[Note: these are rough minutes taken down during the meeting itself by R.L. Chapman. They are intended for archival purposes, see the Summary for a shorter version that will be published in various newsletters. Please excuse the rough edges -- we would appreciate getting feedback from anyone about errors or omissions in this document.] USDA Green Plant Phylogeny Research Coordination Group Workshop 24-28 June 1995 Valley Life Sciences Building University of California, Berkeley, California Brent D. Mishler, Host and CoPI Mark A. Buchheim, PI and Russell L. Chapman, CoPI Participants (arranged in alphabetical order using their initials, by which they are referenced in the following discussion): Angie Newton (AN) Alan Smith (AS) Alison Withey (AW) Bruce Baldwin (BB), Barbara Crandall-Stotler (BCS) Brent Mishler (BDM) Bernard Goffinet (BG) Betty Lemmon (BL) Brian Speer (BS) Chuck Delwiche (CD) Debra Waters (DAW) David Maddison (DM) Doug Soltis (DS) Dale Vitt (DV) Liz Zimmer (EAZ) Efrain De Luna (EDL) Jim Doyle (JD) Jaakko Hyvonen (JH) Jim Manhart (JM) Kathleen Pryer (KP) Karen Renzaglia (KR) Linda Graham (LG) Mark Buchheim (MAB) Mike Sanderson (MS) Peter Crane (PC) Pat Gensel (PG) Paul Kenrick (PK) Russ Chapman (RLC) Rick McCourt (RMM) Dick Olmstead (RO) Ray Stotler (RS) Richard H. Zander (RZ) Terry Hedderson (TAJH) Volker Huss (VH) Bill Hahn (WH) Session 1 - Sunday Morning 25 June 1995 General introduction of participants and business details I.e., the workshop schedule, handling of reimbursements, etc.) * Historical background of the grant * Plans for green algae workshop in conjunction with the Phycological Society of America meeting at Breckenridge in August 1995 * Discussion of goals for the current workshop - the 3 P's: planning, politics, and phylogeny. Should the group per se aim for some product of our efforts (e.g., summary report in some form such as a book and/or electronic media data disk)? Yes. Discussion of OTUs and characters: There is a need for an "available data matrix" to show investigators which data are available. If and when a data matrix for selected exemplar OTUs is completed, there will be some serious data analysis problems, mainly in handling and analyzing such a large data set (200-400 taxa and 4,000-10,000 characters per taxon). Discussion: MAB: in addition to big effort of the group, it would be appropriate for smaller subsets of participants to collaborate on projects within their taxon groups. BDM: We hope that this grant and the activities it sponsors could lead to additional funding from other sources. EAZ: There is a possibility that there will be a new Mellon grant at the Smithsonian Institution (SI) that could support some of the efforts that would be part of this project. RO: Is there a possibility of any support from the NSF cooperative for multi-lab grants? No one had any information on this subject. It was suggested that the appropriate NSF officers be invited to one or more of our workshops, and/or that we have a workshop in the Washington, DC area. It was suggested that it would be appropriate to interact with scientists involved in some of the massive genome projects and that the Washington, DC area would be an appropriate area for such interactions. RLC: The green plant phylogeny project is intended to be as inclsuive as possible, but the grant is not large enough to cover all expenses for all those scientists who might be interested in, and appropriate for, the project-workshops, symposia, etc. Everyone should keep this constraint in mind and help let others know that no one is being prevented from participating in the overall project, but not everyone can be invited to every workshop. BDM: One idea for a group effort product would be to aim to complete a book with a companion CD (or comparable electronic medium) containing the massive data base with annotations, etc. The book and CD would include only previously published data. The goal would be to have this volume complete by the time of the International Botanical Congress in 1999 in St. Louis. All contributors to the data matrix would be included as authors for the matrix and book chapters would be written by various small groups of participants and edited by the PIs and, probably, others. Also, the data matrix would be available electronically. BDM has informally spoken with a representative of Academic Press ( Chuck Crumley) who indicated that there would be interest in such a project. RO: We should consider a publication or electronic posting of the resources available (e.g., a listing of all the green plant DNA samples that are available, etc.). EAZ: The SI is working on its frozen tissue collections and there is some chance that the SI could cooperate in handling the preservation and distribution of frozen plant tissue and/or DNA samples. BDM: It would be best if all genes sequenced for an organisms came from the same DNA samples to ensure that everyone deals with exactly same taxa. EAZ: Most investigators would not mind letting people know what samples they have. RO: That kind of information would be useful and would be appropriate for dissemination via electron media. RLC: Although not explicitly listed in the original proposal, the PIs would like to plan to use some grant funds to get a Green Plant Phylogney WWW page up and running as soon as. Is this a good and acceptable idea? GenResp: Yes and a grant supplement and/or other sources of money should be considered if necessary. CD: Given the time to secure supplemental or new funding, it would be best to use current grant money to get the WWW site going and seek additional funding later if necessary. CD: Is this project supposed to be international in scope and, if so, is there any problem with inviting foreign participation? ANSW: There is no problem other than the high cost of covering the travel expenses for foreign participants. Also, VH indicated that there 25 labs working in Germany working on a similar collaborative effort. VH brought some