From Gene to Organismal Phylogeny: Reconciled Trees and the Gene Tree/Species Tree Problem

Page, Roderic; Charleston, Michael A.

doi:10.1006/mpev.1996.0390

Cited by 389 publications

(244 citation statements)

References 29 publications

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“…lactis, these strains are homothallic), the result of processes of lineage sorting of ancestral genetic polymorphism (Pamilo and Nei, 1988) and/or concerted evolution involving gene duplication or loss (Page and Charleston, 1997), in the case of ribosomal genes. Incongruences between gene trees and species trees are more likely when the time between species splitting is shorter (Pamilo and Nei, 1988;Hudson, 1992).…”

Section: Discussionmentioning

confidence: 99%

An analysis of inter- and intraspecific genetic variabilities in the Kluyveromyces marxianus group of yeast species for the reconsideration of the K. lactis taxon

Belloch¹,

Fernández-Espinar²,

Querol³

et al. 2002

Yeast

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In the present work, we analyse the sequences of the 5.8S rRNA gene and the two internal transcribed spacers 1 and 2 (5.8S-ITS region), obtained from 39 strains belonging to the species Kluyveromyces aestuarii, K. dobzhanskii, K. lactis and K. marxianus, K. nonfermentans and K. wickerhamii, to solve the phylogenetic relationships among these species and also to determine the possible genetic basis for the delimitation of the two currently accepted K. lactis varieties: lactis, including lactose-positive strains isolated from dairy products, and drosophilarum, comprising lactose-negative strains isolated from insects and plant exudates. The determination of the phylogenetic relationships within the species K. lactis, together with the examination of the electrophoretic karyotypes and phenotypic characterization of strains representatives of K. lactis var. lactis and var. drosophilarum, allowed differentiation of two groups of strains. The first, and ancestral, group comprises lactose-negative strains isolated from natural habitats in North America. The second, and derived, group includes both lactose-negative strains isolated from natural habitats in Europe and wine fermentation in South Africa, and lactose-positive strains associated with dairy products. These results suggest that the present taxon K. lactis is a complex of different species, subspecies or, at least, genetically structured populations.

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Section: Discussionmentioning

confidence: 99%

An analysis of inter- and intraspecific genetic variabilities in the Kluyveromyces marxianus group of yeast species for the reconsideration of the K. lactis taxon

Belloch¹,

Fernández-Espinar²,

Querol³

et al. 2002

Yeast

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show abstract

“…Instead, we have presented a method we call gene tree parsimony that operates by finding the species tree that minimizes a weighted sum of the different kinds of conflict-producing events necessary to fit each gene tree to the species tree. The program we used to implement gene tree parsimony, GeneTree (Page and Charleston, 1997), only allows one to minimize either deep coalescence or gene duplication, but not both simultaneously.…”

Section: Discussionmentioning

confidence: 99%

“…First, if there is sequence polymorphism within species, it is not obvious how this can be incorporated into a combined matrix: for species X, which sequences from gene A should be combined with which sequences from gene B? Second, the distinction between homoplasy and gene tree/species tree conflict is ignored (Page and Charleston, 1997). For example, if a gene tree is (AB)C and the true species tree is (AC)B, then any substitutions occurring along the branch of descent leading to (AB) on the gene tree will be interpreted as homoplasy in the context of the species tree, even though they are not homoplasies at all.…”

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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“…With the increasing availability of nuclear gene sequences 25 , reconciled trees may find ready application to the study of the evolution of gene diversity and the inference of organismal phylogeny from multiple, complex gene trees 26 , as well as tools for database analysis 27 . Recent work 28,29 suggests that lineage sorting within a single gene may pose less of a problem for phylogenetic inference than previously thought.…”

Section: Applications Of Reconciled Treesmentioning

confidence: 99%

Trees within trees: phylogeny and historical associations

Page¹,

Charleston²

1998

Trends in Ecology & Evolution

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From Gene to Organismal Phylogeny: Reconciled Trees and the Gene Tree/Species Tree Problem

Cited by 389 publications

References 29 publications

An analysis of inter- and intraspecific genetic variabilities in the Kluyveromyces marxianus group of yeast species for the reconsideration of the K. lactis taxon

An analysis of inter- and intraspecific genetic variabilities in the Kluyveromyces marxianus group of yeast species for the reconsideration of the K. lactis taxon

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

Trees within trees: phylogeny and historical associations

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