@ARTICLE{TreeBASE2Ref20792,
author = {Frida Belinky and Amir Szitenberg and Itay Goldfarb and Tamar Feldstein and Gert W?rheide and Micha Ilan and Doroth?e Huchon},
title = {ALG11 - A new variable DNA marker for sponge phylogeny: Comparison of phylogenetic performances with the 18S rDNA and the COI gene.},
year = {2012},
keywords = {18S rDNA; Alg11; CO1; Cnidaria; Molecular phylogeny; Porifera; Saturation},
doi = {10.1016/j.ympev.2012.02.008},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22387211},
pmid = {22387211},
journal = {Molecular Phylogenetics and Evolution},
volume = {63},
number = {3},
pages = {702--713},
abstract = {Phylogenetic relationships within sponge classes are highly debated. The low phylogenetic signal observed with some current molecular data can be attributed to the use of few markers, usually slowly-evolving, such as the nuclear rDNA genes and the mitochondrial COI gene. In this study, we conducted a bioinformatics search for a new molecular marker. We sought a marker that (1) is likely to have no paralogs; (2) evolves under a fast evolutionary rate; (3) is part of a continuous exonic region; and (4) is flanked by conserved regions. Our search suggested the nuclear ALG11 as a potential suitable marker. We next demonstrated that this marker can indeed be used for solving phylogenetic relationships within sponges. Specifically, we successfully amplified the ALG11 gene from DNA samples of representatives from all four sponge classes as well as from several cnidarian classes. We also amplified the 18S rDNA and the COI gene for these species. Finally, we analyzed the phylogenetic performance of ALG11 to solve sponge relationships compared to and in combination with the nuclear 18S rDNA and the COI mtDNA genes. Interestingly, the ALG11 marker seems to be superior to the widely-used COI marker. Our work thus indicates that the ALG11 marker is a relevant marker which can complement and corroborate the phylogenetic inferences observed with nuclear ribosomal genes. This marker is also expected to contribute to resolving evolutionary relationships of other apparently slow-evolving animal phyla, such as cnidarians.}
}
Citation for Study 12822
Citation title:
"ALG11 - A new variable DNA marker for sponge phylogeny: Comparison of phylogenetic performances with the 18S rDNA and the COI gene.".
Study name:
"ALG11 - A new variable DNA marker for sponge phylogeny: Comparison of phylogenetic performances with the 18S rDNA and the COI gene.".
This study is part of submission 12822
(Status: Published).
Citation
Belinky F., Szitenberg A., Goldfarb I., Feldstein T., W?rheide G., Ilan M., & Huchon D. 2012. ALG11 - A new variable DNA marker for sponge phylogeny: Comparison of phylogenetic performances with the 18S rDNA and the COI gene. Molecular Phylogenetics and Evolution, 63(3): 702-713.
Authors
-
Belinky F.
-
Szitenberg A.
-
Goldfarb I.
-
Feldstein T.
-
W?rheide G.
-
Ilan M.
-
Huchon D.
Abstract
Phylogenetic relationships within sponge classes are highly debated. The low phylogenetic signal observed with some current molecular data can be attributed to the use of few markers, usually slowly-evolving, such as the nuclear rDNA genes and the mitochondrial COI gene. In this study, we conducted a bioinformatics search for a new molecular marker. We sought a marker that (1) is likely to have no paralogs; (2) evolves under a fast evolutionary rate; (3) is part of a continuous exonic region; and (4) is flanked by conserved regions. Our search suggested the nuclear ALG11 as a potential suitable marker. We next demonstrated that this marker can indeed be used for solving phylogenetic relationships within sponges. Specifically, we successfully amplified the ALG11 gene from DNA samples of representatives from all four sponge classes as well as from several cnidarian classes. We also amplified the 18S rDNA and the COI gene for these species. Finally, we analyzed the phylogenetic performance of ALG11 to solve sponge relationships compared to and in combination with the nuclear 18S rDNA and the COI mtDNA genes. Interestingly, the ALG11 marker seems to be superior to the widely-used COI marker. Our work thus indicates that the ALG11 marker is a relevant marker which can complement and corroborate the phylogenetic inferences observed with nuclear ribosomal genes. This marker is also expected to contribute to resolving evolutionary relationships of other apparently slow-evolving animal phyla, such as cnidarians.
