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).
Monday, February 17, 2014
Notes on Quercus types at P – 2014-02-17
**
indicates refiling done or needed, or notes on filing locations
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.
Tuesday, February 11, 2014
Venus, first violet, Ranunculus leaves
This was one of the most beautiful mornings we've had since arriving. I left Cauderan at 7:10, Venus bright in the east, hardly any water on the streets (which is unusual). I grabbed the paper in Pessac, waited 20 minutes for a late train, and by the time we left the sky was glowing orange and yellow. Train to Cestas / Gazinet, and in the inundated ditches along the roadside, enormous buttercup leaves were unfurled, along with patches of light green geranium. The first violet I've seen this year was open but submerged in the ditch. By the time I hit Pierroton, the sun was just coming up over the houses.
RADami ready to use
I redid the tree likelihoods as the likelihood for each tree on the full data matrix, and the plot now is a lot more informative. It turns out that using the summed locus likelihoods was, as I was concerned, giving a falsely linear relationship. The conclusion now is the same -- no obvious secondary tree out there in this dataset -- but with different islands of trees each having a separate distribution of likelihood scores:
 |
| Tree likelihood based on summed loci Including only loci that have a minimum of 20 unique trees, overall likelihood range of 4, and selecting supporting vs. disfavoring loci based on a 2-lnL point threshold. |
 |
| Tree likelihood based on full data matrix Including only loci that have a minimum of 20 unique trees, overall likelihood range of 4, and selecting supporting vs. disfavoring loci based on a 2-lnL point threshold. |
RADami now builds and installs fine on Linux and Windows (8.1; I assume no problems on older windows).
Friday, February 7, 2014
Assemblee Generale, BioGeCo 2014
Today was the annual Assemblée Générale de BioGeCo, held at
the University of Bordeaux in Talence. This is the first day I've seen everyone present on their projects. Remy Petit, the BioGeCo leader for the past three years, opened with a statement on the unit as a whole. BioGeCo holds as its goal to “study the mechanisms governing the evolution of the
diversity of terrestrial ecosystems, from genes to communities,” and to “rebalance ecologie and genetics in a common evolutionary framework.” There is, of course, a very strong tree focus here, and there is a long history of forestry research here.
Today, there are 109 people employed at BioGeCo, 68 salaried (43% lead-researchers, 57% engineers and technicians), 21 PhD students, 18 postdocs and
contract researchers. From 2009 to 2014, increased by 4 chercheurs and 5
engineers.
I made just a few notes on projects that were of interest to me. This is neither exhaustive nor representative, only things that caught my interest:
Highlights in GEMfor [Cécile Robin]
·
Sequencing 150 species of pathenogenic fungi
·
Studying the evolution of natural history traits
(niche differentiation, virulence) using experimental and modeling approaches,
in the light of climate change and colonization of novel environments and
regions
·
The effect of parasitic fungi (oïdium) in the
evolution of oaks
·
Horizontal and vertical transmission of
microorganisms in oaks
·
Role of microorganisms in the health of the
plant (e.g., invisibility of the community by pathenogenic species); this, tied
in with climate change, by looking at microfungal community changes in response
to climatic variation
Highlights in Ecologie des Communautés [Emmanuel Corcket]
·
13 permanent positions (including 9 chercheurs,
3 engineers, 1 technician [?]), 9 contractual
·
Interested in both the distributional (patterns,
processes underlying patterns) and functional (e.g., interactions) components
of biodiversity, and the interactions between communities and their
environments in both directions (e.g., responses to climate change, effects on
nutrient and water cycling)
·
Are trees a countryside (‘paysage’) for
bacterial communities?
·
Impacts of atmospheric deposits on prairie
(‘prairiale’) biodiversity in the Pyrenees.
·
Latitudinal distribution of birds and bats
·
Bird predation and trophic cascades
·
Effects of plant phylogenetic diversity on
herbivory depend on herbivor specialization
·
Interaction between host / nonhost abundance and
insect invasion in pines
·
Restoration as a tool for environmental
remediation and effects on ecosystem processes
·
Risk analysis: movements of forest insect
herbivores; effects of forest insect herbivores on plant growth
·
Herbivory-resistance traits
·
Indirect effect of invasive insects on the
diversity of insular [endemic?] forest birds on Corsica
Ecologie et Génomique Fonctionnelles (EGF) [Annabel Porté]
·
23 permanents; 93 publications in 2011-2013
· The interaction between genotype and phenotype
that affects adaptation
·
Strategy: produce and integrate understanding on
function and structure…
·
Cavitation resistance in pines
o
Genetic architecture (QTL)
o
Physiological
o
Leaf phenology
o
Phylogenetic distribution
·
QTLs underlying budbreak [? – debourrement]
·
Rapid evolution of populations
·
Artificial selection and its effects on genomic
architecture of differentiations
·
A genetic map for oaks with higher density of
markers
o
Genomic signature of adaptation and speciation
in oaks
o
A phylogeny of the genus Quercus
Thursday, February 6, 2014
Fulbright and Paris Herbarium -- post visit
I was unsure what to expect of the Fulbright midyear meeting. The common ground for everyone is being an American in France, which doesn’t seem like all that much to go on. Fortunately, it’s a very interesting group of people, broad-minded and engaged. The main meeting was held in the building where the Marshall Plan was hammered out. The meeting opened with a tour of the building, a tour that closed with a photo of the courtyard in the days after the liberation of Paris, filled with debris from the bombing. Highlights of the meeting for me included conversations with a philosophy of biology student on a causal criterion for natural categories (including, of interest to both of us, the category of species); an electrical engineer working on signal processing, about stochastic computing, the uses of graphs in both signal processing and evolutionary biology, and the rise and fall of Bell Laboratories; a photographer and poet who is working on a book of poems about the first person ever to take a still photo; a chemical engineer, about the importance of learning to be an outsider. The meeting ended with a concert of 20th century French organ music. There was an amazing piece by Messiaen that rattled all of us.
