@ARTICLE{TreeBASE2Ref16024,
author = {Simon Joly and Anne Bruneau},
title = {Incorporating Allelic Variation for Reconstructing the Evolutionary History of Organisms from Multiple Genes: an Example from Rosa in North America.},
year = {2006},
keywords = {},
doi = {10.1080/10635150600863109},
url = {},
pmid = {},
journal = {Systematic Biology},
volume = {55},
number = {4},
pages = {623--636},
abstract = {Allelic variation within individuals holds information regarding the relationships of organisms, which is expected to be particularly important for reconstructing the evolutionary history of closely related taxa. However, little effort has been committed to incorporate such information for reconstructing the phylogeny of organisms. Haplotype trees represent a solution when one non-recombinant marker is considered, but there is no satisfying method when multiple genes are to be combined. In this paper, we propose an algorithm that converts a distance matrix of alleles to a distance matrix of organisms. This algorithm allows the incorporation of allelic variation for reconstructing the phylogeny of organisms from one or more genes. The method is applied to reconstruct the phylogeny of the seven native diploid species of Rosa sect. Cinnamomeae in North America. The glyceralgehyde 3-phosphate dehydrogenase (GAPDH), the triose phosphate isomerase (TPI) and the malate synthase (MS) genes were sequenced for 40 individuals from these species. The three genes had little genetic variation and most species showed incomplete lineage sorting, suggesting these species have a recent origin. Despite these difficulties, the networks (NeighborNet) of organisms reconstructed from the matrix obtained with the algorithm recovered groups that more closely match taxonomic boundaries than did the haplotype trees. The combined network of individuals shows that species west of the Rocky Mountains, Rosa gymnocarpa and R. pisocarpa, form exclusive groups and that together they are distinct from eastern species. In the east, three groups were found to be exclusive: R. nitida ? R. palustris, R. foliolosa, and R. blanda ? R. woodsii. These groups are congruent with the morphology and the ecology of species. The method is also useful for representing hybrid individuals when the relationships are reconstructed using a phylogenetic network.}
}
Citation for Study 1500
Citation title:
"Incorporating Allelic Variation for Reconstructing the Evolutionary History of Organisms from Multiple Genes: an Example from Rosa in North America.".
This study was previously identified under the legacy study ID S1444
(Status: Published).
Citation
Joly S., & Bruneau A. 2006. Incorporating Allelic Variation for Reconstructing the Evolutionary History of Organisms from Multiple Genes: an Example from Rosa in North America. Systematic Biology, 55(4): 623-636.
Authors
Abstract
Allelic variation within individuals holds information regarding the relationships of organisms, which is expected to be particularly important for reconstructing the evolutionary history of closely related taxa. However, little effort has been committed to incorporate such information for reconstructing the phylogeny of organisms. Haplotype trees represent a solution when one non-recombinant marker is considered, but there is no satisfying method when multiple genes are to be combined. In this paper, we propose an algorithm that converts a distance matrix of alleles to a distance matrix of organisms. This algorithm allows the incorporation of allelic variation for reconstructing the phylogeny of organisms from one or more genes. The method is applied to reconstruct the phylogeny of the seven native diploid species of Rosa sect. Cinnamomeae in North America. The glyceralgehyde 3-phosphate dehydrogenase (GAPDH), the triose phosphate isomerase (TPI) and the malate synthase (MS) genes were sequenced for 40 individuals from these species. The three genes had little genetic variation and most species showed incomplete lineage sorting, suggesting these species have a recent origin. Despite these difficulties, the networks (NeighborNet) of organisms reconstructed from the matrix obtained with the algorithm recovered groups that more closely match taxonomic boundaries than did the haplotype trees. The combined network of individuals shows that species west of the Rocky Mountains, Rosa gymnocarpa and R. pisocarpa, form exclusive groups and that together they are distinct from eastern species. In the east, three groups were found to be exclusive: R. nitida ? R. palustris, R. foliolosa, and R. blanda ? R. woodsii. These groups are congruent with the morphology and the ecology of species. The method is also useful for representing hybrid individuals when the relationships are reconstructed using a phylogenetic network.
