24 
PROCEEDINGS OF THE CALIFORNIA ACADEMY OF SCIENCES 
Series 4, Volume 64, Supplement 1 
lar taxonomic group. Early records of bats and other vertebrates generally were reported in the 
literature from field collections; later from observations or net/release, and not from collected spec¬ 
imens. Some invertebrates were collected using pitfall traps with or without bait. 
There has been no organized sampling of groundwater fauna in California. Instead, ground- 
water fauna have been opportunistically discovered during other aquatic sampling programs, either 
for stream bioassessment or for cave bioinventories. These sampling programs employed kick nets 
during benthic sampling or harvest by hand net when visually detected. Nevertheless, these meth¬ 
ods have uncovered a unique and diverse assemblage of macrocrustaceans, primarily amphipods 
and isopods. Meanwhile, microcrustaceans remain largely undocumented, except for bathynel- 
laceans discovered while sorting benthic grab samples. When modem sampling techniques are 
employed and groundwater habitats are systematically sampled in California, a similarly diverse 
microcmstacean fauna probably will be found. 
Our collective data were maintained in computer documents as species lists, cave lists, and 
bibliographies. In 2009, G.O. Graening created the Kryptos database in Microsoft Access®. Kryp- 
tos is a privately owned relational database with data primarily on California’s subterranean 
species, locations, and occurrences, including field collections, observations, and literature records. 
Other tables cover taxonomists and literature. Kryptos was developed further with William R. 
Elliott and others, and queries were designed to generate summary tables for this paper. The data 
in this monograph are dated December 16, 2016. 
Biodiversity, how diverse the species are in a defined area, may be measured in different ways. 
We were interested in examining biodiversity in California caves by using a multivariate metric 
including troblobite endemism, which we knew to be high in many caves. We calculated a biodi¬ 
versity score, B, a composite value of several statistics of interest, as done by Elliott (2007). We 
examined the number of species (species richness or SR) per site, the number of troglomorphic 
species per site (T), and troglobite endemism, e (troglomorphic species with limited distribution) 
per site. The value e is the reciprocal of the number of known sites for an obligate cave species, 
e.g., 1/5 sites = 0.20. We also calculated SE, “site endemism,” that is the sum of e per site. = SR 
x T x SE was used to rank 38 top caves in descending order. In all 38 cases SE was > 0. We trun¬ 
cated the final dataset to the top 20 caves because SR fell below 12 after 20 caves, and we thought 
that insufficient sampling could be a problem in the caves with low SR. B 2 , a similar measure of 
biodiversity, was calculated as SR x T x SST (SST is the number of single-site troglomorphic 
species in the cave). 
Linear regression analysis and statistical tests were performed in the Excel® spreadsheet pro¬ 
gram of Bj vs. cave elevation, SR vs. cave depth, and T vs. cave depth. 
For this paper and beyond, Elliott developed a geographic information system (GIS) using 
QGIS (Quantum GIS), a free, open-source, multi-platform computer program that uses many for¬ 
mats and tools to build maps for publication. Attribute tables and geotiffs were drawn from Kryp¬ 
tos and many online sources: California Polytechnical University/Pomona, California Department 
of Conservation, Caltrans GIS Data, Free California GeoTIFF Maps, Geospatial Innovation Facil¬ 
ity at University of Califomia/Berkeley, State of California Geoportal, University of California/ 
Davis, USDA Forest Service Geodata, USGS National Geologic Map Database, and USGS Nation¬ 
al Map small scale. Point, polyline, and polygon shapefiles were developed as layers in the GIS. 
Researchers needing assistance with data and GIS layers may contact G.O. Graening through The 
Subterranean Institute at http://www.subinstitute.org/California/index.html or graening@csus.edu. 
Many taxonomists were enlisted in identifying species and describing new species, and we 
have listed them in Acknowledgments. Most of the collections eventually were deposited in these 
museums: American Museum of Natural History, New York; California Academy of Sciences, San 
