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Showing posts with label y. Show all posts
Showing posts with label y. Show all posts

Tuesday, October 31, 2017

Vitus, new Krchak introduced into the world!

Hello everyone and sorry for the prolonged hiatus. Did I ever mention that maintaining a bilingual blog is twice the work of maintaining a single language blog?
Also, did I ever mention that taking care of three kids is almost the same like taking care of two, but it still means you will have even less time for your hobbies as a result?

Well, let's get to work then. You aren't here to hear me complain!

So Vitus. Vitus Krchak. Third in this generation (~2010 generation) of Czech Krchaks. We are on the verge of extinction.

So who are we? Male Krchaks? Coming from Hornacko region, in south east Moravia? I started glimpsing into the paternal linage by taking the 23andMe autosomal V4 test, that included several thousand Y chromosome SNPs.


I was denoted I2b* branch, but some small research against the ISOGG Y tree revealed I am actually I-M423, I2a1b branch.
23andMe offers some haplogroup history write-up on their own, but the best source is probably eupedia. There, I learned about the basic I-M423 history.

I clearly saw that SNPs are so much more powerful for Y research than STRs and chose the next step as a I-M423 panel at yseq.net. This is a great price performance ratio, and the yseq.net team goes out of their way to always keep their panels updated with latest developments. Big kudos to Thomas Krahn and team.
This offered me my terminal SNP of I-Y16473 and 4 closest matches - Narog, Telencio, Rohaly and Girya. Poland, Poland, Hungary and Ukraine. Most recent ancestor 200AD. Slavic expansion!
Awesome.
To be able to identify the I-S17250 and it's nearest subclades so clearly with the Slavic expansion in early centuries of AD was a great feeling and justification of the testing effort.



The next step in my Krchak lineage research was a small STR test. This was done for free thanks to a great Czech project "Genealogy and surnames", which tries to map various surnames to haplogroups - genebaze.cz/gap.html (Czech only).
So what did I learn there? How could a small STR test add something to state-of-the-art SNP test? Easily. There SO MANY genealogists, that have only done STR testing, that while SNP testing is superior, to provide better timeline and paternal tree, you should not omit STRs.
In my case, this meant some close Slovak matches, that have not done SNP testing, that hint at correctness of the family lore, that Krchaks came to Hornacko region from Slovakia.
(This is further strengthened but quite close Slovak autosomal matches on my paternal grandfather "quarter" of my DNA.)
Macak. Orava. I hope I will get them to test some SNPs one day.
The ID on ysearch.org is AH7EK. Which is also linked to my WikiTree account.

As I always say, there are two approaches, you can take with your Y reseach. Active or passive.
Passive means waiting, for your matches to test, for them to pave you the SNP way. It is the cheaper road. Yet, it may never get you anywhere.
Active means acting. Testing that NGS Y chromosome test. Finding your novel SNPs. Working with the testing companies to get some of them on their panels and their single SNP tests. Working with your matches to try to verify if they have any of these SNPs common with you. Trying to motivate your distant cousins to do a NGS Y chromosome test too. This will be (much) more expensive but will lead to results so much more likely so much faster.

Of course I choose the active path, so here I was, buying a Big Y test from FTDNA. Or was I?

FTDNA requires you to purchase a STR test, before buying a BigY test. This is probably fair, because you don't want to spend 400$ on your cousin to find he was a NPE.
You can order a 12STR test through a project, to save most money, but I wanted to tackle FTDNA STR database and went for 37STR markers. This added roughly 15 on top of what I had from GAP.

Was it worth it? Not much. Would I do it again? Yes.
The FTDNA limit for matches on 37STR level on FTDNA is very strict to motivate you to purchase 67 or 111 panel. I consider this an ugly money-poaching tactic, but it is, what it is.
FTDNA earns their living off of STR testing after all.

Nothing tangible I got from the 37STR test, but there is always a chance to persuade some of my matches to test BigY. Study modal STR values on various SNP levels, etc.


With the STR test out of my way, the BigY was finally in sight. Except it was further than it seemed, taking over 3 months... Eventually, the test happened, and boy did it deliver.

