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.