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Science Review for the Scott Bar Salamander (Plethodon 

asupak) and the Siskiyou Mountains Salamander (P. 

stormi): Biology, Taxonomy, Habitat, and Detection 

Probabilities/Occupancy

Douglas J. DeGross and R. Bruce Bury

Open-File Report 2007-1352

U.S. Department of the Interior

U.S. Geological Survey
ii Report Title

U.S. Department of the Interior

DIRK KEMPTHORNE, Secretary

U.S. Geological Survey

Mark D. Myers, Director

U.S. Geological Survey, Reston, Virginia: 2007

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Suggested citation:

DeGross, D.J., and Bury, R.B., 2007, Science Review for the Scott Bar Salamander (Plethodon asupak) and the Siskiyou Mountains Salamander (P. stormi): Biology, Taxonomy, Habitat, and Detection Probabilities/Occupancy: Reston, 

Virginia, U.S. Geological Survey, Open-File Report 2007-1352, p. 14. 
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Contents

Introduction.....................................................................................................................................................1

Biology ............................................................................................................................................................1

Taxonomy .......................................................................................................................................................2

Color and Morphology .........................................................................................................................2

Phylogenetics ........................................................................................................................................3

Habitat .............................................................................................................................................................4

Impacts to Habitat.................................................................................................................................6

Timber Harvest and Silvicultural Practices ...............................................................................................6

Fire....... ....................................................................................................................................................7

Mining and Other Ground Disturbing Practices ..............................................................................8

Combined Risk Model...........................................................................................................................8

Detection Probabilities/Occupancy ............................................................................................................8

Conclusions.....................................................................................................................................................8

Systematics............................................................................................................................................8

Habitat ....................................................................................................................................................9

Modeling Salamander Populations and Habitat ..............................................................................9

 Acknowledgments ......................................................................................................................................10

 References ..................................................................................................................................................11
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Science Review for the Scott Bar Salamander (Plethodon 

asupak) and the Siskiyou Mountains Salamander (P. 

stormi): Biology, Taxonomy, Habitat, and Detection 

Probabilities/Occupancy

Douglas J. DeGross and R. Bruce Bury

Introduction

 The Plethodon elongatus Complex in the Klamath-Siskiyou Ecoregion of southern Oregon and northern 

California includes three species: the Del Norte salamander, 

Plethodon elongatus; the Siskiyou Mountains salamander, P. 

stormi; and the Scott Bar salamander, P. asupak. This review 

aims to summarize the current literature and information 

available on select topics for P. stormi and P. asupak. These 

are both terrestrial salamanders belonging to the Family 

Plethodontidae, which contains more species and has a wider 

geographic distribution than any other family of salamanders 

(Wake 1966, 2006; Pough 1989). The genera of this family 

have greatly diversified ecologically across North America, 

Central America, northern South America, Sardinia, southeastern France and northwestern Italy, and have recently been discovered on the Korean peninsula (Min et al. 2005). The genus 

Plethodon is found exclusively in North America and is split 

into three distinct clades, based upon morphology and phylogenetics (Highton and Larson 1979): eastern small Plethodon, 

eastern large Plethodon, and the western Plethodon. The western Plethodon are the greatest representation of Plethodontidae 

in the Pacific Northwest, with 8 species. The two species with 

the most restricted ranges of these regional congeners are the 

Siskiyou Mountains and Scott Bar salamanders.

 These salamanders occupy the interior of the Klamath-Siskiyou Ecoregion which straddles the California and 

Oregon state lines, between Siskiyou County (CA) and 

Jackson and Josephine Counties (OR). The relatively recent 

discovery of P. asupak (Mead et al. 2005) and the limited 

range of both species have created an environment of uncertain 

conservation status for these species. This review will focus on 

four central topics of concern for land and resource managers: 

Biology; Taxonomy; Habitat; and Detection Probabilities/

Occupancy. 

Biology 

Species of the genus Plethodon have fairly rigid physiological requirements. Some unifying characteristics of the 

salamanders in this genus are their fully terrestrial existence, direct development, relatively small size, and lack of 

functional lungs (Dunn 1926, Zug et al. 2001). Although a 

thorough physiological evaluation has not been conducted on 

either P. stormi or P. asupak, moist conditions are required 

by both forms. Plethodon salamanders, due to their lack of 

functional lungs, respire through their permeable skin. This 

process requires moisture to properly allow for cutaneous gas 

exchange (Feder 1983). This obligatory condition is attained 

by the salamanders actively seeking out moist microhabitats, 

including those found by retreating underground, in other 

animal burrows, or the interstitial spaces created by the rocky 

substrates.

Plethodon stormi and P. asupak can be found closest to 

the surface during the region’s wet season, which starts with 

the first fall rains and runs through the spring, or when site 

specific conditions present equable conditions. The region 

has low humidity in summer or other dry spells (mostly late 

spring and early fall) when these organisms are driven into 

subterranean refugia for available moisture and to avoid high 

temperatures. 

Water loss from dry conditions can be lethal to Plethodon

salamanders, and evidence from the Del Norte salamander (P. 

elongatus) indicates sensitivity to these conditions (Ray 1958). 

This would infer limited utilization of habitats or microclimatic environments that occur outside their zone of tolerance 

(Welsh et al. 2007). If sites experience changes in these conditions, it may result in reduction of time spent for foraging and 

reproduction (Feder 1983). No current studies have attempted 

to examine the biological limits or conditions acceptable to 

either P. stormi or P. asupak, but changes in habitat and microclimate variables have been studied in their close relative P. 

elongatus (Biek et al. 2002, Major 2005, Karraker and Welsh 

2006).
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Mobility of P. elongatus appears to be extremely low 

(Welsh and Lind 1992). Due to the environmental extremes of 

the interior Klamath Siskiyou region with freezing winter temperatures and hot, dry summer conditions, most salamanders 

are found during a narrow sampling timeframe (D. DeGross, 

pers. observation). Further, seasonal movements across the 

landscape appear to be even more restricted for the two species found in the interior compared to other salamanders (e.g., 

P. elongatus) living closer to the coast and in less extreme 

conditions. 

Large skin surface to body mass ratios have been correlated to greater water retention (Feder 1983). Mead et al. 

