title: Phylogenetic utility, and variability in structure and content, of complete mitochondrial genomes among genetic lineages of the Hawaiian anchialine shrimp Halocaridina rubra Holthuis 1963 (Atyidae:Decapoda).
abstract: The Atyidae are caridean shrimp possessing hair-like setae on their claws and are important contributors to ecological services in tropical and temperate fresh and brackish water ecosystems. Complete mitochondrial genomes have only been reported from five of the 449 species in the family, thus limiting understanding of mitochondrial genome evolution and the phylogenetic utility of complete mitochondrial sequences in the Atyidae. Here, comparative analyses of complete mitochondrial genomes from eight genetic lineages of Halocaridina rubra, an atyid endemic to the anchialine ecosystem of the Hawaiian Archipelago, are presented. Although gene number, order, and orientation were syntenic among genomes, three regions were identified and further quantified where conservation was substantially lower: (1) high length and sequence variability in the tRNA-Lys and tRNA-Asp intergenic region; (2) a 317-bp insertion between the NAD6 and CytB genes confined to a single lineage and representing a partial duplication of CytB; and (3) the putative control region. Phylogenetic analyses utilizing complete mitochondrial sequences provided new insights into relationships among the H. rubra genetic lineages, with the topology of one clade correlating to the geologic sequence of the islands. However, deeper nodes in the phylogeny lacked bootstrap support. Overall, our results from H. rubra suggest intra-specific mitochondrial genomic diversity could be underestimated across the Metazoa since the vast majority of complete genomes are from just a single individual of a species.
authors.affiliation: a Department of Biological Sciences and Molette Laboratory for Climate Change and Environmental Studies , Auburn University , Auburn , AL , USA .|b Department of Microbiology , University of Alabama at Birmingham , Birmingham , AL , USA , and.
authors.forename: Joshua L
authors.initials: JL
authors.lastname: Justice
authors.affiliation: a Department of Biological Sciences and Molette Laboratory for Climate Change and Environmental Studies , Auburn University , Auburn , AL , USA .|c Department of Biological and Environmental Sciences , Georgia College and State University , Milledgeville , GA , USA.
authors.forename: David A
authors.initials: DA
authors.lastname: Weese
authors.affiliation: a Department of Biological Sciences and Molette Laboratory for Climate Change and Environmental Studies , Auburn University , Auburn , AL , USA .
authors.forename: Scott Ross
authors.initials: SR
authors.lastname: Santos
mesh_terms: D000818:Animals; D033364:Decapoda / Q000145:classification / Q000235:genetics*; D017753:Ecosystem; D019143:Evolution, Molecular; D054629:Genome, Mitochondrial / Q000235:genetics*; D006254:Hawaii; D010802:Phylogeny; D012343:RNA, Transfer / Q000235:genetics; D020080:Tandem Repeat Sequences / Q000235:genetics
chemical_list: D012343:RNA, Transfer
keywords: Control region; duplication; hypervariable; phylogeography; tandem repeat