Gwilliam Michael
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Assessing the role of the Benguela Current as a major biogeographic barrier to marine coastal fishes. Michael Gwilliam A thesis submitted to Aberystwyth University in partial fulfilment for the degree of Doctor of Philosophy. Institute of Biological, Environmental and Rural Sciences Aberystwyth University 2016 Declaration Word Count of thesis: 55,923 This work has not previously been accepted in substance for any degree and is not being concurrently submitted in candidature for any degree. Candidate name MICHAEL GWILLIAM Signature: Date 25/12/2016 STATEMENT 1 This thesis is the result of my own investigations, except where otherwise stated. Where *correction services have been used, the extent and nature of the correction is clearly marked in a footnote(s). Other sources are acknowledged by footnotes giving explicit references. A bibliography is appended. Signature: Date 25/12/2016 [*this refers to the extent to which the text has been corrected by others] STATEMENT 2 I hereby give consent for my thesis, if accepted, to be available for photocopying and for inter-library loan, and for the title and summary to be made available to outside organisations. Signature: Date 25/12/2016 2 Acknowledgements I would like to thank first and foremost my Supervisor Professor Paul Shaw and Dr Niall McKeown. They have both been of exceptional help in writing this thesis in what at times were not ideal circumstances for me. Additionally they have ensured I haven’t gone too far off the academic rails over the last few years. I would also like to thank the help of my colleagues in the Shaw Lab namely Dr Max Blake (soon to be Dr) and Amy Rainbow Unicorn Moonchild Healey for all their help and discussions during the last few years. In particular I would like to acknowledge their help over the last couple of days to ensure submission of this thesis! Our (retired) lab assistant Alun Evans has also been of great help in ensuring the smooth operation of the laboratory work and a great source of advice in where to find and get things done in Aber! I would also like to thank my colleague Dr Hayley Watson for all her help and advice, particularly for initially showing me and Max how to genotype microsatellites (admittedly after being bribed with a bottle of rosé). My Colleagues in South Africa Dr Warren Potts and Alex Winkler have been integral to this project and to whom (along with their colleagues) I would have none of my southern African samples. I would also like to recognise Dr Olgac Guven for collecting my Turkey outgroup samples which have proved invaluable in subsequent analyses. Many thanks also to Sean Roche and the ‘Celtic Spirit’ for attaining our Aberystwyth samples of Black Seabream. My parents have also been of immense help the last couple of years and somewhat integral in ensuring I kept with the PhD to get it submitted! My Friends and family have also been of great help in keeping me motivated. Many Thanks to you all! 3 Dedicated to my late friend Torin Lakeman. Abstract Contemporary biodiversity has been shaped by interactions between intrinsic characters of organisms and extrinsic environmental features that often cannot be reliably predicted. Regions where many species boundaries coincide represent intriguing systems to disentangle factors underpinning eco-evolutionary divergence with relevance to the understanding of how species may respond to climate change. Such regions often harbour complex patterns of inter- and intra-specific biodiversity that are taxonomically challenging. The Benguela cold upwelling system (BCS) has emerged as a major biogeographic barrier promoting and maintaining differences between the Atlantic Ocean and Indo-Pacific Ocean coastal fauna. This research assessed nuclear and mitochondrial DNA variation and applying population genetic and phylogeographic analytical frameworks assessed divergence across the BCS in a number of coastal Sea Bream species (Sparidae). In conjunction with available morphological and ecological data, the results support species level divergence across the BCS in what were previously regarded as conspecific populations in both Spondyliosoma and Diplodus cervinus / hottentotus and direct taxonomic rearrangement. The data also support the potential inadequacy of mtDNA COI barcoding for species discovery in the region due to variable interspecific coalescent depths. Lithognathus mormyrus and Sarpa salpa revealed similar phylogeographic patterns with (1) distinct African and Atlantic / Mediterranean and (2) divergence across the BCS. Phylogenetic analysis supported the ancestral status of African clades and the potential of an Angolan glacial refuge. A salient feature of the results was the signature of historical and largely asymmetric gene flow across the BCS from South Africa to Angola. This episodic permeability has implications for unexpected species’ responses to climate change which are discussed. Collectively, this study provides new insights into the dynamic role of the BCS in shaping marine biodiversity in both the Atlantic and Indo-Pacific regions. 5 Contents Declaration ................................................................................................... 2 Acknowledgements ...................................................................................... 3 Abstract ........................................................................................................ 5 Chapter 1: Introduction ............................................................................ 9 1.1 Introduction ........................................................................................................... 9 1.2 Molecular genetic markers ................................................................................... 9 1.2.1 Microsatellites ................................................................................................ 10 1.2.2 Microsatellite models of evolution ................................................................. 11 1.2.3 mtDNA ........................................................................................................... 11 1.3 Population structure of marine organisms ....................................................... 12 1.3.1 Landscape genetics and phylogeography ....................................................... 13 1.3.2 Applying terrestrial population genetics concepts to the sea ......................... 14 1.3.3 Case Study: Mediterranean Sea ...................................................................... 16 1.3.4 Life history strategies ..................................................................................... 18 1.3.5 Life history characteristics: Sex change ......................................................... 19 1.3.6 Speciation in marine systems ......................................................................... 21 1.3.7 Speciation in the sea ....................................................................................... 22 1.4 The study system: the Benguela Current .......................................................... 23 1.5 Overall project structure and aims ................................................................... 31 1.5.1 Key issues and questions to be resolved ......................................................... 32 Chapter 2: Genetic evidence for cryptic speciation across marine biogeographic boundaries in the Sparid genus Spondyliosoma. ................................................ 34 2.1 Introduction ......................................................................................................... 34 2.1.1 Study species - Spondyliosoma spp. ............................................................... 35 2.1.2 Aims and objectives. ....................................................................................... 39 2.2 Methods ................................................................................................................ 40 2.2.1 Sampling and DNA extraction ....................................................................... 40 2.2.2 Mitochondrial DNA markers .......................................................................... 42 2.2.3 mtDNA data analysis ...................................................................................... 42 2.2.4 Demographic analyses .................................................................................... 44 2.2.5 Microsatellite DNA markers .......................................................................... 45 2.2.6 Microsatellite analysis .................................................................................... 48 2.2.7 Power Analysis ............................................................................................... 49 2.3 Results .................................................................................................................. 51 2.3.1 Mitochondrial DNA diversity ......................................................................... 51 2.3.2 Phylogenetics .................................................................................................. 53 2.3.3 mtDNA population structuring ....................................................................... 64 2.3.4 Demographic tests .......................................................................................... 66 2.3.5 Nuclear Microsatellite DNA diversity and structuring .................................. 67 6 2.3.6 Power Analysis ............................................................................................... 73 2.4