Okay: let me bin these individuals into clades.
Friday, March 28, 2014
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.
Okay: let me bin these individuals into clades.
Monday, March 10, 2014
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:
Then Jeanne comes on Thursday to start working together on the Q. rubra / Q. robur map.
- 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.
Tuesday, March 4, 2014
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.)
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.
*** 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.
*** 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.
*** 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)
*** 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)
*** Synonym of Q. greggii (A.DC.) Trel. (Breedlove, 1987)
Quercus
loesenerii Trel. Isotype: P00754099.
*** Synonym of Q. greggii (A.DC.) Trel. (Breedlove, 1987)
*** 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.
*** 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).
*** Synonym of Q. humboldtii (C.H. Muller, 1958).
Quercus
lindenii A.deC. Isotype: P00754103
*** Synonym of Q. humboldtii (C.H. Muller, 1958).
*** 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
* 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)
* 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.
*** 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).
*** 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).
*** 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).
*** 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.
*** 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
*** 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.
*** 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.
*** 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).
*** 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.
* 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.
Monday, February 17, 2014
Notes on Quercus types at P – 2014-02-17
**
indicates refiling done or needed, or notes on filing locations
Quercus
cubana. Two types of Q. cubana at P (P00754079, P 0075080), and I see
that WCP lists Q. sagraeana Nutt. as a synonym of Q. cubana A.Rich.,
with Q. cubana having an 1841 publication date (where Q. sagraeana has a
publication date of 1841). Presumably Nixon cleared this up in his
dissertation, but I don't have access to that here. Is there any risk that this
is still an open question? If it's tied up, we should let the folks at Tropicos
and WCPs know. If not, we should address it briefly in the paper (this isn't
the paper to deal with such things, but it needs to be addressed if there is
any ambiguity).
Quercus longifolia Liebm. 2 syntypes
(P00754040, P00754041). Filed under Q.
acatenangensis Trel.
Quercus acherdophylla Trel. 3 isotypes
(P00754042—4). Correct name fide Tropicos: Q.
salicifolia Née
Quercus affinis M.Martins & Galeotti non Scheid. 1 isotype (P00754132). Synonym for Q.
martensiana Trel. – tangled synonymy fide Tropicos: also Q. peduncularis Née. and others. See Breedlove, D.E. 1987, Monographic studies of Neotropical Quercus (Cal
Acad?). This specimen is clearly a white oak, while Q. affinis Scheidw. is a red oak.
** Separated Q. affinis M.Martins & Galeotti from
Q. affinis Scheidw.
Quercus nitens M.Martins & Galeotti. Isotype : P00754045 [** Filed under Q. affinis Scheidw.]
Quercus
nitens subintegra A.DC. Isotype : P00754046 [** Filed under Q. affinis Scheidw.]
Quercus agilops [sic.]. There were two
folders labelled with this name, mostly filled with Q. montana. There are four homonyms of Q. aegilops out there, but all reference Cerris spp. ** Refiled.
Quercus ambigua H.B.K. 1 type:
P00129745. Indicated on sheet as
synonym of Q. rugosa Née.
Quercus alpescens Trel. Isotype:
P00754039.
Quercus axillaris E.Fourn. ex Trel. Det on sheet as Q. castanea Née by Mulller;
this is accepted name fide Plant List. Isotype : P00754038.
** Moved the
two Q. axillaris together into one folder ; same collection, filed under
both Q. axillaris and Q. castanea.
Quercus
barbinervis Benth. 1 isotype : P00754123. Indicated on sheet to be synonym of Q. laurina H.&B. (by Breedlove,
1986).
Quercus
benthamii A.DC. 1 isotype: P 00754047. Originally det by Hartweg as Quercus undulata Benth.
Quercus
bourgeai Gerst. 3 isotypes, all duplicates of M. Bourgeau 1013:
P00754048—50; also, one unmounted and unaccessioned sheet of the same
collection (photographed). Indicated on
sheet to be a synonym of Q. laurina H.&.B. (Breedlove, 1986).
