Reconstruction of Ancient Molecular Phylogeny

Guigó, Roderic; Muchnik, Ilya; Smith, Temple F.

doi:10.1006/mpev.1996.0071

Cited by 211 publications

(222 citation statements)

References 4 publications

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“…However, analyses at large taxonomic scales using nuclear genes are likely to encounter problems caused by gene duplication and resulting paralogy. As an example, Guigó et al 30 used a variant of reconciled trees to infer eukaryote phylogeny from 53 gene trees and discovered that only a third of the genes were perfectly consistent with the best fitting eukaryote tree. Although this study has flaws 31 , it suggests that great care must be taken in using nuclear genes as phylogenetic markers -individual genes or gene families can be quite misleading about species relationships.…”

Section: Applications Of Reconciled Treesmentioning

confidence: 99%

Trees within trees: phylogeny and historical associations

Page¹,

Charleston²

1998

Trends in Ecology & Evolution

271

239

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Section: Applications Of Reconciled Treesmentioning

confidence: 99%

Trees within trees: phylogeny and historical associations

Page¹,

Charleston²

1998

Trends in Ecology & Evolution

271

239

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“…Page (1994a), Mirkin et al (1995), and Guigo et al (1996) describe a method for inferring species trees from gene trees that avoids the problems discussed above. Under their method, the preferred species phylogeny is the one that minimizes the number of gene duplications plus gene losses necessary to fit each gene tree to the species tree.…”

Section: Inferring Species Trees From Gene Treesmentioning

confidence: 99%

Inferring Species Trees from Gene Trees: A Phylogenetic Analysis of the Elapidae (Serpentes) Based on the Amino Acid Sequences of Venom Proteins

Slowinski

Knight

Rooney

1997

Molecular Phylogenetics and Evolution

124

103

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Toward the goal of recovering the phylogenetic relationships among elapid snakes, we separately found the shortest trees from the amino acid sequences for the venom proteins phospholipase A 2 and the short neurotoxin, collectively representing 32 species in 16 genera. We then applied a method we term gene tree parsimony for inferring species trees from gene trees that works by finding the species tree which minimizes the number of deep coalescences or gene duplications plus unsampled sequences necessary to fit each gene tree to the species tree. This procedure, which is both logical and generally applicable, avoids many of the problems of previous approaches for inferring species trees from gene trees. The results support a division of the elapids examined into sister groups of the Australian and marine (laticaudines and hydrophiines) species, and the African and Asian species. Within the former clade, the sea snakes are shown to be diphyletic, with the laticaudines and hydrophiines having separate origins. This finding is corroborated by previous studies, which provide support for the usefulness of gene tree parsimony.

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“…An equivalent constructive definition, based on a mapping, called the LCA mapping between the gene tree T and the species tree S, was formulated in [55,88] and widely used [20,39,44,54,77,86,87,88,128]. The LCA mapping between T and S, denoted by M , maps every vertex x of T to the Lowest Common Ancestor (LCA) of L(x) in S. This Interestingly, M (T, S) not only minimizes the duplication cost, but also minimizes the loss and mutation costs [28].…”

Section: Optimization Criteriamentioning

confidence: 99%

“…In the present context, we are thus motivated to define larger classes of reconciliations, including M (T, S), but also sub-optimal solutions (with respect to the number of duplications) [38,54,55,89]. This allows to explore a larger space of reconciliations and alternative evolutionary scenarios for gene families.…”

Section: Optimization Criteriamentioning

confidence: 99%

Analysis of Gene Order Evolution Beyond Single-Copy Genes

El-Mabrouk

Sankoff

2012

Methods in Molecular Biology

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The purpose of this chapter is to provide a comprehensive review of the field of genome rearrangement, i.e., comparative genomics based on representation of genomes as ordered sequences of signed genes. We specifically focus on the "hard part" of genome rearrangement, how to handle duplicated genes. The main questions are: how have present-day genomes evolved from a common ancestor? What are the most realistic evolutionary scenarios explaining the observed gene orders? What was the content and structure of ancestral genomes? We aim to provide a concise but complete overview of the field, starting with the practical problem of finding an appropriate representation of a genome as a sequence of ordered genes or blocks, namely the problems of orthology, paralogy and synteny block identification. We then consider three levels of gene organization: the gene family level (evolution by duplication, loss and speciation), the cluster level (evolution by tandem duplications) and the genome level (all types of rearrangement events, including whole genome duplication).

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Reconstruction of Ancient Molecular Phylogeny

Cited by 211 publications

References 4 publications

Trees within trees: phylogeny and historical associations

Trees within trees: phylogeny and historical associations

Inferring Species Trees from Gene Trees: A Phylogenetic Analysis of the Elapidae (Serpentes) Based on the Amino Acid Sequences of Venom Proteins

Analysis of Gene Order Evolution Beyond Single-Copy Genes

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