External links
About this resource
- Canonical resource URI:
http://purl.org/phylo/treebase/phylows/study/TB2:S1500
- Other versions:
Nexus
NeXML
- Show BibTeX reference
@ARTICLE{TreeBASE2Ref16024,
author = {Simon Joly and Anne Bruneau},
title = {Incorporating Allelic Variation for Reconstructing the Evolutionary History of Organisms from Multiple Genes: an Example from Rosa in North America.},
year = {2006},
keywords = {},
doi = {10.1080/10635150600863109},
url = {},
pmid = {},
journal = {Systematic Biology},
volume = {55},
number = {4},
pages = {623--636},
abstract = {Allelic variation within individuals holds information regarding the relationships of organisms, which is expected to be particularly important for reconstructing the evolutionary history of closely related taxa. However, little effort has been committed to incorporate such information for reconstructing the phylogeny of organisms. Haplotype trees represent a solution when one non-recombinant marker is considered, but there is no satisfying method when multiple genes are to be combined. In this paper, we propose an algorithm that converts a distance matrix of alleles to a distance matrix of organisms. This algorithm allows the incorporation of allelic variation for reconstructing the phylogeny of organisms from one or more genes. The method is applied to reconstruct the phylogeny of the seven native diploid species of Rosa sect. Cinnamomeae in North America. The glyceralgehyde 3-phosphate dehydrogenase (GAPDH), the triose phosphate isomerase (TPI) and the malate synthase (MS) genes were sequenced for 40 individuals from these species. The three genes had little genetic variation and most species showed incomplete lineage sorting, suggesting these species have a recent origin. Despite these difficulties, the networks (NeighborNet) of organisms reconstructed from the matrix obtained with the algorithm recovered groups that more closely match taxonomic boundaries than did the haplotype trees. The combined network of individuals shows that species west of the Rocky Mountains, Rosa gymnocarpa and R. pisocarpa, form exclusive groups and that together they are distinct from eastern species. In the east, three groups were found to be exclusive: R. nitida ? R. palustris, R. foliolosa, and R. blanda ? R. woodsii. These groups are congruent with the morphology and the ecology of species. The method is also useful for representing hybrid individuals when the relationships are reconstructed using a phylogenetic network.}
}
- Show RIS reference
TY - JOUR
ID - 16024
AU - Joly,Simon
AU - Bruneau,Anne
T1 - Incorporating Allelic Variation for Reconstructing the Evolutionary History of Organisms from Multiple Genes: an Example from Rosa in North America.
PY - 2006
KW -
UR - http://dx.doi.org/10.1080/10635150600863109
N2 - Allelic variation within individuals holds information regarding the relationships of organisms, which is expected to be particularly important for reconstructing the evolutionary history of closely related taxa. However, little effort has been committed to incorporate such information for reconstructing the phylogeny of organisms. Haplotype trees represent a solution when one non-recombinant marker is considered, but there is no satisfying method when multiple genes are to be combined. In this paper, we propose an algorithm that converts a distance matrix of alleles to a distance matrix of organisms. This algorithm allows the incorporation of allelic variation for reconstructing the phylogeny of organisms from one or more genes. The method is applied to reconstruct the phylogeny of the seven native diploid species of Rosa sect. Cinnamomeae in North America. The glyceralgehyde 3-phosphate dehydrogenase (GAPDH), the triose phosphate isomerase (TPI) and the malate synthase (MS) genes were sequenced for 40 individuals from these species. The three genes had little genetic variation and most species showed incomplete lineage sorting, suggesting these species have a recent origin. Despite these difficulties, the networks (NeighborNet) of organisms reconstructed from the matrix obtained with the algorithm recovered groups that more closely match taxonomic boundaries than did the haplotype trees. The combined network of individuals shows that species west of the Rocky Mountains, Rosa gymnocarpa and R. pisocarpa, form exclusive groups and that together they are distinct from eastern species. In the east, three groups were found to be exclusive: R. nitida ? R. palustris, R. foliolosa, and R. blanda ? R. woodsii. These groups are congruent with the morphology and the ecology of species. The method is also useful for representing hybrid individuals when the relationships are reconstructed using a phylogenetic network.
L3 - 10.1080/10635150600863109
JF - Systematic Biology
VL - 55
IS - 4
SP - 623
EP - 636
ER -