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Phylogenomic Analysis of Vertebrate Evolution

Hallström, Björn LU (2010)
Abstract
The field of phylogenomics has emerged during the last five years, as the number of fully or partially sequenced genomes has increased rapidly. Using whole genomes for phylogenetic studies greatly increases the accuracy of the trees determined, and can potentially resolve phylogenetic questions that could not be resolved bu studies using only a few gene sequences.

In the current thesis selected phylogentic problems in vertebrate evolution has been studies, with special emphasis on placental mammals. Sequences from several thousand protein-coding sequences (representing almost 3 million nucleotide characters) have been compared between over 30 species of placental mammals. The need for novel bioinformatical methods and approaches... (More)
The field of phylogenomics has emerged during the last five years, as the number of fully or partially sequenced genomes has increased rapidly. Using whole genomes for phylogenetic studies greatly increases the accuracy of the trees determined, and can potentially resolve phylogenetic questions that could not be resolved bu studies using only a few gene sequences.

In the current thesis selected phylogentic problems in vertebrate evolution has been studies, with special emphasis on placental mammals. Sequences from several thousand protein-coding sequences (representing almost 3 million nucleotide characters) have been compared between over 30 species of placental mammals. The need for novel bioinformatical methods and approaches to work with such large amounts of data has been solved with customised software.

The large-scale analyses has resolved several previously uncertain relationships with strong statistical confidence. However, a small number of divergences remained unresolved, despite the extensive data sampling. As other possibilities were ruled out as less likely, the natural explanation for this lack of resolution is probably to be found in speciation related processes. All the identified problematic relationships are characterised by rapid subsequent speciation events. In such scenarios, incomplete sorting of ancient polymorphism and species hybridization are processes that could create mosaic genomes in which different parts of the genomes will show incompatible trees.

Divergences such as these are not well-represented as a classic bifurcating tree, instead attempts to illustrate them as phylogenetic networks have been made to more accurately describe the speciation. (Less)
Please use this url to cite or link to this publication:
author
supervisor
opponent
  • Prof von Haeseler, Arndt, University of Vienna
organization
publishing date
type
Thesis
publication status
published
subject
keywords
mammals, phyogenetics, phylogenomics, vertebrates, evolution
pages
116 pages
defense location
Genetic building, Sölvegatan 29, Lund, Sweden
defense date
2010-03-04 09:30
ISBN
978-91-628-8033-0
language
English
LU publication?
yes
id
6e7ef848-9036-4d66-96bf-5519174cf8d8 (old id 1543638)
date added to LUP
2010-02-08 13:06:57
date last changed
2016-09-19 08:45:16
@phdthesis{6e7ef848-9036-4d66-96bf-5519174cf8d8,
  abstract     = {The field of phylogenomics has emerged during the last five years, as the number of fully or partially sequenced genomes has increased rapidly. Using whole genomes for phylogenetic studies greatly increases the accuracy of the trees determined, and can potentially resolve phylogenetic questions that could not be resolved bu studies using only a few gene sequences. <br/><br>
	In the current thesis selected phylogentic problems in vertebrate evolution has been studies, with special emphasis on placental mammals. Sequences from several thousand protein-coding sequences (representing almost 3 million nucleotide characters) have been compared between over 30 species of placental mammals. The need for novel bioinformatical methods and approaches to work with such large amounts of data has been solved with customised software.<br/><br>
	The large-scale analyses has resolved several previously uncertain relationships with strong statistical confidence. However, a small number of divergences remained unresolved, despite the extensive data sampling. As other possibilities were ruled out as less likely, the natural explanation for this lack of resolution is probably to be found in speciation related processes. All the identified problematic relationships are characterised by rapid subsequent speciation events. In such scenarios, incomplete sorting of ancient polymorphism and species hybridization are processes that could create mosaic genomes in which different parts of the genomes will show incompatible trees.<br/><br>
	Divergences such as these are not well-represented as a classic bifurcating tree, instead attempts to illustrate them as phylogenetic networks have been made to more accurately describe the speciation.},
  author       = {Hallström, Björn},
  isbn         = {978-91-628-8033-0},
  keyword      = {mammals,phyogenetics,phylogenomics,vertebrates,evolution},
  language     = {eng},
  pages        = {116},
  school       = {Lund University},
  title        = {Phylogenomic Analysis of Vertebrate Evolution},
  year         = {2010},
}