Author Topic: Interesting Data from the yeast Genome Study  (Read 5311 times)

Offline klickitat jim

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Re: Interesting Data from the yeast Genome Study
« Reply #75 on: May 17, 2018, 11:19:28 PM »
Well, building up whatever's in a bottle of SNPA, as I posted above.  It is clearly a top fermenting yeast (crappy pic):
https://drive.google.com/file/d/1TdiBFYtdSdx7C269ES3VdC3baDFEzaF1/view?usp=drivesdk
But that said, it actually smells less estery at this point than a starter of 2124 would.  So.  Whatever this tells.
Don't feel confident I have quite enough for a lager pitch after my last step-up -- so tomorrow's pre-Prohibition lager just got redesignated a pre-Prohibition "sparkling ale."  Then I'll have plenty, and next time hope to do a "lager" fermentation, and see if it seems plausible this yeast once made "lagers" at Ballantine.  Will follow up at that time.  (See, now I feel like putting "lager" and "ale" in quotes from now on...)
Up until recently, in Texas, "ale" meant over 5% ABV. So ale... lager... IPA... these are all meaningless terms

Offline ynotbrusum

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Re: Interesting Data from the yeast Genome Study
« Reply #76 on: May 18, 2018, 11:35:14 AM »
Even “hybrid” can now have different meanings - a Kölsch style hybrid ale using lager yeast? Or a Kölsch style ale using hybrid yeast? It depends on the yeast...but then the yeast itself has to be genotyped for “certainty”?
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Offline Robert

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Re: Interesting Data from the yeast Genome Study
« Reply #77 on: May 20, 2018, 11:01:52 PM »
Well, building up whatever's in a bottle of SNPA, as I posted above.  It is clearly a top fermenting yeast (crappy pic):
https://drive.google.com/file/d/1TdiBFYtdSdx7C269ES3VdC3baDFEzaF1/view?usp=drivesdk
But that said, it actually smells less estery at this point than a starter of 2124 would.  So.  Whatever this tells.
Don't feel confident I have quite enough for a lager pitch after my last step-up -- so tomorrow's pre-Prohibition lager just got redesignated a pre-Prohibition "sparkling ale."  Then I'll have plenty, and next time hope to do a "lager" fermentation, and see if it seems plausible this yeast once made "lagers" at Ballantine.  Will follow up at that time.  (See, now I feel like putting "lager" and "ale" in quotes from now on...)

Well something strange.  After just 36 hours the yeast had quit and flocced out, at only 36%AA.  Never seen anything like this in all my years of brewing.  What's more, the beer was completely insipid -- no hop or malt aroma or flavor, just a little bready yeastiness, no apparent foam capacity -- weird.  Suspect either the yeast in the bottle isn't the yeast in the ferment (though it may have been years ago) or it's just not adapted to my fermentation conditions (needs open fermentation?) Or something I haven't thought of, I'm stumped. Anyway, it was a fun idea, but it's a dumper, as I'll have time to brew again this week.

(Think I'll buy some 1056 though...)
« Last Edit: May 20, 2018, 11:23:57 PM by Robert »
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Offline denny

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Re: Interesting Data from the yeast Genome Study
« Reply #78 on: May 21, 2018, 03:47:28 PM »
Well, building up whatever's in a bottle of SNPA, as I posted above.  It is clearly a top fermenting yeast (crappy pic):
https://drive.google.com/file/d/1TdiBFYtdSdx7C269ES3VdC3baDFEzaF1/view?usp=drivesdk
But that said, it actually smells less estery at this point than a starter of 2124 would.  So.  Whatever this tells.
Don't feel confident I have quite enough for a lager pitch after my last step-up -- so tomorrow's pre-Prohibition lager just got redesignated a pre-Prohibition "sparkling ale."  Then I'll have plenty, and next time hope to do a "lager" fermentation, and see if it seems plausible this yeast once made "lagers" at Ballantine.  Will follow up at that time.  (See, now I feel like putting "lager" and "ale" in quotes from now on...)

Well something strange.  After just 36 hours the yeast had quit and flocced out, at only 36%AA.  Never seen anything like this in all my years of brewing.  What's more, the beer was completely insipid -- no hop or malt aroma or flavor, just a little bready yeastiness, no apparent foam capacity -- weird.  Suspect either the yeast in the bottle isn't the yeast in the ferment (though it may have been years ago) or it's just not adapted to my fermentation conditions (needs open fermentation?) Or something I haven't thought of, I'm stumped. Anyway, it was a fun idea, but it's a dumper, as I'll have time to brew again this week.

