Molecular insights to crustacean phylogeny [Elektronische Ressource] / vorgelegt von Bjoern Marcus Reumont

Bjoern Marcus Von Reumont

Sujets

• Biologie

Informations

• Publié par: rheinische_friedrich-wilhelms-universitat_bonn
• Publié le: 01 janvier 2010
• Nombre de lectures: 24
• Poids de l'ouvrage: 8 Mo

Extrait

MOLECULAR INSIGHTS TO CRUSTACEAN PHYLOGENY
DISSERTATION
zur Erlangung des Doktorgrades (Dr. rer. nat.)
an der Mathematisch-Naturwissenschaftlichen Fakultät
der Rheinischen Friedrich-Wilhelms-Universität Bonn
vorgelegt von
BJOERN MARCUS VON REUMONT
Bonn – Oktober 2009

Angefertigt mit der Genehmigung der Mathematisch-Naturwissenschaftlichen Fakultät
der Rheinischen Friedrich-Wilhelms-Universität Bonn.




Diese Dissertation wurden am Zoologischen Forschungsmuseum Alexander Koenig in
Bonn durchgeführt.











Tag der mündlichen Prüfung 29.01.2010
Erscheinungsjahr 2010






Betreuer

Prof. Dr. Johann-Wolfgang Waegele
Prof. Dr. Bernhard Y. Misof






[…] Make up your mind, plan before and follow that plan.
[…] An unforgivenable sin is quitting. Never give up and keep on going. The only
struggle should be to solve the problem or survive. […] Focus on the task and on
the moment. […]
Excerpts of a cave diving manual
This basic philosophy for cave diving is not only useful in cave diving but also generally in
live and was indeed helping not only once conducting this thesis. And while diving…
Dedicated to my family and all good friends – a permanent, safe mainline Contents Molecular insights to crustacean phylogeny
CONTENTS
SUMMARY / ZUSAMMENFASSUNG
1. INTRODUCTION 1
1.1 CRUSTACEANS AND THEIR CONTROVERSIAL PHYLOGENY – A SHORT OVERVIEW 22 CONTRADICTING PHYLOGENY HYPOTHESES OF MAJOR CRUSTACEAN GROUPS 6
1.3 EARLY CONCEPTS OF ARTHROPODS AND MAJOR CLADES IN A MODERN BACKGROUND 84 QUINTESSENCE OF RECENT ARTHROPOD STUDIES 11
1.5 METHODOLOGICAL BACKGORUND 13
1.5.1 THE FUNDAMENT OF ALL MOLECULAR ANALYSES – TAXON CHOICE & 14ALIGNMENT RECONSTRCUTION1.5.2 SINGLE GENE DATA – INCORPORATING BACKGROUND KNOWLEDGE TO rRNA ANALYSES 15
1.5.3 PHYLOGENOMIC DATA – A GENERAL OVERVIEW 16
1.6 AIMS OF THE THESIS 197 SHORT INTRODUCTION AND OVERVIEW OF ANALYSES [A-C] 20
2. MATERIAL AND METHODS 21
2.1 SPECIES CHOICE, COLLECTION AND FIELDWORK 212 LABORATORY METHODS 26
2.3 DATA ANALYSES METHODS PRIOR TO PHYLOGENETIC TREE RECONSTRUCTION 30
2.3.1 SEQUENCE PROCESSING AND QUALITY CONTROL 312.3.2 MULTIPLE SEQUENCE ALIGNMENT 322.3.3 ALIGNMENT OPTIMIZATION BASED ON SECONDARY STRUCTURE INFORMATION 32
2.3.4 EVALUATING STRUCTURE AND SIGNAL BY NETWORK RECONSTRUCTION 332.3.5 ALIGNMENT EVALUATION AND PROCESSING 33
2.4 ANALYSES [A]| CAN 16S, 18S AND COI IMPROVE CRUSTACEAN PHYLOGENY WITHIN 35
A RTHROPODS? COMPARING “USUAL” STANDARD VS. SECONDARY STRUCTURE BASED APPROACHES.
2.4.1 OBJECTIVES 352.4.2 TAXON SAMPLING 352.4.3 ANALYSIS DESIGN 35
2.4.4 PHYLOGENETIC TREE RECONSTRUCTION 37
2.5 ANALYSIS [B]: IS IMPLEMENTATION OF SECONDARY STRUCTURE BASED ALIGNMENT 40
OPTIMIZATION AND TIME-HETEROGENEITY A SOLUTION TO SOLVE PHYLOGENY WITHIN ARTHROPODS?
