San Diego Management & Monitoring Program


High-throughput sequencing reveals distinct regional genetic structure among remaining populations of an endangered salt marsh plant in California

Type: journal article

Article abstract: Conservation of rare species requires careful consideration to both preserve locally adapted traits and maintain genetic diversity, as species’ ranges fuctuate in response to a changing climate and habitat loss. Salt marsh systems in California have been highly modifed and many salt marsh obligate species have undergone range reductions and habitat loss with concomitant losses of genetic diversity and connectivity. Remaining salt marshes are threatened by rising sea levels, and so these habitats will likely require active restoration and re-establishment eforts. This study aims to provide a reference point for the current status of genetic diversity and range-wide population structure of a federally and state listed endangered plant, salt marsh bird’s-beak (Chloropyron maritimum subsp. maritimum) that can inform future preservation and restoration eforts. We used historical data and current monitoring information to locate and sample all known occurrences throughout the range of this subspecies in southern California, and three additional occurrences from Baja California, Mexico. We used fow cytometry and single nucleotide polymorphic markers (SNPs), generated by double-digest restriction-site associated DNA sequencing (ddRAD), to assess relative ploidy, and estimate genetic diversity and population structure across the region. Overall, we found fve distinct genetic clusters that coincide with geographic regions. Genetic diversity was greatest in the southern part of the range including Baja California and San Diego. These fndings can bolster management and restoration eforts by identifying potentially isolated occurrences and areas that are the richest sources of allelic diversity, and by providing insight into the amount of genetic diferentiation across the taxon’s range.

Authors: Milano, Elizabeth; Mulligan, Margaret; Rebman, Jon; Vandergast, Amy;

Journal title: Conservation Genetics

Year: 2020

Keywords: Chloropyon maritimum; genetic diversity; population structure; Rare plant; rare plants; Salt Marsh bird's beak;

Species: Salt marsh bird's-beak

Vegetation communities: salt marsh