New terminal SNP with my match Larry Telencio. I-FGC40352. Super awesome. Super exciting. Y-tree in the making.
On top of that I got 8 unnamed variants (that actually included two named SNPs, but nevermind).
Potential for further research closer to present. Give it to me!

Was I done? Not yet. The NGS test are notoriously hard to analyze. And FTDNA does not do a very good job. That is why everyone who takes Y research seriously goes one step further and orders detailed analysis of his BAM file for 49$ on https://www.yfull.com.
There are three milestones:

  1. SNP results - this is the foundation of the analysis, finding any new terminal SNPs
  2. STR results - this offers a more profound look at the STR landscape
  3. new Tree being published - this finally offers the age estimate of your new terminal SNP

All in all, I am fairly advanced in terms of my Y research, that my son will carry.
Still, more things remain.

Persuading close matches to test BigY or my novel SNPs. I hope I will succeed with some of them (you).
Buying BigY for known distant cousins so that we can better define the older novel SNPs and the most recent one, as well as get the branch on various trees (YFull, ISOGG, FTDNA).

Another year, another step forward. I am looking forward to learning more in 2018.

Saturday, December 10, 2016

Nedávný výzkum otcovské linie

Můžete si o mě třeba myslet, že jsem držgrešle, ale rád neutrácím bezhlavě a za svoje peníze chci, co si zasloužím. Když jsem v říjnu uviděl slevu na yseq.net, konečně jsem se rozhoupal lépe prozkoumat svou otcovskou linii - Krcháky. Data z 23andMe (haploskupina I-M423) mě dovedly jen do doby před asi 14000 lety, kdy v Evropě ustupovali ledovce a náš předek tu byl lovcem a sběračem (zemědělství se začalo objevovat snad o 4 tisíce let později, v JV Evropě o šest, a u nás v té střední asi o 8 či víc).
Není pravda, že bych vůbec netušil co se mezi těmí 14000 a současností dělo. Docela silně jsem byl přesvědčen, že patříme do haploskupiny I-S17250 (https://www.yfull.com/tree/I-S17250/), která souvisí s expanzí (proto-)Slovanů z Černomořské a Kaspické stepi na západ.

Pro ostřílené borce DNA testování to může vypadat jako rouhání, ale stále ještě nemám žádné STR markery. Mělo by se to změnit příští rok, kde získám alespoň prvních 27 markerů, v rámci českého projektu Genetika a příjmení. Zatím tedy mohu pro patrání po otcovské linii a shodách používat jen snipy.

Co jsem se tedy dověděl na YSeq?
Je to pravda, Krcháci jsou I-S17250! Slované jak poleno. Teoretický výzkum na jedničku.
Ale pod tímhle snipem už byly mé dohady liché. Na základě výsledků jiných Čechů jsem předpokládal I-Z16971 nebo I-Z16983.

Jaké bylo mé překvapení, když jsem zjistil, že jsem I-Y4882! (https://www.yfull.com/tree/I-Y4882/)
A tedy, že Krcháci byli Východní, nikoliv Západní Slovani! Čas přepsat rodinou historii :D

Zatím jsem A1328- a A811-. Příští týden bych měl dostat výsledky pro A7358 a Y16473. Pokud bude vše negativní, ještě existuje nová větev A12505 k ověření. A jinak jsem úplně sám.

Nicméně v podstatě nezávisle na výsledku musím začít šetřit na Next Generation Sequencing test. Žádná z podvětví Y-4882 totiž není moc prozkoumaná, takže ať už do nějaké známe větve patřit budu, nebo ne, posunout dopředu se půjde jen co nejkompletnějším sekvenováním chromosomu Y.

Narrowing down my Y heritage

You can call me a cheapskate, but I just like to get my money's worth ;) Seeing a sale on yseq.net in October, I jumped on it, to finally get closer to present than I-M423's ~14000 years (I had from 23andMe).
Well what I say is not completely true, by looking around, I strongly suspected, I will belong to I-S17250 when tested (https://www.yfull.com/tree/I-S17250/).

