the survey-and-manage list because they were known from so few sites that it was difficult to determine if the plan would adequately protect them. Little-known species such as the Siskiyou Mountains salamander, red tree vole, rare snails and slugs, and numerous species of mushrooms were included on the list. The survey-and-manage provisions of the Northwest Forest Plan resulted in a surge of funding for surveys and research for these species, resulting in unprecedented gains in understanding for many of them.
At the same time, the state of California, which protects the Siskiyou Mountains salamander as threatened under the stateœs Endangered Species Act, was requiring surveys for Siskiyou Mountains salamanders as part of timber harvest planning on private lands. Because of the unprecedented survey efforts, biologists found more salamanders that appeared to be the new species south of the Klamath River.
Woodland salamanders (the genus that includes the Siskiyou Mountains, Del Norte and Scott Bar salamanders) are notoriously hard to identify. Adapted for life in the forest floor, their bodies are long and thin, their legs small. Fully terrestrial, they lay their eggs in small subterranean cavities where the mother guards the eggs until they hatch as miniature adults, bypassing the larval or tadpole stage common in many amphibian species. Because the salamanders do not have lungs and exchange gases through their skin, they, like their eggs, require moist environments. Woodland salamanders are territorial and have elaborate courtships that often last for hours. They use a complex system of chemical pheromones secreted from specialized glands to communicate, and possess sophisticated adaptations to receive these chemical messages. Woodland salamanders donœt appear to move around much; over geologic time, their stationary life can result in the occasional isolation of populations and subsequent formation of new species.
Traditionally, biologists have applied the biological species concept to determine if pairs of similar populations are the same or different species. Individuals from the two populations are considered the same species if they are able to interbreed and produce fertile offspring. If some sort of barrier to reproduction exists, then the two populations represent different species. However, this definition is hard to apply in the wild given the secretiveness of most species. In the absence of reproductive information, taxonomists have used surrogates such as skeletal structure or the shape and relative proportions of the organism to infer the relationship between populations.
With the advent of a DNA analysis technique known as polymerase chain reaction in the 1980s, researchers could read the four-letter genetic code from a tiny sample of cells collected in the wild and reconstruct evolutionary history. Relationships between populations could be inferred and cryptic species identified. Rather than indirect measures of species relationships, researchers now had a tool that allowed a direct measure of the genetic distance between populations and an estimation of the time since populations last shared a common ancestor.
After Cuenca and Claytonœs discovery, researchers estimated that the Scott Bar salamander and its sister species, the Siskiyou Mountains and Del Norte salamanders, last shared a common ancestor during the Pliocene (about 2ס million years ago), a period of mountain building that created the modern Siskiyou Mountains from a broad plain and produced climatic changes that isolated populations and promoted the formation of new species.
The rugged and remote Siskiyou Mountains donœt give up their secrets easily. Even though two populations of Scott Bar salamanders were close to a state highway, the species remained unknown, in part because of the landscape salamanders inhabit. Woodland salamanders hide under rocks and downed logs in wet conditions. During dry, hot weather or when temperatures fall close to or below freezing, salamanders retreat into the rocky soils.
The range of the Scott Bar salamander is dry; ridge after ridge of the Klamath Mountains strip storms of their moisture as they sweep in from the north Pacific. After storms pass over the 7,000- to 8,000-foot peaks of the Marble Mountains and arrive on Scott Bar Mountain, they rarely produce significant precipitation. In interior regions summer temperatures are higher, and periods of freezing weather during the winter are common. On Scott Bar Mountain, far from the dampening effect of the ocean, nights are cold for much of the year and daytime temperatures are hot and dry during the remainder. Researchers who set out to capture Scott Bar salamanders must study weather forecasts and be able to head to the field on short notice. While finding Del Norte salamanders is relatively easy through much of the year along the foggy, frost-free coast, Scott Bar salamanders may be active only on a limited number of days between January and late May, or they may not appear on the surface at all in any given year.
In this part of the world, salamander season comes early, before clean-up crews reach the forests, so reaching remote sites during salamander weather can take hours. Washed-out roads or downed trees can force researchers to turn back miles from their destination. Other times they arrive at a site only to find that it is too dry to find salamanders. The field workers face a host of other difficulties in the woods: Poison oak grows on the rocky soils and as weather warms in the spring, ticks become active. Flipping rocks can startle scorpions, and in the canyon bottoms, crews occasionally turn up a rattlesnake. Rivers roar to life in the spring runoff season. To access one newly discovered population of Scott Bar salamanders, biologists packed inflatable kayaks down a steep trail and used them to cross the Scott River.
