Seguin Moreau

Remy Petit and I met today with colleagues at Seguin Moreau, one of the largest wine-barrel producers in France. Wine barrels are made of white oak, in particular of Quercus petraea, which is higher in whiskey lactone than Quercus robur (the other common French oak) and American white oak (Q. alba). The day was fascinating from the standpoint of the oaks themselves and the barrel making. The photos below show only some of the highlights of barrel-making. Any errors are my own, as this text has not been reviewed.

Andrei and Remy inspecting incoming wood.

Wood that comes to the factory stands outside for several years (about 1 year for every centimeter of thickness). The alternation between saturation and drying draws secondary compounds out to the surface of the board, where they are washed away by the rain. The thickers boards here are used for large fermenting vats (see below), while the thinner boards...




... are used for standard wine barrels. The foam visible in the water running off of the wood to the left is caused by the tannins.







To keep the wood at an appropriate moisture level for barrel construction, flats of wood are stored under a large, open-air roof. You can see in the topmost board on the middle stack here a little warp; this is fine, and is caused by the fact that the boards of Q. petraea are cut to follow the grain, to ensure water-tightness. This is not necessary in Q. alba, which has larger tyloses. As a consequence, only about 25% of the original log makes it to this stage in Q. petraea, whereas about 60% of the Q. alba log makes it (to my recollection; these numbers could be a bit off).

Once inside, the boards are shaped into staves, and the staves are lined up on a barrel-sized pattern. There is about 1mm of wiggle room in this process.

Batches of staves are then assembled into barrels, which are open at the bottom, pounded into alignment, and then moved off to the next stage...



... where they are toasted over an open flame. During toasting, the bottoms of the barrels are hugged into shape

Toasting

and hugging.

 The resultant barrel smells like warm bread inside. It's delicious.

The edges of the barrel are then beveled, and a rim is cut to accept the top.

The barrel tops are made of a variety of woods, including Robinia pseudo-acacia, depending on the wine variety. The wood is pressed together with reeds between the boards to ensure that the top is airtight. This is the only monocot I noticed in the factory.

















The tops are cut round and pounded into place, with a sort of bread dough (truly! flour and water) between the top and the barrel proper to ensure a tight seal.

 The barrel is sanded smooth...

... laser-printed with the Seguin Moreau logo...

 ... pressure tested twice to ensure air-tightness, and then packaged up for shipping.










The largest barrels are truly enormous. As I understand it, the barrels below are used for fermenting chambers.

 

FST distributions, between vs. within clades

The pattern of among-clade divergence becomes more interesting when I compare the clades. What I did here is I looked at FST within the white oaks, splitting all the white oaks (exc. for Virentes) from the Mexican / AZ clade; and FST within the red oaks, splitting all the red oaks except for Q. palustris and pals from the Mexican / AZ clade. These were the outcomes I imagined, and why I suspected each of them:

1. If diversification is neutral, then I expect conserved regions of the genome to be, on average, shared between the white and red oaks. This would be reflected by a correlation in FST within the white oaks compared to FST within the red oaks.
2. If diversification is driven by divergent selection on some regions of the genome but not others, I might find either:
   
   a. positive correlation, if the same regions of the genome were under divergent selection during diversification of the major white oaks clades as were under selection during divergence of the major red oak clades; or
   
   b. negative correlation, if white oak divergence was driven by selection at different loci than red oak divergence.

I subsetted the ca. 33000 RADseq loci from my last clustering analysis based on the criteria that loci were present in at least 5 members of each of the two white oak clades or at least 5 members of the two black oak clades, and variable at least at one nucleotide position. Then I mapped these all back to the Q. robur SNP map, 800-bp contigs, as described here: 2014-03-10. It is not the same set of markers that successfully maps in each case. Here are the markers that map in the two groups:

FST by linkage group within Quercus section Lobatae,
where the two populations are the eastern North American
red oaks (excluding Q. palustris and allies) and the Mexcian /
Arizonian red oaks.

FST by linkage group within Quercus section Quercus,
where the two populations are the eastern North American
red oaks (excluding Virentes and the Roburoids)
and the Mexcian / Arizonian red oaks.

I looked first to see whether there is any kind of correlation on a locus-by-locus basis, but this is noisy:

Biplot of FST within section Quercus (y axis) against section
Lobatae (x axis)

But we have a map! binning by 3 cM, and averaging FST within those bins, still gives a pretty noisy plot:

But, remarkably, the story seems to be a lot cleaner at bin sizes of 30 cM or higher:

Map position of divergence in 30 cM windows,
red oaks and white oaks, with all 12 linkage
groups concatenated.