information on this consortium. Their experience indicates that a mega-project (i.e., a project wherein specific participants are designated to work on specific parts of a single project doesn't work so well. Apparently, some subsets of the group work more closely and effectively than do others, and, thus, the not all parts of the project are being completed. Therefore, the Green Plant Phylogeny Reserch Coordination Group idea of providing guidelines for appropriate exemplar taxa and appropriate characters, will allow everyone and anyone to participate, but will not alot or allocate discreet tasks to specfic groups. BDM: It should be noted that the German green plant study group is a bit larger and more diverse (e.g., it includes population biologists who are not interested in phylogeny per se). VH has some of the summaries of the research activities of various laboratories in the German group. BDM will distribute these. BDM: there are also groups in Japan working on similar green plant phylogenetic problems. EAZ: Dr. Mitsu Hatsu Hasebe is a key contact person for learning more about the research activities of the Japnese workers. BDM: The three PIs do indeed see this project as international; and we hope to participate in a significant way at the joint USA-Canadian botanists meeting in Montreal in 1997. EAZ: We ought to present information on this project at other types of meetings such as systematics and evolutionary biology meetings, and molecular evolution meetings, not just at plant biology meetings. The upcoming paleobiology meetings are another possibility. PG: Something could be mentioned at the Santa Barbara IOP (International Organization of Paleobotany) meeting next year. BDM: Incorporating the fossil data is another of our tasks. PC: But we must remember that most of the fossil data that can be easily integrated into the data base has been (i.e., with respect to the angiosperms). CD: This is another case wherein the electronic data base can be very helpful. RLC: All participant can help with the following three tasks: 1)names (& addresses & other info.) on other who should be involved in this enterprise. 2)names of newsletters, bulletin boards, etc. for dissemination info. about this project 3)meetings that should be considered for possible workshops or reports from this group. DM: By 1999 the paper book maybe secondary and the electron medium would be the main thing. Also, probably cheaper. BDM: Yes, but there would still be lots of poor countries wherein electronic media access would be limited. DM: this was discussed in terms of electronic taxonomic keys and access in poor countries wherein access to electronic media is easier and/or cheaper. RLC: It is important to note that any earnings from such a book or product would NOT go to PIs or contributors, but rather to a research fund for plant phylogenetics. DM: the financial aspects would be the same for book versus electronic media version. PK: What about the editing of the proposed data base? BDM: Yes there would have to be editing and that is why limiting entries to published data (in peer-reviewed journals) would ensure some quality control. EAZ: The Institute for Genomic Research (TIGR) has a project on database links to museum specimens and molecular data. RO: GENBANK provides no quality control. WH: GENBANK is working on the taxonomic aspects on their database. He and RLC were at a recent workshop. He thinks they are getting ready announce an alignment database, and they may be getting ready for accepting information on vouchers. BDM: We can probably come up with the standards for submission. BS: What happens if labs are no longer interested in keeping their DNAs? It would be good to have repositories for DNA collections. WH: The ATTC may accept and store DNA samples. EAZ: It would be good to have the SI involved in the frozen samples collection (Mike Braun has a grant for this). WH: How large a project would this be? ANSW: The space is not so critical, rather it is the distribution to requestors and the eventual depletion of the samples. There would be questions about the original IDs etc. BDM: The current grant could look into this. Is the general idea of afour year goal of a report/publication appropriate and acceptable? ANS: Yes. CD: such a project would require at least a couple of people working on it. BDM: If we want to do, the first thing would be to contact more publishers. GEN DISC: of practical aspects. BS: The BSA has a slide collection that might provide needed pictures. JM: There are a lot of images on the Web that could be pulled down. GEN DISC: on legal aspects of copyrights etc. DM: Many of the presses will be publishing on paper and electronically simultaneously. Also, he will talk about the Tree of Life project later in this meeting. CD:******************** there are also funded projects in Scandinavia (CD) and Amsterdam (TAJH). RMMcC has phytoplankton data base from one of these. EAZ someone at the LMS will be getting information on some other data base activities involving museums. BDM We are in agreement on a such a project, but small subgroups will have to be involved. We will try to involve many people including foreigners. There would have to be coordinators for various subtopics. BDM The fern people are publishing their summary already so that area would be covered. KP how would this affect people's publication activity? BDM Shouldn't be a problem if we stick to using published data. BDM MacClade needs to accept bigger footnotes. BDM this group, as a group would not publish much if any new data (except an occasional sequence or two). BDM so we should talk to publishers. EAZ Be sure the publishers are dedicated to electronic media. BDM What other political issues are there? RO But if this being duplicated elsewhere, what do you do (e.g., Germany). BDM Shouldn't be too bad a problem especially in terms of Germany (different thrust). Same thing for Japan. BB It would be helpful to include people who are working on very fine level taxomic questions in a database. RO include these people in electronic database. JH What about a data base of literature references? Yes there should be some of the pertinent literature included to support the matrix. JM At Tx A&M colleagues are often asking questions for which our data bases would be helpful. RZ databases should be transportable to various platforms. DM MacClade data matrices are NEXUS files. That is not what people would want ultimately. DM how many data bases etc.? People database, DNA samples data base, alignment database, character matrix databases for morphology and molecules. RO would this be a project goal? Yes, two large NEXUS files (MoBot paper, fern people have one). RO rbcL data set. BDM My original idea was for simply making nexus files available. DM searchable database would be ultimate goal. DISC of files and convertibility. 