PhyloGeographer Updated to YFull v7.09.01

All goals of the last development cycle were met.

7 New Geographic Codes Used For the First Time

  • Hebron, Palestine
  • Midelt, Morocco
  • Musundam, Oman
  • Ju┼żnobanatski okrug, Serbia
  • Kurbin, Albania
  • Causeway Coast and Glens, Northern Ireland
  • Isle of Bute, Scotland

Changes to Data

  • On 12/5 YFull had 21,296 samples – that’s 1001 more than my last update on 10/25. In six weeks they grew 5%! There should be even more soon given the Black Friday sales.
  • Haplogroup Statistics
  • 69 ancient samples from the New Collaboration System
  • I personally added all the samples from the recent ancient Roman and Italy study, based on classifications by Ted Kandell and for J-M241, Flor Veseli
  • Fixed bug in my code that was excluding 99 samples from far west Africa, west of -7 degrees longitude. They are all now in PhyloGeographer.

Changes to Algorithm

  1. Non-basal samples now being included – penalized by a factor of sample age / most specific determined clade TMRCA. Only samples who are at least half as old as this TMRCA are used.
  2. Geographic consistency of a subclade is now taken into account in the initial averaging – clades whose children have higher average distance to one another are now counted up to half as much as their more geographically consistent siblings in the weighted average to compute an initial location of the parent
  3. Change to refinement step for clades with exactly two subclades / samples – now uses linear interpolation to refine a clade’s position to be the point along the segment formed by its two children which is closest to the clade’s parent
  4. A second refinement pass has been added to the original process, which results in more intuitive, less jerky paths
  5. Less successive subclades computed on top of one another

Changes to My Ancestor’s Path Interface

Improved display of My Ancestor’s Path

Dates text and line changed to orange, font size decreased, line thickness increased

Changes to Crossing Paths Interface

  1. Can now enter a SNP directly (previously had to use time slider and check boxes)
  2. Removed staggering number of mouse hover controls that had prevented larger haplogroups from loading
  3. Toggle added to hide/show subclade labels
  4. Fixed bug that had prevented A0 from displaying due to major subclade having no geolocated samples

To see all these changes go here and select your haplogroup via the dropdown.

Goals for Next Update

  1. Finish the research articles for my Patreon patrons
  2. Get more people to collaborate by adding ancient samples, especially now that I have logic for including lower resolution samples
  3. Fix My Ancestor’s Path zoom issue
  4. Comigration Discovery – finish back end first, then have rudimentary view
  5. Geographic Code Map Viewer – to help find possible mistakes in my coordinates
  6. Create more specific haplogroup filtering in the Ancient Sample Map View

Things on my mind for the future

  • Allow collaborators to specify a corrected haplogroup location
  • Compute each subclade’s MRCA as a straight line that traveled from his birth location to where he may have died

I appreciate your patronage

I’m able to make this progress because I am not working full time for other people.

The PhyloGeographer project is not funded by any company, agency or institution.

If you want to fund it you can by donating to me here.

I also offer consulting services for interpreting Y chromosome tests and developing a testing strategy to achieve your goals. I charge $40 an hour and charge $40 minimum for new clients. To get started, you can send me your contact information through the comment form on this page.

Check out the services I offer on Patreon, including mapping, articles and sneak preview videos of my development.

 

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