Spatial Analysis of Plague in California - Recent Advances and Issues in Environmental Science - page 120

collected in the Modoc plateau, eastern Mojave, or Colorado Desert bioregions during
the surveillance period.
We identifi ed a total of 166 unique locations for positive rodent samples (Figure
2a). The California ground squirrel ( Spermophillus beecheyi ) was the rodent species
with the largest total number of specimens (12,546; Table 1) and number of posi-
tive specimens (559; Table 1), representing 105 of these unique geocoded locations.
Because California ground squirrels are a key indicator species for plague epizootics
[36] and human disease risk in California [10], we also ran models for this subset of
data only.

Table 1. Number of total samples and positive samples for the rodent species most commonly
collected during plague surveillance in California.

Species Common Name Total samples Positive

samples

Prevalence
(proportion seropositive)

Spermophilus beecheyi California ground squirrel 12546 559 0.045

Tomias senex Shadow chipmunk 2701 174 0.064

Golden-mantled ground
squirrel

Spermophilus lateralis 2685 19 0.007

Peromyscus maniculatus Deer mouse 1776 20 0.011

Neotoma fuscipes Dusky-footed woodrat 1622 10 0.006

Yellow-pine chipmunk 1014 58 0.057

Tamias a moe nus

Tamias speciosus Lodgepole chipmunk 658 43 0.065

Tamiasciurus douglasii Douglas' squirrel 475 44 0.093

Spermophilus beldingi Belding's ground squirrel 408 21 0.051

Tamias quadrimaculatus Long-eared chipmunk 400 16 0.040

Neotoma lepida Desert woodrat 307 2 0.007

Tamias merriami Merriam's chipmunk 277 18 0.065

Neotoma cinerea Bushy-tailed woodrat 186 6 0.032

Peromyscus boylii Brush mouse 117 2 0.017

Peromyscus truei Pinon Mouse 108 0 0.000

T amias minim us Least chipmunk 96 2 0.021

Peromyscus crinitus Canon mouse 82 1 0.012

Glaucomys sabrinus Northern Flying squirrel 71 0 0.000

Total 25529 995 0.039

Only records of positive rodents were included for niche modeling, as negative
samples (Figure 2b) were frequently obtained from areas that had also yielded posi-
tive samples, or from which too few specimens had been collected to be considered
representative. The 3,788 sampling events had yielded negative samples, but 2,296 of
these were at locations where positive samples had also been collected. Of the remain-
ing 1,492 sampling events, only fi ve locations had been sampled more than 20 times,
which we estimated as the minimum number of samples that would need to be taken
to confi rm a location as a true absence.