Meusemann, Karen A.: The “Atelocerata” – A vanishing hypothesis? : Molecular phylogeny of arthropods with focus on primary wingless hexapods. - Bonn, 2012. - Dissertation, Rheinische Friedrich-Wilhelms-Universität Bonn.
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author = {{Karen A. Meusemann}},
title = {The “Atelocerata” – A vanishing hypothesis? : Molecular phylogeny of arthropods with focus on primary wingless hexapods},
school = {Rheinische Friedrich-Wilhelms-Universität Bonn},
year = 2012,
month = sep,

note = {Arthropods encompass more than three quarters of all described living species. Among arthropods, hexapods are the most abundant group and show an enormous diversity. To understand evolutionary processes of and within hexapods, it is necessary to resolve phylogenetic relationships, especially early hexapod splits within an arthropod framework. Several contradicting hypotheses have been suggested in the last decade addressing the monophyly of hexapods, and placements and relationships of primary wingless hexapod orders. As a possible sister group of hexapods, traditionally myriapods have been suggested, uniting hexapods and myriapods to a clade "Atelocerata". Alternatively several crustacean taxa (branchiopods or copepods) have been proposed as a possible sister group of hexapods associated with the "Pancrustacea" hypothesis where hexapods and crustaceans are united into a clade. This study concentrates on the analyses of molecular data and aims to resolve deep hexapods relationships within an arthropod context using two different methodological approaches.
In the first approach, large phylogenomic (multi-gene and taxon) data sets based on nuclear protein coding genes derived from Expressed Sequence Tags (ESTs) are analyzed. This approach uses raw data sets with more than 100 taxa and more than 700 genes, and optimal data subsets with more than 100 taxa and more than 100 most informative genes to reconstruct phylogenetic trees. This is the first phylogenomic study which takes all entognathous, primary wingless hexapod orders into account. For this study, new EST data have been generated for each entognathous (Protura, Diplura and Collembola) and one ectognathous primary wingless hexapod order (Archaeognatha). A new approach based on a hill climbing algorithm is introduced to select most informative taxa and genes from raw data matrices. The aim is to select an optimized data subset with high information content. Therefore, MARE, (MAtrix REduction, has been developed by our work group. Optimized data subsets (SOS) are selected by taking information content of single genes (partitions) and the complete matrix into account without loosing to much taxa. For phylogenomic data sets addressing phylogenetic relationships, such an approach has never previously been applied. Instead, available studies rely on thresholds of available data or on maximal connected groups of data presence. Effects of selecting optimized data subsets towards high information content are examined with respect to phylogenetic reconstructions. Altogether, phylogenomic data can substantially advance our understanding of arthropod evolution and resolve several conflicts among existing hypotheses.
Optimized data subsets show strong support for a sister group relationship of onychophorans and euarthropods. Within pancrustaceans, analyses yield paraphyletic crustaceans and monophyletic hexapods and robustly resolved deep hexapod relationships. Within neopteran insects, endopterygote (holometabolous) insects are monophyletic where hymenopterans branch off first with strong support. Analyses show a remarkable sensitivity to methods of analyses for the placement of myriapods. Altogether, results of this thesis show that new heuristics for the selection of optimized submatrices and other applied tools to improve data quality pay off their effort.
The second approach to resolve deep hexapod relationships within an arthropod framework relies on two well known nuclear ribosomal RNA genes (large subunit 28S and small subunit 18S rRNA). Both genes are popular markers for studies addressing metazoan, arthropod and hexapod phylogeny. Analyses using an arthropod data set with 148 taxa of all important arthropod groups including both nuclear rRNA genes are improved by employing plausible models of sequence evolution. This rRNA study incorporates background knowledge on the evolution of nuclear ribosomal RNA gene sequences, in particular, into various steps of data processing. Mainly, automated methods have been used, an automated secondary structure guided alignment approach (RNAsalsa) and the software Aliscore for alignment masking. Further, mixed RNA/DNA models have been applied to avoid artifacts due to interdependence and covariation of paired sites of rRNA genes. Concurrently, reconstruction methods have been used that account for variation of evolutionary rates among lineages (non-stationarity). Although split-decomposition networks indicated conflicting signal in the data set, analyses modeling non-stationary statistically outperform stationary approaches. Topologies show strong support for a pancrustacean clade. The placement of some myriapod orders remains suspicious, a sister group of hexapods cannot robustly be resolved. Analyses taking non-stationarity into account unequivocally propose monophyletic Hexapoda. Relationships among entognathous primary wingless hexapods are resolved and Ectognatha are maximally supported. Within endopterygotes, hymenopterans are strongly proposed as a sister group of remaining holometabolous insects. Again, advanced methods in data quality assessment and modeling pay off its effort.},

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