(2005) produced evidence that P. stormi and P .asupak appear 

to be larger in size, or more robust, than P. elongatus. If the 

interior animals are more robust, it likely reflects an evolutionary response to life in the more arid interior. Variable number 

of trunk vertebrae has been inferred as a possible temperaturedependent phenotypic response (Jockusch 1997) in the western Plethodontid genus, Batrachoseps. In the Plethodon elongatus Complex, fewer costal grooves (i.e., shorter trunk) and 

the larger forelimbs observed in P. stormi and P. asupak result 

in a more robust body form than what is found in P. elongatus

(Mead et al. 2005). Thus, the higher elevations of the interior 

of the Klamath-Siskiyou Ecoregion, greater climatic extremes 

(hotter summers and colder winters), and the glacial history of 

the region could be the driving forces of the evolutionary patterns observed in the Plethodon elongatus Complex. 

Taxonomy 

The systematics of the Plethodon elongatus Complex has 

been an active area of study as two distinct and novel forms 

have been identified over the last 40 years. The first identified 

member of the Complex was Plethodon elongatus that was 

described from a coastal population in Del Norte County, California (Van Denburgh 1916). When P. stormi was described 

(Highton and Brame 1965), it was found inland of P. elongatus 

and geographically isolated from the nearest known population 

of P. elongatus by at least 9 miles (14.4 km) (Brodie 1971). 

However, as more field observations were made of these congeners, the gap in geographic separation continued to shrink, 

and regional observations of morphological similarities began 

to emerge in the interior of the region (Brodie 1970; Bury 

1973, 1999). Inferences to inland populations of P. elongatus

sharing morphological characters with nearby P. stormi led 

to the proposition of intergrades in the interior of the region 

(Bury 1973), as well as combination of both forms under one 

species with subspecies designations (Stebbins 2003). Morphological traits and color were used in these early analyses 

(Brodie 1970; Bury 1973, 1999) to designate systematic relationships or describe geographic variation in features. Most 

recently, P. asupak was described more interior to P. elongatus

and south to southeast of P. stormi (Mead et al. 2005). 

Past studies and inferences of current studies on this 

complex have indicated the potential for additional taxonomic 

delineations or distinct population segments within the group 

(Bury 1973, Mahoney 2004, Mead et al. 2005, DeGross 2004, 

DeGross and Bury unpublished). However, none of these 

variants has been described in the literature. The systematic 

relationships of the group remain of high biological interest 

due to its marked geographic variation over relatively short 

geographic distances and the recent description of a new species.

Color and Morphology 

Coloration differences between P. elongatus and P. 

stormi were originally the field diagnostic for their separation into different taxonomic units (Highton and Brame 1965, 

Brodie 1970). The ground color of P. stormi is usually black 

in juveniles and varies from light brown to purplish brown in 

subadults and adults (Highton and Brame 1965, Nussbaum 

et al. 1983). They lack a dorsal stripe, but may have many 

iridiphores (small spots) over the lateral surfaces and dorsum 

of the body. Juvenile P. elongatus in most interior locations 

have a distinct, dorsal red-brown stripe on a dark brown body 

color (Brodie 1971, Stebbins 2003, Bury 1999), however the 

adult stripe becomes lighter (olive-tan) or less distinct with 

age. Few localities were known at the time of the description 

of P. stormi, and Brodie (1971) reported that the two forms 

were allopatric (adjacent areas) in distribution. Past and present analyses and observations suggest that field identification 

based upon color alone can be problematic between the members of this complex, especially in western Siskiyou County, 

California. 

Brodie (1970, 1971) reported that the number of trunk 

vertebrae in P. stormi (mode = 18) is one fewer than P. elongatus (mode = 19). Also, P. stormi has proportionally longer 

limbs than P. elongatus (Highton and Brame 1965, Bury 1999, 

Mead et al. 2005). Earlier, the variation observed by Brodie 

(1971) and Bury (1973) across the ranges of P. elongatus and 

P. stormi in coloration and morphological characters led Stebbins (2003) to consider a subspecies designation for inland P. 

elongatus, rather than full species status as P. stormi; however, 

this was a species account in a field guide and provided no 

specific rationale for the designation. 

One locality of particular note and importance in the 

identification of these species was Seattle Creek, California, 

in the upper Klamath River basin. A fairly large series of 

specimens was first collected there by Bury (1973; specimens 

at Museum of Vertebrate Zoology), and reported on later by 

several authors (Brodie 1971; Bury 1973, 1999; Mead et al. 

2005). A few samples taken from this locality would later be 

designated P. stormi from genetic analyses (Mahoney 2001, 

Pfrender and Titus unpublished, DeGross 2004, Mahoney 

2004, Mead et al. 2005, Mead 2006, DeGross and Bury 

unpublished). Animals measured from this population and 

southward in the Klamath River drainage suggested clinal 
Heading 1 3

variation in morphological traits between inland and coastal 

populations of P. elongatus (Bury 1973, 1999). Morphological 

analysis of both forms in the region demonstrated variation 

in vertebral counts between and within each form, consistent 

with prior findings (Bury 1999). Studies of variation in morphological traits (Brodie 1971; Bury 1973, 1999) reported a 

reduction of modal number of vertebrae (and, in turn, number 

of costal grooves) moving from coastal to inland P. elongatus

(n = 19) and then to P. stormi (n = 18).

The most recent analysis of morphological traits (Mead 

et al. 2005) demonstrated variation and overlap between and 

within each of the three forms (P. elongatus, P. stormi, and 

P. asupak). However, they demonstrated a general trend of 

increased robustness with reduced number of costal folds and 

longer forelimbs of the inland forms compared to those closer 

to the coast. They also noted some subtle sexual dimorphism 

within each group. 

Phylogenetics

 The phylogenetic relationships among forms of this 

complex have been relatively well studied, especially in comparison to other western Plethodons. One of the driving forces 

to understand species’ relationships among the complex is the 

protected status of these salamanders under federal or state 

species-management programs, including: Federal Survey 

and Manage list (USDA and USDI 1994), proposed listing as 

federal threatened and endangered species (Greenwald 2004), 

and the California State threatened species list (P. stormi) and 

Species of Special Concern List (P. elongatus). The designation or degree of protected status may rely, in part, upon how 

the forms are broken into discrete species units. 

