Phylogeny and phylogeography of the caddisfly Rhyacophila pubescens, PICTET 1834, (Trichoptera), with special consideration of its habitat specificity [Elektronische Ressource] / vorgelegt von Christine Engelhardt

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120 pages

English

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Publié par	universitat_duisburg-essen
Publié le	01 janvier 2009
Nombre de lectures	12
Langue	English
Poids de l'ouvrage	3 Mo

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Phylogeny and phylogeography of the caddisfly Rhyacophila pubescens, PICTET
1834, (Trichoptera), with special consideration of its habitat specificity

Inaugural-Dissertation
zur
Erlangung des Doktorgrades
Dr. rer. nat.
des Fachbereichs
Biologie und Geografie
an der Universität Duisburg-Essen

vorgelegt von
Christine Engelhardt
aus München
Februar 2009

Tag der mündlichen Prüfung
22. Juni 2009
Prüfer:
Vorsitzender des Prüfungsausschusses: Prof. Dr. B. Sures
Prof. Dr. D. Hering
PD Dr. P. Haase
Prof. Dr. H. Burda
Die der vorliegende Arbeit zugrunde liegenden Experimente wurden in der
Abteilung für Limnologie und Naturschutzforschung des Forschungsinstituts
Senckenberg und in der Abteilung für Hydrobiologie der Universität Duisburg-
Essen durchgeführt.

1. Gutachter:
2. Gutachter:
3. Gutachter:
Vorsitzender des Prüfungsausschusses:
Tag der mündlichen Prüfung:
Table of contents
List of figures
List of tables
Abbreviations
Introduction……………………………………………………………………..………….8
General introduction..…………………………………………………………………..……...8
Phylogeographic patterns in aquatic insects………………………..……………………….....9
Chapter 1 Phylogeny of the Rhyacophila tristis-group with special
consideration of R. pubescens (Insecta: Trichoptera)…………………..……….14
Introduction………………………………………………………..…..……………..…...…14
Taxonomy of the genus Rhyacophila…………………………………………….…………...14
The R. tristis-group and questions addressed in this chapter……………………………..…..14
Materials and methods……………………………………………………………………...16
Specimens examined………………………….………………………………………………16
DNA extraction and amplification……………….……………………………………..….....16
Sequencing and sequence editing……………………………………………...……………..17
Phylogenetic inference ……………………………………………………………………….17
Results…………………………………………………………………………………..……18
The datasets…………………………………………………………………….…………..…18
Monophyly of R. pubescens ……………………………………………………………….....19
Relationships in the R. tristis-group inferred by different phylogenetic
methods…………………….………………………………………………………………....20
Discussion………………..…………………………………………………….…………..…25
Phylogenetic relationships of Rhyacophila pubescens…………………………………….....25
Monophyly of the R. tristis-group and relatedness between
species..…………………….………………………………………………………………....26
Performance of the genetic markers..………………………………………………………....27 Conclusions and outlook……….…………………………………………………………....27
Chapter 2 Population genetic structure of the caddisfly Rhyacophila
pubescens, PICTET 1834, north of the Alps..……………..………………………....31
Introduction………………………………………………………..…..……………..…...…31
Effects of population fragmentation………………………………………….….…………...31
Habitat specificity of R. pubescens………………………………………………………...…32
Questions addressed in this chapter………………………………………………………..…33
Materials and methods……………………………………………………………………...33
Specimens examined………………………….………………………………………………33
DNA extraction and amplification……………….……………………………………..….....38
Sequence editing and alignment………………………………………..……...……………..38
Calculation of networks and statistical analyses ………….………………………………….38
Results…………………………………………………………………………………..……39
Sequence data and haplotype networks.……………………………………….…………..…39
Population differentiation………………………………………………………………….....41
Discussion………………..…………………………………………………….…………..…45
Genetic differentiation of Rhyacophila pubescens and possible microendemism………........45
Insular distribution pattern and demographic history…………………………………...…....47
Postglacial history……………….....………………………………………………………....48
Conclusions and outlook ……….……………………...…………………………………....50
Chapter 3 Range wide phylogeography of Rhyacophila pubescens inferred
from mtCOI and AFLP´s……………………………...…..……………………….......51
Introduction………………………………………………………..…..……………..…...…51
Phylogeographic patterns in Europe………………………………………….….…………...51
Questions addressed in this chapter……………………...………………………………...…52
Materials and methods……………………………………………………………………...52
Mitochondrial DNA: Specimens examined.….………………………………………………52 DNA extraction and amplification……………….……………………………………..….....53
Statistical methods………….………………………………………………………………...53
Amplified Fragment Length Polymorphism: DNA amplification.……..……...……………..55
Statistical methods………….………………………………………………………………...56
Results…………………………………………………………………………………..……57
Mitochondrial DNA: Haplotype networks and haplotype distribution......…….…………..…57
Population differentiation………………………………………………………………….....61
Barriers to gene flow…………………………………………………......…….…………..…61
Demographic expansion…………...……………………………………………………….....62
Migration……………...…………...……………………………………………………….....64
Amplified Fragment Polymorphism: Structure of the AFLP-dataset…..………………….....65
Assigment tests…..…...…………...……………………………………………………….....68
Discussion………………..…………………………………………………….…………..…72
Population genetic structure north and south of the Alps…………………………….…........72
Population history of R. pubescens…...……………………………………………………....75
Conclusions……………………...……………………...…………………………………....77
Summary and
conclusions……...……………………...…………………………………………..……....88
Deutschsprachige
Zusammenfassung………………...………………………………………………..…....94
References……...……………………...…………………….………………..………......103
Acknowledgments……...……………………......………………………….…………..120

