FrogEyes
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Several interesting papers have appeared this year in a journal new to me:
Xia, Y., H.-f. Gu, R. Peng, Q. Chen, Y.-c. Zheng, R.W. Murphy, and X.-m. Zeng. 2012. COI is better than 16S rRNA for DNA barcoding Asiatic salamanders (Amphibia: Caudata: Hynobiidae). Molecular Ecology Resources 12: 48–56. DOI: 10.1111/j.1755-0998.2011.03055.x.
The 5' region of the mitochondrial DNA (mtDNA) gene cytochrome c oxidase I (COI) is the standard marker for DNA barcoding. However, because COI tends to be highly variable in amphibians, sequencing is often challenging. Consequently, another mtDNA gene, 16S rRNA gene, is often advocated for amphibian barcoding. Herein, we directly compare the usefulness of COI and 16S in discriminating species of hynobiid salamanders using 130 individuals. Species identification and classification of these animals, which are endemic to Asia, are often based on morphology only. Analysis of Kimura 2-parameter genetic distances (K2P) documents the mean intraspecific variation for COI and 16S rRNA genes to be 1.4% and 0.3%, respectively. Whereas COI can always identify species, sometimes 16S cannot. Intra- and interspecific genetic divergences occasionally overlap in both markers, thus reducing the value of a barcoding gap to identify genera. Regardless, COI is the better DNA barcoding marker for hynobiids. In addition to the comparison of two potential markers, high levels of intraspecific divergence in COI (>5%) suggest that both Onychodactylus fischeri and Salamandrella keyserlingii might be composites of cryptic species.
Available free: COI is better than 16S rRNA for DNA barcoding Asiatic salamanders (Amphibia: Caudata: Hynobiidae) - XIA - 2011 - Molecular Ecology Resources - Wiley Online Library
Che, J. H.-M. Chen, J.-Q. Jin, J.-X. Yang, K. Jiang, Z.-Y. Yuan, R.W. Murphy, and Y.-P. Zhang. 2012. Universal COI primers for DNA barcoding amphibians. Molecular Ecology Resources 12(2): 247–258. DOI: 10.1111/j.1755-0998.2011.03090.x.
DNA barcoding is a proven tool for the rapid and unambiguous identification of species, which is essential for many activities including the vouchering tissue samples in the genome 10K initiative, genealogical reconstructions, forensics and biodiversity surveys, among many other applications. A large-scale effort is underway to barcode all amphibian species using the universally sequenced DNA region, a partial fragment of mitochondrial cytochrome oxidase subunit I COI. This fragment is desirable because it appears to be superior to 16S for barcoding, at least for some groups of salamanders. The barcoding of amphibians is essential in part because many species are now endangered. Unfortunately, existing primers for COI often fail to achieve this goal. Herein, we report two new pairs of primers (?, ?) that in combination serve to universally amplify and sequence all three orders of Chinese amphibians as represented by 36 genera. This taxonomic diversity, which includes caecilians, salamanders and frogs, suggests that the new primer pairs will universally amplify COI for the vast majority species of amphibians.
Available by request from Dr. Bob Murphy at the University of Toronto, or by download from your favorite academic library.
Relatively few amphibians [especially non-frogs] are included in the published paper, but I think this is the published version of a presentation I have previously reported. The latter included a more extensive survey of salamanders, including multiple populations and undescribed species.
GREENWALD, K. R. and LISLE GIBBS, H. (2012), A single nucleotide polymorphism assay for the identification of unisexual Ambystoma Salamanders. Molecular Ecology Michigan University, 316 Mark Jefferson, Ypsilanti, MI 48197, USA
Unisexual (all female) salamanders in the genus Ambystoma are animals of variable ploidy (2N-5N) that reproduce via a unique system of ‘leaky’ gynogenesis. As a result, these salamanders have a diverse array of nuclear genome combinations from up to five sexual species: the blue-spotted (A. laterale), Jefferson (A. jeffersonianum), smallmouth (A. texanum), tiger (A. tigrinum) and streamside (A. barbouri) salamanders. Identifying the genome complement, or biotype, is a critical first step in addressing a broad range of ecological and evolutionary questions about these salamanders. Previous work relied upon genome-related differences in allele size distributions for specific microsatellite loci, but overlap in these distributions among different genomes makes definitive identification and ploidy determination in unisexuals difficult or impossible. Here, we develop the first single nucleotide polymorphism assay for the identification of unisexual biotypes, based on species-specific nucleotide polymorphisms in noncoding DNA loci. Tests with simulated and natural unisexual DNA samples show that this method can accurately identify genome complement and estimate ploidy, making this a valuable tool for assessing the genome composition of unisexual samples.
Check your favorite academic library to download a copy.
I should note that all of these salamanders apparently share a single female ancestor of an extinct species related to A.barbouri. One could in theory assign all the gynogenetic forms to the oldest 'hybrid' species name, as they share the same ancestor and their oddball [and somewhat intermixing] reproduction.
