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Population Genetics and Evolutionary History of Some Deep-Sea Demersal Fishes from the Azores-North Atlantic

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Population Genetics and Evolutionary History of Some Deep-Sea Demersal Fishes from the Azores-North Atlantic University of Southampton Research Repository ePrints Soton Copyright © and Moral Rights for this thesis are retained by the author and/or other copyright owners. A copy can be downloaded for personal non-commercial research or study, without prior permission or charge. This thesis cannot be reproduced or quoted extensively from without first obtaining permission in writing from the copyright holder/s. The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the copyright holders. When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given e.g. AUTHOR (year of submission) "Full thesis title", University of Southampton, name of the University School or Department, PhD Thesis, pagination http://eprints.soton.ac.uk UNIVERSITY OF SOUTHAMPTON School of Ocean and Earth Sciences POPULATION GENETICS AND EVOLUTIONARY HISTORY OF SOME DEEP- SEA DEMERSAL FISHES FROM THE AZORES - NORTH ATLANTIC by Maria Ana Aboim Thesis submitted as part of the requirements for the awarding of the degree of Doctor of Philosophy March 2005 i Graduate School of the Southampton Oceanography Centre This PhD dissertation by Maria Ana Aboim has been produced under the supervision of the following persons Supervisors: Doctor Alex Rogers Doctor Gui Menezes Professor Paul Tyler Chair of Advisory Panel: Professor Alan Kemp Member of Advisory Panel: Professor John Shepherd ii DECLARATION OF AUTHORSHIP I, Maria Ana Couto Pinto Aboim , declare that the thesis entitled Population genetics and evolutionary history of some deep-sea demersal fishes from the Azores – North Atlantic and the work presented in it are my own. I confirm that: this work was done wholly or mainly while in candidature for a research degree at this University; where any part of this thesis has previously been submitted for a degree or any other qualification at this University or any other institution, this has been clearly stated; where I have consulted the published work of others, this is always clearly attributed; where I have quoted from the work of others, the source is always given. With the exception of such quotations, this thesis is entirely my own work; I have acknowledged all main sources of help; where the thesis is based on work done by myself jointly with others, I have made clear exactly what was done by others and what I have contributed myself; parts of this work have been published as: - Aboim MA, Menezes GM, Schlitt T and Rogers AD (2005) Genetic strucutre and history of populations of the deep-sea fish Helicolenus dactylopterus (Delaroche, 1809) inferred from mtDNA sequence analysis. Molecular Ecology , 14 , 1343-1354. - Aboim MA, Rogers AD, Menezes GM, Maggioni R and Pearson CVM (2003) Isolation of polymorphic microsatellite markers for the demersal fish Helicolenus dactylopterus (Dela Roche 1809). Molecular Ecology Notes . 3,18-20. Signed: ……………………………………………………………………….. Date:……………………………………………………………………………. iii UNIVERSITY OF SOUTHAMPTON FACULTY OF SCIENCE SCHOOL OF OCEAN AND EARTH SCIENCE Doctor of Philosophy POPULATION GENETICS AND EVOLUTIONARY HISTORY OF SOME DEEP-SEA DEMERSAL FISHES FROM THE AZORES -NORTH ATLANTIC by Maria Ana Aboim ABSTRACT MtDNA sequences and microsatellite loci were used as independent molecular markers to reveal the genetic population structure in three deep-sea demersal fish species from the North Atlantic. In the Azores archipelago, the demersal fishery is the second most important after tuna and Helicolenus dactylopterus , Beryx splendens and Beryx decadactylus are among the most captured species. Partial sequences for the mitochondrial control region and cytochrome b gene were obtained for the three species using universal primers. The diversity encountered for these markers is consistent with diversity found on other marine fishes, except for B.decadactylus in which the d-loop and cyt b diversity was lower than expected. Haplotype data indicated a strong genetic differentiation between Helicolenus dactylopterus NW, Cape Verde and NE Atlantic populations suggesting long distance colonisation processes by jump dispersal events along major oceanic currents. Eight microsatellite loci were developed for H.dactylopterus in order to resolve population structure at a finer intraregional scale (within Portuguese waters). Significant deviations from allelic frequencies expected under Hardy-Weinberg equilibrium were detected at several loci. Analysis of F IS revealed significant differences from zero as a result of heterozygote deficiency. Estimates of F ST , R ST and AMOVA were also significant, suggesting that the population structure of this species within Portuguese waters was not homogeneous. 