Biplot, FST of red oaks on FST of
white oaks, 30 cM windows.
Pearson's r = -0.583, P = 0.0028.

This effect I was expecting to potentially show up at fine scales, due to selection at the scale of individual genes. In both groups we are looking at a cladogenetic split that is probably > 10 million years old (the split between the red and white oaks is about 30 million years old). Is there any chance, though, that we are really picking up on a strong divergence in the selective pressures driving divergence at the bases of the red and white oak clades, and that affected divergence patterns across 1/2-chromosome size blocks of the genome? 

Where is the divergence? v1

Okay, here's where I had reached last week:

This is a map of FST (y-axis) against map position... of course, what it reflects is mostly just low-divergence (low phylogenetic informativeness) loci (near zero) vs loci that do a good job of distinuishing the reds and the whites. A fixation index is probably not what I want for this project. It does, however, show us what loci are strongly divergent. I wonder what this would look like if we mapped (1) the red-white break, (2) a major within-white break, and (3) a major within-red break on the same plot?

Okay: let me bin these individuals into clades.

How much overlap?

354 loci in the last RAD dataset have at least 10 red oaks and 10 white oaks and are mapped to the Quercus robur contigs.

RAD map v1

Last week I mapped the RAD sequences back to the oak contigs. After clustering the contigs, there are 3327 unique contigs, of which 23 were removed because they either don't have a map position or map to two positions > 3 cM distant. So we now have 803 RAD loci mapped to 587 Quercus robur contigs... that's a lot farther along than we were two weeks ago. To do the first four days this week:

• Quantify divergence between any two groups of individuals defined on the tree for mapped loci
• Plot divergence on this map
• Relate this map to the Q. rubra map
• Start analyzing the fuller set of RADs on the Morton server
• work with Isabella on mapping the larger contigs... status?

Then Jeanne comes on Thursday to start working together on the Q. rubra / Q. robur map.

RADami on CRAN

http://cran.r-project.org/web/packages/RADami/index.html

Notes on Quercus types at P – 2014-02-18

This is a late post! Just to get these in the record b/f I move on to the next thing...

Quercus excelsa Liebm. Isotype : P00754092

Quercus falcata Michx. Isotype: P00754029 (C.H. Mueller, 1958) ; I don’t know the variability in this species, but this looks to me to be a mixed collection. Also listed as isotypes on the P catalog, but not indicated as such on the sheets: P00754031—33.

Quercus triloba Michx. 3 isotypes : P00754026, 8 (C.H. Mueller, 1958), unbarcoded (anonymous det.) ; 1 unspecified type: P00754027 (C.H. Muller, 1958).
These have a look intermediate between Q. falcata and Q. marilandica.
*** Synonym of Q. falcata Michx. (Muller dets.)

Quercus galeottii Mart. 2 isotypes : P00754036, 7.

Quercus furfuracea Liebm. 2 types (unspecified) : P00754034, 5.

Quercus germana v. echidiea Trel. 1 isotype: P00754016.
*** Previously det. as Quercus subsquarossa [?] A.Camus, by A. Camus.

Quercus ghiesbreghtii Mart. & Gal. 2 isotypes: P00754017, 8.

Quercus glabrescens Benth. Isotype: P00754019.

Quercus conjungens Trel. Isotype: P00754025
*** Synonym of Q. glaucoides Mart. & Gal., following Govaerts and Frodin 1999.
* Filed under Q. glaucoides.

Quercus glaucescens H. & B. Isotype: P00129726 (Bonpland collection, with written notes)

Quercus oerstediana Liebm. var. crenifolia Trel. Type (unspecified): P00754020.
*** Ghiesbreght label (1842) dets as Q. synthetic Trel., and indicates this is a synonym of Q. oerstediana Liebm. non R.Br. var. crenifolia Trel.
*** Filed under Q. glaucescens.

Quercus glaucophylla V.Seem. Isotype : P00754024 (Breedlove, 1987)
*** Synonym of Q. glaucoides Mart. & Gal. (Breedlove, 1987)

Quercus greggii (A.DC.) Trel.

Quercus revoluta var. dysophyllopsis Trel. 2 isotypes : P00754100, 1. (A. Camus)
*** Synonym of Q. greggii (A.DC.) Trel. (Breedlove, 1987)

Quercus loesenerii Trel. Isotype: P00754099.
*** Synonym of Q. greggii (A.DC.) Trel. (Breedlove, 1987)

Quercus grahamii Benth. var. brevipes Trel. isotype : P00754098 (Breedlove, 1987).

