I have opened this new thread to share our views, questions and opinions about the phylogeny of haplogroup E3b. As we know, E3b is an old and diverse haplogroup which comprises several subclades.
My initial assumption is that just as haplogroups can be predicted by statistical analysis of marker values of individual haplotypes, we can also predict or "infer" the subclades within our haplogroup by using the proper software tools to analyze a sample of E3b haplotypes.
The objective is to create a diagram or tree that will allow us to visually represent the main bifurcations of haplogroup E3b into its main subclades and then identify individual haplotypes by their Id. label in the ending branches.
The data that I've been using comes from the E3b project but since new members are joining all the time, some haplotypes are being upgraded from 12 markers to 25 or 37, etc., it is necessary to periodically update the E3b cladograms.
To look at a sample E3b cladogram click here.
The colors were added to highlight what I believe to be the three main subclades, that is E3b3, E3b1 and E3b2 in the order of appearance.
(I'll be posting a cladogram with the latest data soon.)
As to the software tools used to create the tree, there is a wide assortment of available software packages but I have opted for using some of the same tools that have proven useful in other DNA projects, namely McGee's YDNA comparison tool, PHYLIP (Phylogeny Inference Package), Tree View and Tree Explorer, plus a couple of other image conversion applications.
For an excellent primer on Phylogenetics I recommend visiting the National Center for Biotechnology Information .
What follows is some basic terminology about phylogenetic trees copied from the above page.
http://www.ncbi.nlm.nih.gov/About/pr.../treechart.gif
More to come...
My initial assumption is that just as haplogroups can be predicted by statistical analysis of marker values of individual haplotypes, we can also predict or "infer" the subclades within our haplogroup by using the proper software tools to analyze a sample of E3b haplotypes.
The objective is to create a diagram or tree that will allow us to visually represent the main bifurcations of haplogroup E3b into its main subclades and then identify individual haplotypes by their Id. label in the ending branches.
The data that I've been using comes from the E3b project but since new members are joining all the time, some haplotypes are being upgraded from 12 markers to 25 or 37, etc., it is necessary to periodically update the E3b cladograms.
To look at a sample E3b cladogram click here.
The colors were added to highlight what I believe to be the three main subclades, that is E3b3, E3b1 and E3b2 in the order of appearance.
(I'll be posting a cladogram with the latest data soon.)
As to the software tools used to create the tree, there is a wide assortment of available software packages but I have opted for using some of the same tools that have proven useful in other DNA projects, namely McGee's YDNA comparison tool, PHYLIP (Phylogeny Inference Package), Tree View and Tree Explorer, plus a couple of other image conversion applications.
For an excellent primer on Phylogenetics I recommend visiting the National Center for Biotechnology Information .
What follows is some basic terminology about phylogenetic trees copied from the above page.
- Node: represents a taxonomic unit. This can be either an existing species or an ancestor.
- Branch: defines the relationship between the taxa in terms of descent and ancestry.
- Topology: the branching patterns of the tree.
- Branch length: represents the number of changes that have occurred in the branch.
- Root: the common ancestor of all taxa.
- Distance scale: scale that represents the number of differences between organisms or sequences.
- Clade: a group of two or more taxa or DNA sequences that includes both their common ancestor and all of their descendents.
- Operational Taxonomic Unit (OTU): taxonomic level of sampling selected by the user to be used in a study, such as individuals, populations, species, genera, or bacterial strains.
http://www.ncbi.nlm.nih.gov/About/pr.../treechart.gif
More to come...
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