11:10 BDM provided comments on plans for this afternoon and subgroups (tracheophyte group, liverwort and hornwort group, group, charophyte group, and moss group) and the task of listing the appropriate examplar taxa. The alternative to using an exemplar approach vs. consensus sequence for group of taxa in group. Also, how can you encourage cooperation within the group? Mechanisms for reaching our 1999 goal? RLC Presented a reminder for participants to turn-in suggestions for people, newsletters, and meetings. DM What about the criteria for choosing exemplar taxa? BDM Good question will discuss today. EAZ It would be more logical to discuss this before we discuss exemplar choice. JD The data analysis is scheduled for after the other discussions. RZ and MS We all need to discuss the criteria etc. General discussion and agreement. Discussion of exemplar selection: 1) availability (material and/or other data already available and character rich; good criterion?); 2) nomenclatorial types; 3) model systems; 4) "basal" taxa and/or isolated taxa, "plesiomorphic taxa," within a known specific subgroup i.e. avoid highly autapomorphic taxa where appropriate ; 5) * broad representation for diverse groups (even sampling) of "true" tree, no long branches, fossils; [ comments: 4 says exclude taxa, 5 says include taxa; can't avoid; need to keep number small]; 6) anomalous taxa? that are not within well defined groups (remnants); [sister- group = the Chlorophyceae; sister-group to Chlorophyceae = Streptophytes; JM we need to be sure about the out groups; need to use other out groups; CD working on some of these taxa, but this is not too critical to what we are doing here; JM We would want to root this at some point therefore we need to be sure about the outgroup; CD This meeting could help drive the collection of needed data for critical taxa; AS subgroups can prioritize exemplar taxa; the selection is guided by the idea of resolving the broad level relationships and the limit a few hundred OTUs; RZ We should select taxa at the base of long branches (not at the end of long branch); JD sometimes the selection of taxa is great (e.g. Liriodendron and Magnolia a good choice, but other selections based on what is readily available are bad); CD these kinds of questions are good for the group in question and can be discussed in the subgroups; for the Charophyceae some of the critical taxa are not in culture] break at 11:45 meet back at 1:00 use SE door 1:15 Session 2 Reminder for afternoon goals: each subgroup should choose a scribe who might report the results later. Discuss exemplar taxa and then discuss mechanisms. Even if we are not done it would be better to meet here at 4:00 for a general session and progress reports. 4:00 Session 3 Group Session - Reports Charophyceae Group - Mark Buchheim Just a few orders, not such a difficult task. Some model organisms included. Some interest in the Coleochaetales and new task. Did discuss the out group issue; more or less agreed that Charophyceae could be out group to land plants or Chlorophyceae to the Streptophytes. Only a small number of exemplar taxa ~20 Hornworts and Liverworts - Brian Speer and Barbara Crandall-Stotler Exemplar Hepatics B. Crandall-Stotler, B. Lemmon, K. Renzaglia, B. R. Speer, R. Stotler, D. Waters (* = essential, S=spermatid, U=ultrastructure, R=rbcL, 18=18S, !=data pending) Anthocerotophyta * Anthoceros "punctatus" (NA) R * Megaceros (tosanus? flagellaris? d'Puerto Rico?)R? * Notothylas orbicularis S * Phaeoceros carolinianus S U Sphaerocarpales Riella affinis * Spharocarpos texanus S R Monocleales * Monoclea gottschii S U R 18 Marchantiales * Conocephalum conicum U R 18 * Corsinia coriandrina ! Dumortiera hirsuta R 18 Exormotheca pustulosa * Marchantia "polymorpha" S R 18 Neohodgsonia mirabilis Oxymitra paleacea ! * Riccia glauca ! * Ricciocarpos natans R * Targionia hypophylla (Europe) ! Metzgeriales * Blasia pusilla S U * Fossombronia brasiliensis 18 * Haplomitrium hookeri S U R? 18 Haplomitrium mnioides S R * Hymenophyton flabellatum Makinoa crispata R * Metzgeria crassilipis Noteroclada confluens * Pallavicinia lyellii S? U R 18 * Pellia epiphylla S R 18? * Riccardia multifida S? Treubia tasmanica S Jungermanniales * Anthelia juritzkana * Barbilophozia barbata * Bazzania trilobata R? 18 Calypogeja muelleriana R? * Cephalozia lunulifolia (bicuspidata?) * Herbertus aduncus R? * Jubula pennsylvanica R * Jungermannia leiantha 18 Lejeunea Lembidium * Lepicolea (sp. from Cent. Amer.) * Lophocolea heterophylla R * Marsupella emarginata S? Micropterygium * "Omphalanthus" filiformis * Plagiochila porelloides * Porella pinnata R 18 Pteropsiella (frondiformis?) * Ptilidium pulcherimum * Radula tenax (Florida) * Scapania nemorea Schistochila * Temnoma * Trichocolea tomentella 18 Vetaforma dusenii (Argentina) Other taxa * Naiadita (fossil) 3-4 hornworts 8-10 simple thalloids (Metzgeriales) 14 leafies (Jungermanniales) 1 Naiadita 1-2 Spherocarpus 1 Monoclean 6-8 Marchantiales 1 "fossil liverwort" total: 41 some research questions covered by these taxa include some aspects of morphology