Green Plant Phylogeny Research Coordination Group
Green Algae Working Group
DuBois Center, Northern Arizona University
7:15 p.m. - 9:40 p.m.
6 August 1998
Attending: Mark Buchheim, Rick McCourt, Debra Waters, Russ Chapman, Marvin Fawley, Rick Zechman, Ken Karol
Marvin Fawley email@example.com
Kenneth G. Karol firstname.lastname@example.org
Richard M. McCourt email@example.com
Frederick Zechman firstname.lastname@example.org
Russell L. Chapman email@example.com
Debra Waters firstname.lastname@example.org
Absent: Louise Lewis
Mark Buchheim opened the discussion with comments on the goals for the IBC in St. Louis. He noted that August 15th, 1998, is the deadline forfinal plans for the symposia, and he will need all names and full addresses, including e-mail, of co-authors by August 12th. Conversation ensued regarding various aspects of the symposia.
Chuck Delwiche definitely wants to be included in the symposia. Regarding prasinophytes: Michael Melkonian's prasinophyte material is all done but not published. Marvin Fawley says Melkonian has indicated he hasn't had time to get it all done. Marvin Fawley is not doing prasinophytes. rbcL sequence for Mesostigma is available. Prasinophytes are paraphyletic (Rick McCourt).
Marvin Fawley & Rick McCourt discussed problems with deep branching in data sets.
Mark Buchheim talked about the data set for micromonads--Marvin Fawley has coccoid data, Michael Melkonian has most of other. Marvin Fawley can make a story, but would be much better with the Melkonian data.
Mark Buchheim tells Rick Zechman that the symposium is going to be an outline for the publication. Rick Zechman will present symposium for the Ulvophyceace, perhaps with co-authors.
Rick Zechman asks about synthesis of all data. What has happened?
Russ Chapman says not possible now to begin synthesis because we don't have all data to work with. Rick Zechman says perhaps we could do morphology, using Mishler paper as guideline.
Mark Buchheim says individual group leaders could develop a morphology data set for their group. Why not try to get it done this fall(ahead of April abstract deadline). Perhaps working independently as co-authors, could then get all data together for synthesis. Mark Buchheim would like to have this done by late fall. This also has to be integrated into an embryophyte synthesis, although we have to choose characters forour group.
Mark Buchheim asks for reactions to this plan. He thinks we won't be able to work on big data set all at once; that doesn't seem possible unless we could all meet frequently. Rick McCourt recommends a meeting onthe east coast. Mark Buchheim says there will be a meeting the weekend of October 4th, consisting of Brent Mishler, Russ Chapman, and Mark Buchheim. Liz Zimmer will be organizing. Discussed organizing a larger meeting around that for working on big data set, but decided against having ameeting then, although Rick McCourt, Ken Karol, and Chuck Delwiche might meet with the others.
Rick Zechman says if we had a list of species and a master character list and have all people fill in, then could put that on a diskand disseminate to all. Thinks it is crucial to have this master character list. We have master taxon list already, but Mark Buchheim says it is unrealistic even for focus groups. He has pared down the chlorophyceae, but not other groups. Between now and when next meet, this list must be made realistic.
Russ Chapman says must have target group, and it must always be complete, and data matrix should always be updated and made available.Then with that matrix, actual data to be analyzed will be self-pruned because we don't have data. No need to have prepruned list, but just let available data decide which data will be left out. Data matrix should bedone as soon as possible and put on the web site. Have two or three genes (SSU, rbcL, nuclear) were are supposed to work on. Molecular data availability chart should be simple.
Don't know status of morphological data at present.
Mark Buchheim: we don't really have morphology data availability matrix. At Seattle meeting tried to identify broad character list, but the characters are so vague.