Quercus
bourgeai Gerst. var. ilicifolia
Trel. 1 isotype: P00754051. Indicated
on sheet to be synonym of Q. laurina H.&B. (Breedlove, 1986).
Quercus boyacanus Cuatr. 1 isotype:
P00754052.
Quercus brandegei Goldm. 2 sheets, no
collecting date, but old. Only to “Basse-Californie”, by M.L. Diguet, HERB.
MUS. PARIS. Probably a date could be assigned.
Quercus
canbyi Trel. 2 isotypes: P00754053, 4. Originally det. as Q. graham Benth. by C.G. Pringle.
------ below this point, Breedlove dets are
consistently indicated; above, inconsistent ------
Quercus canbyi Trel. forma berlandieri Trel. Isotype :
P00754055. (Breedlove 1987)
Quercus
candicans Née f. michoacana Trel.
Isotypes, all duplicates of Pringle 3955 : P00754059—61. (Breedlove
1987)
Quercus
acuminata M.Martins & Galeotti. Isotype: P00754056. Filed under Q. candicans Née and listed
as illegitimate in The Plant List.
Quercus
alamo Bentham. Type (unspecified) : P00754057. Filed under Q. candicans Née
Quercus
intermedia M.Martins & Galeotti. Isotype : P00754058. Filed under Q. candicans Née
Quercus
candolleana Trel. 2 isotypes: P00744195, 6. Det as Q. acutifolia Née (Breedlove 1987). Later synonymized (on
sheet) to Q. vexans Trel following Govaerts and Frodin 1999.
Q.
carmenensis C.H.Mull. 1 type (unspecified): P00754062.
Q. rossii f. arsenii Trel. Isotype:
P00754063. Synonymized to Q. diversifolia
Née (Breedlove 1987); Synonymized to Q. castanea Née following Govaerts and
Frodin 1999.
Q.
pulchella
H.&B. Type (unspecified): P00129710.
Synonymized to Q. castanea Née following Govaerts and Frodin 1999.
Q. axillaris E.Fourn. ex Trel. Isotype :
P00754064. ** Filed under Q. castanea; indicated to be Q. castanea on det (C.H.
Muller 1958; J.R. Bacon 2004).
Q. chihuahensis
Trel. 3 isotypes, all duplicates of Pringle 355: P00754065—7. Originally
det as Q. undulata Torr. var. breviloba Engelm.
Q.
chrysophylla H.&B. 3 isotypes, including 2 duplicates of Bonpland
4062: P00129742—4.
Quercus
coccolobifolia Trel. 1 type (unspecified): P00754118. Synonym of Q. jonesii Trel.
Q.
praineaya
Trel. 2 isotypes, both duplicates of Pringle 8854: P00754068,9. Synonym of Q. coffeicolor Trel.
Q.
colombianus Trel. Isotype: P00754070
Q.
conglomerata Trel. Isotype : P00754165 (Breedlove 1987). Synonym
of Q. rugosa Née (Breedlove 1987).
Previously det. as Q. reticulata (C.H. Muller, 1958).
Q.
nitida M.Martins & Galeotti. Type (unspecified) : P00754071. Synonym
of Q. conspersa Benth. following Govaerts and Frodin 1999. ** filed under Q.
conspersa
Quercus
convallata Trel. Type (unspecified) : P00754073.
Quercus corrugata var. graminiflora Trel. Isotype : P00754075 (C.H. Muller,
1958).
Quercus corrugata Hooker. Isotype :
P00754074 (C.H. muller, s.d.).
Quercus orbiculata Trel. Isotype :
P00754077. Synonym : Q. crassifolia
Bonpl. ** Filed under Q. crassifolia.
Quercus
stipularis H.&B. 3 isotypes : P00129748—50. ** Filed under Q.
crassifolia.
Quercus
crassifolia H.&B. Type (unspecified): P00129735—7.
Quercus spinulois H.&B.