 The first phylogenetic analysis to compare these salamanders utilized gene electrophoresis of more conservative 

gene-coding regions (Highton and Larson 1979). This original 

phylogenetic comparison of P. stormi and P. elongatus produced a Nei’s genetic distance of D = 0.33, where D increases 

with decreasing relatedness. Further, Nei’s normalized identity 

(I) of genes (decreases with decreasing relatedness) confirmed 

only two pairs of western Plethodons to be closely related, P. 

elongatus and P. stormi (I = 0.72), and P. vandykei and P. idahoensis (I = 0.71) which had a D = 0.35. The values observed 

for the Vandykei Complex infer slightly greater genetic 

divergence than those of the P. elongatus species Complex 

which seems intuitive with the disjunct distribution and large 

geographic distance between forms in the P. vandykei Complex (gap extending from the Washington Cascades to Idaho). 

By the late 1990s, mitochondrial DNA (mtDNA) 

sequence analysis had become the most widely utilized technique for evaluating population designations. The first mtDNA 

phylogenetic analysis to assess the relationship of these 

closely related forms supported a sister species designation 

between P. stormi and P. elongatus (Mahoney 2001). However, 

the scale of inference of this first study for interior populations 

was somewhat small due to only one population of P. stormi

being used in the analysis. 

A more focused phylogenetic analysis of P. stormi 

sampled populations from the Applegate River drainage (along 

the Oregon and California state line) south to the Klamath 

River, California (Pfrender and Titus unpublished). This report 

found a lack of genetic diversity in P. stormi within the Applegate River drainage, likely due to a recent range expansion 

and genetic bottleneck as individuals dispersed into the lower 

reaches of the watershed. However, salamanders sampled further south over the Siskiyou Mountain crest displayed significant divergence. Overall for P. stormi, three strongly supported 

mtDNA clades were recognized (Pfrender and Titus unpublished), and later published (Mead et al. 2005): (1) the Applegate drainage samples (North clade); (2) the adjacent populations on the southside of the Siskiyou crest, which formed a 

monophyletic group with the Applegate populations (South 

clade); and (3) a more deeply divergent clade from south of 

the Klamath River and east of Grider Creek, California. 

A parallel study of mtDNA diversity across the range of 

P. elongatus (Mahoney 2004) sampled the lower two-thirds of 

the P. elongatus range (i.e., primarily in California), as well 

as across the range of P. stormi. Mahoney (2004) identified 

three distinct clades within her samples of P. elongatus and 

confirmed the two clades of P. stormi on either side of the 

Siskiyou Mountains reported by Pfrender and Titus (unpublished). Additionally, one sample from south of the Klamath 

River and east of Grider Creek Ridge formed its own discrete 

clade in analyses, further supporting the findings of Pfrender 

and Titus (unpublished). Inferences were made as to the origin 

of phylogenetic patterns observed in P. stormi and the relationship it has with its sister taxa, P. elongatus. It was deduced 

that glaciation and changes in climate in the Klamath-Siskiyou 

Ecoregion seem to be the most plausible explanation of the 

complex patterns and species distribution seen in this group of 

salamanders. 

A fourth, more extensive study utilized both mtDNA and 

morphological analyses to assess, with greater sampling, the 

form found south of the Klamath River, and led to designation 

of the third discrete form of the complex, P. asupak (Mead 

et al. 2005). The study added additional support for the two 

clades within the range of P. stormi (North and South), and 

demonstrated that P. asupak was a more basal lineage than the 

group formed by P. elongatus and P. stormi. 

Time frames of divergence can be estimated from results 

of MtDNA analyses. If one were to adopt the conservative 

time frame (slow mtDNA clock) of speciation for poikilotherms set forth by Avise et al. (1998) with approximately 

0.5% sequence divergence per million years, there is a long 

history of separation in the Elongatus Complex that precedes 

the most recent glacial periods of the region. An average of 

2.22% sequence divergence between the two clades of P. 

stormi (North and South) translates to over 4 million years of 

separation (Mead et al. 2005). Values of sequence divergence 

between P. elongatus and both clades (North and South) of P. 

stormi are 8.62% and 7.59%, respectively, which relate to 17 
4 Report Title

and 15 million years of separation. The amount of sequence 

divergence between P. asupak and the North clade of P. stormi, 

the South clade of P. stormi, and P. elongatus are 11.5%, 

11.68%, and 12.85% respectively, and these correspond to 23-

26 million years of separation. These values are estimates, but 

the time elapsed since divergence for each form in the Elongatus Complex precedes the region’s Pleistocene and Holocene 

glaciations as well as the warming trends associated with each. 

Limited levels of gene flow are reported from these 

analyses, with only 2 of 63 individuals of P. stormi tested from 

the contact zones (one from West Grider and the other from 

Horse Creek) demonstrating truly mixed ancestry (i.e., demonstrating more ‘inheritance’ of its genome from the opposite 

form). These findings support the reproductive isolation of P. 

stormi and P. elongatus, a classical criterion used to designate 

species. Past confusion that stemmed from morphological similarities near Happy Camp, California, have been clarified with 

substantial molecular evidence delineating P. stormi exclusively north of the Klamath River and west of Seiad Valley to 

Happy Camp, California. The one population (Seattle Creek 

population) that previously had been defined as P. elongatus or 

intergrades (Brodie 1970; Bury 1973, 1999) has produced only 

P. stormi mtDNA haplotypes (DeGross 2004, Mahoney 2004, 

Mead et al. 2005, Mead 2006). Still, relatively few samples 

have been analyzed for genetic identification in this area. 

Besides no P. elongatus mtDNA haplotypes in samples from 

this locality, only one specimen out of nine analyzed from 

the microsatellite analysis demonstrated a limited admixed 

(<13% P. elongatus; > 87% P. stormi) genome (DeGross 2004, 

DeGross et al. unpublished).