Russ Chapman asks Rick Zechman if he took Mishler data matrix andworked on a more developed matrix. Rick Zechman is willing to share, but he first wants to make sure he didn't take anything important out; he has a list of deletions. Rick Zechman found lots of 'bad' characters for the Ulvophyceae. Marvin Fawley says he thinks that will be the case for all groups. Rick Zechman has 34 taxon by 120 character matrix list derived from Mishler et al paper and has ulvophyte tree based on this data matrix.It is a parsimony tree of morphology characters. It is for publication, so proprietary. His data matrix will be shared. Russ Chapman: this could be the skeleton for data availability matrix for everyone else.
Rick Zechman: many of the characters will not be useful for other groups, because he picked characters for specifically for the ulvophytes,but it will be a starting point for others to tack onto. Added 10 newcharacters for ulvophytes. He did not retain all of the taxa that were in Mishler publication, but he is pretty sure he left them all in.
Mark Buchheim sums up: Rick Zechman will give us a template for data availability. Are we going to share with embryophyte people or will it be useful? Russ Chapman: they should be compatible in that there willbe a lot of non-applicable characters, but some will and there should be overlap. The master matrices should be inclusive. Mark Buchheim agrees all should be inclusive.
Mark Buchheim will find out if Louise Lewis, Paul Kenrick, and Gar Rothwell are interested in taking a look at the template. Louise Lewis maybe working on a data matrix. Gar Rothwell is a paleobotanist at Ohio University. Mark Buchheim doesn't know if he is still involved in symposium, since he may be a symposium presenter in another symposium and he can't present in both. Paul Kenrick is supposed to find out.
There were no breakout groups for present meeting, as there weren't enough attendees.
Ken Karol asked if we have cut down number of molecules. Mark Buchheim is concerned we won't even have one gene complete for a big matrix. Very few rbcL for chlorophyceae except in certain groups--some orders are completely missing. Page 5 of handout Mark Buchheim presented gives a realistic list for IBC for chlorophyceae matrix. There are many zeros in the matrix. There is 18S data and partial 28S data. 21 out ofthe 28 taxa are missing rbcl. Mark Buchheim says maybe too large a data matrix for analysis. Discussion ensued as to who is working on rbcL, and what can be accomplished in time for meetings. A problem is that even if the sequences were completed, they could not be peer-reviewed and published in time, and therefore should not be put in the matrix.
Russ Chapman: big gaps remaining in the data matrix could be sources of future funding; however, if there are only a few taxa that could be quickly sequenced, even if the sequences were not published in time for IBC data analysis, it would be good to show that the group had cooperated in getting the sequences done.
Marvin Fawley--the list is out of date, lots more prasinophytesare done. Take home assignments: find out what the data availability really is for rbcL.
Assignments to update matrix:
Ulvophytes- Rick Zechman
Charophytes - Ken Karol (molecular)
Mark Buchheim will do chlorophyceae
Debra Waters will ask Thomas Friedl to do Treubuxiophyceae.
August 31 is deadline to get this information to Mark Buchheim.
This will be submitted to web site. Needs to be in Excell format. This deadline is for molecular data only!!!!
SHOULD BE in the format of: not done, done and in GenBank, done but not available-- plus or minus matrix. In theory, this could be posted on list server and others asked to input additional information. Could send URL and ask people to look at it and fill in once it is completed and uploaded.
Mark Buchheim-by end of month will have completed assignments and looked at Rick Zechman's data matrix.
Mark Buchheim: need to work on morphology right away--should we set deadline? Need to get data sets to one or two people soon. Could discuss by e-mail ahead of time. Concerned will run out of time and won't have a synthesized data set of morphology.
Mark Buchheim: when should we start thinking about analyzing data? Must first decide what global taxa are. Are we going to have a global analysis with all taxa? or pick exemplars of each group? Rick Zechman: probably have a lot to do with how we want to treat unknown scores. Mark Buchheim: would be reluctant to run an analysis for presentation that was lacking a molecular sequence, but might be okay for morphology. Need to focus on taxa with a complete data set all the way down the line; should be reluctant to have ANY analyses with missing data. Rick Zechman: what would really help would be if we could have flow chart and time line with names associated with what needs to be done when and who can coordinate and who will be recipients of final data sets for analysis. Brent may not be involved in IBC, but certainly with publication.
