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Dissertation zugänglich unter
URN: urn:nbn:de:gbv:18-87340
URL: http://ediss.sub.uni-hamburg.de/volltexte/2017/8734/

Molecular phylogenetic analyses of Ecdysozoa and Haemosporida

Molekularphylogenetische Analysen der Ecdysozoa und Haemosporida

Borner, Janus

 Dokument 1.pdf (10.226 KB) 

SWD-Schlagwörter: Phylogenie , Malaria , Spinnen , Tausendfüßer , Priapswürmer , Hakenrüssler , Plasmodium , Hämosporidien , Sporentierchen , Evolution , Kontamination
Freie Schlagwörter (Deutsch): Ecdysozoa
Basisklassifikation: 42.21
Institut: Biologie
DDC-Sachgruppe: Biowissenschaften, Biologie
Dokumentart: Dissertation
Hauptberichter: Burmester, Thorsten (Prof. Dr.)
Sprache: Englisch
Tag der mündlichen Prüfung: 07.09.2017
Erstellungsjahr: 2017
Publikationsdatum: 15.09.2017
Kurzfassung auf Englisch: The advent of molecular phylogenetics has revolutionized our understanding of the tree of life. In my PhD thesis, I have aimed to elucidate various aspects of the deep phylogeny of Ecdysozoa and Haemosporida employing classical PCR-based approaches, next-generation sequencing, and bioinformatic data mining techniques.

The superphylum Ecdysozoa was first proposed based on phylogenetic analyses of 18S rRNA sequences. Among others, it comprises the two most species-rich animal phyla, Arthropoda and Nematoda. The Ecdysozoa concept was initially received with considerable skepticism and controversy as it contradicted traditional animal systematics; and while it is now widely accepted in the scientific community, the relationships within Ecdysozoa have remained poorly understood. To improve our understanding of the deep phylogeny of Ecdysozoa, new transcriptome data from a number of ecdysozoan species belonging to previously undersampled taxa were generated. All phylogenetic analyses found strong support for the monophyly of Ecdysozoa. The scalidophoran taxa Priapulida and Kinorhyncha were recovered in a sister group relationship at the base of Ecdysozoa. Within Euarthropoda, I found strong support for a common origin of Myriapoda, Crustacea, and Hexapoda (Mandibulata hypothesis) thus rejecting the notion of a sister group relationship between Myriapoda and Chelicerata (Myriochelata hypothesis), which was recovered in a number of earlier molecular analyses. Molecular clock analyses resulted in divergence time estimates that are notably younger than the estimates of most previous studies based on sequence data. However, the molecular dates still significantly predate the earliest fossil evidence and point to an Ediacaran origin of Arthropoda followed by diversification of the extant arthropod subphyla in the Cambrian.

Haemosporida are intracellular blood parasites with a complex life cycle that infect a great variety of vertebrate hosts. Haemosporidians are member of the phylum Apicomplexa and include the agents of human malaria (genus Plasmodium). Despite being the focus of numerous studies, there is still no consensus on the deep phylogeny of Haemosporida. As genome sequencing projects have focused on mammalian parasites of the genus Plasmodium, sequence data from the other haemosporidian genera was only available for a small set of standard genes, which are not ideal for reconstructing the earliest events in haemosporidian evolution. This limited gene sampling is due to numerous challenges involved in developing nuclear markers for this diverse group. By employing a newly developed bioinformatic pipeline for primer design and by carefully optimizing design parameters and PCR protocols, I was able to obtain sequence data from a number of nuclear genes in haemosporidian species belonging to the genera Haemoproteus, Leucocytozoon, Polychromophilus, and Plasmodium. Phylogenetic analyses resulted in highly congruent topologies consistently placing Leucocytozoon at the base of Haemosporida. Surprisingly, the phylogenetic analyses recovered Polychromophilus, a genus of bat-infecting parasites, as the sister group to a monophyletic clade comprising all Plasmodium parasites. This relationship has not been proposed before but is well supported and appears plausible when considering various aspects of parasite life history. Within Plasmodium, a sister group relationship between the avian and the mammalian species was found.

Contamination by DNA from external sources (e.g. cloning vectors or human DNA) is a common problem in NGS projects. If the contaminating sequences are not identified and remain in the datasets after sequence assembly and deposition into public databases, subsequent analyses may yield confusing results that can lead to false conclusions. Moreover, the identification of parasite-derived contaminations may also enable the discovery of novel parasite lineages and shed light on previously unknown host-parasite associations. In order to quantify the extent of contamination by apicomplexan parasites in the public genome and transcriptome databases and to extract as many parasite-derived contigs from the contaminated animal assemblies, I developed a software pipeline that uses a series of sequence similarity searches to identify contigs of parasite origin. In total, 953 assemblies of terrestrial animals were analysed and, in 51 assemblies, a combined 20,907 contigs from apicomplexan parasites were found. For most of the contaminating parasite species, no molecular data had been available previously and, for some of them, large amounts of the parasite's gene repertoire could be extracted from the sequence assemblies. Phylogenetic inference yielded a well-resolved tree and the contaminating parasite species could be identified as members of the apicomplexan taxa Gregarinasina, Coccidia, Piroplasmida, and Haemosporida.


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