 The evidence of sympatry (occurring in same area) 

and a narrow zone of contact between P. elongatus and P. 

stormi in the Indian Creek drainage of western Siskiyou 

County, California, further confirms the distinct taxonomy 

between these two forms. The current region of contact 

between P. stormi and P. asupak north of the Klamath River 

and south of Horse Creek appears complicated. Further 

sampling and nuclear analyses are needed to define where 

each species occurs. Comparatively, there are deep levels of 

divergence between these three species of salamanders and are 

most likely reflective of the extremely complex geologic and 

climatic history of the Klamath-Siskiyou Ecoregion.

Habitat

 To date, only one peer-reviewed scientific study has 

rigorously analyzed the habitat correlates for these salamander species (Welsh et al. 2007). Anecdotal and observational 

reports of habitat use are relatively well documented, especially for Plethodon stormi (Nussbaum 1974, Nussbaum et 

al. 1983, Clayton and Nauman 2005, Nauman 2005, Bull et 

al. 2006, Farber 2007). Many P. asupak sites on private lands 

(Farber 2007) as well as several on managed public lands 

(Bull et al. 2006) had past timber harvesting and other ground 

disturbances. However, these studies are all retrospective. The 

habitat correlates study of Welsh et al. (2007) included study 

sites that would later be identified through molecular techniques as inhabited by P. asupak. 

Overall, available moisture and rocky talus appear to be 

the two most important habitat conditions for these two species. The reduced annual precipitation and climatic extremes 

of the inland portion of the Klamath-Siskiyou Ecoregion, in 

comparison to more coastal environments, likely has a major 

influence on habitats that support populations of P. stormi or P. 

asupak. Average daily temperatures of the Klamath Mountain 

Province in the summer, when solar insolation is the greatest 

in the mid-latitudes of the northern hemisphere, are about 32o 

C (90o F). The winter average daily temperature is 0o C (32o 

F) and winter is the season receiving the greatest percentage 

of the region’s annual precipitation 50–190 cm (20–75 in). 

This seasonal precipitation generally falls as rain below 1219 

m (4000 ft) and snow above (USDA Forest Service 1994b). 

Besides influencing suitable habitat, these environmental 

variables will drive seasonal surface activity of salamanders 

such as mate selection and reproduction, and therefore genetic 

exchange.

The first identification of P. stormi from the upper 

reaches of the Applegate River Valley in Jackson County, 

Oregon, was from one or two talus slopes (Storm 1966). This 

species was reported as being associated with talus slopes 

for several decades (Highton and Brame 1965, Nussbaum 

1974, Herrington 1988, Blaustein et al. 1995). The first indepth distributional analysis (Nussbaum 1974) of the species 

described differences in habitat correlates for this species as 

well as interior populations of the closely related P. elongatus

compared to coastal habitats of P. elongatus. He reported the 

interior populations at elevations of 488–1078 m (1340 –3540 

ft), with the densest populations occupying talus deposits or 

fissured rock outcrops on heavily-wooded, north-facing slopes. 

Early on, many of the populations of P. stormi occurred in 

talus slopes along road cuts, which exposed the underlying 

rock substrate and created accessible habitat for biologists to 

search for salamanders. Talus environments provide interstitial spaces where organisms, like Plethodon salamanders, 

can move with relative ease to find cool, moist subterranean 

retreats. Additionally, the immediate forest habitat observed at 

occupied sites was conifer-hardwood, mixed canopy (Highton 

and Brame 1965). Surface activity in the more arid interior 

was restricted to the wet season of late fall through spring, and 

only on very wet days could individuals be found in or under 

downed wood and leaf litter (Nussbaum et al. 1983). 

The most recent reports of habitat conditions for both 

P. stormi and P. asupak have been addressed by: (1) observational studies recording conditions found at previously 

occupied sites (Bull et al. 2006, Farber 2007); (2) a Federal 

report which used a stratified random design to select survey 

sites (Nauman and Olson 2004b); and (3) a scientific publication (Welsh et al. 2007). Additionally, three other documents 

will soon be available to better understand the requirements 

and habitat conditions of these species (Nauman and Olson 
Heading 1 5

in press, Reilly et al. in press, Suzuki and Olson in press). Of 

these, the study by Welsh et al. (2007) has the greatest spatial 

inference because they used a rigorous experimental design 

that randomly selected sites across the range of both species. 

In contrast, the least inference is provided by Farber (2007), 

which was a retrospective study of 36 known populations. 

Still, findings of each study are informative about the conditions at sites occupied by salamanders. 

Welsh et al. (2007; published version of the interim 

report of Ollivier et al. 2001) is the most statistically rigorous 

evaluation of habitat correlates as well as additional habitat 

variables for parent geology and GIS-based climate models. 

Welsh et al. (2007) had site selection criteria at three different 

spatial scales. The coarsest scale was “biogeographical” and 

assessed possible sites across the entire range of the species 

based upon underlying geology and forest type. The second 

was “possible habitats” and was based upon the USGS Township and Range system. Within each township, 4 of the 36 sections (each 1-mile2

) were randomly selected. Further, they had 

to have the requirement of available rock substrate. The final 

scale was the seral stage of forest types within each section, 

and they selected four to represent each classification in each 

of the selected townships: pre-canopy (0-30 yrs), young (31-99 

yrs), mature (100-199 yrs), and old-growth (200+ yrs). 

They sampled 239 sites within the range of both P. stormi 

and P. asupak from March 1995 to June 1998 and recorded 

associated habitat correlates from 120 continuous and 8 categorical independent habitat variables. These variables were 

broken into three spatial scales: landscape; macrohabitat; and, 

microhabitat. Further, data from the north and south slopes 

of the Siskiyou crest were assayed for inherent differences. 

They sampled 163 sites from the northern slope of the crest 

and species range of P. stormi, and 76 from the south slope 

or southern portion of the range of P. stormi and the northern 

portion of P. asupak. Of the 163 sites surveyed on the northern 

slope, only 46 (28%) produced P. stormi. Of the 76 south slope 

sites, only 15 (20%) produced P. stormi or P. asupak. They 

found climate variables (annual precipitation, solar incidence, 

and soil temperature) were present in the most informative 

multi-scaled models. Precipitation patterns observed across the 

landscape and across temporal scales were more consistent on 

the northern slope in the Applegate Valley, Oregon, than on the 

southern slope in California. Models for habitat on the south 

slope had consistently higher predictive capabilities than the 

northern slope models. Across all spatial scales, the models 

that either represented or acted as surrogates for climatic conditions were the best predictors of salamander presence. These 

models indicated an emphasis for forest stands that have the 

ability to sustain moist microclimates, and therefore meet the 

physiological and biological requirements of these salamanders. Thus, those requirements are different for the northern 

and southern slopes, and the availability of habitats meeting 

those requirements are not equally distributed across both 

landscapes. Use of these data to prioritize unsurveyed habitats 

has great utility. 

