High genetic diversity among fossorial lizard populations (Anniella pulchra) in a rapidly developing landscape (Central California)

California is a biodiversity hotspot facing unbridled human population growth, especially in Central California. One of the poorly known, sensitive species in this area is the California legless lizard (Anniella pulchra), a fossorial worm-like reptile. We report mt and nuDNA sequences from 69 museum-vouchered samples of Anniella (A. pulchra and its sister species A. geronimensis) from 48 localities. Our genetic survey reveals substantially more genetic diversity within A. pulchra than previously reported. Our two independently evolving markers (mt and nuDNA) reveal five major lineages of A. pulchra. Two of the five major lineages of A. pulchra correspond to a north-south split found in other widespread California reptiles. These northern and southern clades also correspond to a previous study showing variation in chromosomal number. Unlike most other Californian reptiles, A. pulchra has major genetic lineages that are endemic to Central California including two that are endemic to the San Joaquin Valley and Carrizo Plain. Although A. pulchra is threatened throughout its range, the distinct San Joaquin lineages are seriously imperiled by urban sprawl. Some of the localities for the newly recognized genetic lineages have already been destroyed by development.