Range-wide and local drivers of genetic structure in an endangered California vernal pool endemic crustacean

Abstract

Phylogeographic and landscape genetic structure were studied for the endangered vernal pool tadpole shrimp (Lepidurus packardi) with the goal of identifying genetic units below the species level and understanding local patterns of gene flow. A portion of the mitochondrial cytochrome c oxidase I (COI) gene was sequenced from 208 individuals from throughout the range of the species (26 sites). The COI gene indicated the presence of five distinct clades or lineages within L. packardi. A majority of these clades were found in the southern portion of the species’ range. Sequence divergence between these clades was exceptionally high and historical demographic analysis did not indicate any changes in female effective population sizes. The divergent clades represent a pattern that is observed in other notostracan species. The presence of a single clade with a wide geographic distribution (northern portion of the study) suggests this area has experienced historical/recent gene flow, and is in contrast to the southern portion of the species range where divergent clades lie in close geographic proximity to one another. Amplified fragment length polymorphisms (AFLPs) and COI sequence data of 125 individuals samples from 14 pools revealed a pattern of isolation by distance across a 17 km span. The significant isolation by distance pattern suggests equilibrium processes override non-equilibrium processes (strong founder effects) at smaller geographic scales. These results suggest greater conservation attention to the southern portion of the species range (San Joaquin Valley) and the continuance of management practices that may assist in mitigating migration at local scales.