Recently, two landscape-scale habitat models for P. 

stormi in the Applegate watershed were developed from 

mapped habitat variables from an earlier study (Ollivier et 

al. 2001). The model developed by Reilly et al. (in press ) 

included rocky soil types with adequate interstitial spaces, forest canopy closures above 70%, and conifer forest types with 

average tree size > 43 cm (17 in) Diameter Breast Height. An 

additional GIS-based variable “illumination index” was used, 

which incorporated seasonal hillside shading with aspect. 

Using a different modeling approach, Suzuki and Olson (in 

press) used the same variables as Reilly et al. (in press ) and 

added distribution of three tree species: Douglas-fir, Oregon 

white oak, and white fir. They found the occurrence of salamanders was associated (p < 0.05) positively with rocky soils 

and negatively with Oregon white oak and white fir; 84% of 

occupied sites were correctly classified by their model. Additionally, this model incorporated variables for risk to and persistence of salamanders (see section “Combined Risk Model”). 

Another study (Nauman and Olson in press) randomly 

sampled sites on federal lands south of the Siskiyou crest for 

P. stormi and P. asupak. Their objective was to investigate 

patterns of occupancy with federal land allocation termed 

matrix or reserve. They found Plethodons at 26% of their 

sampled points, with higher detection rates in lower elevation 

lands where matrix lands dominated and higher precipitation 

occurred.

Two reports (Farber et al. 2001, Farber 2007) focus on 

salamanders and habitat at sites with previous disturbance and, 

in several cases, multiple disturbances: 94% of the 36 sites 

from the 2007 report had one or more disturbances recorded 

on site. Of the 36 sites with salamanders, 31 (86%) of the sites 

had northerly facing aspects, and canopy closure ranged from 

0% to 100%. A mean of 68% canopy closure was reported at 

the original 18 occupied sites (Farber et al. 2001), but no mean 

is provided for canopy closure at the 36 sites (Farber 2007).

Finally, Bull et al. (2006) reported field surveys conducted on 92 known sites for the two salamander species (P. 

stormi, P. asupak) to document habitat elements, substrate, and 

disturbance. The majority of the sites (87%) were on private 

lands stewarded by Timber Products Company and Fruit 

Grower Supply Company, and the remaining sites were on 

federal lands. Of their 92 sites, their subsequent habitat data 

analyses were reported for the 68 sites where P. stormi were 

detected. Conifers dominated the basal area, but hardwoods 

were present and provided cover at 37 (54%) of the sites with 

detections. Percent of rock > 2.54 cm (1 in) covering > 50% 

of the plot was found at 35 sites (51.5%). Evidence of timber 

harvest (stumps) was observed at 31 sites (46%) and reported 

moderate (10-50%) and high (>50%) basal removal at 54% 

and 26% of these sites, respectively (Bull et al. 2006). Further, 

at 30 (44%) sites with animal detections there was at least 

50% soil disturbance.

The historically accepted view of these animals being tied 

to talus slopes in forested areas has been somewhat substantiated in several studies, but it remains unclear as to the obligatory reliance of salamanders on these habitats. The amount of 
6 Report Title

over-story canopy and its shade on the forest floor seem intuitive with the requirement of moisture and moisture retention 

by salamanders. However, there are reports that these organisms can exist at sites lacking over-story canopy and, in lieu 

of past disturbances, both manmade and naturally occurring. 

Collectively, a better understanding has developed that these 

species require moist habitat and adequate access to subterranean refugia. Climate, topography, and canopy therefore can 

act as surrogates for and affect microhabitat moisture. These 

characters in combination with talus and fissured substrate 

seem to provide optimal habitat for these species of salamanders.

In summary, several studies have found these salamanders to be associated with diverse habitat variables, including 

those indicative of older forest conditions, wet climatic conditions, rocky substrates, tree species (e.g., conifers or mixed 

forest), and topographic conditions (e.g., slopes). The relative 

importance of these various features appears complex and may 

not be easily resolved in a single set of factors to classify all 

sites across their ranges. If key site conditions favoring these 

salamanders include rocky substrates and cool, moist conditions, then salamanders may live at some sites with less influence from forest canopy conditions. For example, north-facing 

aspects, darker-illumination indices, and precipitation patterns are three additional factors that can play dominant roles 

in microsite conditions for salamanders (see discussions in 

Nauman and Olson 2004b, Nauman 2005, Welsh et al. 2007, 

Reilly et al. in press, Suzuki and Olson in press). 

Impacts to Habitat

The ranges of both P. stormi and P. asupak fall in the 

interior of the Klamath-Siskiyou Ecoregion where rocky substrates abound and cool, moist environmental conditions are 

found in the late fall and early spring (Clayton and Nauman 

2005, Mead et al. 2005, Welsh et al. 2007). Several disturbances may have effects on the habitats of both P. stormi and 

P. asupak. In particular, the region has a long history of mining 

(Orr and Orr 2000), timber harvesting (Jules et al. 1999), 

recreation, and road building that provides access for these 

activities to remote areas. Additionally, natural phenomena 

like wildfires (Frost and Sweeney 2000, Major 2005, Bury 

2005) alter habitat conditions and play a role in dictating biotic 

assemblages throughout the region. Here, we synthesize the 

limited body of literature on the effects various disturbances 

have on these species and their habitats. 