2.5.1 OBJECTIVES 402.5.2 TAXON SAMPLING 402.5.3 ANALYSIS DESIGN 41
2.5.4 PHYLOGENETIC TREE RECONSTRUCTION 42
2.6 ANALYSES [C]: ENLIGTHS PHYLOGENOMIC DATA CRUSTACEAN PHYLOGENY WITHIN ARTHROPODS 46
– OR STICK OLD PROBLEMS TO THE ANALYSES OF THIS NEW LARGE SCALE DATA?
2.6.1 OBJECTIVES 462.6.2 TAXON SAMPLING 462.6.3 ANALYSIS DESIGN 47
2.6.4 PHYLOGENETIC TREE RECONSTRUCTION 53Molecular insights to crustacean phylogeny Contents
2.7 ANALYSIS OF HEMOCYANIN STRUCTURE IN REMIPEDIA 55
2.7.1 OBJECTIVES 552.7.2 ANALYSIS DESIGN 552.7.3 PHYLOGENETIC TREE RECONSTRUCTION 55
3. RESULTS 57
3.1 ANALYSES [A]| CAN 16S, 18S AND COI IMPROVE CRUSTACEAN PHYLOGENY WITHIN 57
A RTHROPODS? COMPARING “USUAL” STANDARD VS. SECONDARY STRUCTURE BASED APPROACHES.
3.1.1 DATA SIGNAL AND SPLIT SUPPORTING PATTERNS 573.1.2 BASE COMPOSITIONS 603.1.3 PHYLOGENETIC RECONSTRUCTION 61
3.1.4 PROBLEMATICS OF THE DATA 65
3.2 ANALYSIS [B]: IS IMPLEMENTATION OF SECONDARY STRUCTURE BASED ALIGNMENT 66
OPTIMIZATION AND TIME-HETEROGENEITY A SOLUTION TO SOLVE PHYLOGENY WITHIN ARTHROPODS?
3.2.1 FINAL DATASET AND SPLIT SUPPORTING PATTERNS 663.2.2 COMPOSITIONAL HETEROGENEITY OF BASE FREQUENCY 683.2.3 PHYLOGENETIC MODEL TESTING & RECONSTRUCTIONS 69
3.2.4 RESULTING TOPOLOGIES 71
3.3 ANALYSES [C]: ENLIGTHS PHYLOGENOMIC DATA CRUSTACEAN PHYLOGENY WITHIN ARTHROPODS 75
– OR STICK OLD PROBLEMS TO THE ANALYSES OF THIS NEW LARGE SCALE DATA?
3.3.1 RESULTING TOPOLOGY OF THE UNREDUCED DATASET 753.3.2 RESULTING TOPOLOGIES OF THE REDUCED, OPTIMAL DATA SUBSET 763.3.3 DIFFERENCES IN ML AND BAYESIAN TOPOLOGIES OGF THE REDUCED DATA SUBSET 78
3.3.4 PROBLEMATICS IN RESULTING TOPOLOGIES OF THE BAYESIAN CHAINS 78
3.4 ANALYSIS OF HEMOCYANIN STRUCTURE IN REMIPEDIA 813.4.2 PHYLOGENETIC RECONSTRUCTION AND RESULTING TREE 81
4. DISCUSSION 83
4.1 SEPARATE METHODOLOGICAL DISCUSSION OF ANALYSIS [A-C] 83
4.1.1 ANALYSES [A] 834.1.2 ANALYSES [B] 854.1.3 ANALYSES [C] 88
4.2 PANCRUSTACEAN PHYLOGENY DISCUSSION 913 ARTHROPOD PHYLOGENY DISCUSSION 103
4.4 GENERAL MEHTODOLODICAL DISCUSSION 1075 CONCLUSIONS AND FURTHER ASPECTS 114
5. REFERENCES 117
6. ABREVIATIONS 140
7. INDEX OF FIGURES AND TABLES 141
8. ACKNOWLEDGEMENT 143
9. SUPPLEMENT I
10. CURRICULUM VITAE –E RKLÄRUNG Above picture: Derocheilocaris typicus, a specimen of the Mystacocarida
Cover picture: Some of the rather small but beautiful crustaceans (from above
left: Branchiura, Mystacocarida, Copepoda, Ostracoda, Cladocera, Branchiopoda
and Remipedia.Molecular insights to crustacean phylogeny Abstract / Zusammenfassung
ABSTRACT
A key role in arthropod phylogeny plays a group of organisms that was already in the focus
th
of taxonomic research of Charles Darwin in the mid of the 19 century, namely the
Crustacea. This extremely divers group comprises small species like the Mystacocarida
(Derocheilocaris typicus) with only 0.3 mm body size or such big representatives like the
Japanese giant crab (Macrocheira kaempferi) with a span width of almost 4 m. Generally
