Phylogenetic relationships and introduction history inferred from complete mitochondrial genomes of four smelts (Osmeridae) of the modern San Francisco Estuary

Abstract

We announce complete mitogenomes of four smelts (Osmeridae) of the San Francisco Estuary (SFE): endemic Hypomesus transpacificus, native H. pretiosus and Spirinchus thaleichthys, and non-native H. nipponensis. The genomes each contained 13 protein coding, 2 ribosomal RNA and 22 transfer RNA genes, a control region (D-loop), and a putative origin of replication of the light strand (OL); gene order followed other osmerids. Total genomes were 16,767 base-pairs (bp) for H. transpacificus; 16,672bp for H. pretiosus; 16,811bp for S. thaleichthys; and 16,779bp for H. nipponensis. GC content was from 47.8% (S. thaleichthys) to 49.4% (H. pretiosus). Phylogenetic analyses of mitogenomes placed H. transpacificus sequences within the H. pretiosus [Oregon + SFE] clade and most closely related to H. pretiosus [SFE], whereas affinities of derivative cytochrome b sequences supported a Lake Suwa origin for SFE H. nipponensis.