evolution within the groups maybe more taxa needed to cover the diversity problem of finding pure cultures of these bryophytes noted (e.g. two different genera of hornworts growing together with the sporophytes only of one of the species showing) QUEST: what are the oldest leafies? ANSW: Permian (Palaviciniidaes) Mosses - Dale Vitt 60 taxa, 20 orders but some of these are low priority for the big land picture little discussion of mechanisms: circulate the news Tracheophytes - Dick Olmstead 2-4 cycads 12 conifers 3 gnetales 2 psilophytes 3-6 lycophytes 2 equisetaceae 25 ferns 35 angiosperms total: ~ 85-90 (excl. fossils) what fossil taxa should be added? total, total: ~200 DISCUSSION: DM: each group draw phylogeny with age of origins and see if there are long branches. BS: need entire phylogeny for perspective. CD: We don't have many Charophyceae, 80+ taxa would cover almost every genus we have. RLC: we kept our number low, but we would need more to study the Zygnematales well. Maybe we should have a list of questions within each group. BCS & KR: QUEST: In the character matrix will there physiological data? LG: recent paper in AJB information about auxins in an evolutionary context. auxin modifications that influence its activity and Charophytes and Liverworts were basal while other bryophytes and tracheophytes were more dervied: thus this is an example of physiological data that could be used in a phylogenetic analysis. Monday 26 June 1995 9:00 a.m BDM: comments on the exemplar taxa activity: subgroups should plan to submit a finalized version on their list via the subgroup chair or recorder/reporter by the end of summer: end of August; now groups should decide who will do what here and now; develop the character matrix for the exemplar taxa; RLC: does everyone agree we should start the WWW page etc.? Yes. Does anyone else want to be involved in setting this up? No. Can and should Brent proceed with it here at Berkeley? Yes. Also, mirror the page to other sites. DM: photos of PIs too. RLC: good idea to help people see each so to speak. BDM: Also, photos of organisms should be added. tomorrow afternoon another big group meeting (what databases we want and who will develop it) 1:15 Monday afternoon session - brief research presentations BDM: 1 person in each group circulate character data matrix to group for comment etc. and then to Brent exemplar OTUs and data matrix etc. Therefore, brief OTU group meeting tomorrow morning for 1/2 hour to assign responsibility for these activities etc. (meet at 9:00 for no more than 1 hour.) Much of this can be done by email after this meeting. Comments on travel (lobby at Foothills has travel info.) they will pick up at the campus. Wednesday: they will work on airport trips (to Oakland = 1/2 hour normally, 2 hours by van; can take BART too). RLC: 6 min MAB: 3:35? Sphaeroplea , Atractomorpha , Radiofilum , Ankyra; Spheroplea is not really filamentous long branch leading to this clade looking at zygote morphology and cross wall morphology ITS data support the morphology data Sphaeroplea not monophyletic, some species come out with Atractomorpha Q/A: Where do the Streptophytes fit into this picture VH:18S rRNA data (they are doing some 16S rRNA); they have recent paper in Molec. Evol. tree without Dasycladales, sued Charopytes as out groups; earlier work on Chlorella; Thomas Friedl Trebouxiophyceae; basal ulvophytes (above the miscellanaeous Prasinophytes); published tree with Mantoniella in the Chlorophytes - Charales are the basal group in the Streptophytes; Chlorokybus sister to Zygnematales; ML analysis: similar; have also done some plastid sequences: Coleochaete sister to land plants, Charales basal; 18S of Charophyceae with RLC sequences bryophytes incl. seq. from Capesius; branches short - hard to resolve - BUT liverworts are polyphyletic; she added 3 more bryophytes, he has 2 trees Pteridophytes: lycopodium basal, Psilotum derived -this paper doesn't include Ophioglossum sequences; he is also looking at fossil data; 2 Psilotum nudum sequences too many errors in one (ours?) DAW check on this - compare our sequence to the new GENBANK sequence - determine if corrections are needed RMM: 2:02 looking at morphology and molecular data: rbcL (cpDNA), ndhF (cpDNA) 3 prime end highly divergent from land plants VATPase (Gogarten) review of the families; tree based on rbcL data Entransia was in Zygnematales now comes out with the Coleochaetales Charales (W&I idea with diagrams on slide) two sections of Tolypella (sec. Rothia and sec. Tolypella) and the two taxa are sister to each other (not paraphyletic) morphological tree 25 million year old gyrogonite DNA sample comes out basal to the Charales ndhF data (about 700 bases near 5 prime end): here Coleochaete is sister to the land plants introns in V-ATPase A subunit: in Coleochaete but missing in Hornworts JM:1:51 pm original interest in angiosperms rbcL tree with lots of poorly supported placements (lycophytes derived with some mosses etc.) ; reviewed info. on fern allies and 16S data, throwing out the Selaginella sequence pulls the Isoetes up next to the seed plants angiosperms and gymnosperms variation in "str operon" genes; had interesting result for Spirogyra and Marchantia (intron) ; showed matrix with taxa and introns-in-gene info. (23s rbcL, tRNA's), so he is now continuing the look for introns Q/A: DS; What do the different genes tell us? 5:06 Chuck Delwiche: Coleochaete orbicularis, C. nitellarum, and C. scutata etc. descriptions and comments (Chaetospheridium) ; he has most of the species in culture and has DNA for those that can be grown in quantity; did rbcL with Jim Manhart's data for the higher plants; arrangements among the orders of Charophyceae very variable in rbcL data analyses Studying plasstid evolution: looked at protein tufA and ML analysis in paper he just published in Molec Phylogenetics and Evolution 1995 4:110-128. He thinks tufA is changes a bit fast for these analyses is not too bad, but placement