I spent yesterday morning at the Paris herbarium with Béatrice Chassée of the International Oak Society, getting a sense of the oak collection as a whole and working through some of the eastern North American Lobatae. I got through all of what I wanted to today and have a good sense of what material I need to go through when I’m back up here in two weeks. Then Béatrice and I had lunch at the Paris mosque and talked about IOS, Journal of International Oaks, oak collections around the world. Then off to the train, and back home.
I spent yesterday morning at the Paris herbarium with Béatrice Chassée of the International Oak Society, getting a sense of the oak collection as a whole and working through some of the eastern North American Lobatae. I got through all of what I wanted to today and have a good sense of what material I need to go through when I’m back up here in two weeks. Then Béatrice and I had lunch at the Paris mosque and talked about IOS, Journal of International Oaks, oak collections around the world. Then off to the train, and back home.
Tuesday, February 4, 2014
Fulbright meeting, Paris
Today and tomorrow are the midyear meeting in Paris for France Fulbright and Chateaubriand Scholars. The train left out of Gare St. Jean (Bordeaux) at 8:23, exactly as the sun was rising. As we went out of town to the north, the sun was lighting up the towers over the bridge beside the CAP Sciences Museum. This side of town I don’t know at all (we live on the west side, in Caudéran, and my commute to work takes me over to Pessac to catch the train, so I have missed north Bordeaux altogether so far). Like the rest of Bordeaux, this side grades into vineyards pretty quickly; there’s a chateau now off to the east, active, another we’ve just passed that appears to be an individual’s home, no longer active in grape-growing or wine-making. Fourteen minutes out and we’ve just passed another village, all I could see of which is the cathedral surrounded by its cemetery. There are horses and little round haystacks in the sodden fields, and the ditches are brilliant with duckweed or something else bright green. The train is full of people going about their business, one knitting, another reading the paper. I asked my son David two nights ago what his favorite part of the trip has been so far, from the minute we left Downers Grove. He said it was the flight over. He didn’t know why. It certainly wasn’t for lack of enjoying the rest of the trip: he’s been happy, even exuberant, over so much on this trip. But I understand. The time between destinations transcends what we do at either end. Neither here nor there, a time when plans are evolving, interruptions are minimal, you are with family or strangers or by yourself, and you have time to think and watch out the window, and nothing else you can do. “Old men ought to be explorers / Here and there does not matter / We must be still and still moving” (T.S. Eliot, East Coker). When you travel, constraints and desires come into a different kind of balance.
Last time we took this trip our trip from Paris to Bordeaux to begin this project. The trees were all full of round masses of bright green stuff, which we took to be some kind of squirrel’s nest. Anyone reading this who knows better will recognize immediately that this was in fact mistletoe. It’s all over here, today perhaps a bit greener than it was at the end of December. The fields are much wetter. We’ve had loads of rain since we’ve been here. I wonder if the horses get colds from standing in it all day?
Back to work. I’m trying to finish up documenting the codebase for RADami today. That has been a ridiculously slow process with little to write about, but I think I can finish it up on the train and the manuscript revised and resubmitted this week, so I can get on with new RAD work next week. One realization: there may be a bias in the partitioned RAD visualization the way I’ve been doing it, because the expectation is linear with a slope of 1.0 when (1) the tree likelihood is calculated as the sum of locus log-likelihoods for all loci based on just the loci used for the partitioned analysis, rather than the global likelihood for all loci; and (2) locus log-likelihoods are assigned based on topological identity with pruned trees that are voted on by each locus. I’m not sure this introduces a bias. It should reduce noise, as there is noise associated with requiring a locus to vote on trees that are topologically identical to one another when pruned down to just those taxa that are in the locus, but not topologically identical when all taxa are included. Because the optimization runs only until it stops improving by epsilon, trees that all lie at one point in the likelihood surface may appear to be at different positions. So in this sense the visualization as written biases us toward finding a tighter fit plot; but does it bias us toward a linear relationship? I’ll set this up to run the global likelihood on each tree as well, and see whether that plot is also so nice.
Last time we took this trip our trip from Paris to Bordeaux to begin this project. The trees were all full of round masses of bright green stuff, which we took to be some kind of squirrel’s nest. Anyone reading this who knows better will recognize immediately that this was in fact mistletoe. It’s all over here, today perhaps a bit greener than it was at the end of December. The fields are much wetter. We’ve had loads of rain since we’ve been here. I wonder if the horses get colds from standing in it all day?
Back to work. I’m trying to finish up documenting the codebase for RADami today. That has been a ridiculously slow process with little to write about, but I think I can finish it up on the train and the manuscript revised and resubmitted this week, so I can get on with new RAD work next week. One realization: there may be a bias in the partitioned RAD visualization the way I’ve been doing it, because the expectation is linear with a slope of 1.0 when (1) the tree likelihood is calculated as the sum of locus log-likelihoods for all loci based on just the loci used for the partitioned analysis, rather than the global likelihood for all loci; and (2) locus log-likelihoods are assigned based on topological identity with pruned trees that are voted on by each locus. I’m not sure this introduces a bias. It should reduce noise, as there is noise associated with requiring a locus to vote on trees that are topologically identical to one another when pruned down to just those taxa that are in the locus, but not topologically identical when all taxa are included. Because the optimization runs only until it stops improving by epsilon, trees that all lie at one point in the likelihood surface may appear to be at different positions. So in this sense the visualization as written biases us toward finding a tighter fit plot; but does it bias us toward a linear relationship? I’ll set this up to run the global likelihood on each tree as well, and see whether that plot is also so nice.
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