Molecular genetic studies on species and population structure of North Atlantic redfish (genus Sebastes; Cuvier 1829) [Elektronische Ressource] / vorgelegt von Cathrin Schmidt

Schmidt Francis

Informations

• Publié par: universitat_hamburg
• Publié le: 01 janvier 2005
• Nombre de lectures: 14
• Langue: English
• Poids de l'ouvrage: 5 Mo

Extrait

MOLECULAR GENETIC STUDIES
ON SPECIES AND POPULATION STRUCTURE OF
NORTH ATLANTIC REDFISH
(GENUS SEBASTES; CUVIER 1829)

















Dissertation

zur Erlangung des Doktorgrades des Fachbereiches Biologie
der Universität Hamburg

vorgelegt von

Cathrin Schmidt


Hamburg 2005































Genehmigt vom
Fachbereich Biologie der
Universität Hamburg
auf Antrag von Professor Dr. A. TEMMING
Weiterer Gutachter der Dissertation :
Professor Dr. R. HANEL
Tag Disputation: 17. Juni 2005der
den 02. Juni 2005Hamburg,
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Professor Dr. Arno Frühwald
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University of Harrburg.
St. JohnProf. Dr. Michael
Researchfor Marine and Climate Vice Director, Center
Scienceand Fisheries Institute for Hydrobiology
of HarnburgUniversity
Olbersweg24
22767 Hamburg
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[phone]Tel
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email michael. stj ohn @uni-hamburg.de































TABLE OF CONTENTS

TABLE OF CONTENTS I-V
SUMMARY 1
GENERAL INTRODUCTION 4
An introduction to redfish5
The genus Sebastes (Cuvier 1829)
Distribution and habitat of North Atlantic Sebastes
Life history and reproduction6
Species structure and species identification of North Atlantic Sebastes 6
Intermediate individuals and hybridisation8
Population structure of commercially exploited redfish in the Irminger Sea and adjacent
waters 9
Molecular markers 12
Polymerase chain reaction (PCR) 12
Mitochondrial DNA (mtDNA)13
Microsatellites14
Amplified fragment length polymorphism (AFLP)16
Aims and outline 18