of plants is questionable because the gene was transferred to the nucleus in landplants. He wnts to study the nuclear gene in Coleochaete. Euglena plastid comes out with greens. He has done extenisvve other analyses on rbcL. Dinoflagellates has a form 2 rubisco perhaps transformed this gene from mt to ct one way or another He is also working on tree of life with Norm Pace's group (mentioned new info. on new group isolated from hot mud) 3:24 pm Linda Graham: character state transitions: 1) charo zygotes -> embryo sugar transporter genes, proteins, & regulation 2) primary plasmodesmata charos -->early divergent bryophytes 3) resistant wall compounds (other than sporopollenin) charos --> bryophytes fossil records of bryophytes ancient fossil evidence of land plants: spores and spore tetrads (Jane Gray thought they were from liverworts) there are Silurian fossils that look like LWs, so maybe these early spores are from LW; there was also scraps of cells not from animals, 470 mil yr old plant tissue? Diane Edwards studied other fossils like these and suggested they might be from plant cuticle layers etc. BUT these samples are not associated with underlying tissue; she showed slide of extant organism (Sphagnum capsule boiled in conc. sulfuric acid) that is similar to the fossil; they autofluoresce (highly crossed linked polyphenolics); material from liverwort (capsule wall after acid treatment), the elaters (el-lahters ? vs. ee- lay-ters?) survived; they are now doing SEM study etc. from where did bryophytes get the resistant material? Coleochaete has acid-resistant material; Charophytes invented these compounds NMR studies underway with a colleague these compounds are different from sporopollenin they are NOT base resistant and have a different FITC spectrum 4) origin of cuticle: charos --> bryos 3:41 Brian Speer: looking at relationships within the Marchantiales (a small order) incl. Riella, Riccia, Marchantia, Monoclea, etc.; he is focussing on the genus Targionia ; there is a lot to be cleared up for liverworts; cladogram showing Sphaerocarpus, Toximitra, Targionia, etc. (spore dehiscence types); rbcL studies BDM: may give enough resolution for his study Q/A Where would you root that? BDM if you try to root with algae, the long branches cause problems and algae end up in the bryophytes etc. Q/A Is there a reason for the long branches? Maybe there is GC bias and Louise Lewis is looking at that. Brian would like to know if it is related to environmental factors (one group is subject to drying out frquently and the other isn't, so maybe there is a relationship) 3:53 pm Barbara Crandall-Stotler: students working on various problems; in hepaticology we are futher behind in good testable phylogenetic hypotheses; diaspores - how long do they survive in nature (e.g. after fires); one student working on Monoclea . Checklist of liverworts and hornworts of North America. Their checklist is being published and it will be added to the plant data base. Showed Shuster's complex diagram of his hypothesis p. 336 and 340 now they are focussing on the non-leafy hapatics; 40 genera in the Metzgeriales, total of 72 morphological characters; simple thalloids are not always very simple, some have good vascular-like system; also doing light and em microscopy to determine homology of morphological characters; they are planning to develop morphological data base and culture exotic taxa BDM: they made all of the observations themselves 4:07 pm Terry Hedderson: really a life history specialist, but used 18S to look at broad relationships: basal hornworts; LW and Mosses are sister taxa in parsimony and ML analyses and he has run with up to 46 tracheophytes; also look at liverworts with hornworts as OG, topology not stable, but monophyletic jungermanniales; quite clearly we are going to need more taxa and maybe new gene; looking at the mosses: basal Sphagnum, the two clades, some support for Dale Vitt's hypothesis concerning some of these; (peristomes evolved twice, operculum have evolved multiple times) these results differ from Volker Huss; all ambiguous regions have been removed 4:16 Brent Mishler: interested in haplopideous mosses, but had to look at green plant phylogeny; now going back to finer levels and focussing on lower level questions; we hope the day of single gene trees will end; rbcL data incl. some of Jim Manhart's data; new tree from Louise (rate difference between leafies and thalloid liverworts), gets LW tree that seem to be different because of the rooting: basal Spaerocarpales, then Marchantiales, then Calobryales, the Metzgeriales sister to Jungermanniales current moss rbcL (week old tree): some similarities with Terry's tree (high degree of congruence); this is not a weighted analysis, hornworts were the OG, LW as OG gives different topology; in the giant rbcL data adding the LW mess up topology among the tracheophytes Q/A BIG THREE BDM LW are basal, 4:30 Richard H. Zander - 76 genera in moss family (Pattioideacae) rooted with a selection of taxa that may not be right, but the tree does fit traditional approach; he "doesn't have a fumehood" 4:41 Dick Omstead - What constitutes sufficient taxon sampling? (his own work is on the Asteridae) looked at subgroup Lamiales: in much of this work there is a lot of unresolved relationship; zoomed in on Labiaceae and had lots of seq data BUT the nodes are weakly supported....maybe bursts of rapid radiation...he believes this reflects the eveness of sampling and having short internodes; analysis: recent study of the Scrofs (snapdragons, etc.) results suggested not monophyletic (version 4 of PAUP); tried NJing with PAUP got different result (no BS values for the NJ analysis); ML analysis in PauP; he is just raising questions of which we should be mindful; What constitutes good data? Olmstead and Sweere Sys. Bot. 1995 (issue 1) Look at substitution rates and compare to random rate (0.5). rbcL was 1, ndhF was about one therefore a basis for waiting What about codon positions? probability of change varies greatly at each position, but there is not such a great difference among the three positions AND for these ct genes there is NO basis for weighting Now he is working on comparing independent data sets for nsdF gene to see if there can be a basis for weighting individual positions. Slow gene vs. fast gene is not a good set of terms despite the convenience; there is not s statistically significant difference when you look at the standard deviation 5:07 Q/A EAZ any specially useful data to examine this etc.? 7:29 pm Monday Pat Gensel: fossils of early land plants; she is working on the Trimerophytes____________?