Xia, Y., H.-f. Gu, R. Peng, Q. Chen, Y.-c. Zheng, R.W. Murphy, and X.-m. Zeng. 2012. COI is better than 16S rRNA for DNA barcoding Asiatic salamanders (Amphibia: Caudata: Hynobiidae). Molecular Ecology Resources 12: 48–56. DOI: 10.1111/j.1755-0998.2011.03055.x.
The 5' region of the mitochondrial DNA (mtDNA) gene cytochrome c oxidase I (COI) is the standard marker for DNA barcoding. However, because COI tends to be highly variable in amphibians, sequencing is often challenging. Consequently, another mtDNA gene, 16S rRNA gene, is often advocated for amphibian barcoding. Herein, we directly compare the usefulness of COI and 16S in discriminating species of hynobiid salamanders using 130 individuals. Species identification and classification of these animals, which are endemic to Asia, are often based on morphology only. Analysis of Kimura 2-parameter genetic distances (K2P) documents the mean intraspecific variation for COI and 16S rRNA genes to be 1.4% and 0.3%, respectively. Whereas COI can always identify species, sometimes 16S cannot. Intra- and interspecific genetic divergences occasionally overlap in both markers, thus reducing the value of a barcoding gap to identify genera. Regardless, COI is the better DNA barcoding marker for hynobiids. In addition to the comparison of two potential markers, high levels of intraspecific divergence in COI (>5%) suggest that both Onychodactylus fischeri and Salamandrella keyserlingii might be composites of cryptic species.
Available free: COI is better than 16S rRNA for DNA barcoding Asiatic salamanders (Amphibia: Caudata: Hynobiidae) - XIA - 2011 - Molecular Ecology Resources - Wiley Online Library
Che, J. H.-M. Chen, J.-Q. Jin, J.-X. Yang, K. Jiang, Z.-Y. Yuan, R.W. Murphy, and Y.-P. Zhang. 2012. Universal COI primers for DNA barcoding amphibians. Molecular Ecology Resources 12(2): 247–258. DOI: 10.1111/j.1755-0998.2011.03090.x.
DNA barcoding is a proven tool for the rapid and unambiguous identification of species, which is essential for many activities including the vouchering tissue samples in the genome 10K initiative, genealogical reconstructions, forensics and biodiversity surveys, among many other applications. A large-scale effort is underway to barcode all amphibian species using the universally sequenced DNA region, a partial fragment of mitochondrial cytochrome oxidase subunit I COI. This fragment is desirable because it appears to be superior to 16S for barcoding, at least for some groups of salamanders. The barcoding of amphibians is essential in part because many species are now endangered. Unfortunately, existing primers for COI often fail to achieve this goal. Herein, we report two new pairs of primers (?, ?) that in combination serve to universally amplify and sequence all three orders of Chinese amphibians as represented by 36 genera. This taxonomic diversity, which includes caecilians, salamanders and frogs, suggests that the new primer pairs will universally amplify COI for the vast majority species of amphibians.
Available by request from Dr. Bob Murphy at the University of Toronto, or by download from your favorite academic library.
Relatively few amphibians [especially non-frogs] are included in the published paper, but I think this is the published version of a presentation I have previously reported. The latter included a more extensive survey of salamanders, including multiple populations and undescribed species.
GREENWALD, K. R. and LISLE GIBBS, H. (2012), A single nucleotide polymorphism assay for the identification of unisexual Ambystoma Salamanders. Molecular Ecology Michigan University, 316 Mark Jefferson, Ypsilanti, MI 48197, USA
Unisexual (all female) salamanders in the genus Ambystoma are animals of variable ploidy (2N-5N) that reproduce via a unique system of ‘leaky’ gynogenesis. As a result, these salamanders have a diverse array of nuclear genome combinations from up to five sexual species: the blue-spotted (A. laterale), Jefferson (A. jeffersonianum), smallmouth (A. texanum), tiger (A. tigrinum) and streamside (A. barbouri) salamanders. Identifying the genome complement, or biotype, is a critical first step in addressing a broad range of ecological and evolutionary questions about these salamanders. Previous work relied upon genome-related differences in allele size distributions for specific microsatellite loci, but overlap in these distributions among different genomes makes definitive identification and ploidy determination in unisexuals difficult or impossible. Here, we develop the first single nucleotide polymorphism assay for the identification of unisexual biotypes, based on species-specific nucleotide polymorphisms in noncoding DNA loci. Tests with simulated and natural unisexual DNA samples show that this method can accurately identify genome complement and estimate ploidy, making this a valuable tool for assessing the genome composition of unisexual samples.
Check your favorite academic library to download a copy.
I should note that all of these salamanders apparently share a single female ancestor of an extinct species related to A.barbouri. One could in theory assign all the gynogenetic forms to the oldest 'hybrid' species name, as they share the same ancestor and their oddball [and somewhat intermixing] reproduction.