Comparison of mitochondrial and nuclear genetic variation of common Acartia species in the San Francisco Estuary

Delineation of Acartia spp. is essential to assess the biodiversity of copepods in marine ecosystems. Previous phylogenetic analyses show lack of monophyly for A.tonsa and A.hudsonica. Reported average DNA sequence divergence among some Acartia spp. includes >16% for mitochondrial cytochrome oxidase c (COI) and 13%-25% for 18S rRNA. We investigated the genetic diversity of SFE Acartia in comparison to other Acartia spp. sequences from Genbank. Copepods were collected from the SFE across a range of temperatures and salinities and sequenced at COI and nuclear 18S loci for Bayesian phylogenetic comparison. We found £23% COI divergence and >35% 18S divergence among paired comparisons of A. tonsa, A. hudsonica and A. californiensis. Acartia hudsonica SFE haplotypes clustered more closely with northeast Pacific coast (-25% COI divergence) than with northeast Atlantic (-30% divergence) samples. Acartia californiensis from SFE showed <13% divergence in comparison with Genbank haplotypes. SFE and Atlantic coast A. tonsa were -15% 18S and 31-33% COI divergent. These results support high sequence divergence among Acartia species. Further analysis of additional loci is needed to understand the phylogenetic and population structure of SFE Acartia species relative to other populations.