___ Psilophyton and Pertica: lack leaves, no roots (basically "stick on sticks morph."}; some gametophytic material but not much, generally we have sporophyte material; some preservation is fine and can be studied at light and em levels; she faces a shortage of characters for cladistic analysis of these taxa; she is interested in spores and comparisons of fossil and extant taxa; characters such as wall laminations, aspects of the apertures in spore, maybe some details about the thickenings in the wall, etc. might be useful 7:44 pm Kathy Pryer (worked with Brent on ferns, now at the Field Museum) She works on lycophytes; part of pteridological symposium group combined rbcL data (107 rbcL sequences) analyze with ML, NJ, and MP (only 72 taxa could be used for ML); notes on ML tree: heterosporous ferns come together as a monophyletic ferns; the tree ferns are also a strong monophyletic group; indusium missing in two different groups; with help from Judy Skog et al. she put together a morphological data set82 characters for 61 ferns plus OG taxa; comments on the footnote feature in MacClade; OG = Equisetum, Lycopodium, Cycad, and two fossils; morphology tree: consensus tree (of 1000's of mp trees), combined rbcL and morphology consensus tree (of 10 mp trees) AS: old ideas incl. theory that there were multiple origins of indusiums; Psilotum and Botrychium came together (controversial, but also supported by rbcL data) 8:10 pm Doug Soltis: work of Doug and Pam during sabbatical at SI: land plant survey with several collaborators incl. RLC Angiosperms with several collaborators (Nickrent, Hahn, Johnson, Kron, Kuzoff, Hoot, Chaw, Sweere, Chase, Zimmer, Sytsma) OG Gnetales Concerns: 1) 18S sequences are highly prone to insertion and deletion; 2) these indels make alignment difficult; and 3) too conservative for angiosperm work a) some of the alignment problems are cause by erroneous sequences b) location of indels and phylogenetic importance; msot indels confined to specific regions of 18S (3 regions) c) ease of alignment: examined problems he had with RT sequencing etc. and once you can sequence through tough regions, things get easier; d) mosaics of regions: rate of evolution 18S vs. rbcL: 18s has long regions of stasis and hot spots much more so than rbcL therefore a mosaic e) compensatory changes phylogenetic results: Amborella at base! followed by clade of Austrobaileya/Illicium/Scisandra followed by Nymphaea followed by Annonaceae/Lauraceae/Calycanthaceae 1) supports woody Magnolids rather than paleoherbs as most ancient extant angiosperms 2) monocots are monophyletic 3) large "Saxifragales" clade is preset, sometimes sister to remaining higher dicots 4) Expanded Caryophyllidae: incldues Droseraceae and Neppethaceae (as in rbcL analysis) 5) Mustard-oil plants for a clad (as in morpholoigcal + rbcL analyses) 6) Hammelidae cleearly polyphyletic (as in rbcL) 7) Expanded Asteridae (as in rbcL analyses) future plans: move into 26S sequencing; phylogenetic analysis of 400 angiosperms suing the 18s and 26S regions; comparison with rbcL and morphology 8:35 Liz Zimmer: review of ongoing projects at the SI and participants; some current results; automated sequencers have really made significant positive changes; sequencing of both strands possible on a routine basis; Q/A Brian Speer re: inclusion of certain taxa Tuesday 27 June 1995 9:15 BDM: travel info Dave Madison: Tree@Phylogeny.Arizona.edu BDM: by late this summer we need the list of exemplar taxa and the list of characters, and current data matrix; OTU groups need to workout mechanisms; OTU groups should feel free to contact other members; overall goal is to stimulate truly comparative research on these exemplars; we could ask some individuals to help complete specific needed studies; meet in OTU groups for 1 hr, reconvene at 10:30 9:30 Charophyte OTU group 1:30 Plenary Session: Logistics: at circular turn around by check out office 5:30: Russ, Volker, Linda & daughter, AllisonWithey (Duke) to Oakland 7:00: Angie, Terry, Effrain 11:15: SF airport: Betty, Debra, Rick and Paul (Ken & Rick) tonight: Terry O'Brein and van to SF Jack London Square in Oakland (Dutch East Indian food) 1:35 Morphology & Molecules Subgroup Reports Molecular Data: Dick Olmstead: reviewed what sequence data were available and was desirable rbcL and 18S already pretty complete; ct genes atpB, 16s rRNA, ndhF, 23s RNA ct gene; nuc: 26 S rRNA, RNA pol2 subunit 2, tally of over 10,000 base pairs from those genes excl. the last RNA pol2; also, number of molecular characters dealing with genome structure in ct genome (Jim Manhart will develop the info.); also, primer database worldwide coudl be useful; nomenclature for primers (universal means for designate: Bill Hahn and Chuck Delwiche will work on that); also discussed where we my want to go with multiple lab grant proposal - perhaps talk to people at the NSF before doing anything; also, parallel proposals in US and Europe; EAZ not only NSF, also USDA and DOE; need to think big in terms of private sources, Europe, etc.; discussed DNA availability - no volunteers to over see the effort - OTU groups could handle this separately; what is available in independent labs might be a problem; BS: Should we include whether the sequences are based on both directions? Should include lots of information. EAZ: Maybe somebody would want to pursue the DNA availability idea; maybe somebody is doing it; Many people may being doing some of this. Lists of sequence availability: Dick Olmstaed will compile ct DNA sequences; Liz and Doug will handle nuclear sequences; Non-molecular Data: Russ Chapman for Linda Graham: 11:55 Morphological (non-molecular characters) I) What kinds of character types can we define that would be useful across all green plants (globably useful)? 