Going nuclear: gene family evolution and vertebrate phylogeny reconciled

Cotton, James A.; Page, Roderic

doi:10.1098/rspb.2002.2074

Cited by 83 publications

(50 citation statements)

References 47 publications

(63 reference statements)

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“…More efficient collection techniques for large molecular data sets are already having a major impact on the field. Moreover, more powerful and new phylogenetic algorithms [e.g., Bayesian, Markov Chain, Monte Carlo methods (Huelsenbeck et al 2001); and the metapopulation genetic algorithm (Lemmon & Milinkovitch 2002)] and alternative new approaches such as reconciled trees (Cotton & Page 2002), as well as faster computers facilitate the estimation of phylogenetic relationships even when using large sequence data sets (Liu et al 2001). …”

Section: Discussionmentioning

confidence: 99%

Recent Advances in the (Molecular) Phylogeny of Vertebrates

Meyer

Zardoya

2003

Annu. Rev. Ecol. Evol. Syst.

181

142

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Tetrapodas Abstract The analysis of molecular phylogenetic data has advanced the knowledge of the relationships among the major groups of living vertebrates. Whereas the molecular hypotheses generally agree with traditional morphology-based systematics, they sometimes contradict them. We review the major controversies in vertebrate phylogenetics and the contribution of molecular phylogenetic data to their resolution: (a) the mono-paraphyly of cyclostomes, (b) the relationships among the major groups of rayfinned fish, (c) the identity of the living sistergroup of tetrapods, (d ) the relationships among the living orders of amphibians, (e) the phylogeny of amniotes with particular emphasis on the position of turtles as diapsids, (f ) ordinal relationships among birds, and (g) the radiation of mammals with specific attention to the phylogenetic relationships among the monotremes, marsupial, and placental mammals. We present a discussion of limitations of currently used molecular markers and phylogenetic methods as well as make recommendations for future approaches and sets of marker genes.

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Section: Discussionmentioning

confidence: 99%

Recent Advances in the (Molecular) Phylogeny of Vertebrates

Meyer

Zardoya

2003

Annu. Rev. Ecol. Evol. Syst.

181

142

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“…A phylogenetic tree representing the ordinal relationships among the species was used to infer amino acid changes during descent of the tetrapods. Phylogenetic relationships were taken from previously published studies (35,36,(39)(40)(41)(42). Inferred amino acid changes were reconstructed with DELTRAN in a maximum parsimony framework by using PAUP* 4.0b10 (43).…”

Section: Esmentioning

confidence: 99%

Rapid electrostatic evolution at the binding site for cytochrome c on cytochrome c oxidase in anthropoid primates

Schmidt

Wildman

Uddin

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

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Cytochrome c (CYC) oxidase (COX), a multisubunit enzyme that functions in mitochondrial aerobic energy production, catalyzes the transfer of electrons from CYC to oxygen and participates in creating the electrochemical gradient used for ATP synthesis. Modeling three-dimensional structural data on COX and CYC reveals that 57 of the >1,500 COX residues can be implicated in binding CYC. Because of the functional importance of the transfer of electrons to oxygen, it might be expected that natural selection would drastically constrain amino acid replacement rates of CYC and COX. Instead, in anthropoid primates, although not in other mammals, CYC and COX show markedly accelerated amino acid replacement rates, with the COX acceleration being much greater at the positions that bind CYC than at those that do not. Specifically, in the anthropoid lineage descending from the last common ancestor of haplorhines (tarsiers and anthropoids) to that of anthropoids (New World monkeys and catarrhines) and that of catarrhines (Old World monkeys and apes, including humans), a minimum of 27 of the 57 COX amino acid residues that bind CYC were replaced, most frequently from electrostatically charged to noncharged residues. Of the COX charge-bearing residues involved in binding CYC, half (11 of 22) have been replaced with uncharged residues. CYC residues that interact with COX residues also frequently changed, but only two of the CYC changes altered charge. We suggest that reducing the electrostatic interaction between COX and CYC was part of the adaptive evolution underlying the emergence of anthropoid primates. mitochondria ͉ electron transport chain ͉ molecular coevolution C ytochrome c (CYC) and the subunits of CYC oxidase (COX) are mitochondrial-functioning proteins that play a central role in aerobic energy production. By catalyzing the transfer of electrons from CYC to oxygen, COX greatly increases an electrochemical gradient used for ATP synthesis. As a consequence of their critical function, mutations altering the structures of either CYC or COX must face the close scrutiny of natural selection. Among vertebrates, relatively few amino acid replacements have occurred in the structures of CYC and COX. However, against this background of slow rates of CYC and COX evolution, upsurges in COX and CYC amino acid replacement rates occurred during the emergence and evolution of the larger brained primates (members of Anthropoidea) (1-12). Here, by using atomic resolution structural data on bovine COX (13) and horse CYC (14) and an experimentally verified model of the interaction between COX and CYC (15, 16), we identify, among the Ͼ1,500 amino acid residues of COX, 57 residues that are likely to bind CYC during delivery of electrons to oxygen. We then demonstrate that the amino acid replacement rate acceleration in anthropoid lineages is especially pronounced in the subset of COX residues that can bind CYC. We further demonstrate that, among these CYC-binding COX residues, many amino acid replacements were from charge-bearing [electros...

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“…We then show, in Section 3, that deciding if a gene tree is a DS-tree can be answered in linear time 4 , and that in such a case, there is a single species tree that is compatible with the corresponding Duplication/Speciation history. In the case where a given gene tree T is not a DS-tree, T can be derived from a DS-tree by a series of gene losses.…”

Section: Introductionmentioning

confidence: 99%

“…It can be described as "fitting a gene tree into a species tree", which is not obvious due to the possible incongruence between the two trees [10]. The main algorithmic approach developed to solve this problem, the gene tree/species tree reconciliation, allows to identify the duplications with respect to the speciation events in the species tree [4,13]. It is based on a mapping of the gene tree into the species tree, that can be done in linear time [15,3,16].…”

Section: Introductionmentioning

confidence: 99%

Inferring a Duplication, Speciation and Loss History from a Gene Tree

Chauve

Doyon

El-Mabrouk

2008

SciVee

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Abstract. We consider two questions related to the evolution of gene families. First, given a gene tree for a gene family, can the evolutionary history of this family be explained with only speciation and duplication events, and without gene loss. We show that this question can be answered in linear time, and that such a gene tree induces a single species tree consistent with a history with no loss. We then present a heuristic for the following problem: if a gene tree can not be explained without gene loss, what is the minimum number of losses involved in an evolutionary history of the gene family. We finally evaluate our algorithms on a dataset of plants gene families.

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Going nuclear: gene family evolution and vertebrate phylogeny reconciled

Cited by 83 publications

References 47 publications

Recent Advances in the (Molecular) Phylogeny of Vertebrates

Recent Advances in the (Molecular) Phylogeny of Vertebrates

Rapid electrostatic evolution at the binding site for cytochrome c on cytochrome c oxidase in anthropoid primates

Inferring a Duplication, Speciation and Loss History from a Gene Tree

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