Keywords
18S rDNA; Alg11; CO1; Cnidaria; Molecular phylogeny; Porifera; Saturation
External links
About this resource
- Canonical resource URI:
http://purl.org/phylo/treebase/phylows/study/TB2:S12822
- Other versions:
Nexus
NeXML
- Show BibTeX reference
@ARTICLE{TreeBASE2Ref20792,
author = {Frida Belinky and Amir Szitenberg and Itay Goldfarb and Tamar Feldstein and Gert W?rheide and Micha Ilan and Doroth?e Huchon},
title = {ALG11 - A new variable DNA marker for sponge phylogeny: Comparison of phylogenetic performances with the 18S rDNA and the COI gene.},
year = {2012},
keywords = {18S rDNA; Alg11; CO1; Cnidaria; Molecular phylogeny; Porifera; Saturation},
doi = {10.1016/j.ympev.2012.02.008},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22387211},
pmid = {22387211},
journal = {Molecular Phylogenetics and Evolution},
volume = {63},
number = {3},
pages = {702--713},
abstract = {Phylogenetic relationships within sponge classes are highly debated. The low phylogenetic signal observed with some current molecular data can be attributed to the use of few markers, usually slowly-evolving, such as the nuclear rDNA genes and the mitochondrial COI gene. In this study, we conducted a bioinformatics search for a new molecular marker. We sought a marker that (1) is likely to have no paralogs; (2) evolves under a fast evolutionary rate; (3) is part of a continuous exonic region; and (4) is flanked by conserved regions. Our search suggested the nuclear ALG11 as a potential suitable marker. We next demonstrated that this marker can indeed be used for solving phylogenetic relationships within sponges. Specifically, we successfully amplified the ALG11 gene from DNA samples of representatives from all four sponge classes as well as from several cnidarian classes. We also amplified the 18S rDNA and the COI gene for these species. Finally, we analyzed the phylogenetic performance of ALG11 to solve sponge relationships compared to and in combination with the nuclear 18S rDNA and the COI mtDNA genes. Interestingly, the ALG11 marker seems to be superior to the widely-used COI marker. Our work thus indicates that the ALG11 marker is a relevant marker which can complement and corroborate the phylogenetic inferences observed with nuclear ribosomal genes. This marker is also expected to contribute to resolving evolutionary relationships of other apparently slow-evolving animal phyla, such as cnidarians.}
}
- Show RIS reference
TY - JOUR
ID - 20792
AU - Belinky,Frida
AU - Szitenberg,Amir
AU - Goldfarb,Itay
AU - Feldstein,Tamar
AU - W?rheide,Gert
AU - Ilan,Micha
AU - Huchon,Doroth?e
T1 - ALG11 - A new variable DNA marker for sponge phylogeny: Comparison of phylogenetic performances with the 18S rDNA and the COI gene.
PY - 2012
KW - 18S rDNA; Alg11; CO1; Cnidaria; Molecular phylogeny; Porifera; Saturation
UR - http://www.ncbi.nlm.nih.gov/pubmed/22387211
N2 - Phylogenetic relationships within sponge classes are highly debated. The low phylogenetic signal observed with some current molecular data can be attributed to the use of few markers, usually slowly-evolving, such as the nuclear rDNA genes and the mitochondrial COI gene. In this study, we conducted a bioinformatics search for a new molecular marker. We sought a marker that (1) is likely to have no paralogs; (2) evolves under a fast evolutionary rate; (3) is part of a continuous exonic region; and (4) is flanked by conserved regions. Our search suggested the nuclear ALG11 as a potential suitable marker. We next demonstrated that this marker can indeed be used for solving phylogenetic relationships within sponges. Specifically, we successfully amplified the ALG11 gene from DNA samples of representatives from all four sponge classes as well as from several cnidarian classes. We also amplified the 18S rDNA and the COI gene for these species. Finally, we analyzed the phylogenetic performance of ALG11 to solve sponge relationships compared to and in combination with the nuclear 18S rDNA and the COI mtDNA genes. Interestingly, the ALG11 marker seems to be superior to the widely-used COI marker. Our work thus indicates that the ALG11 marker is a relevant marker which can complement and corroborate the phylogenetic inferences observed with nuclear ribosomal genes. This marker is also expected to contribute to resolving evolutionary relationships of other apparently slow-evolving animal phyla, such as cnidarians.
L3 - 10.1016/j.ympev.2012.02.008
JF - Molecular Phylogenetics and Evolution
VL - 63
IS - 3
SP - 702
EP - 713
ER -