(Think I'll buy some 1056 though...)

I guarantee you that the yeast in the bottle is the same yeast they ferment with.
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Offline Robert

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Re: Interesting Data from the yeast Genome Study
« Reply #79 on: May 21, 2018, 06:00:37 PM »
^^^^^
I'll buy that.  Probably was too big an ask for it to adapt to totally different conditions right out of the gate. It was off like a rocket, then flocced, and I had no means of rousing it.  Anyway, I picked up a pitch of 051, which I wouldn't have been inspired to do either if not for this topic.   :)

EDIT At least I've seen that SNPA yeast is emphatically top fermenting and top cropping --  it ain't a lager yeast. FWIW.
« Last Edit: May 21, 2018, 07:31:42 PM by Robert »
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Offline dmtaylor

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Re: Interesting Data from the yeast Genome Study
« Reply #80 on: May 22, 2018, 02:08:33 AM »
As I'd indicated previously (and copied below), based on my reviews of the genome study results, I didn't think 1056 and WLP051 could be equivalent.  I wasn't sure if 1056 might be a lager yeast, while WLP051 probably IS a lager yeast.

EDIT: And... forgot to mention... I *do* believe Sierra Nevada is 1056.  WLP051 on the other hand is supposedly Anchor Liberty.  Source: http://www.mrmalty.com/yeast.htm

...to be clear, WLP051 and Wyeast 1056 are NOT equivalent.  They are very very distant cousins.

BRY-96 = Wyeast 1056, AND NOTHING ELSE!  NOTHING else is exactly equivalent!  1056 is unique!

BRY-97 = WLP051 = 1272, AND NOTHING ELSE!  Nothing else is exactly equivalent!  And if I'm right in my interpretation as explained above, then all 3 of these might be pastorianus...

...the pastorianus *might* indeed be limited to just BRY-97 = WLP051 = 1272...

EDIT #2: Hell... now expert "qq" says he doesn't think 1272 is actually the same as WLP051, but rather is more closely related to WLP002 and WLP007... and "German" ale yeast WLP029!  He found a different study separating 1272 from WLP051.  To be clear: Of all these, WLP051 is the only one identified verily as pastorianus.  http://beer.suregork.com/?p=4000

Hmm.... gonna be a while longer before we get all this stuff straight.
« Last Edit: May 22, 2018, 02:31:35 AM by dmtaylor »
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Offline Robert

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Re: Interesting Data from the yeast Genome Study
« Reply #81 on: May 22, 2018, 02:49:48 AM »
Well, my 051 starter is behaving just like I'd expect of my usual 2124 starters.  As sure as I am that the SNPA (bottle) yeast (by any other name) is an "ale" yeast, I, inveterate lager brewer, am gonna bet 051 is a "lager" yeast.  Whatever that means.  It's like asking a prospective employee for their family's work history instead of assessing their own skills.
« Last Edit: May 22, 2018, 02:51:23 AM by Robert »
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Offline Northern_Brewer

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Re: Interesting Data from the yeast Genome Study
« Reply #82 on: November 15, 2018, 01:07:46 PM »
The original link contains 3 places on the tree for "WLP019/WLP051/WY1056".  I do NOT take this to mean that these 3 yeasts are identical!  Far from it!  I think they just weren't sure which one went where.

Exactly - Suregork et al did a remarkable job of guessing most of the White Lab strains based on a handful of database hits and then just spotting patterns in the countries of origin - California/England/Germany/Ireland is a slightly weird combination of countries but it perfectly matches WLP001-4 for instance. But there were problems with a bunch of sequences described as from "California" or the US.

There were a couple of unidentified sequences from California and a couple of Californian WLPs that hadn't been placed, so it was just guessed that the two "gaps" corresponded somehow. Unfortunately White Labs didn't include them in the strains they unblinded in response to Suregork's work - the thought is that they may have actually sequenced variants that were banked by local Californian breweries and so were covered by confidentiality clauses. So we don't know for certain about those ones, but most of the other identities we can be fairly sure about.

