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Genetic threats to the integrity and persistence of endangered species can be significant and develop rapidly. These threats include the breakdown of locally adapted gene pools, and more extreme phenomena such as the dissolution of species boundaries. Anthropogenic homogenization of the landscape is often the underlying cause, manifested as an increase in biotic connectivity, and a decrease in structural and spatial habitat heterogeneity. In southern California, the narrowly endemic San Diego fairy shrimp Branchinecta sandiegonensis is federally endangered due to high levels of vernal pool habitat loss. Human disturbance is associated with the increased presence of the widely distributed generalist B. lindahli in the native range of B. sandiegonensis. Regional sympatry for these closely related species has now become local co-occurrence in anthropogenically created basins and disturbed pools, with possible hybridization. To assess this threat, we developed a new morphological hybrid index that ranges from 1.0 for typical B. lindahli adult females to 3.0 for typical B. sandiegonensis. Index scores in undisturbed habitats that are typical for each “pure” species are 1.3 and 2.6 respectively. In disturbed areas, females have a wider range of intermediate scores. Using mitochondrial DNA markers that are diagnostic to each species, we also determined that putative hybrids at all mixed sites share their maternal lineage with the more common species at the site. We hypothesize that anthropogenic activities have increased genetic, taxonomic and functional homogenization in southern California’s vernal pools, and may constitute a significant threat to the species integrity and persistence of the San Diego fairy shrimp.

journal of crustacean biology

Landscape homogenization threatens the genetic integrity of the endangered San Diego fairy shrimp Branchinecta sandiegonensis (Branchiopoda: Anostraca)