Chapter 4
Phylogeny of Animals: Genomes Have
a Lot to Say
Ferdinand Marlétaz and Yannick Le Parco
Abstract Multiple lines of evidence have been proposed to resolve the tree of metazoans. Views based on morphology and development were often questioned because
they relied on characters whose evolutionary orientation is difficult. Molecules offer
an independent perspective and the employment of some genes, such as ribosomal RNA subunits (SSU/LSU) or Hox genes, have led to a profound reshaping
of the metazoan tree, leading to the “New View” of animal phylogeny. However,
classical molecular approaches have not succeeded in settling some long-standing
issues in animal relationships. Recently, extensive genome data have been collected for a large set of organisms including several evolutionarily relevant marine
species. This has allowed the development of phylogenomic approaches, which
have the potential to overcome the limitations of single-gene phylogenies by inferring trees on the base of whole genome evidence. This new approach has triggered
several advances regarding metazoan relationships such as the reevaluation of chordate relationships and the re-positioning of some problematic minor phyla with
improved accuracy. These studies have also raised new questions about the processes that underlie morphological evolution, as well as the future of molecular
phylogenetics.
4.1 Introduction
The first attempt to establish a classification of animals was made by Aristotle in
De generatione animalium, which defined five main groups according to the degree
of perfection of their generation and the relative warmness of their blood: mammals, ovoviviparous sharks, birds and reptiles, marine animals (fishes, cephalopods
& crustaceans) and finally insects (Aristotle 1965). Just one of these categories,
the marine animals, contains representatives of the whole tree of animals, if defined
F. Marlétaz (B)
Station Marine d’Endoume, UMR 6540 DIMAR, CNRS & Université de la Méditerranée,
Marseille, France
e-mail: ferdinand.marletaz@me.com
119
J.M. Cock et al. (eds.), Introduction to Marine Genomics,
Advances in Marine Genomics 1, DOI 10.1007/978-90-481-8639-6_4,
C
Springer Science+Business Media B.V. 2010
Phylogeny of Animals: Genomes Have
a Lot to Say
Ferdinand Marlétaz and Yannick Le Parco
Abstract Multiple lines of evidence have been proposed to resolve the tree of metazoans. Views based on morphology and development were often questioned because
they relied on characters whose evolutionary orientation is difficult. Molecules offer
an independent perspective and the employment of some genes, such as ribosomal RNA subunits (SSU/LSU) or Hox genes, have led to a profound reshaping
of the metazoan tree, leading to the “New View” of animal phylogeny. However,
classical molecular approaches have not succeeded in settling some long-standing
issues in animal relationships. Recently, extensive genome data have been collected for a large set of organisms including several evolutionarily relevant marine
species. This has allowed the development of phylogenomic approaches, which
have the potential to overcome the limitations of single-gene phylogenies by inferring trees on the base of whole genome evidence. This new approach has triggered
several advances regarding metazoan relationships such as the reevaluation of chordate relationships and the re-positioning of some problematic minor phyla with
improved accuracy. These studies have also raised new questions about the processes that underlie morphological evolution, as well as the future of molecular
phylogenetics.
4.1 Introduction
The first attempt to establish a classification of animals was made by Aristotle in
De generatione animalium, which defined five main groups according to the degree
of perfection of their generation and the relative warmness of their blood: mammals, ovoviviparous sharks, birds and reptiles, marine animals (fishes, cephalopods
& crustaceans) and finally insects (Aristotle 1965). Just one of these categories,
the marine animals, contains representatives of the whole tree of animals, if defined
F. Marlétaz (B)
Station Marine d’Endoume, UMR 6540 DIMAR, CNRS & Université de la Méditerranée,
Marseille, France
e-mail: ferdinand.marletaz@me.com
119
J.M. Cock et al. (eds.), Introduction to Marine Genomics,
Advances in Marine Genomics 1, DOI 10.1007/978-90-481-8639-6_4,
C
Springer Science+Business Media B.V. 2010