title: Curious bivalves: Systematic utility and unusual properties of anomalodesmatan mitochondrial genomes.
abstract: Mitogenomic trees for Bivalvia have proved problematic in the past, but several highly divergent lineages were missing from these analyses and increased representation of these groups may yet improve resolution. Here, we add seven new sequences from the Anomalodesmata and one unidentified semelid species (Bryopa lata, Euciroa cf. queenslandica, Laternula elliptica, Laternula truncata, Lyonsia norwegica, Myadora brevis, Tropidomya abbreviata, "Abra" sp.). We show that relationships in a mitogenomic tree for the Class are improved by the addition of seven anomalodesmatans from this highly divergent clade, but are still not completely consistent with relationships recovered in studies of nuclear genes. We suggest that some anomalous relationships (for instance the non-monophyly of Bivalvia) may be partially explained by compositional heterogeneity in the mitogenome and suggest that the addition of more taxa may help resolve both this effect and possible instances of long branch attraction. We also identify several curious features about anomalodesmatan mitogenomes. For example, many protein-coding gene boundaries are poorly defined in marine bivalves, but particularly so in anomalodesmatans, primarily due to non-conserved boundary sequences. The use of transcriptomic and genomic data together enabled better definition of gene boundaries, the identification of possible pseudogenes and suggests that most genes are translated monocistronically, which contrasts with many other studies. We also identified a possible case of gene duplication of ND5 in Myadora brevis (Myochamidae). Mitogenome size in the Anomalodesmata ranges from very small compact molecules, with the smallest for Laternula elliptica (Laternulidae) only 14,622bp, to Bryopa lata (Clavagellidae) which is at least 31,969bp long and may be >40,000bp. Finally, sampled species show a high degree of sequence divergence and variable gene order, although intraspecific variation in Laternula elliptica is very low.
authors.affiliation: Natural History Museum, Cromwell Rd, London SW7 5BD, United Kingdom. Electronic address: s.williams@nhm.ac.uk.
authors.forename: S T
authors.initials: ST
authors.lastname: Williams
authors.affiliation: Natural History Museum, Cromwell Rd, London SW7 5BD, United Kingdom.
authors.forename: P G
authors.initials: PG
authors.lastname: Foster
authors.affiliation: Natural History Museum, Cromwell Rd, London SW7 5BD, United Kingdom.
authors.forename: C
authors.initials: C
authors.lastname: Hughes
authors.affiliation: Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EQ, United Kingdom.
authors.forename: E M
authors.initials: EM
authors.lastname: Harper
authors.affiliation: Natural History Museum, Cromwell Rd, London SW7 5BD, United Kingdom.
authors.forename: J D
authors.initials: JD
authors.lastname: Taylor
authors.affiliation: Natural History Museum, Cromwell Rd, London SW7 5BD, United Kingdom.
authors.forename: D T J
authors.initials: DTJ
authors.lastname: Littlewood
authors.affiliation: Natural History Museum, Cromwell Rd, London SW7 5BD, United Kingdom.
authors.forename: P
authors.initials: P
authors.lastname: Dyal
authors.affiliation: Natural History Museum, Cromwell Rd, London SW7 5BD, United Kingdom; Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, United Kingdom(1).
authors.forename: K P
authors.initials: KP
authors.lastname: Hopkins
authors.affiliation: Natural History Museum, Cromwell Rd, London SW7 5BD, United Kingdom.
authors.forename: A G
authors.initials: AG
authors.lastname: Briscoe
mesh_terms: D000596:Amino Acids / Q000235:genetics; D000818:Animals; D049872:Bivalvia / Q000235:genetics*; D003062:Codon / Q000235:genetics; D020440:Gene Duplication; D023061:Gene Order; D054629:Genome, Mitochondrial; D023281:Genomics; D010802:Phylogeny; D014176:Protein Biosynthesis; D011544:Pseudogenes / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics; D016415:Sequence Alignment
chemical_list: D000596:Amino Acids; D003062:Codon; D012343:RNA, Transfer
keywords: Bivalve; Enrichment; Gene boundaries; Mitochondrial genome; Pseudogenes; Systematics