This may seem like a heresy to the old-timers, but I still have no STR markers tested on my paternal line. Should change next year, with my first 27. So I only have SNPs to utilise in my Y-research so far.

So what have I learned at YSeq?
I was true, I am actually I-S17250! Good job figuring that one out.
But downstream, it was all miss, no hit. Based on other Czechs, I suspected I-Z16971 or I-Z16983.

What was my surprise to learn, I am actually I-Y4882! (https://www.yfull.com/tree/I-Y4882/)
This seems to be an East Slavic SNP, where I always saw my Krchaks as West Slavs till the last week. Time to change the family history :D

So far, I am A1328- and A811-. Next week should bring us results for A7358 and Y16473.
Based on that, if I am all negative, I still have a new A12505 to check.

Almost regardless of the result, I need to start saving for that NGS Y test though. None of the Y-4882 sub-branches is much explored, so either being placed in one of them or being an original one still leads to the same solution - NGS.

Saturday, November 19, 2016

Nové Y-ové haplogroupy na 23andMe

Tenhle týden se nám dostalo nového hezkého update od 23andMe. Máme teď k dispozici Y haploskupiny založené na snipech - alternativních DNA bazích. Bohužel se tahle novinka dostala jen na jejich nové stránky (a tam zatím Evropany nepouštějí).

Tady to podrobně popisují v blogu: https://blog.23andme.com/ancestry/updates-to-23andme-paternal-haplogroup-assignments/

My se zaměříme na podstatu změny.
Na začátku se Y strom tvořil pomocí písmen a číslic. Pokud jsme měli nějakou haplogrupu, např. R, tak první rozvětvení jsme označili jedničkou, další dvojkou, atd.: R1, R2. Pro další větvení jsme použili písmena - R1a, R1b, a pak zase čísla R1a1, R1a2 atd.
Problém byl v tom, že nalezení nových dělení nám mohlo (a typicky taky dělalo) tyhle větvení přeházet. Čím blíže současnosti, tím víc se vše měnilo a nebylo stabilni.
Proto jsme zavedli definici pomocí snipů - ty označují, která konkrátní mutace k danému větvení vedla. Pokud došlo mutací na pozici L160 k vytvoření nové větve, je jedno jestli je třetí nebo patá. Tohle značení je mnohem stabilnější.

A tohle tedy David Poznikskvělý výzkumník chromozomu Y, na 23andMe zavedl.
Obnovil údaje na úroveň ledna 2016, pomocí ISOGG stromu.

Nyní tedy každý uvidí, jak vypadá jeho kousek Y linie:

Tohle hlavně zamezí zmatkům. Ani nevíte, kolikrát přišel do našeho FTDNA projektu nebo Facebookové skupiny někdo zcela popletený výsledky z 23andMe.

Rovněž bude mnohem jednodušší pomocí 23andMe výsledků objednat ten správný SNP panel z FTDNA nebo YSeq.

Skvělá práce od Davida, těším se, že o něm neslyšíme naposledy!
(pro technicky znalé - můžete se podívat na jeho prográmek, kterým výsledky zaktualizoval)

New Y haplogroups at 23andMe

What a nice and useful update from 23andMe. We now have SNP-based haplogroup info! As expected, this feature only made it to new experience (yes, as a European, I am still at the old one).

The blog: https://blog.23andme.com/ancestry/updates-to-23andme-paternal-haplogroup-assignments/
What do we have here?
David Poznik, great Y chromosome researcher, is working hard to bring us some improvements.
He has updated all the results to recent (January 2016) ISOGG phylotree.

Now everyone will have a small image representing his position in the tree:

First and foremost, this will help reduce confusion, as unexperienced users often didn't understand the old notation, it's relation to the new SNP one. (People were coming to my FTDNA project of Facebook group with misunderstandings from 23andMe all the time.)

It will be also easier to jump to SNP panels at FTDNA or YSeq based on this info.

All-in-all great work from David, and I hope to see more from him!
(For tech savvies, you can check out his utility they used for this haplogroup update.)