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Evaluating support for the current classification of eukaryotic diversity.

Parfrey LW, Barbero E, Lasser E, Dunthorn M, Bhattacharya D, Patterson DJ, Katz LA - PLoS Genet. (2006)

Bottom Line: We assess three aspects of each supergroup: (1) the stability of its taxonomy, (2) the support for monophyly (single evolutionary origin) in molecular analyses targeting a supergroup, and (3) the support for monophyly when a supergroup is included as an out-group in phylogenetic studies targeting other taxa.Our analysis demonstrates that supergroup taxonomies are unstable and that support for groups varies tremendously, indicating that the current classification scheme of eukaryotes is likely premature.We highlight several trends contributing to the instability and discuss the requirements for establishing robust clades within the eukaryotic tree of life.

View Article: PubMed Central - PubMed

Affiliation: Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, Massachusetts, United States of America.

ABSTRACT
Perspectives on the classification of eukaryotic diversity have changed rapidly in recent years, as the four eukaryotic groups within the five-kingdom classification--plants, animals, fungi, and protists--have been transformed through numerous permutations into the current system of six "supergroups." The intent of the supergroup classification system is to unite microbial and macroscopic eukaryotes based on phylogenetic inference. This supergroup approach is increasing in popularity in the literature and is appearing in introductory biology textbooks. We evaluate the stability and support for the current six-supergroup classification of eukaryotes based on molecular genealogies. We assess three aspects of each supergroup: (1) the stability of its taxonomy, (2) the support for monophyly (single evolutionary origin) in molecular analyses targeting a supergroup, and (3) the support for monophyly when a supergroup is included as an out-group in phylogenetic studies targeting other taxa. Our analysis demonstrates that supergroup taxonomies are unstable and that support for groups varies tremendously, indicating that the current classification scheme of eukaryotes is likely premature. We highlight several trends contributing to the instability and discuss the requirements for establishing robust clades within the eukaryotic tree of life.

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Support for Membership and Supergroup Monophyly from “Excavata”-Targeted Molecular GenealogiesMember taxa: Di, Diplomonadida; Rt, Retortamonadida; Cp, Carpediemonas; Tr, Trimastix; Ox, Oxymonadida; Ht, Heterolobosea; Eu, Euglenozoa; Ml, Malawimonas; Jk, Jakobida; Pa, Parabasalia; Dy, Diphylleia. Hypothesized subgroups:  Fornicata clade (Di + Rt + Cp) monophyletic,  Preaxostyla clade (Ox + Tr) monophyletic, ♦ Discicristata clade (Ht + Eu) monophyletic. The position of Diphylleia, Dy, was not considered when scoring the monophyly of “Excavata” as the inclusion of this organism within “Excavata” is controversial and has been removed from recent classifications (see text). See Figure 4 for further notes. References cited in this figure are [33,40,49,60,115,123–128].
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pgen-0020220-g006: Support for Membership and Supergroup Monophyly from “Excavata”-Targeted Molecular GenealogiesMember taxa: Di, Diplomonadida; Rt, Retortamonadida; Cp, Carpediemonas; Tr, Trimastix; Ox, Oxymonadida; Ht, Heterolobosea; Eu, Euglenozoa; Ml, Malawimonas; Jk, Jakobida; Pa, Parabasalia; Dy, Diphylleia. Hypothesized subgroups: Fornicata clade (Di + Rt + Cp) monophyletic, Preaxostyla clade (Ox + Tr) monophyletic, ♦ Discicristata clade (Ht + Eu) monophyletic. The position of Diphylleia, Dy, was not considered when scoring the monophyly of “Excavata” as the inclusion of this organism within “Excavata” is controversial and has been removed from recent classifications (see text). See Figure 4 for further notes. References cited in this figure are [33,40,49,60,115,123–128].

Mentions: “Excavata” rarely form a monophyletic group in molecular systematic studies targeting this supergroup (two of nine; Figure 6). Moreover, the position of putative members, jakobids, Malawimonas, parabasalids, and Diphylleia vary by analysis (Figure 6). Three distinct subclades, all of which are supported by ultrastructural characters [40], are generally recovered (Fornicata [six of six], Preaxostyla [six of six], and Discicristata [five of eight]; Figure 6).


Evaluating support for the current classification of eukaryotic diversity.

