title: Molecular phylogenetics of a South Pacific sap beetle species complex (Carpophilus spp., Coleoptera: Nitidulidae).
abstract: Several species of sap beetles in the genus Carpophilus are minor pests of fresh produce and stored products, and are frequently intercepted in biosecurity operations. In the South Pacific region, the superficially similar species C. maculatus and C. oculatus are frequently encountered in these situations. Three subspecies of C. oculatus have been described, and the complex of these four taxa has led to inaccurate identification and questions regarding the validity of these taxa. A molecular phylogenetic study using the mitochondrial gene cytochrome c oxidase I (COI) and two nuclear markers comprising the rDNA internal transcribed spacer 2 (ITS2) and the D1-D2 region of the large (28S) ribosomal RNA subunit showed that C. maculatus, and C. o. cheesmani were easily differentiated from the two other subspecies of C. oculatus. COI also showed differentiation between C. o. gilloglyi and C. o. oculatus, but this was not shown when third codon positions were removed and when RY-coding analyses were conducted. Generalised mixed Yule-Coalescent (GMYC) models were fitted to trees estimated from the COI data and were analysed using a multimodel approach to consider the evidence for three taxonomic groupings of the C. oculatus group. While the arrangement with the highest cumulative weight was not the arrangement ultimately accepted, the accepted taxonomy also had an acceptable level of support. ITS2 showed structure within C. oculatus, however C. o. oculatus was resolved as paraphyletic with respect to C. o. gilloglyi. COI showed evidence of sequence saturation and did not adequately resolve higher relationships between species represented in the dataset. 28S resolved higher relationships, but did not perform well at the species level. This study supports the validity of C. maculatus as a separate species, and provides sufficient evidence to raise C. o. cheesmani to the level of species. This study also shows significant structure within and between C. o. gilloglyi and C. o. oculatus, giving an indication of recent speciation events occurring. To highlight the interesting biology between these two taxa, C. o. gilloglyi is retained as a subspecies of C. oculatus. These results give clarity regarding the taxonomic status of C. maculatus and the subspecies of C. oculatus and provide a platform for future systematic research on Carpophilus.
authors.affiliation: Bio-Protection Research Centre, PO Box 84, Lincoln University, Lincoln 7647, Canterbury, New Zealand. sam.brown@lincoln.ac.nz
authors.forename: Samuel D J
authors.initials: SD
authors.lastname: Brown
authors.forename: Karen F
authors.initials: KF
authors.lastname: Armstrong
authors.forename: Robert H
authors.initials: RH
authors.lastname: Cruickshank
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D002467:Cell Nucleus / Q000235:genetics; D001517:Coleoptera / Q000145:classification* / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000235:genetics; D049810:Genetic Speciation; D016013:Likelihood Functions; D008957:Models, Genetic; D010802:Phylogeny; D012339:RNA, Ribosomal, 28S / Q000235:genetics; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D004272:DNA, Mitochondrial; D021903:DNA, Ribosomal Spacer; D012339:RNA, Ribosomal, 28S