An assessment of aquatic amphibian biodiversity on the California Lost Coast

Figures & data

Figure 1. Study area maps. Left: Distribution of Dicamptodon spp. observations between San Francisco and the California-Oregon border reported on iNaturalist as of January 17, 2022. The study area corresponds to the gap in coastal observations outlined in black. Right: Survey sites included in this study (n = 29).

Table 1. List of species included in survey with the number of sites where each species was detected based on visual encounter surveys (VES) or eDNA sampling (eDNA).

Common name	Scientific name	VES	eDNA	# bp sequences	longest sequence
Northwestern pond turtle^a	Actinemys marmorata	1	x	x	x
Northwestern salamander	Ambystoma gracile	1	0	56	1,525
Toad^b	Anaxyrus sp.	5	3
Western toad	A. boreas			466	3,870
Yosemite toad	A. canorus			129	2,852
Black toad	A. exsul			21	2,433
Amargosa toad	A. nelsoni			12	2,450
Black salamander	Aneides flavipunctatus	9	0	2,100	201,973
Wandering salamander	Aneides vagrans	1	0	30	1,069
Tailed frog	Ascaphus truei	5	1	386	17,790
Giant Salamander^b	Dicamptodon sp.	20	17
Idaho giant salamander	D. aterrimus			151	172,643
California giant salamander	D. ensata			200	2,372
Coastal giant salamander	D. tenebrosus			165	2,710
Bullfrog	Lithobates catesbeianus	0	0	552,292	21,245,044
Pacific chorus frog	Pseudacris regilla	2	0	48,494	68,155
Northern red-legged frog	Rana aurora	2	1	74	2,402
Foothill yellow-legged frog	Rana boylii	10	5	214	2,011
Southern Torrent Salamander	Rhyacotriton variegatus	1	0	123	216,063
Rough-skinned newt	Taricha granulosa	3	0	69	205,000,000
Red-bellied newt	Taricha rivularis	0	2	115	16,310

Last two columns indicate for each species the number of base pair sequences and longest sequence cataloged in GenBank (https://www.ncbi.nlm.nih.gov/nuccore) as of February 2022.

^aPond turtles were not included in the eDNA survey.

^bResults from analysis of eDNA samples did not resolve toads (Anaxyrus) or giant salamanders (Dicamptodon) to s single species. Possible matches are listed under each heading. Species with species ranges overlapping the survey area are indicated in bold. Note that D. tenebrosus was not indicated by the lab as a possible match.

Figure 2. Estimated stream occupancy and upper 95% confidence limit of four most commonly observed aquatic amphibian species in the King Range National Conservation Area, California.

Table 2. Comparison table for occupancy and detection models of the four most commonly observed species in the King Range National Conservation Area; foothill yellow-legged frog, coastal/California giant salamander, western toad, and black salamander.

Model	nPars	AIC	AICc
Foothill yellow-legged frog
best	7	82.73	86.3
detection.null	3	90.58	91.2
occupancy.null	6	90.31	92.9
global	12	86.90	103.4
Giant salamander
best	6	86.3	88.9
occupancy.null	4	95.12	96.2
global	12	92.62	103.2
Western toad
best	6	46.65	49.2
occupancy.null	4	56.14	57.3
detection.null	4	56.54	57.7
global	12	56.39	67
Black salamander
best	6	63.92	66.5
detection.null	4	65.77	66.9
global	11	65.43	74.3
occupancy.null	5	73.95	75.7

Variables included in the best models are presented in Table 3. Variables included in the global detection models included: survey length, average canopy cover, and percent coverage by medium substrate coverage for all species, survey type for all species except black salamanders, percent coverage by boulders for foothill yellow legged frogs and giant salamanders, and percent coverage by large substrates for western toads and black salamanders. Variables included in the global occupancy model included: length of stream surveyed, slope, canopy coverage, and percent coverage by fine and medium substrates for all species; and percent coverage by large substrates for foothill yellow legged frogs, giant salamanders and black salamanders, and percent coverage by boulders for western toads.

Table 3. Most supported occupancy and detection models for the four most commonly observed species in the King Range National Conservation Area; foothill yellow-legged frog, coastal/California giant salamander, western toad, and black salamander.

Species	Variables included	Influence	z	P(>|z|)
Foothill yellow-legged frog
Detection model	survey type	VES > eDNA	–1.63	0.102
	surveyed distance	positive	1.78	0.076
	% medium substrate	negative	–2.11	0.035
	% boulders	negative	–2.97	0.003
Occupancy model	average canopy cover	negative	2.46	0.014
Giant salamander
Detection model	surveyed distance	positive	1.01	0.312
	average canopy cover	positive	4.84	<0.001
	% boulders	positive	2.1	0.036
Occupancy model	% sandy substrate	negative	–1.66	0.097
Western toad
Detection model	survey type	eDNA > VES	1.39	0.164
	average canopy cover	negative	–0.299	0.003
Occupancy model	Slope	negative	–0.927	0.354
	% fine substrate	positive	0.597	0.550
Black salamander
Detection model	Survey type	VES > eDNA^a	x	x
	% medium substrate	negative	–2.36	0.018
	% large substrate	negative	–2.5	0.0126
Occupancy model	Surveyed distance	positive	1.27	0.202
	Average canopy cover	positive	1.47	0.141

Data availability

All data used in this study available upon request to the authors.