Molecular phylogeny of the panpulmonate groups Stylommatophora and Hygrophila

The phylogenetic relationships at the base of the stylommatophoran land snails and slugs have proven to be controversial, particularly the position of the Scolodontidae in relation to other stylommatophoran taxa. Likewise, the phylogenetic relationships within the hygrophilan freshwater snails and limpets are uncertain. This study provides molecular phylogenies for the Stylommatophora and Hygrophila at multiple scales including deep phylogenetic relationships of the major stylommatophoran and hygrophilan clades and family level relationships within the Orthurethra and Lymnaeoidea. In chapter 3, four standard markers: almost the full-length large subunit (LSU) rRNA gene (also incorporating part of the 5.8S gene), almost the full-length small subunit (SSU) rRNA gene, part of the histone three (H3) gene and the 1st and 2nd codon positions of the CO1 gene were used with the aim of resolving the basal divisions within the Stylommatophora and evaluating the phylogenetic utility of these markers. The deep phylogenetic relationships at the base of the Stylommatophora are now clearly resolved. The Scolodontidae are shown categorically to be the sister group to all other stylommatophoran taxa with robust support and with all phylogeny reconstruction methods. Based on this result, a taxonomic revision for the basal groups within the Stylommatophora has been proposed by reclassifying the ‘achatinoid’ and ‘non-achatinoid’ clades at a lower rank than the Scolodontina in order to properly reflect the deep-level relationships within the Stylommatophora. The original LSU 1-5 fragment used extensively in studies of the Stylommatophora is found to be the most informative gene fragment among the genes used in this study. Expanding the length of the LSU gene and combining it with other genes is necessary to fully resolve the relationships within the Stylommatophora, particularly those at the base of the clade. The family-group interrelationships within the Orthurethra were examined in chapter 4 using the ribosomal (r) RNA gene cluster [including part of the 5.8S gene, the complete ITS-2 region, and almost the full-length large subunit (LSU; 28S) gene]. There is robust support for the basal division between the Chondrinidae and the rest of the Orthurethra in our tree. Likewise, the monophyly of the Chondrinidae, Cerastidae, Vertiginidae, Achatinellidae and Partulidae is well supported while the Pupillidae, Enidae, and Valloniidae are not recovered as monophyletic groups in our orthurethran tree. Although there is relatively little support for the deep-level relationships among the main orthurethran groups, some groupings are strongly supported. The validity of the families and subfamilies within the Hygrophila was investigated in chapter 5 using the ribosomal (r) RNA gene cluster [including part of the 5.8S gene, the complete ITS-2 region, and almost the full-length large subunit (LSU; 28S) gene]. This study provides the most comprehensive sampling of the Hygrophila clade to date. The principle division of the Hygrophila into two monophyletic groups (the Chilinoidea and Lymnaeoidea) is robustly supported in our tree. The Acroloxidae, Lymnaeidae and Physidae are fully supported as monophyletic families. However, the Planorbidae are not supported as a monophyletic group due to the clustering of Bulinidae within the family. The subfamilies Amphipepleinae within the Lymnaeidae and both the Planorbinae and Ancylinae within the Planorbidae are strongly supported as monophyletic groups while the Aplexinae and Physinae within the Physidae and the Lymnaeinae within the Lymnaeidae are not recovered as monophyletic subfamilies. Based on the results of this study, a taxonomic revision for the hygrophilan families has been suggested by either retaining the Bulinidae as a family but reclassify the Ancylinae as a family outside the Planorbidae consistent with previous classifications or lowering the Bulinidae to subfamilial rank alongside the Ancylinae within the family Planorbidae. The interrelationships among the lymnaeoidean families (Acroloxidae, Bulinidae, Burnupiidae, Lymnaeidae, Physidae and Planorbidae) are reasonably well resolved in chapter 5 using a single standard marker, though they are not fully supported. Therefore, to better resolve these relationships we have undertaken a more detailed phylogenetic analyses in chapter 6 using four standard molecular markers [LSU (incorporating 5.8S), SSU, H3 and 1st and 2nd codon positions of the CO1gene] for a representative taxa from the main hygrophilan groups within a framework of the Panpulmonata combined with a phylogenomic analysis based on transcriptome sequences data for a representative from each of the main lymnaeoidean families (Acroloxidae, Lymnaeidae, Physidae and Planorbidae). The observed interrelationships among the lymnaeoidean families based on the four standard markers are consistent with those obtained in chapter 5, but surprisingly support for the major division decreases raising uncertainty about the topology. However, the problematic interrelationships between the lymnaeoidean families are well resolved in our phylogenomic analysis, with the Acroloxidae recovered as the sister group to a clade comprising the Lymnaeidae, Physidae and Planorbidae, the Physidae recovered as the sister group of a cluster comprising the Lymnaeidae and Planorbidae, and the Lymnaeidae and Planorbidae recovered as sister taxa