Timber Harvest and Silvicultural 

Practices

The most widespread ground-disturbing activity in the 

region is timber harvest (Bury and Pearl 1999). Due to the 

loss of overhead canopy from removal of trees and consequent 

increased exposure of occupied sites to altered microclimate 

regimes, timber harvesting has been implicated as the single 

greatest threat to these species (Nussbaum 1974, Blaustein et 

al. 1995, Petranka 1998, Bury and Welsh 2005). No study to 

date has experimentally addressed the effects of any timber 

harvest practices on P. stormi and P. aspuak. However, field 

research on the related P. elongatus suggests more salamanders in older than younger forests (Welsh 1990, Welsh and 

Lind 1992). Our understanding of the relationships of these 

animals to timber harvest now relies on retrospective studies 

of the species’ habitat relationships and occupancy of sites 

with various disturbance histories.

There are unpublished reports (Farber et al. 2001, Bull 

et al. 2006, Farber 2007) that document both P. stormi and P. 

asupak at areas with little natural canopy cover, or pre-canopy 

sites where past disturbance has removed the majority of or all 

of the overhead forest structure. These observational studies 

primarily represent habitats found on private and matrix lands 

in the Klamath River drainages. These habitats may not be 

representative of or are the most optimal for the species, and 

inferences should not be made about habitat use across the 

range of either salamander. There is unpublished evidence 

that P. stormi living in early seral stages of harvested forests 

have reduced body condition and skewed age distributions 

with higher proportions of animals as juveniles and sub-adults 

(Welsh et al. pers. comm., unpubl. data). They also report this 

to be a population structure to be indicative of sink (declining) 

populations. 

Occupancy (e.g., presence of few animals) at sites and 

the proportion of all life stages may be providing only a 

coarse estimator of influence of timber harvest effects on these 

animals. Effects of these disturbances may not be lethal to all 

members of a population, but may be seen in terms of their 

densities, survivorship, reproduction, or altered demographics. While demographic data for some retrospective case study 

sites are becoming known, they do not address the effect of 

the disturbance on the animals at the site. Related to this, 

detectability of salamanders can change with demography and 

survey method used across studies. Among available studies 

(cited above), survey methods were not similar. In particular, 

Ollivier et al. (2001) surveyed small plots, 7 x 7 m. It is possible that their effort most often resulted in detections at sites 

only with abundant salamander populations, and hence, their 

findings may reflect more optimal habitat associations. It is 

likely that P. stormi and P. asupak are relatively rare salamanders with patchy distributions across the landscape and 

therefore, relatively low detection rates should be expected. 

For example, Welsh et al. (pers. comm., unpublished data) 

compared P. stormi and P. elongatus and found the latter to be 

3.5 times more readily detected across all forest age classes 

than was P. stormi.

There are currently only two anecdotal studies that monitor sites for P. stormi in areas with timber harvest. Both were 

on north-facing slopes of Siskiyou Mountain ridges. Both 

produced very different observations of salamanders postharvest. One was a paired-plot survey, conducted by the U.S. 
Heading 1 7

Forest Service (D. Clayton pers. comm.) where they surveyed 

for salamanders in spring 1992 immediately following a forest 

clear cut in fall 1991. They found 40 salamanders in the first 

spring post-harvest (10 salamanders per person hour), one 

juvenile the following year, and then no animals for another 

eight years. In spring 2001, a juvenile was again found after a 

search by two field crews (D. Degross, personal experience). 

In the immediate vicinity, another timber harvest operation 

used helicopter yarding instead of cable yarding (employed 

at the previous harvest site) and activities were monitored by 

Fruit Growers Supply Company (Taylor 2007). As a condition 

of the California Endangered Species Act Biological Opinion, 

the project area was surveyed for P. stormi. They surveyed 

salamanders on 39 plots (35 harvested and 4 controls) prior to 

harvest, one year post-harvest, and again 10 years post-harvest. Counts of salamanders did not change significantly over 

each of three observation periods (Taylor 2007). While persistence of salamanders is documented for this study site, no 

detection probabilities for each plot were quantified, making 

conclusions about there being stable salamander populations 

uncertain.

A variety of published studies are available that examine 

various management impacts on the closely related P. elongatus. However, the range of P. elongatus covers a greater geographical area, diversity of habitats, and closer proximity to 

the Pacific Ocean than either P. asupak or P. stormi. Therefore, 

before making any inferences to P. stormi and P. asupak, one 

must consider that the effects of land-use practices may not be 

strongly correlated unless the study is from the more interior 

portion of the range of P. elongatus. With existing information on plethodontid salamander physiology, it is reasonable 

to believe that anthropogenic alterations to forest habitats in 

the drier interior of the Klamath-Siskiyou region would have 

more of a negative impact on P. stormi and P. asupak than it 

would have on P. elongatus closer to the Pacific Ocean that 

has milder conditions overall.

Evidence of P. elongatus across forest conditions and 

forest edges has been reported by several authors, but with 

variable results that are influenced by proximity of sites to 

the coast (Diller and Wallace 1994, Welsh and Lind 1995, 

Biek et al. 2002, Karraker and Welsh 2006). However, results 

from at least one of these studies indicated there were effects 

to individual’s body conditions (Karraker and Welsh 2006). 

Furthermore, Welsh and Lind (1995) demonstrated a significant relationship with high forest canopy (>80%) and numbers 

of Plethodons. Welsh and Lind (1995) show a habitat model 

where P. elongatus were highly correlated with conditions 

prevalent in old-growth forests that have the pre-requisite 

microclimates required by these salamanders. Other inferences 

suggest that site-specific microclimates would have the greatest influence on occupancy of salamanders, particularly in the 

interior of the species’ range (Diller and Wallace 1994, Welsh 

and Lind 1995, Biek et al. 2002). 

 In the Pacific Northwest, examination of microclimate modification of Douglas-fir forests after silvicultural 

practices suggests less optimal environmental conditions 

for both species of salamanders (Chen et al. 1993, Chen et 

al. 1995, Rykken et al. 2007). The relevance of these studies stems from the region-wide representation of this forest 

type, and it is a dominant forest component in lower elevation 

habitat zones of the Klamath-Siskiyou Ecoregion (Staus 2002) 

where many private timber lands reside. The effects on microclimate conditions are variable depending on the characteristic 

and the distance from the edge into the forested habitat (Chen 

et al. 1995). Landscape-scale characters play a pivotal role 

on the impacts that loss of canopy or a silvicultural edge may 

have on forested habitats. Latitude, aspect, and local weather 

patterns are all considerations when assessing the impact of 

edges on microclimates (Chen et al. 1995). 