Quercus hahnii Trel. Isotype: P00754102

Quercus hartwegii Benth. Isotype: P00754093.
*** Synonym of Q. obtusata Bonpl., following Govaerts and Frodin 1999.

Quercus humboldtii Bonpl. Isotype: P00129753

Quercus tolimensis H.&B. Isotype : P00129751.
*** Synonym of Q. humboldtii (C.H. Muller, 1958).

Quercus lindenii A.deC. Isotype: P00754103
*** Synonym of Q. humboldtii (C.H. Muller, 1958).

Quercus impressa Trel. Isotype: P00754104

Quercus cinerea var. humilis Michx. 2 isotypes: P00754106, 7 (C.H. Muller, 1958).
* Filed under Q. incana Michx.
*** Q. cinerea Michx. is a synonym of Q. incana Michx. (Tropicos)
*** Det as Q. pumila Walt., Q. cinerea humilis Michx. (C.H. Muller, 1958).
*** Quercus cinerea Michx. v. humilis (Walter) A.DC. is the ref in Tropicos.
*** Authorship unclear

Quercus cinerea Michx. 4 isotypes: P00754108—11.
* Filed under Q. incana Michx.
*** Q. cinerea Michx. is a synonym of Q. incana Michx. (Tropicos)

Quercus insignis M. & G. Isotype : P00754113

Quercus intricata Trel. 2 types (unspecified and perhaps depauperate ; how small are the leaves on this sp. ?) : P00754114, 5.
*** Originally det as Q. microphylla Née by Pringle.

Quercus laeta Liebm. var heterophylla Trel. Type (unspecified) : P00754119. Det as Q. laeta f. [forma? deliberately left blank?] by Trelease, 1913.

Quercus jaralensis Trel. 2 isotypes : P00754116, 7.

Quercus lanceolata H.&B. 2 types (unspecified) : P00129724, 5 (the first a Bonpland collection with notes), 1 isotype: P00129719 (Breedlove, 1987; det as Q. laurina H.&B., Muller 1958)
*** synonym for Q. laurina H.&B. (Breedlove, 1987).

Quercus lancifolia Cham. & Schl. 1 possible lectotype : P00754121; 1 lectotype : P00754120 (Breedlove 1987); det A. Camus and there designated “Type”

Quercus lanigera Mart. & Gal. Isotype: P00754122.
*** Breedlove (1987) annotated other sheets in this folder as Q. castanea Née, but someone came along and annotated them to Q. lanigera M&G (nomenclatural).

Quercus lecomteana Trel. 2 isotypes : P00754127, 8 (Trelease, 1913) ; 1 type : P00754126 (Trelease, 1913).
*** Breedlove (1987) annotated to Q. repanda H&B (nomenclatural).

Quercus laurina H.&B. 3 isotypes (Bonpland 4143: P00129720,1,2); 1 type: P00129723.

Quercus leiophylla A.DC. Isotype : P00754131.

Quercus leiophylla A.DC. f. subintegra Trel. Isotype : P00754130 (Breedlove, 1987).
*** both of the above det to Q. lancifolia S.&C. (Breedlove 1987), then back Q. leiophylla A.DC. following Govaerts and Frodin 1999.

Quercus olivaeformis Michx. Type (unspecified and unscanned) – Photo taken.
*** Synonym of Quercus macrocarpa

Quercus mollis Mart. & Gal. Type ?: P00754134 (Trelease 1913). But annotations by Trelease and C.H. Muller (1958) suggest that in fact Galeotti 104 is the isotype (this collection is Galeotti 103).
*** Annotated to Q. crassifolia H.&B. (Breedlove 1987), then to Q. chicamolensis Trel. following Govaerts and Frodin 1999.

Quercus mexicana f. lanosa Trel. Isotype : P00754133 (Breedlove 1987). Det Trelease, 1913
*** Det to Q. crassipes (C.H. Muller 1958, Breedlove 1987), then there is a synonym det slip to Q. mexicana H.B.K. following Govaerts and Frodin 1999.

Quercus mexicana H.&B. 3 isotypes : P00129716, 7, 8 (duplicates of Bonpland 4060).

Quercus panduriformis Trel. 2 types (indicated on one of labels, and these are duplicates, but not scanned or barcoded or stamped “TYPE”).
*** Both det to Q. magnoliaefolia Née (Muller 1958).

Quercus obovalifolia Fourn. 3 isotypes: P00754135, 6, 7.
* Filed under Q. oblongifolia Torr.
*** WCSP gives Q. crassipes as the accepted name for this species.

Quercus obtusata H.&B. 3 isotypes: P00129713, 4, 5.