On Monday, October 14, 2013 2:12:02 PM UTC-7, Cathal Garvey wrote:
Yes, the genes selected for barcoding are definitely useful for phylogeny. With the exception of things like V(D)J recombination in immune receptors, there's no such thing as a "bio-hash" - just genes that evolve at different rates. Pick a slow evolving gene, and you won't be able to tell species apart, but you might be able to reconstruct deeper branchings between phyla. Pick a very fast evolving gene, and you might be able to tell strains or sub-strains apart, but a fast evolving gene will typically only be useful within a specific taxonomic range (and may not have the same rate of mutation across that entire range). The genes picked for the Barcodes of Life project are typically picked to give enough separation between species and genera, but may not have enough resolution to tell different strains apart - or to reconstruct the evolution of a new species, such as modern wheat from its ancestral strains.
To quote barcodeoflife.org:
This Plos One paper has a lot more info:
To tease apart the evolution of a specific species, you may need to look at features that mutate much faster, such as microsattelites or transposable elements:
See also:
Patrik
-- Does barcoding have any relevance to phylogeny? I thought it was like a
"bio-hash", with the output guaranteed to be unique but not necessarily
have any other useful purpose.. :)
Yes, the genes selected for barcoding are definitely useful for phylogeny. With the exception of things like V(D)J recombination in immune receptors, there's no such thing as a "bio-hash" - just genes that evolve at different rates. Pick a slow evolving gene, and you won't be able to tell species apart, but you might be able to reconstruct deeper branchings between phyla. Pick a very fast evolving gene, and you might be able to tell strains or sub-strains apart, but a fast evolving gene will typically only be useful within a specific taxonomic range (and may not have the same rate of mutation across that entire range). The genes picked for the Barcodes of Life project are typically picked to give enough separation between species and genera, but may not have enough resolution to tell different strains apart - or to reconstruct the evolution of a new species, such as modern wheat from its ancestral strains.
To quote barcodeoflife.org:
The gene region that is being used as the standard barcode for almost all animal groups is a 648 base-pair region in the mitochondrial cytochrome c oxidase 1 gene ("CO1"). COI is proving highly effective in identifying birds, butterflies, fish, flies and many other animal groups. COI is not an effective barcode region in plants because it evolves too slowly, but two gene regions in the chloroplast, matK and rbcL, have been approved as the barcode regions for plants.
This Plos One paper has a lot more info:
The outcome of these trials was that although some markers could be eliminated from consideration (e.g. rpoC1 and rpoB showed markedly lower discriminatory power), there was no straightforward solution as to which should form the plant barcode, as each of the candidate markers had different strengths and weaknesses. The majority preference of the CBOL Plant Working group was to recommend a core-barcode consisting of portions of two plastid coding regions, rbcL+matK, to be supplemented with additional markers as required [11]. The rbcL barcode consists of a 599 bp region at the 5′ end of the gene, located at bp 1–599 (including primer sites) in the complete Arabidopsis thaliana plastid genome sequence (gi 7525012:54958–56397). The matK barcode region consists of a ca. 841 bp region at the center of the gene, located between bp 205–1046 (including primer sites) in the complete A. thaliana plastid genome sequence (gi 7525012:2056–3570).
To tease apart the evolution of a specific species, you may need to look at features that mutate much faster, such as microsattelites or transposable elements:
Microsatellite markers: an overview of the recent progress in plants
Marker utility of miniature inverted-repeat transposable elements for wheat biodiversity and evolution
Marker utility of miniature inverted-repeat transposable elements for wheat biodiversity and evolution
See also:
Genetic Diversity, Evolution and Domestication of Wheat and Barley in the Fertile Crescent
Genetic diversity, evolution and domestication of Triticeae in the Fertile Crescent
Genetic diversity, evolution and domestication of Triticeae in the Fertile Crescent
Patrik
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