 Species of the genus Plethodon rely on a specific 

set of environmental conditions in which they can be surface 

active to acquire greater food resources and find potential 

mates (Feder 1983). In direct correlation with the surface 

activity of these terrestrial salamanders, microclimate variables are temporally and spatially variable (Chen et al. 1999). 

South-facing slopes that are inhabited by P. stormi and P. 

asupak may only provide a limited period per year of suitable moist and thermally equable conditions for these species 

to carry out biological functions. Multivariate factors should 

be evaluated on a site-specific basis. For example, Welsh and 

Lind (1992) reported extremely high densities of P. elongatus

on a south-facing slope of old-growth Douglas-fir forest, but 

on an adjacent clear-cut that has been continuously sampled 20 

years post-harvest (since 1987), no animals have been detected 

since 2002, and the few that were previously found were 

mostly juveniles. Detections in the old-growth stand continue 

to remain high and represent all age classes of salamanders 

(Welsh, unpublished data).

Fire

 Fire regimes throughout the Klamath-Siskiyou Ecoregion are as variable as topography, species assemblages, and 

the climates present in the region. Wildfires in the region tend 

to burn in the late summer and early fall (Pilliod et al. 2003). 

This timeframe does not correspond with the surface activity 

of the terrestrial salamanders of the region, and therefore is 

assumed to not have direct impacts on salamander populations 

(Bury 2004). However, these events may have indirect effects 

on the salamanders. Large-scale wildfires and prescribed burning projects affect available wood resources and leaf litter for 

seasonal cover on the forest floor for salamanders. Further, 

removal of overhead canopy will decrease the ability of the 

forest to retain moisture until vegetation is re-established on 

site. Fire suppression practices of the past decades exacerbate 

the issue by allowing the accumulation of fuels on the forest 

floors (Bury et al. 2002, Major 2005). No study has been conducted to examine the effects of prescribed burning on these 

species, but the seasonal choice for these fuel management 

operations is the spring when there is remnant moisture still 

available in leaf litter and understory vegetation, helping con-
8 Report Title

trol the rate and behavior of the burn. The springtime practice 

of broadcast burning and even pile burning could have a direct 

effect on the salamander species based upon seasonal use of 

cover objects on the surface by these salamanders. However, 

no evidence is currently available to support this hypothesis. 

Mining and Other Ground Disturbing Practices

 The terrane stratigraphy of the Klamath Siskiyou 

exposes abundant mineral resources (Orr and Orr 2000). 

Evidence of abandoned mines near sites with P. stormi and P. 

asupak may suggest that mining activities have little adverse 

effect on salamanders. However, much of the Klamath River 

drainage in the vicinity of Seiad Valley and Happy Camp, 

California has been hydraulically mined, as evidence of tailings that now make up the majority of the banks of the river 

(D. Degross, personal observation). Much like road building 

or road cuts, mining removes and undermines the integrity of 

salamander habitat and then exposes the remaining underlying 

rock and talus of an area, creating exposure of the remaining 

substrate to the surface and reducing the complexity of the 

habitat (Nussbaum 1974, Diller and Wallace 1994). Several 

known sites of both of these salamanders are adjacent to mine 

or quarry sites, and many sites across both ranges lie in road 

cuts, but this is most likely a remnant of surveyor bias. 

Combined Risk Model

 Recently, the USDA Forest Service, USDI Bureau of 

Land Management, and the USDI Fish and Wildlife Service 

signed a conservation strategy for the northern populations of 

P. stormi. This strategy incorporated a risk assessment (Suzuki 

and Olson in press) to provide for conservation of this species within the Applegate River drainage, Oregon. This model 

used a habitat suitability model (Reilly et al. in press) as well 

as incorporation of 4 factors quantifying risk and 2 factor 

quantifying species persistence. Occurrence of P. stormi was 

positively correlated with the distribution of rocky substrates 

and negatively associated with June solar illumination, Oregon 

white oak and white fir trees. This model assisted in the location of key conservation areas for the salamander, and it will 

aid managers to delineate suitable sites to maintain the species 

across the landscape. 

Detection Probabilities/Occupancy

 The majority of studies on P. stormi and P. asupak 

have utilized either time constrained and/or area constrained 

survey techniques (Farber et al. 2001, Bull et al. 2006, Welsh 

et al. 2007, Nauman and Olson in press). These methods produce relative abundance estimates calculated from catch per 

unit effort (i.e., salamanders/ person hours or area). From these 

estimates, researchers calculate the proportion of an area occupied by the species based upon the proportion of sites with 

observations (Bailey et al. 2004). However, when comparing 

these results to those of other studies, or even the same study 

over different years, an assumption is made that the probability 

of detection is the same temporally and spatially. Understanding detection probabilities for each site, method, and year is 

needed to make more valid comparisons. 

Importantly, detection probability (i.e., animals are 

present) has been shown to vary with local habitat conditions 

(Bailey et al. 2004, Dodd and Dorazio 2004) to the extent 

that it can lead to flawed conclusions. It should be calculated 

in field studies of western Plethdontid salmanders (N. Chelgren et al. unpublished data). Further, within the range of P. 

stormi and P. asupak, the time window for optimal site conditions allowing for salamander surface activity and, therefore 

detection, is small and highly variable across their respective 

ranges. Aspect, forest type and seral stage, amount of available 

cover, and seasonal precipitation all influence site microhabitat 

conditions and the window of opportunity for detecting these 

terrestrial salamanders. As these characters change across the 

landscape, so do respective detection probabilities for sites. It 

is imperative from this point forth to account for differences in 

detection probabilities between areas when making comparisons of salamander occupancy and abundance. 

Compounding these probabilities is the patchy distribution of these species across the landscape and their variable densities at sites where they are found. The range-wide 

habitat correlate assessments for these species (Ollivier et al. 

2001, Welsh et al. 2007) are the only studies that randomly 

selected sites, and therefore can infer range wide patterns. 

These studies incorporated single-site visits using area-constrained searches to produce relative abundance estimates, 

and therefore were not able to produce detection probabilities. 

Mounting evidence demonstrates that single site visits grossly 

underestimate relative abundance values (Bailey et al. 2004). 