2 Pairwise comparisons of F ST , R ST and genetic distances (D SW and ( σ) ) between populations revealed a significant separation of the Azores and Peniche (continental Portugal) populations as well as a moderate differentiation among subpopulations of the Azores archipelago . Beryx splendens and Beryx decadactylus are two congeneric species with many similarities in known biology. Analysis of haplotype data revealed striking differences in structure and history of the populations of these two species. MtDNA sequences confirmed that Beryx splendens is constituted by one panmitic population within the Northeast Atlantic as has been previously hypothesised by other authors. Surprisingly, indices of genetic diversity were lower in the closely-related B.decadactylus and there was a strong genetic differentiation between Cape Verde and the rest of the NE Atlantic populations when analysed for the same molecular markers. Differences found are discussed based on the limited knowledge of these species especially with respect to life- history. Population structure results are discussed in relation to historical and on-going hydro- geographic events. Evidence for the strong influence of several events previous to the last glacial maximum (LGM) on the population demographic history and evolution of deep-sea demersal fish species in the North Atlantic was found. iv “Animals living in…the sea waters… are protected from the destruction of theirs species by man. Their multiplication is so rapid and their means of evading pursuit or traps are so great, that there is no likelihood of his being able to destroy the entire species of any of these animals.” Lamarck (19 th century) “…Probably all the great sea-fisheries, are inexhaustible; that is to say nothing we do seriously affects the number of fish. And any attempt to regulate these fisheries seems consequently… to be useless.” Thomas Huxley “70% of world’s fishery resources are in deep trouble and world’s fisheries cannot be sustained for much more without severe appliance of new management laws. In spite of some management policies have been put in practice since 1993, 35% of stocks show declining yields, 25% are flat and 40% are still developing and there’s no space for growth in landings.” FAO (1997) “ It’s difficult to reach the deep-sea and follow the organisms that live there. So, we went to the deep of the cells to find the place where life since the beginning is recorded.” Anonymous v ACKNOWLEDGEMENTS I would like to thank to all the people and institutions that somehow were involved in this work: To my supervisor Dr.Alex Rogers for introducing me to the amazing field of genetics and for guiding me troughout 5 years of research. To Dr. Gui Menezes for teaching me and let me know one of the most amazing places in the world, the Azores archipelago. To Prof.Paul Tyler, for the patience and for taking me under his wing. To all the people that were part of the “Molecular Ecology Group” at SOC, it was wonderfull to work with you all and learn how to investigate as a team. Special thanks to Cath and Rodrigo, my guides in profession and in life too. To people in Norman’s lab for the advices and exchange of knowledge. Very gratefull and fulfilling. To Mark Dixon first of all for the Sequencing and GeneScanning facilities and also for all the time, pacience and advices troughout the process. To the r/v Arquipélago’s tripulation, research team and other inhabitants of the Azores archipelago for the best times of this project, and for teaching me everything I know about the sea, what it means to work in marine science and the porpose of all this work. Thank you for the humanity lessons as well. Thank you to all my friends and family (including adoptive ones as well) for taking care of me, for giving me the psicological support that making a thesis implies, and for the help in so many different ways. Gratefully you are too many to put on a list! Maria and Andreia thank you for showing me some other paths biologists can chose or take, so I could continue on this one. André thank you for the art work. Finally, I would like to thank FCT (Fundação para a Ciência e Tecnologia) for supporting this work and make it possible by awarding me with the PhD Fellowship (SFRH/BD/1122/2000). This work as also been partially funded by the European Comission DGXIV/C/1 as study contract 97/081 “Seasonal changes in biological and ecological traits of demersal and deep-water fish species in the Azores”. vi CONTENTS Abstract iv Acknowledgements vi Contents vii List of Tables x List of Figures xi PART I – INTRODUCTION 1 1.INTRODUCTION AND GENERAL BACKGROUND 2 1.1 The Deep-sea 2 1.2 Deep-sea resources and exploitation 4 1.2.1 Deep-sea biodiversity 4 1.2.2 Deep-sea fisheries 5 1.3 Fisheries Management
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