Isotype : P00754078. Synonymized to Q. stipularis H&B (CH
Muller, 1958), then to Q. crassifolia H&B (Breedlove, 1987). ** Filed under
Q. crassifolia
Quercus
confertifolia H.&B. Isotype : P00129739 ; Type
(unspecified) : P00129738. Synonym of Q. crassipes Bonpl. ** Filed under
Q. crassipes Bonpland.
Quercus
crassipes var. angustifolia
H.&B. 4 isotypes : P00129730—33 (the last annotated by CH Muller,
1958); 1 type (unspecified): P00129729. Synonym of Q. crassipes Bonpl. ** Filed
under Q. crassipes Bonpland.
Quercus
splendens var. pallidior A.DC. Isotype:
P00754076 (Breedlove 1987). Synonym of Q. crassifolia H&B (Breedlove 1987);
synonym of crassifolia. ** Filed under Q. crassipes Bonpland. – I refiled to Q. crassifolia.
Quercus subavenia Trel. Isotype:
P00754081 (A. Camus, s.d.). Synonym of Q. depressa H&B.
Quercus depressa H.&B. 2 isotypes
(Bonpland 4145): P00129727, 8.
Quercus fournieri Trel. Holotype : P00077457 (Breedlove 1994). Originally det
as Q. ferruginea H&B. ** filed under Q. dysophylla Benth. (but not redet.
to this by Breedlove). The Plant List treats both as hybrid names, with Q. x
fournieri a synonym of Q. x dysophylla.
Quercus sideroxyla H&B f. ciliifera Trel. Syntype :
P00754082 (A. Camus). Synonymized to Q. eduardii Trel. (Breedlove, 1987 ;
Bacon, 2004). ** Filed under Q. eduardii
Quercus
langlassei Trel. 2 Isotypes : P00754088, 9. Synonym of Q. elliptica Née (Govaerts and Frodin,
1999). ** Filed under Q. elliptica.
Quercus
chiquihuitilloi Trel. 2 isotypes : P00754083, 4. Synonym of Q. elliptica Née (Breedlove, 1987). ** Filed under Q. elliptica.
Quercus oajacana Liebm. isotype :
P00754086. Synonym of Q. elliptica
Née (Breedlove, 1987). ** Filed under Q. elliptica.
Quercus
linguaefolia Liebm. Isotype : P00754087. Synonym of Q. elliptica Née (Breedlove, 1987). ** Filed under Q. elliptica.
Quercus
pubinervis M.Martins & Galeotti. Isotype : P00754085 (Breedlove,
1987). Synonym of Q. elliptica Née
(Breedlove, 1987). ** Filed under Q. elliptica.
Quercus
emoryi Torr. var. chihuahuensis
Trel. Isotype: P00754091. Synonym of Q.
chihuahuensis Trel. (J.R. Bacon, 2004). At E, this thing seems to be
annotated to Q. grisea by Breedlove (1987). ** Filed under Q. emoryi. ** Move
to Q. chihuahuensis?
Quercus
emoryii Torr. var. san-ysidroana
Trel. Isotype: P00754090. Synonym of Q. emoryi Torr. (J.R. Bacon, 2004). **
Filed under Q. emoryi.
Wednesday, February 12, 2014
got it!
I think this is it! Here, I do the standard partioned RAD plot of loci favoring (panel A) vs disfavoring (panel C) loci, then a regression on the main distribution of trees in panel A (the other trees on panel A are not plausible). Overlaying the 95% prediction interval on the main part of the partitioned RAD analysis regression, no points are excluded except tree 122, which does not have anything obviously bad about it.
If there is a disproportionately supported tree (in terms of number of loci supporting it, as a function of the log likelihood), we'd expect it to fall outside the prediction interval on the upper side. We don't see any such.
Okay. This is how it goes into the paper! what I need now is simulated data to see how well this performs, but that will have to wait.
If there is a disproportionately supported tree (in terms of number of loci supporting it, as a function of the log likelihood), we'd expect it to fall outside the prediction interval on the upper side. We don't see any such.
Okay. This is how it goes into the paper! what I need now is simulated data to see how well this performs, but that will have to wait.
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