Phylogenomics of the pulmonate land snails
AuthorTeasdale, Luisa Cinzia
AffiliationSchool of BioSciences
MetadataShow full item record
Document TypePhD thesis
Access StatusThis item is embargoed and will be available on 2019-03-20. This item is currently available to University of Melbourne staff and students only, login required.
© 2017 Dr. Luisa Cinzia Teasdale
The pulmonates are the most speciose gastropod lineage and are highly diverse in morphological form and habitat. The evolutionary relationships among the pulmonates have remained controversial despite a long history of scientific study. Recent molecular studies have placed traditionally pulmonate (air-breathing) and non-pulmonate taxa into Panpulmonata; however, the relationships within this new group are still poorly understood. Incongruence between molecular studies has generally resulted from a lack of informative loci but the advent of next generation sequencing technologies means it is now feasible to produce large genetic datasets for non-model organisms. The main aim of my thesis was to investigate the timing and pattern of evolutionary relationships within the Panpulmonata, at multiple taxonomic scales, using phylogenomic datasets. The qualification of orthology is a significant challenge when developing large, multi-locus datasets for phylogenetics from transcriptome assemblies. In Chapter 2, I identified 500 orthologous single-copy genes from 21 transcriptome assemblies across the Eupulmonata (mostly terrestrial land snails and slugs) using a thorough approach to orthology determination, involving manual alignment curation and gene tree assessment. I further qualified orthology by sequencing the genes from the genomic DNA of 22 representatives of the Australian land snail family Camaenidae using exon capture. Through comparison, I also found that automated orthology determination approaches can be susceptible to transcriptome assembly errors. I then used the orthologous genes identified in Chapter 2 to investigate the pattern and timing of evolution across Panpulmonata in Chapter 3. My dataset included representatives of all major clades within Panpulmonata including a wide representation of the stylommatophoran land snails, the most successful lineage of terrestrial molluscs. Maximum likelihood and Bayesian analyses confirm that Panpulmonata is monophyletic, and that Pulmonata is not monophyletic, implying that air-breathing has likely evolved more than once. Within Panpulmonata I show strong support for relationships previously unsupported or weakly supported in molecular analyses, including the Geophila, and the Pylopulmonata, a clade that unites the operculate panpulmonates. Molecular dating suggests a Permian or Early Triassic origin for Panpulmonata and a Triassic/Jurassic boundary origin for Eupulmonata and the freshwater Hygrophila. In addition to investigating deep relationships within Panpulmonata, I used a similar approach to investigate phylogenetic relationships on a shallower scale within a land snail family, the Rhytididae. Australia has the highest taxonomic diversity of the Rhytididae, a carnivorous family of land snails with a Gondwanan distribution. Previous higher classifications of the Australian Rhytididae are based on limited morphological characters and have not been assessed with molecular evidence. I present a molecular phylogeny of the Australian Rhytididae based on a large multi-locus dataset comprising nuclear exons sequenced using exon capture. I identified four major monophyletic lineages within the Australian Rhytididae. I also show that there is a high amount of unrecognised diversity, particularly in the smaller rhytidids. Contrary to shell morphology, on which the current taxonomy is based, a number of currently recognised genera are either polyphyletic or paraphyletic. The Australian lineages all resulted from an apparent pulse of diversification approx. 45-30 Ma. Given the South African Nata and the New Zealand Delos and Schizoglossa also belong to this clade, this date suggests that cross-water dispersal has played a role in the evolution of this group.
Keywordsphylogenomics; Pulmonata; Panpulmonata; Stylommatophora; phylogenetics; orthology; exon capture
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