1) BL: great deal of information on microtubule organization on plants, cytoskeletal characters: a) MTOCs, b) PPB (preprophase band) and cortical microtubules, c) immunolocalization (less laborious than EM, less expensive?); can use serial sections; relates to the extracellular matrix 2)LG: gross meristem structure (SEM approach) (n.b., for both sporophytes and gametophyte plants where appropriate); lots of data not collected yet; BL: this is a basic plant feature DISC: are the meristems different in the generations? or just turned-on differentially? PG: same group of genes or different group of genes? Work in bryophytes? There is work on protonema, can the workers also look at sporophytes? There will be global comparisons of homeostatic genes. 3) LG: additional studies relating meristem development 4)PG: sperm ultrastructure, other aspects of reproductive processes including timing of meiosis 5)PG: Can types of meristems be handled as character states? JD: Tricky because it can be different in different plants (e.g. meristems in gametophytes and sporophytes can be homolgous or different) 6)BC-S: Global characters will be things like plastid organization. 7)RZ: Be careful about terminology for reproductive processes (e.g. monoecious and dioecious etc.). 8)JD: Problem of blocks of missing data for all characters that are not truly global. 9)BCS: Spore wall characters might be more global and extracellular matrix characters too. 10)RZ: Pigments (e.g., chlorophylls but chl b has multiple origins) might be used. 11)RLC: Why keep non-molecular data? JD: We want to get information from fossils to help our understanding. RZ: Study the evolution of morphology by superimposing morphological characters on the molecular trees. PC: We need fossils to understand the total diversity that ever lived and that can't come from molecular data. Any general explanation of plant evolution must include the extinct plants. JD: Much of the information is already available. 12) specialists could help redevelop, redefine some of those characters in the MOBOT paper 13) developmental shifts, to soon to use 14)exemplar blots!!! BDM that could be probed for various genes RZ: Morphological characters are important to understnading form and function. LG: Morpholoigcal studies provide insights into ecological questions and adapations, and these can't be addressed with sequence data. JD: Yes, are we interested only in the phylogeny or in the evolutionary development and the understanding of the biology of green plants. KR: Morphology helps provide standards by which to assess molecular trees. 12)RLC: additional fossil characters? PC: Yes, megaspore characters and the evolution of meiosis. PG: Spore aperture already covered. BL: Endosperm development (the third generation). 13)JD: Heterospory and other aspects of megaspore and microspores. 14)PG: Initiation of reproduction. 15)BL: Wall development (including in some cases, fine structure) and extracellular matrix. 16)PK: A lot of plant characters available in fossils of plants vis-a- vis animals. 17) phytochrome function 18)presence or absence of certain genes DISCUSSION: PK need definitions (e.g. for xylem present or absent) II) How can we encourage people to contribute to this effort? BCS: People work on their own little projects. LG: Obviously the new home page would help spread the word. PG: The evolution meeting and BOT SOC (Plant Sciences Bulletin) BCS: Bryol. group working on matrix for 1997 for Montreal meeting, could this be done through BOT SOC.? LG: Should we have someone write an article for Plant Sci. Bulletin? Yes Reports at various meetings etc. AIBS Business Meeting ? Pat Gensel and Linda Graham could contact some people at AIBS. LG: Maybe beneficial to have plenary sessions etc. at various major meetings; for example at Seattle BSA meeting (LG, PG, & EAZ). III) Are there major questions or changes in approach that we should raise? 1)Treating our exemplar taxa as special taxa (cf. endangered species) in our efforts to promote this undertaking. 2)SEM observations of meristems. 12:05 OTU GROUPS: 1) Charophyceae: Mark Buchheim: MAB, with Chuck Dilwiche's help, will compile the list of exemplars and data availability matrix; 34 exemplar taxa 2)Liverworts and Hornworts: Exemplar list up to 50. Barbara Crandall-Stoler: KR and BL responsible for matrix of morphological data availability, BCS will cordinate; Brian Speer and Debra Waters will collect moleclular data availability information; BCS and RS will complete developmental data availability matrix; announcements will be made in Mexico City for living collections of exemplars; BCS & RS woudl accept material and make voucher and culture; KR would embed for em study in plastic; would advertise availability of the matrix in BBS meeting and elsewhere (e.g., AIBS), AIB meeting. 