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Untangling the Octopus Vulgaris Species Complex Using a Combined Genomic and Morphological Approach

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Untangling the Octopus Vulgaris Species Complex Using a Combined Genomic and Morphological Approach Untangling the Octopus vulgaris species complex using a combined genomic and morphological approach Michael Douglas Amor BSc (Hons) Submitted in total fulfilment of the requirements for the degree of Doctor of Philosophy Department of Ecology, Environment and Evolution School of Life Sciences La Trobe University, Victoria, Australia October, 2016 i Contents Untangling the Octopus vulgaris species complex using a combined genomic and morphological approach ................................................................................................................ i Contents...................................................................................................................................... ii Abstract ...................................................................................................................................... iv Statement of authorship ........................................................................................................... v Statement of co-authorship ...................................................................................................... v Statement of material included for the award of another degree .................................... viii Acknowledgements .................................................................................................................. ix 1. Introduction ........................................................................................................................... 1 1.1 Cryptic speciation ..................................................................................................... 1 1.2 Cryptic speciation among cephalopods ................................................................ 3 1.3 The Octopus vulgaris group .................................................................................... 4 1.4 Implications for unresolved taxonomy ................................................................... 9 1.5 Species tree inference .................................................................................................. 9 1.6 Recent advancements in sequencing technology .................................................. 11 1.7 Thesis overview ........................................................................................................... 13 2. Allopatric speciation within a cryptic species complex of Australasian octopuses .. 16 2.1 Abstract ......................................................................................................................... 16 2.2 Introduction ................................................................................................................... 17 2.3 Methods ......................................................................................................................... 21 2.3.1 Molecular methods ................................................................................................... 21 2.3.2 Morphological methods ........................................................................................... 24 2.4 Results ........................................................................................................................... 28 2.4.1 Molecular analyses .................................................................................................. 29 2.4.2 Morphological analyses ........................................................................................... 32 2.5 Discussion ..................................................................................................................... 36 2.6 Supplementary information ........................................................................................ 45 3. Morphological assessment of the Octopus vulgaris species complex evaluated in light of molecular-based phylogenetic inferences. ............................................................ 58 3.1 Abstract ......................................................................................................................... 58 3.2 Introduction ................................................................................................................... 59 3.3 Methods ......................................................................................................................... 63 3.3.1 Sampling .................................................................................................................... 63 3.3.2 Molecular analyses .................................................................................................. 66 3.3.3 Morphological analyses ........................................................................................... 67 3.3.4 Comparative analyses ............................................................................................. 69 ii 3.4 Results ........................................................................................................................... 70 3.4.1 Phylogenetic relationships ...................................................................................... 70 3.4.2 Morphological relationships .................................................................................... 72 3.5 Discussion ..................................................................................................................... 81 3.6 Supplementary information ........................................................................................ 87 4. Genome-wide sequencing uncovers cryptic diversity and mito-nuclear discordance in the Octopus vulgaris species complex. ........................................................................ 101 4.1 Abstract ....................................................................................................................... 101 4.2 Introduction ................................................................................................................. 102 4.3 Methods ....................................................................................................................... 106 4.4 Results ......................................................................................................................... 113 4.5 Discussion ................................................................................................................... 120 4.6 Supplementary information ...................................................................................... 126 5. Reconstructing the biogeographic history of speciation within the Octopus vulgaris species group. ....................................................................................................................... 132 5.1 Abstract ....................................................................................................................... 132 5.2 Introduction ................................................................................................................. 133 5.3 Methods ....................................................................................................................... 136 5.4 Results ......................................................................................................................... 143 5.5 Discussion ................................................................................................................... 150 5.6 Supplementary information ...................................................................................... 155 6. Discussion ......................................................................................................................... 157 6.1 Thesis overview ......................................................................................................... 157 6.2 Implications ................................................................................................................. 158 6.3 Limitations ................................................................................................................... 160 6.4 Future research .......................................................................................................... 161 6.5 Summary ..................................................................................................................... 165 7. References ........................................................................................................................ 166 iii Abstract Benthic octopuses (family Octopodidae) are a highly valuable global fisheries resource (worth >$US1/2 billion per annum). However, taxonomic relationships within the Octopodidae remain unresolved, which impedes their appropriate management. The type species of the genus Octopus, Octopus vulgaris, has historically been considered cosmopolitan. Recent studies, however, suggest O. vulgaris may represent a complex of morphologically similar, yet genetically distinct, species (the “Octopus vulgaris complex”). My thesis aims to investigate the species-level relationships within the O. vulgaris complex. In chapter two, I found congruence between morphological and mitochondrial DNA-based evidence, suggesting that allopatric populations of O. tetricus from the east and west coasts of Australia are distinct species. In addition, Asian O. vulgaris formed a monophyletic clade with both Australian species, which was distinct from other O. vulgaris populations. In chapters three and four, I investigate the species-level diversity within the O. vulgaris complex using unprecedented levels of morphological and genomic
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