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Genetic Biodiversity of the European Barnacle Chthamalus Montagui

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Genetic Biodiversity of the European Barnacle Chthamalus Montagui University of Plymouth PEARL https://pearl.plymouth.ac.uk 04 University of Plymouth Research Theses 01 Research Theses Main Collection 2009 GENETIC BIODIVERSITY OF THE EUROPEAN BARNACLE CHTHAMALUS MONTAGUI FONTANI, SONIA http://hdl.handle.net/10026.1/2733 University of Plymouth All content in PEARL is protected by copyright law. Author manuscripts are made available in accordance with publisher policies. Please cite only the published version using the details provided on the item record or document. In the absence of an open licence (e.g. Creative Commons), permissions for further reuse of content should be sought from the publisher or author. GENETIC BIODIVERSITY OF THE EUROPEAN BARNACLE CHTHAMALUS MONTAGUI by SONIA FONTANI A thesis submitted to the University of Plymouth in partial fulfilment for the degree of DOCTOR OF PHILOSOPHY School of Biological Science Faculty of Sciences In collaboration with Marine Biological Association of the UK, Plymouth ENEA - Marine Environment Research Centre S. Teresa, Italy June 2009 SONIA FONTANI GENETIC BIODIVERSITY OF THE EUROPEAN BARNACLE CHTHAMALUS MONTAGUI Abstract Biodiversity ultimately is genetic diversity. Genetic diversity within species is eroded before negative trends in biodiversity become evident as loss of species or habitats. Hence, monitoring biodiversity at the genetic level may indicate what will happen at higher levels of organisation if the trend is allowed to continue. There is a pervasive belief that marine ecosystems are less vulnerable to biodiversity loss than terrestrial ones, due to marine species' high dispersal ability and connectivity, large geographic ranges, low genetic differentiation among populations and high genetic variation within populations. Many studies offer compelling evidence that it is not so: loss of genetic variation due to natural and anthropogenic factors has been detected even in marine species with potentially high dispersal. In this context the genetic pattern of the European barnacle Chthama/us montagui, a species with high dispersal capability, was investigated from three different perspectives using polymorphic microsatellite loci as molecular markers. The effect of structures created to protect coastal areas in the Adriatic Sea, was investigated to test the hypothesis that artificial substrates can act as "corridors" facilitating gene flow among previously isolated populations. The genetic pattern of central populations was compared to that of peripheral/marginal populations over the range of C. montagui in the UK, to test the hypothesis that marginal and peripheral populations tend to be less genetically variable than central ones. For both studies results were consistent with the formulated hypotheses at the 3 analysed loci. Finally, a broader survey of the NE Atlantic and Mediterranean range of this barnacle was carried out to assess spatial scales of genetic variation. A clear differentiation between Atlantic and Mediterranean samples was detected; however, the major source of genetic variation was within sites at a very small spatial scale. The information gained generates insights for marine genetic management and conservation planning. 1 List of Contents Chapter 1 - General Introduction ......................................................... 11 1.1 The context of the project ............................................................. 12 1.2 Genetic biodiversity ...................................................................... 13 1.2.1 Marine genetic biodiversity ...................................................... 18 1.2.2 Human factors influencing marine genetic biodiversity ................ 22 1.3 Molecular techniques and markers .................................................. 26 1. 3.1 Allozymes .............................................................................. 29 1.3.2 DNA fingerprinting ............... ~ .................................................. 30 1.3.3 DNA sequencing ..................................................................... 35 Chapter 2 - Barnacle biology, systematics and genetics, with particular reference to Chthama/us montagui ....................................................... 37 2.1 Taxonomy of Chthamalus montagui ................................................ 38 2.2 External morphology ..................................................................... 39 2.3 Distribution .................................................................................41 2.4 Reproduction, settlement and recruitment ...................................... .43 2.5 Growth and longevity ....................................................................47 2.6 Genetic approaches to taxonomy and phylogeny of barnacles ........... .48 2.6.1 Markers for taxonomy and phylogeny of barnacles ...................... 50 2. 7 Population genetics of barnacles ..................................................... 51 2. 7.1 Markers for population genetics of barnacles .............................. 55 Chapter 3- Materials and methods ...................................................... 56 3.1 Fieldwork ................................................................ , ................... 59 3.2 Laboratory work ........................................................................... 60 3.2.1 DNA extraction .......................................................................60 3.2.2 Microsatellite markers ............................................................. 62 3.2.3 PCR reaction, DNA sequencing and fragment analysis ................. 62 3.3 Genetic data analysis ....................................................................65 Chapter 4 - The influence of habitat corridors generated by artificial substrates on the genetic pattern of Chthamalus montagui ..................... 73 4.1 Introduction and specific alms ........................................................ 74 4.2 Materials and methods ..................................................................79 4.3 Results ........................................................................................85 4.4 Discussion ...................................................................................99 Chapter 5 - Effects of marginality and peripherality on the genetic variability of Chthamalus montagui ................................................................... 105 5.1 Introduction and specific aims ...................................................... 106 5.2 Materials and methods ................................................................ 110 5.3 Results ...................................................................................... 117 5.4 Discussion ................................................................................. 133 Chapter 6 - Spatial scales of genetic variation in Chthama/us montagui .. 139 6.1 Introduction and specific aims ...................................................... 140 6.2 Materials and methods ................................................................ 145 6.3 Results ...................................................................................... 151 6.4 Discussion ................................................................................. 171 Chapter 7 - Final Discussion .............................................................. 178 Appendices ..................................................................................... 186 Reference List ................................................................................. 215 2 List of Tables Table 3.1 - Microsatellite loci with core repeats, primer sequences, optimal annealing temperature {TA), GeneBank accession number (from Pannacciulli et al., 2005) .............................................................. 62 Table 3.2: Master Mix employing Qiagen HotStar Taq DNA Polymerase and Q solution ...................................................................................63 Table 3.3: Master Mix employing JumpStart Taq DNA Polymerase (Sigma) . .................................................................................................63 Table 3.4:Main software employed in the genetic data analysis ............... 65 Table 4.1 - Sampling location, site used in the genetic analysis, abbreviation, geographical coordinates and type of substratum ......... 82 Table 4.2 - Summary of genetic variability per sites at each microsatellite locus and all loci: number of sampled individuals (N), number of observed alleles per locus (NA); allelic richness based on 25 individuals (A); Nel's 1987 unbiased expected heterozygosity (HE); observed heterozygosity (H0 ); Weir and Cockerham's (1984) estimate of Wright's (1951) fixation index (F15). F1s values in bold indicate significant departures from HWE after standard Bonferroni correction. For site abbreviations see Table 4.1. .......................................................... 90 Table 4.3 - Test for Hardy-Weinberg equilibrium {F15, Weir and Cockerham, 1984) using Fisher's method, estimation of exact probability values (P- value) by a Markov-chain randomization ......................................... 92 Table 4.4 - Tests for linkage disequilibrium in each location and for each locus pair, estimation of exact probability values (P-value) and standard error (S.E.) determined by a Markov-chain randomization (1,000,000 dememorlzations, 1,000 batches and 50,000 iterations per batch). Significant P-values in bold ........................................................... 93 Table 4.5 - F-statistics (Weir and Cockerham's,
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