Russ Chapman: in terms of symposium, he envisions each speaker and coauthor will have completed matrices and run analyses, but that we still would like to see a global analysis for overall, which would be possible if all matrices were completely compatible. Is this a goal? Otherwise hewould just review the overall.
Marvin Fawley: within different groups different genes are important, and this can't be overlooked. Russ Chapman: so global analysis will not necessarily give the same results as analyses of different groups, but the discrepancies can be explained at the same time and this will be interesting. Mark Buchheim: focus groups can use whatever data will be available for that group, and leaders will be responsible for making the choices. Russ Chapman: yes, but for example, for 18S and morphology each group should provide data that for the global analysis. The global analysis could concentrate on only one gene plus morphology, and each group should give complete data for that gene, same for morphology. Each group must help with the global analysis , yet can do what they want for the focus group.
Marvin Fawley: December should be target date for data matrices.Will we need overview data also?
Russ Chapman: seems that if each focus group could get to the abstract stage before the abstracts are due and provide him with info, that would give some time before the abstracts are due to prepare the 'overview' abstract. If each group has data matrices ready, could do global analyses well in advance, but need lots of time, because will have to send the data off. Need someone else to do global alignments. All focus group alignments should be done the same way.
1 September we should start making decisions about:
global analysis--what taxa, begin assembling data set of available data. Propose global taxa to group, ask if the list of taxa is sufficient given what they want to talk about at symposium, will not add any taxa that are not on exemplar list for the global analysis.
Rick Zechman: Global alignment should be starting point for all focus groups. Global alignment should be locked in. Mark Buchheim--is becoming more and more important that global analysis have as many genes as possible.
Russ Chapman - fundamental question- do we include taxon for which we only have one or two genes? Or should we do global just for genes for which we have all data.
Rick Zechman, Debra Waters, Russ Chapman: We need a "hired gun" to do data analysis for global. Each group will do their own--don't have to do the same kind of analysis.
Need to resolve question about missing data--how will we resolve? Rick McCourt assignment--will try to do a missing data test and make the results available by September 1--or will at least report.
Mark Buchheim global taxon sampling dependent on this!! So, should be building molecular data matrix based on what we learn from Rick McCourt's data test. Ken Karol will also approach Huelsenbeck about doing global data analysis--we will offer him trip to IBC and co-authorship.
Then need to begin working on alignments, based on what learn from above. Must decide how to provide data to 'hired gun'--as alignments or as sequences.
Ken Karol recommends putting sequences in Sequencher then taking results and putting in CL (freeware).
8/31 data matrix will be e-mailed to Mark Buchheim, then to Brent Mishler, and also to algae-L, asking for anyone who knows of sequences that will be put in GenBank by end of year to please notify.
9/1 should have the info to put together list of global taxa
1 December all matrices completed. Mark Buchheim: need to get global alignment together as soon as possible (begin to get together). Whois going to do this? Ken Karol already has all rbcLs that are in GenBank in an alignment, so he can go ahead and complete. Mark will begin workingon 18S
ORDER OF TAXA in ALL MATRICES MUST BE THE SAME
Final discussion about symposia at IBC:
Mark Buchheim: need to contact coauthors and get lists to him.
Marvin Fawley & Rick McCourt: prasinophytes need to be moved and charophytes need to be put with embryophytes. Number of symposium speakers should be 7. Marvin Fawley will check with Melkonian and see if he is interested at all in global prasinophytes. Marvin Fawley will let Mark Buchheim know what is to be done--he may give a talk on prasinophytes.Then if so, Mark Buchheim will contact Louise Lewis and see if Louise Lewis and Rick McCourt can be co-authors on a basal streptophytes with charophytes and basal embryophytes. Marvin Fawley will decide whether the prasinophytes can be subsumed into overview, with Marvin Fawley and Russ Chapman as co-authors.
meeting adjourned: 9:40