List of figures
Fig. 1 Map of entire distribution range of R. pubescens………….…………………………11
Fig. 1.1 Neighbor-joining phylogenetic tree of Rhyacophila specimens………………….….21
Fig. 1.2 One of the eight most parsimonious trees obtained by Maximum Parsimony
analysis..........................................................................................................................23
Fig. 1.3 50% majority rule consensus tree obtained with B/MCMC method………………...24
Fig. 2.1 Sampling locations across the northern part of the distribution range of R.
pubescens………………………………………………………………………..…….34
Fig. 2.2 Median-joining network of R. pubescens haplotypes in mountain ranges north of the
Alps…………………………………………………………………………………...40
Fig. 2.3 Pairwise mismatch distributions of selected mountain ranges (Franconian Alb, Swiss
Jura, Northern Hungary) and for the complete data set………………………………44
Fig. 3.1 Median-joining haplotype network of R. pubescens………..…..………………...…59
Fig. 3.2 Unrooted 50% majority rule consensus tree of R. pubescens haplotypes…………...60
Fig. 3.3 Map of R. pubescens´ range with sampled sites marked with white squares……..…62
Fig. 3.4 Mismatch distributions for populations north and south of the Alps………………..63
Fig. 3.5 Relative migration rate values (Nm) between each population pair for the stepping
stone model for the Western Alps region……………………………………..…….65
Fig. 3.6 Neighbor-joining phenogram of Nei´s D values for mountain regions………….…..66
Fig. 3.7 Principal Coordinate Analysis based on squared Euclidean distances………………67
Fig. 3.8 Results of BAPS analysis with admixture based on mixture clustering………..……69
Fig. 3.9 Clusters found in the AFLP-dataset with Structurama assignment test…………..…70
Fig. 3.10 Results of assignment test…………………………………………………………..71
Fig. 3.11 Shannon´s index and down-weighed marker value for AFLP samples for each
mountain region……………………………………………………………………….72
List of tables
Tab. 1.1 Sampling sites of Rhyacophila specimens………………………………...……...…29
Tab. 1.2 Results of single genes and combined dataset using Maximum Parsimony and
Bayesian approach………………………………………………………………...….18
Tab. 1.3 Maximum Parsimony bootstrap support values and posterior probabilities for the
clade of R. pubescens specimens……………………...…………………………..….20
Tab. 2.1 Sampling locations and haplotypes of R. pubescens populations ……………….….35
Tab. 2.2 Population differentiation by exact tests of population differentiation and pairwise
F …….…………………...…………………………………………………..…..….42 ST
Tab. 2.3 Analysis of molecular variance (AMOVA) for grouping of the 15 sampled mountains
into six major mountain ranges…………………………………………………..…...43
Tab. 2.4 Neutrality test results for selected mountain regions……………………………..…45
Tab. 3.1 Sampling sites of R. pubescens………….…………………………………………..78
Tab. 3.2. Results of exact tests of population differentiation…………………………...…….85
Tab. 3.3 Gene diversity estimators of R. pubescens in mountain ranges across the range
detected by AFLP´s…………………………………………………………………...87

Abbreviations
Asl above sea level
bp base pairs
DNA deoxyribonucleic acid
mt mitochondrial
mts mountains
nu nuclear
PCR Polymerase chain reaction
Introduction

Introduction
General introduction
In biological research the field of phylogeography is relatively young. Phylogeography
comprises many disciplines, like molecular genetics, population genetics, phylogenetic
biology, geology and historical geography (Avise 2000). In the 1980ies mtDNA studies of
natural populations showed that branches in intraspecific gene trees were linked to
geographical distribution. The term phylogeography was created to describe relationships
between gene genealogies and geography. Phylo