accepted are six major crustacean taxa, the Malacostraca (Latreille, 1802), Branchiopoda
(Latreille, 1817), Remipedia (Yager, 1981), Cephalocarida (Sanders, 1955), Maxillopoda
(Dahl, 1956) and Ostracoda (Latreille 1802). The validity of the taxon Maxillopoda is to date
still disputed. The monophyly of some crustacean groups like the Malacostraca and
Branchiopoda is generally accepted, but for several other groups unclear. This thesis aims to
resolve internal relationships of the major crustacean groups inferring phylogenies with
molecular data. The crustaceans are in addition of eminent interest to enlight the question
how land was successfully conquered by arthropod taxa. New molecular and
neuroanatomical data support the scenario that the Hexapoda might have evolved from
Crustacea. The thesis further seeks to address the possible close relationship of Crustacea
and Hexapoda. That issue is closely linked to the partly still debated position of crustaceans
within arthropods and the supposable sister-group of the Crustacea.
Most molecular studies of crustaceans relied on single gene or multigene analyses in which
for most cases partly sequenced rRNA genes were used. However, intensive data quality and
alignment assessments prior to phylogenetic reconstructions are not conducted in most
studies. Additionally, a complex modeling and the implementation of compositional base
heterogeneity along lineages are missing. One methodological aim in this thesis was to
implement new tools to infer data quality, to improve alignment quality and to test the
impact of complex modeling of the data. Two of the three phylogenetic analyses in this
thesis are also based on rRNA genes.
In analysis (A) 16S rRNA, 18S rRNA and COI sequences were analyzed. RY coding of the
COI fragment, an alignment procedure that considers the secondary structure of RNA
molecules and the exclusion of alignment positions of ambiguous positional homology was
performed to improve data quality. Anyhow, by extensive network reconstructions it was
shown that the signal quality in the chosen and commonly used markers is not suitable to
infer crustacean phylogeny, despite the extensive data processing and optimization. This
result draws a new light on previous studies relying on these markers.
In analyses (B) completely sequenced 18S and 28S rRNA genes were used to reconstruct
the phylogeny. Base compositional heterogeneity was taken into account based on the
finding of analysis (A), additionally to secondary structure alignment optimization and
alignment assessment. The complex modeling to compare time-heterogeneous versus time-
homogenous processes in combination with mixed models for an implementation of
secondary structures was only possible applying the Bayesian software package PHASE. The
results clearly demonstrated that complex modeling counts and that ignoring time-Abstract / Zusammenfassung Molecular insights to crustacean phylogeny
heterogeneous processes can mislead phylogenetic reconstructions. Some results enlight the
phylogeny of Crustaceans, for the first t