title: Phylogenetic analysis of molluscan mitochondrial LSU rDNA sequences and secondary structures.
abstract: Mollusks are an extraordinarily diverse group of animals with an estimated 200,000 species, second only to the phylum Arthropoda. We conducted a comparative analysis of complete mitochondrial ribosomal large subunit sequences (LSU) of a chiton, two bivalves, six gastropods, and a cephalopod. In addition, we determined secondary structure models for each of them. Comparative analyses of nucleotide variation revealed substantial length variation among the taxa, with stylommatophoran gastropods possessing the shortest lengths. Phylogenetic analyses of the nucleotide sequence data supported the monophyly of Albinaria, Euhadra herklotsi + Cepaea nemoralis, Stylommatophora, Cerithioidea, and when only transversions are included, the Bivalvia. The phylogenetic limits of the mitochondrial LSU rRNA gene within mollusks appear to be up to 400 million years, although this estimate will have to be tested further with additional taxa. Our most novel finding was the discovery of phylogenetic signal in the secondary structure of rRNA of mollusks. The absence of entire stem/loop structures in Domains II, III, and V can be viewed as three shared derived characters uniting the stylommatophoran gastropods. The absence of the aforementioned stem/loop structure explains much of the observed length variation of the mitochondrial LSU rRNA found within mollusks. The distribution of these unique secondary structure characters within mollusks should be examined.
authors.affiliation: Biodiversity and Systematics, University of Alabama, Tuscaloosa, Alabama 35487, USA.
authors.forename: C
authors.initials: C
authors.lastname: Lydeard
authors.forename: W E
authors.initials: WE
authors.lastname: Holznagel
authors.forename: M N
authors.initials: MN
authors.lastname: Schnare
authors.forename: R R
authors.initials: RR
authors.lastname: Gutell
mesh_terms: D000818:Animals; D001482:Base Composition; D001483:Base Sequence; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification; D004272:DNA, Mitochondrial / Q000737:chemistry / Q000235:genetics*; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015394:Molecular Structure; D008974:Mollusca / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D012335:RNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D004272:DNA, Mitochondrial; D004275:DNA, Ribosomal; D012335:RNA, Ribosomal; D004247:DNA