Hence, earlier findings (e.g., Ollivier et al. 2001, Welsh et 

al. 2007) are likely to be conservative perspectives of habitat 

conditions, perhaps where the more abundant populations of 

salamanders occur. Repeat sampling visits within a season 

alleviate the underestimates, but may be a challenge for both 

of these species due to their rare and patchy distribution across 

the landscape as well as the small window of optimal seasonal 

conditions for detection. 

Conclusions

Systematics 

The utilization of combined phylogenetic and morphometric analyses has produced substantial evidence for differentiating species in the Plethodon elongatus group. The limited 

degree of contact and consistent phylogenetic breaks observed 

from multiple analyses supports designation of at least three 
Heading 1 9

species. Still, the evolutionary processes acting upon these 

salamanders remain poorly understood and, therefore, more 

rigorous biogeographic analyses should help our understanding of these processes and may alter our interpretations. The 

conservation status of P. stormi and recent discovery of P. 

asupak have been instrumental in increasing the sampling and 

analyses across the range of both, but gaps in knowledge persist. Assessment of gene flow between P. asupak and the two 

other species, now that populations of each have been found 

adjacent to one another, seems integral in better understanding the evolutionary history and trajectory of the Plethodon 

elongatus Complex.

Habitat

 Rocky talus substrates with interstitial space appear 

to be an integral habitat characteristic for the presence of 

P. stormi and P. asupak in the interior of the Klamath Siskiyou Ecoregion. The ability for these salamanders to move 

vertically from the surface to subterranean refugia to avoid 

dessication appears to be provided by talus and fissured rock 

environments. The seasonally limited conditions for these 

organisms to be surface active can be enhanced by microhabitat, macrohabitat, and landscape conditions that act as 

surrogates or extend the period for moist climate. The development of models to predict occupancy of salamanders (Welsh 

et al. 2007, Reilly et al. in press, Suzuki and Olson in press) 

has greatly improved the ability to assess potential habitat 

and conservation strategies for P. stormi. The major variables 

of the models were based upon conditions found in lateseral forests and habitats which do not receive a lot of solar 

insolation throughout the year. These conditions invariably 

include aspect, solar incidence, closed canopies, larger DBH 

categories, and vegetative species (indicative of mesic conditions). Although in-depth physiological studies have yet to be 

conducted for P. stormi and P. asupak, the requirements of the 

species in the genus Plethodon are fairly restrictive, and rely 

primarily on available moisture. Habitat components of sites 

where these species occur may be variable, but the ability of 

a site to sustain population appears correlated to more mesic 

conditions.

 The role of specific forest types and seral stages as 

elements of salamander habitat may vary with local site conditions. The only analysis of habitat associations with presenceabsence data across both species ranges (primarily P. stormi) 

alluded to the strong role that landscape-level attributes, such 

as precipitation patterns and aspect, play in predicting habitat 

occupancy (Welsh et al. 2007). However, it is the microclimate 

conditions at occupied sites that appear to allow these species 

to spend more time on the surface seasonally, and likely persist 

as a thriving population. Some evidence suggests that these 

species are able to occupy a variety of habitats, forest types, 

and can withstand habitat disturbance (Farber et al. 2001, Bull 

et al. 2006, Farber 2007). However, these unpublished studies 

did not produce any gauge for changes in individual body condition, site specific population structure, or provide any baseline population data to compare their results. In many of these 

sites the disturbance footprint has been from tree harvesting, 

and no experimental study has rigorously inspected cause 

and effect responses of the practices to P. stormi or P. asupak

across their range. The amount of land allocated within the 

range of each species for timber practices is 24% (14% federal 

matrix lands and 10% private lands), but these allocations currently provide 36% of all known sites for these species (Bull et 

al. 2006). In general, these lands present better conditions for 

persistence of salamanders because they reside at lower elevations that receive more wet precipitation than higher elevation 

habitats (Nauman and Olson 2004b). 

The combination of variable habitats and greater occupancy of salamanders observed on these historically disturbed 

low-elevation habitats in private and matrix land allocations 

warrants further inspection south of the Siskiyou crest (in the 

ranges of P. asupak and southern populations of P. stormi). 

Risk analysis much like that of Suzuki and Olson (in press), 

for northern populations of P. stormi, would be useful to designate areas for conservation purposes. Further, we need more 

information to assess demographics and critically evaluate 

persistence of populations at sites and across the landscape. 

It will be a challenge to accomplish these goals because these 

species have secretive habits, and fossorial existence for much 

of the year. This leads to our current inability to quantify 

robust population estimates, and estimation of genetically 

effective population (Ne

) size. The majority of known sites for 

these species in California, are on private lands and in Northwest Forest Plan non-withdrawn federal lands (i.e., subject 

to timber harvest). If the goal is to conserve these species of 

salamanders, then identifying and protecting habitats known to 

support healthy populations of these animals across the region 

is needed.

Modeling Salamander Populations and Habitat

 Development of accepted conservation of these 

species and their habitat management is difficult due to these 

salamanders’ secretive habits, our inability to rigorously 

quantify population size, and their patchy distribution across 

the landscape. Models have recently been developed to aid 

in both these arduous tasks. The habitat suitability model by 

Reilly et al. (in press), and the combined risk model of Suzuki 

and Olson (in press) have provided useful tools for focusing 

conservation efforts of P. stormi and its potential habitat in the 

Applegate River drainage, Oregon. A similar model would 

greatly improve efforts for southern populations of P. stormi

and P. asupak. Additionally, detection probabilities and occupancy models have been developed for terrestrial salamanders 

to assess spatial and temporal variation in sampled populations. These calculations will be critical in assessing land 

management practices effects on populations, due to site complexity, population differences across the landscape, seasonal 

climatic differences, and many other variables researchers are 
10 Report Title

unable to control when rigorously evaluating population level 

changes and effects. 

 Acknowledgments

The paper was improved from comments provided by J. 

Bettaso, N. Chelgren, D. Clayton, D. Olson, R. Nauman, and 

H. Welsh. Support was provided by the US Fish and Wildlife 

Service, with assistance from the U.S. Geological Survey, and 

Oregon State University. 
Heading 1 11

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