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E3b project cladograms

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  • Bill Harvey
    replied
    E3b median-joining diagram : for 37 markers also?

    Victor ,

    This newest version gives the same basic info as the prior format (my personal favorite of the three recent trees) but seems to accentuate the difference M81 shows in relationship to M78 and M123 - these latter indicate a distinct separation from one another but not as sharply as M81 shows a separation from the other two clades in your latest effort.

    Is this primarily due to only having one test in the M123 clade? - whereas the other two have numerous test samples.

    I would like to see the results of all 37 markers in a run using the same format as your prior tree. I would like to begin trying to sort out the potential M123 testees from all the rest and am curious as to whether the additional 12 markers will be of any assistance in determining specific modal differences?

    If it is a lot of work - just forget about doing it. I'll probably take forever to figure it out anyway!

    Bill

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  • Victor
    replied
    E3b median-joining diagram

    One more visual representation of the same data:
    http://img.villagephotos.com/p/2005-.../e3b_25_MJ.jpg

    Leave a comment:


  • Victor
    replied
    Originally posted by Bill Harvey
    Victor,

    Ok - thanks for the taxonomic link and the definitions.

    If I am reading this correctly the "Root" for this tree would simply be an extension (to the left or "upstream") of the first horizontal line that joins the three clades - and that extension would be labeled E3b M-35+ as all ancestors of anyone in this specific tree would have this SNP as well as all descendants.

    Then the intersection of the first vertical line would be the node (M-123+) for E3b3 clade.

    The intersection with the 2nd vertical line would be the nodes designating E3b1 (M-78+) and E3b2 (M81+) being the upper and lower segments respectively of this vertical line.

    It does appear that the last four haplotypes included in the M-78+ group may be forming a sub-clade - it would be interesting to see one of the closely grouped threesome be "deeper" SNP tested.

    Thanks for your cladogram efforts!

    Bill
    You're right, Bill. The diagram doesn't actually show the root but it would be, as you say an extension to the left of the first line that joins the three clades.

    The following new diagram offers a new perspective and I made my interpretation of what clades the branches represent.

    http://img.villagephotos.com/p/2005-...25_dec03cb.jpg

    What I've noticed since I started doing the cladograms when there were only close to 40 records is that as new records are added the haplotypes get rearranged a little bit within their own cluster. What has remained more or less constant are the three main branches, including the top one which at the moment represents a single haplotype.

    Victor

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  • Bill Harvey
    replied
    Root location on current E3b cladogram

    Victor,

    Ok - thanks for the taxonomic link and the definitions.

    If I am reading this correctly the "Root" for this tree would simply be an extension (to the left or "upstream") of the first horizontal line that joins the three clades - and that extension would be labeled E3b M-35+ as all ancestors of anyone in this specific tree would have this SNP as well as all descendants.

    Then the intersection of the first vertical line would be the node (M-123+) for E3b3 clade.

    The intersection with the 2nd vertical line would be the nodes designating E3b1 (M-78+) and E3b2 (M81+) being the upper and lower segments respectively of this vertical line.

    It does appear that the last four haplotypes included in the M-78+ group may be forming a sub-clade - it would be interesting to see one of the closely grouped threesome be "deeper" SNP tested.

    Thanks for your cladogram efforts!

    Bill

    Leave a comment:


  • Victor
    started a topic E3b project cladograms

    E3b project cladograms

    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.
    • 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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