CHAPTER 1
SPECIES STRUCTURE AND PHYLOGENETIC RELATIONSHIPS AMONG NORTH ATLANTIC
REDFISH (GENUS SEBASTES; CUVIER 1829) BASED ON MITOCHONDRIAL NADH
DEHYDROGENASE SUBUNIT 3 DNA SEQUENCE DATA 21
1. Abstract 23
2. Introduction 24
3. Material and methods 26
3.1 Sample collection 26
3.2 Sample analysis29
3.2.1 DNA extraction29
3.2.2 DNA quantitation29
3.2.3 In vitro amplification of the mitochondrial ND3 gene by polymerase chain
reaction (PCR) using universal primers29
3.2.4 Gel electrophoresis31
3.2.5 Cycle sequencing of PCR products 31
3.2.6 Analysis of the sequencing reactions on an automated sequencer 32
3.2.7 Cloning of PCR products32
I3.2.8 Sequencing of plasmid vectors 35
3.2.9 Construction of redfish specific ND3 primers35
3.2.10 Optimising PCR conditions for the newly designed primers GLY-Red-New
and ARG-Red-New36
3.2.11 Sequencing of PCR products using the newly developed redfish specific
primers GLY-Red-New and ARG-Red-New 36
3.3 Data analysis 37
3.3.1 Sequence alignment37
3.3.2 Sequence composition and variation37
3.3.3 Site saturation38
3.3.4 Phylogenetic tree reconstruction38
3.3.5 AMOVA (analysis of molecular variance) and Φ statistics 45 ST
4. Results 46
4.1 Sequence composition and diversity 46
4.2 Haplotype frequencies and distribution55
4.3 Phylogenetic analysis58
4.4 AMOVA (analysis of molecular variance) and Φ66ST
5. Discussion 67
5.1 Sequence evolution and substitution analysis 67
5.2 Phylogeny, species structure and the evolutionary history of North Atlantic
Sebastes 70
5.3 Patterns of haplotype distribution75
5.3.1 S. marinus on the Flemish Cap – a case of interspecific introgression of
mitochondrial DNA?75
5.3.2 "Giant" S. marinus - another example of ancient introgression events within
North Atlantic Sebastes?79
5.3.3 S. marinus on the shelves of Greenland and Iceland comprises genetically
different mitochondrial lineages 82
5.3.4 Haplotype distribution in the "deep-sea" and "oceanic" type of S. mentella – an
indication of population structure?84
5.4. Divergence times in North Atlantic Sebastes evolution – an approximate time frame
86
6. General conclusions and perspectives 88
Appendix I 90
Appendix II 94
Appendix III 95 IICHAPTER 2
GENETIC SPECIES AND POPULATION STRUCTURE OF NORTH ATLANTIC REDFISH
(GENUS SEBASTES; CUVIER 1829) BASED ON MICROSATELLITE POLYMORPHISM 99
1. Abstract 100
2. Introduction 101
3. Material and Methods 104
3.1 Sample collection 104
3.2 DNA extraction107
3.3 DNA quantitation107
3.4 Polymerase chain reaction (PCR)107
3.5 Analysis of microsatellite fragments on an automated sequencer 109
3.6 Determination of allele sizes109
3.7 Genotyping110
3.8 Statistical analysis 110
3.8.1 Descriptive statistics110
3.8.2 Factorial correspondence analysis (FCA) 112
3.8.3 Model-based cluster analysis113
3.8.4 F-statistics and analysis of molecular variance (AMOVA) 118
3.8.5 Isolation by distance 120
3.8.6 Genetic distances and multidimensional scaling (MDS) 120
4. Results 122
4.1 Allelic composition, Hardy Weinberg and linkage equilibrium 122
4.2 Factorial correspondence analysis (FCA)125
4.3 Results of the model-based cluster analyses127
4.3.1 Species structure and species assignment 127
4.3.2 Species hybridisation135
4.3.3 Population structure of S. marinus139
4.3.4 Population structure of S. mentella144
4.4 AMOVA and F-statistics 144
4.4.1 Pairwise F and R values145ST ST
4.4.2 Analysis of molecular variance (AMOVA) 158
4.5 Isolation by distance164
4.6 Multidimensional scaling analysis (MDSA)165
5. Discussion 170
5.1 Levels of genetic diversity170
5.2 Heterozygote deficiencies170
5.3 Species structure of North Atlantic redfish – a case of cryptic speciation in the
genus Sebastes? 173 III5.4 Precision of species assignment and admixed genotypes 178
5.5 Interspecific hybridisation 181
5.6 Population structure184
5.6.1 General patterns of population structure in North Atlantic redfish 184
5.6.2 Population structure of S. marinus185
5.6.3 Population structure of the newly identified potential cryptic species of North
Atlantic Sebastes189
5.6.4 Population structure of S. mentella189
5.6.5 Factors complicating the analysis of the population structure of North Atlantic
redfish species 195
5.7 A comparison of F- and R-statistics and their efficiency in detecting inter- and
intraspecific genetic differentiation in North Atlantic redfish 195
6.General conclusions and perspectives 198
Appendix I 202
Appendix IIa 206
Appendix IIb 207
Appendix III 208
Appendix IV 213

CHAPTER 3
A STUDY ON THE GENETIC STRUCTURE OF NORTH ATLANTIC REDFISH (GENUS SEBASTES;
CUVIER 1829) BASED ON AMPLIFIED FRAGMENT LENGTH POLYMORPHISM (AFLP)
MARKERS 217
1. Abstract 218
2. Introduction 219
3. Material and methods 220
3.1 Sample collection 220
3.2 Sample analysis223
3.2.1 DNA extraction223
3.2.2 DNA quantitation223
3.2.3 AFLP analysis223
3.2.4 Analysis of AFLP fragments on an automated sequencer 227
3.3 Data analysis228
3.3.1 Descriptive statistics and genetic diversity indices 228
3.3.2 Analysis of inter- and intraspecific genetic structure using model-based cluster
analysis 229 IV