3)Mosses: BDM Moss exemplar list now 50; BDM will work on morphology data (character) availability matrix; BG will work on DNA availability; try for 1997 meeting in Montreal??? report on relationships mosses (and liverworts too) as an intermediate goal for the moss subgroup; each subgroup should aim for intermediate goal; DISCUSSION: help from BSA (Barbara Schall) and ASPS (SCT president) for plenary sessions, symposia, etc. 4)Tracheophytes: Peter Crane: About 200 taxa on the list, but this may come down to 80-90 key taxa and some fossil taxa; need to get down to the species level for some of these for angiosperms and conifers; Peter Crane will keep filling in the matrix; Alan Smith, Dick Olmstead, Liz Zimmer Kathleen Pryer, and Doug Soltis will help with the molecular data availability matrix; Paul Kenrick and Pat Gensel work on fossil data availability; have a fern focus meeting in Montreal in 1997; Dave Madison had raised a question about the technical problems (lg. data sets, what to do with missing data, questions of homology) BDM: We are planning to have at least one meeting on data analysis. Miscellaneous Other Issues: 1.Meetings vs. other expenditures: original plan was for 10 meetings; need to think about this issue: a) bryophyte meeting: in Montreal 1997 b) fossil meeting: in association with big meeting IPC & IOP (Santa Barbara) in 96, maybe in 98; focussed workshop would be better or do both c) fern meeting: 1997, 1998 d) Charophtye fossil meeting e) seed plant f) data analysis, high performance computing , algorithms, (Chuck Delwiche growing interest among HPC people in phylogenetic analysis, HPC prize); CD: also a need for specific plans for last year of the project, how to handle this massive data g) IBC in 1999 i) meeting in Washington incl. genome project people; SI meeting money to help supplement; combine with some other focus meeting 1995 UCB and PSA (algae) 1996 fossil Charophytes (2nd week in July in Wisconsin) but they are anticladistics Seattle: global characters (morph. characters) Baton Rouge: February - data analysis, large data sets, algorithms meeting DC meeting grant proposals 1997 Montreal: bryophytes, ferns (incl fossils) 1998 seed plants fossils final report coordination and planning whole group nuts & bolts meeting (EAZ try to raise money) general comment: have both public symposium and private workshop, yes; seed plants meeting: later better than sooner; 1999 IBC in St. Louis 2) Workshops: suggestions of people who should be included should go to the PIs; EAZ maybe people can get help toward their expenses; we could send letters saying that we would cover 1/2 of the costs. 3) Grants: maybe have foreign guests at the Washington meeting (e.g. Prof. Hoeker); also NCBI people, TIGR 4) CD: Funds availabile for eastern European scientists, former soviet union scientists 5) National Research Competitive Grant Program, Collaborative Plant Biology Program Plant USDA Grant Number 94-37105-0713 6) Databases: a) data availability matrix or matrices for OTUs (maybe NEXUS file); continuously updated; organized by OTU groups b)actual data matrix: prepare near the end not as an early draft version; release before IBC; NEXUS format with footnotes etc. (250 exemplars plus Chlorophyceae) for OTUs only c) put older matrices in TREE BASE not on our WWW page d) some info. would go into TREE OF LIFE database e) DNA availability matrix (what is published, what is available, what is planned, tissue list, ongoing projects) could be lab-based and updated by labs with links to individualsetc. EAZ: good way to get started and people would be willing to help; RO: more information than just info. that relates to this project; the DNA availability matrix is being compiled in two pieces: cpDNA by Ollmstead and nuDNA by D. Soltis and L. Zimmer f)culture availability for all OTUs not just exemplars (RLC check on Japanese culture collection web site and then we link to it); try to indicate which taxa are exemplar taxa g)primer list (will be compiled by Bill Hahn at the Smithsonian Institution and Chuck Delwiche at Indiana U.; sequences and availability; follow standard format; incl. reference sequence for numbering; incl. notes on the universality of these primers; reference list to publications with first use of these primer and the sequences h)vouchers? there should be a field in the final data base there should an entry for reference to the vouchers and who determined them etc.; list of experts willing to identify (Alan Smith: ferns; Ray Stoler: hornworts and liverworts); the ASSC??? is working on a list of taxomic experts i)Plant-Taxonomists-On-Line (PTO): RO will check into current status; it is on the Gopher; BDM: maybe we could spend some funds to help sustain this General Discussion: RLC: How to maximize participation with finite funds? EAZ: Encourage altruism, get people to match. BDM: Have invitees bring 1 person and set the number at 1/2 of what can be afforded. CD: Use this money as seed money. BDM: Not just money, also max. size practical limits invitees. EAZ: Opportunity to take our project to a molecular meeting (Elliot Meyerwitz will be coordinating and there is 1997 meeting for Molecular Evolution meeting); we should be represented. RO: Would be glad to talk to the Society Systematics Biologists about our activity and Pam Soltis is on the Council; therefore, get to Dick Olmstead asap (that is, by July 8th. EAZ: All participants should review minutes before we circulate further. CD: Must be careful about those who couldn't be invited to the meeting because of financial limits etc. The project is open to all. BCS: Everyone is invited to work on the matrix . There is no attempt to preclude participation. BDM: Data availability matrix will help many people. The intervening meeting might have written products too and the participants would all get credit. The final book would be edited and all writers would get credit. The data matrix would have even more authors. EAZ: The large co-authored papers bring the authors into conflict for NSF. BS: Minutes should emphasize that we are here to promote coordination and cooperation, and want to encourage participation . EAZ: Important to emphasize that we are not trying to intrude on the research activities of others. BDM: Since to be included in the final project authors must publish their data, there may be a bit of a stimulus to the field. RO: Perhaps put out a brochure. BDM: OK to talk with publishers? Yes. Recommendations: Smithsonian Press? Academic Press, Cambridge, Sinauer, Chapman & Hall, Hartcourt Brace, Univ. Chicago Press, O'Reilly and Associates in Sebastopol CA (computer based publishing), Cal Academy (has marked CD tree of life etc.) 5:00 adjourn