Have you seen Yfull's and YSEQ's new heatmap?

+4 votes
583 views

Hunter Provyn and Thomas Krahn have developed a heatmap, that shows the relative frequency of Y-DNA haplogroups. 

After you have found your own haplogroup you can climb in the Ytree back to your major branch like R or I.

in The Tree House by Ole Selmer G2G6 Mach 3 (30.2k points)
This will prove to be attractive to a lot of people who have been investigating their own Y-lines

2 Answers

+7 votes
 
Best answer

Thom stated in a catchy metaphor kinda what I was thinking after looking at this yesterday; so I agree. I think it's a way-cool idea, but it just doesn't seem quite ready for prime time.

Reading the methodology page closely, it still isn't clear precisely what is being displayed. Ancient samples are mentioned, and the bulk of the data is being pulled from YFull (which is understandable; the bioinformaticist who's presenting the data had a falling-out with FTDNA some time back).

It seems the heatmap is trying to display contemporary density, not anthropological timeframe origins. The author's main app, BTW, "Mygrations," is quite good (again, as far the available data go) at approximating an animated yDNA anthropological timeline: https://phylogeographer.com/snp-lookup/.

But for the heatmaps, ancient samples really don't matter much: there are so few significantly sequenced ancient remains (most have only limited SNP and/or STR results because they were done circa pre-2015) that they really wouldn't blip the radar on a contemporary population heatmap.

Having been a customer of YFull's for a couple of years, I honestly don't know where reasonably accurate geolocation information could be coming from in their database...unless it is not from contemporary user-submitted data at all. For my paid account, YFull has my mailing address and my subjective estimate of the country my EKA was born in. So for me YFull has USA and GBR on file: where I lived when I purchased the service, and where I think my EKA hails from.

I could have guessed Fiji for my EKA because for none of the SNPs/haplogroups I tried was there ever any results at all on the heatmap in North or South America. Nada. And for many, there are small hotspots out in the middle of the Atlantic Ocean.

More yDNA test takers are in North America than anywhere else, and FTDNA and its database are the industry's 800-pound gorilla for yDNA. There are very large numbers of R1b and, downstream, M269 men in North America. That absolutely is not displayed in the heatmaps. In fact, for M269 and several steps deeper, down to DF27, North America remains zeroed but a perennial hot-spot shows up in the Philippines. Southeast Asia. Almost exactly the opposite side of the world from where actual contemporary concentrations of M269 or DF27 would be.

A separate issue with YFull is they have long maintained some instances of analyses and haplotree branch taxonomy that are in distinct disagreement with FTDNA. As an example--while both SNPs were first discovered and named by FTDNA--YFull and FTDNA have me placed on entirely different branches of R-BY3332. YFull thinks I (and by extrapolation the 36 test-takers in my Williams yDNA subproject) am BY3332 > BY19276 (which is an analog of L881). FTDNA has us as BY3332 > BY22166 > BY22194 > BY35076 > BY35083. So in other words, that haplotree branching occurred sometime around 4,000 years ago and FTDNA and YFull thinks our ancestors took two different branches of the tree at that time. Depending on your individual results, there can be a huge disconnect between the data reported by FTDNA, who does the vast majority of full-sequence DNA testing right now, and YFull, who does no testing at all.

As a final comment, for those who try the utility, keep in mind that it seems to be case-sensitive for the input. Too, valid input is inconsistent. For example, if you want to look at haplogroup G or E, just type "G" or "E". Doesn't worth with others like I, J, K, R, etc. "R1b" works, "R1b1" doesn't. L151 is barely there; its parent branch, P310, is nonexistent, while its child branch, P312, shows high densities throughout Europe...and, of course, the Philippines. So if at first your searches don't succeed, try reformatting the input query, or moving up or down the particular haplotree branch. And take the results with a grain of salt.

by Edison Williams G2G6 Pilot (309k points)
selected by Ole Selmer
+4 votes
It has sizzle but where's the steak?
by Thom Anderson G2G6 Mach 5 (53.2k points)

I think it shows pretty well that the Swedish vikings mainly went eastward just looking at your haplogroup I-Y37109 

By missing the steak, I mean that I see little that makes me understand how these data are derived and what they mean.

Maybe some gravy here Frequency Heatmaps Usage

Well, fudgesicle! Thanks, Ole. That little question mark above the intensity adjustment was there all along. I ignored it because I thought it was just a popup describing what happens when you increase or decrease the intensity. The developer would really do himself a favor if he were to change that link title to something like "FAQs."

Another associated help page that would probably be more useful if it were presented as a link from the main heatmap page: https://phylogeographer.com/what-do-all-these-codes-mean/.

And the M269/DF27 mystery in Southeast Asia? I think that's solved, thanks to you.

And why, very strangely at first glance, the map shows nada for North America. See https://phylogeographer.com/yfull-world-sampling-rate-map/: "Paternal line country origins self reported from YFull customers."

It really isn't a population heatmap at all; and it also isn't an anthropological origin heatmap. It's a self-reported "I think my 3g-grandfather came from here" heatmap.

The Philippine mystery: Only 12 test-takers in YFull's database said that their earliest known patrilineal ancestors were already in the Philippines. A grand total of one of them happened to test deep in the DF27 subclade. Which means, of course, his patrilineal line didn't originate in the Philippines at all, or Oceania or Asia. But the result is that he displays as a one-man hotspot of that decidedly European haplogroup, out there by himself in the Pacific Ocean.

Only Native Americans have their origin in North America. The rest of us pretty much understand the fact that we're mutts, amalgams of peoples who came from almost everywhere else. The YFull data that's feeding the map shows that, in 1960 numbers, the U.S. had a population of 180.67 million...but shows only 1,102 yDNA test takers are in the U.S. Sweden, by contrast, is showing an even larger number of test takers than the U.S.--1,134--but a 1960 population of 7.48 million, only 4.1% that of the U.S.

The heatmaps are more fun to play with now that I understand them better. But I'd still contend that we have some skewed bioinformatics going on here; that the maps aren't doing a great job of conveying what I believe they're trying to convey.

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