But the picture is becoming clearer on the main US strains involved in the
Ballantine's ->Siebel BRY-96/97 -> Anchor/Sierra Nevada
chain. Bear in mind that :
Strains get mixed up, labels get switched, beer gets contaminated, stuff happens.
If Ballantine's was _anything_ like British breweries of the time, it would have been using a blend of at least two strains in its ale fermentations, but may well have been using just one for its lager.
Siebel would presumably have purified them down to single strains.
The West Coast breweries could easily end up with multistrains, either deliberately or by contamination.
Yeast evolve over time. Not hugely, but enough to be different at the DNA level and eventually at the beer level.

So what is the DNA telling us?

First - only WLP051 seems to be a lager strain, the rest seem to be ale strains. If WLP051 came from Anchor as is claimed, I'd guess it somehow came from Anchor Steam and not Liberty.

The latest sequencing puts Lallemand BRY-97 in the Mixed group - ie a distant cousin of Windsor/S-33 and nothing to do with the main group of brewery yeasts that includes the Chicos and Whitbread B. There needs to be more analysis of exactly how it fits in though. Since Lallemand own Siebel, presumably they got it direct from the banked version.

The main "Chico" group seems to have a single origin and is most closely related to WLP025 Southwold, presumably from Adnams. Adnams are interesting, they got their yeast from Morgans in Norwich in 1942 after an infection, in the 1970s it was 5 strains that they reduced down to two after stability problems.  But the relationship isn't close - the split could have happened 300 years ago if you believe the Gallone timings (which I don't entirely).

WLP008 East Coast ("Sam Adams") is a distant cousin of the Chicos which could have split off in the mid 19th century.

The remaining Chicos are much more tightly related, they might have split from each other within the last 30-40 years, some more recently than that. In that group you have WLP001, US-05, WLP090 San Diego and Pacman for certain. I don't think we have something that definitively ties 1056 to that group but I would expect it to be in there - it's subtly different to WLP001 but not that different. Although I don't have a definitive source, the Chicos are commonly claimed to be diploid (ie two sets of chromosomes like us) but Pacman for one is definitely tetraploid (four sets). Doubling the chromosome count is something that's quite "easy" to do and seems to be quite common in domestication, particularly in yeast.

We don't have sequence data for 1272, all we have are some basic interdelta "fingerprints" from Richard Priess which suggest it's close to WLP002 and WLP007 in the Whitbread B family. It's worth emphasising that this can only be tentative even with perfect data and in this case the gels are a bit contradictory, but the family does include "clean" yeasts like WLP029 Kolsch and WLP030 Thames Valley so it's plausible. We can be reasonably confident that 1272 is an ale yeast, which means it's nothing to do with WLP051. But the identification in the Whitbread B family is not certain, there's maybe a 25% chance it's something else, which opens up the possibility that it's similar to BRY-97 but it's not probable.

An intriguing option would be to do some DNA work on the East Coast Yeast strains that supposedly come from Ballantine - ECY-10 Old Newark Ale and ECY-12 Old Newark Beer are meant to be the ale and beer strains respectively. Unfortunately they only seem to be produced sporadically, and ECY don't distribute to Europe AFAICT - I don't suppose anyone happens to have some in a fridge/freezer/beer? Given the huge differences between Chico, BRY-97 and WLP051 it should be possible to distinguish them using pretty basic DNA techniques.

It's worth emphasising that although this stuff is really interesting from geek and historical points of view, you shouldn't sweat it too much from a brewing point of view. As others have said, it's brewing performance that matters. But DNA can open fresh perspectives - like using WLP051 California V Ale to make a classic low-temperature pilsner, or adapting an APA that you normally make with 1272 American Ale II to use the better-floccing WLP030 Thames Valley instead. Neither of those would be obvious things to do if you just looked at the names, but make perfect sense from a DNA point of view.




« Last Edit: November 16, 2018, 02:57:10 PM by Northern_Brewer »

Offline dmtaylor

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Re: Interesting Data from the yeast Genome Study
« Reply #83 on: November 15, 2018, 10:23:46 PM »
We don't have sequence data for 1272, all we have are some basic interdelta "fingerprints" from Richard Priess which suggest it's close to WLP002 and WLP007 in the Whitbread B family. It's worth emphasising that this can only be tentative even with perfect data and in this case the gels are a bit contradictory, but the family does include "clean" yeasts like WLP029 Kolsch and WLP030 Thames Valley so it's plausible. We can be reasonably confident that 1272 is an ale yeast, which means it's nothing to do with WLP051. But the identification in the Whitbread B family is not certain, there's maybe a 25% chance it's something else, which opens up the possibility that it's similar to BRY-97 but it's not probable.