Under these difficult conditions, with a limited, unpredictable window of opportunity to catch animals, collecting for the population genetic study proceeded slowly after Clayton and Cuencaœs initial discovery, with every spring salamander season providing a little more information. In 2001, conservation planning for the Siskiyou Mountains salamander became a priority for federal agencies and the Forest Serviceœs Corvallis Forestry Sciences Laboratory hired Dr. Louise Mead to complete the analysis and put together the manuscript describing the new species, pushing it through the lengthy and often difficult process of peer review and scientific publication. Because the research team knew that the description of a new species would be controversial, data from two different genes and a traditional analysis of morphology were used in the description. The concordance between the two genes and morphology data provided the evidence they needed to establish their find as a separate species.
But even as the new species was being established, changes in land management laws were affecting it. In 2004, the Bureau of Land Management and the Forest Service, the two land management agencies governed by the Northwest Forest Plan, eliminated the survey-and-manage provision of the plan altogether. The original version had required salamander surveys prior to timber harvest, road building and other land management projects for the Siskiyou Mountains salamander and protection of all known sites. After a review in 2001, the requirement for surveys was dropped in the northern half of the Siskiyou Mountains salamander range but all known sites continued to be protected. In the southern half of the range surveys continued. After the termination of the survey-and-manage provisions, federal land managers placed about 160 of the former survey-and-manage species on agency sensitive species lists. Sensitive species regulations provide a lower standard of protection, only requiring that land management projects must not lead toward endangered species listing, or the loss of species viability.
Without survey-and-manage requirements, the future for the Scott Bar and Siskiyou Mountains salamanders is uncertain. The two species have small ranges—the Scott Bar salamander has the smallest range of any salamander in the Pacific Northwest—and both are vulnerable to disturbance. Past impacts are difficult to measure for species like these. There is a history of extensive placer and hydraulic mining, and associated logging, that likely affected local populations after European and Chinese miners first settled the area following the discovery of gold at Scott Bar in 1850. As mining declined in the first half of the twentieth century, the timber industry grew, further affecting populations. In spite of this, Siskiyou Mountains salamanders have been found in disturbed areas, indicating that they have some ability to survive impacted habitats. Larger blocks of quality habitat remain on the north side of Siskiyou Mountain.
Less is known about the habits of the Scott Bar salamander. The roadless north side of Scott Bar Mountain, nearly unexplored, may hold more populations, but the known range is small. In this dry landscape, woodland salamanders may be particularly susceptible to land management activities.
But scientific activity around the Siskyiou Mountains and Scott Bar salamanders continues. Forest Service and BLM staff are reviewing a conservation assessment and strategy, written before the survey-and-manage requirements were eliminated, for populations north of Siskiyou Mountain, on federal lands.
Agencies are proceeding cautiously. Recently, the Medford, Oregon, BLM decided not to apply forest-thinning treatments to an area designated as a salamander conservation site in the draft conservation strategy. The Klamath National Forest, which includes the entire range of the Scott Bar salamander and the southern half of the Siskiyou Mountains salamander, is applying the same management direction to both species. Because the two species are hard to tell apart in the field, the boundary between their ranges is still unclear. Many of the factors that resulted in sensitive species listing for the Siskiyou Mountains salamander also apply to the Scott Bar salamander, so the Forest Service has decided to treat the Scott Bar salamander as sensitive. According to Forest Biologist Karen West, “we will avoid or minimize impacts to these species from our management activities and we will conduct surveys or assume suitable habitat to be occupied and address the effects of management actions in our Biological Evaluations.”
While federal agencies move cautiously with the management of the salamanders, the California Department of Fish and Game has submitted a petition to the State Fish and Game Commission recommending elimination of the state protections that protect both species on private lands, and states in its petition that “The Department further believes that no special management provisions or protections under the California Environmental Quality Act or Forest Practice Rules are necessary to conserve this species.”
Federal and state agencies have either reduced or proposed reducing protections for these species, though the Center for Biological Diversity has petitioned the U.S. Fish and Wildlife Service to list both the Siskiyou Mountains and Scott Bar salamanders under the Federal Endangered Species Act in June 2004, and recently filed a notice of its intent to take the Fish and Wildlife Service to court over its failure to respond to the petition within one year as required by the Endangered Species Act.
The recipients of this unprecedented attention—the salamanders—continue on, oblivious to the petitions and reports written about them. Living out a pattern millions of years old, hidden in the forest floor, they wait for the next rainy season. Recent work in the Trinity River watershed to the Southwest has suggested that other undiscovered species may live there and maybe, in the large wilderness areas of the region, other salamander species remain undiscovered. With a little rain and a little luck, field biologists will stumble upon more new species, each one providing a piece of the biological puzzle.