Parfrey LW, Barbero E, Lasser E, Dunthorn M, Bhattacharya D, Patterson DJ, Katz LA - PLoS Genet. (2006)

Support for Membership and Supergroup Monophyly from “Excavata”-Targeted Molecular GenealogiesMember taxa: Di, Diplomonadida; Rt, Retortamonadida; Cp, Carpediemonas; Tr, Trimastix; Ox, Oxymonadida; Ht, Heterolobosea; Eu, Euglenozoa; Ml, Malawimonas; Jk, Jakobida; Pa, Parabasalia; Dy, Diphylleia. Hypothesized subgroups:  Fornicata clade (Di + Rt + Cp) monophyletic,  Preaxostyla clade (Ox + Tr) monophyletic, ♦ Discicristata clade (Ht + Eu) monophyletic. The position of Diphylleia, Dy, was not considered when scoring the monophyly of “Excavata” as the inclusion of this organism within “Excavata” is controversial and has been removed from recent classifications (see text). See Figure 4 for further notes. References cited in this figure are [33,40,49,60,115,123–128].
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC1713255&req=5

pgen-0020220-g006: Support for Membership and Supergroup Monophyly from “Excavata”-Targeted Molecular GenealogiesMember taxa: Di, Diplomonadida; Rt, Retortamonadida; Cp, Carpediemonas; Tr, Trimastix; Ox, Oxymonadida; Ht, Heterolobosea; Eu, Euglenozoa; Ml, Malawimonas; Jk, Jakobida; Pa, Parabasalia; Dy, Diphylleia. Hypothesized subgroups: Fornicata clade (Di + Rt + Cp) monophyletic, Preaxostyla clade (Ox + Tr) monophyletic, ♦ Discicristata clade (Ht + Eu) monophyletic. The position of Diphylleia, Dy, was not considered when scoring the monophyly of “Excavata” as the inclusion of this organism within “Excavata” is controversial and has been removed from recent classifications (see text). See Figure 4 for further notes. References cited in this figure are [33,40,49,60,115,123–128].
Mentions: “Excavata” rarely form a monophyletic group in molecular systematic studies targeting this supergroup (two of nine; Figure 6). Moreover, the position of putative members, jakobids, Malawimonas, parabasalids, and Diphylleia vary by analysis (Figure 6). Three distinct subclades, all of which are supported by ultrastructural characters [40], are generally recovered (Fornicata [six of six], Preaxostyla [six of six], and Discicristata [five of eight]; Figure 6).

Bottom Line: We assess three aspects of each supergroup: (1) the stability of its taxonomy, (2) the support for monophyly (single evolutionary origin) in molecular analyses targeting a supergroup, and (3) the support for monophyly when a supergroup is included as an out-group in phylogenetic studies targeting other taxa.Our analysis demonstrates that supergroup taxonomies are unstable and that support for groups varies tremendously, indicating that the current classification scheme of eukaryotes is likely premature.We highlight several trends contributing to the instability and discuss the requirements for establishing robust clades within the eukaryotic tree of life.

View Article: PubMed Central - PubMed

Affiliation: Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, Massachusetts, United States of America.

ABSTRACT
Perspectives on the classification of eukaryotic diversity have changed rapidly in recent years, as the four eukaryotic groups within the five-kingdom classification--plants, animals, fungi, and protists--have been transformed through numerous permutations into the current system of six "supergroups." The intent of the supergroup classification system is to unite microbial and macroscopic eukaryotes based on phylogenetic inference. This supergroup approach is increasing in popularity in the literature and is appearing in introductory biology textbooks. We evaluate the stability and support for the current six-supergroup classification of eukaryotes based on molecular genealogies. We assess three aspects of each supergroup: (1) the stability of its taxonomy, (2) the support for monophyly (single evolutionary origin) in molecular analyses targeting a supergroup, and (3) the support for monophyly when a supergroup is included as an out-group in phylogenetic studies targeting other taxa. Our analysis demonstrates that supergroup taxonomies are unstable and that support for groups varies tremendously, indicating that the current classification scheme of eukaryotes is likely premature. We highlight several trends contributing to the instability and discuss the requirements for establishing robust clades within the eukaryotic tree of life.

Show MeSH
Related in: MedlinePlus