Your insights, as always, are very insightful.  Thanks and kudos.

My latest hypothesis that I would like to gather more data for is that perhaps 1272=WLP019 Cal Ale IV.

Another hypothesis I have is that US-05 is actually a lager yeast possibly related to WLP810 San Fran Steam yeast.

Another hypothesis of mine is that WLP051 is a recent branch off Chico.  It only turned into a lager in the last 40 years or so, and did so on its own and has no other known progeny.

All these hypotheses are again based on several hours worth of staring at last year's research and trying to make sense of it all.  I'm probably wrong on most of them, but odds are that I might possibly be correct on at least one of them.  Crossing fingers and waiting for more research results.

I'd certainly be curious to hear your or anyone's thoughts on these.  Go ahead and refute, I can handle it.

Cheers.
Dave

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Offline denny

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Re: Interesting Data from the yeast Genome Study
« Reply #84 on: November 15, 2018, 10:27:03 PM »
Another hypothesis I have is that US-05 is actually a lager yeast possibly related to WLP810 San Fran Steam yeast.

I know for a fact where 05 came from and that ain't it!
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Offline dmtaylor

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Re: Interesting Data from the yeast Genome Study
« Reply #85 on: November 15, 2018, 11:28:30 PM »
Aw man!  It was a longshot.  It wasn't identified as a lager yeast so, yeah.  Would like to know where it's from if you're allowed to share.  It does have its own evolutionary branch.
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Offline Northern_Brewer

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Re: Interesting Data from the yeast Genome Study
« Reply #86 on: November 16, 2018, 03:18:36 PM »
My latest hypothesis that I would like to gather more data for is that perhaps 1272=WLP019 Cal Ale IV.

Anything's possible with WLP019 - it's kinda mysterious how it doesn't hit the radar. Maybe it's a duplicate of something else (like that Swedish stout strain that turned out to be Ringwood), maybe there's  a commercial confidentiality thing. I'm not sweating it too much, not least because it seems to be permanently tucked away in the Vault... If one could get one's hands on it, then it would be easy to do a basic DNA fingerprint test on it.

Another hypothesis I have is that US-05 is actually a lager yeast possibly related to WLP810 San Fran Steam yeast.

Absolutely not, it's been sequenced twice and is definitely a Chico ale. As I said above, only WLP051 seems to be a lager out of the ones we're talking about. If it's on Suregork's chart and isn't in red, then it's an ale.

Another hypothesis of mine is that WLP051 is a recent branch off Chico.  It only turned into a lager in the last 40 years or so, and did so on its own and has no other known progeny.

Vanishingly unlikely compared to other possibilities. We only know of lager hybrids forming twice in 1000 years - you're claiming that it's happened in the same brewery that is also know for making steam beer with lager yeast? Do you have next week's lottery numbers as well?

Offline denny

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Re: Interesting Data from the yeast Genome Study
« Reply #87 on: November 16, 2018, 03:45:12 PM »
Aw man!  It was a longshot.  It wasn't identified as a lager yeast so, yeah.  Would like to know where it's from if you're allowed to share.  It does have its own evolutionary branch.

Sorry, but I'm not.  But if you really wanted to dig,I think the info is out there.
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Offline Northern_Brewer

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Re: Interesting Data from the yeast Genome Study
« Reply #88 on: November 16, 2018, 07:07:22 PM »
There's more grist to the mill, Suregork has updated with Wyeast and dry strains :
https://www.homebrewtalk.com/forum/threads/from-the-lab-family-tree-of-white-labs-yeast.642831/#post-8444803

Offline Robert

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Re: Interesting Data from the yeast Genome Study
« Reply #89 on: November 17, 2018, 01:46:41 AM »
There's more grist to the mill, Suregork has updated with Wyeast and dry strains :
https://www.homebrewtalk.com/forum/threads/from-the-lab-family-tree-of-white-labs-yeast.642831/#post-8444803
Well, there goes my weekend.  ;)
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