Deep Time Project: A Comprehensive Phylogenetic Tree of Living and Fossil Angiosperms

Comments and questions: Dr. Doug Soltis


Last modified: May 17, 2002


Copyright © FLMNH. This site is maintained by the FLMNH.














Back to Top
















Back to Top















Back to Top















Back to Top















Back to Top


















Back to Top


The Scientist 15[5]:12, Mar. 5, 2001

'Deep Gene' and 'Deep Time'

Evolving collaborations parse the plant family tree

By Barry A. Palevitz

Amid last month's hoopla over the human genome sequence and what it says about humans, plant biologists announced two new efforts aimed at a firmer understanding of plant evolution--who is related to whom and how--a discipline better known as systematics. Constructing evolutionary family trees is harder than investigating personal genealogies--biologists don't have the equivalent of birth registrations or family bibles to consult. Fossils tell them what ancient plants use to look like, but placing them in context with living organisms is difficult at best. Even the systematics of existing plants can be contentious, as researchers disagree on lumping plants together or splitting them apart in search of the most natural taxonomy.

Scientists liken constructing phylogenetic trees to tracing all the branches and trunks of a real tree, like an oak, with only characteristics of its outermost twigs to go on. That's because present day organisms are the sole survivors--called "terminals" by systematists--of multiple, diverging lineages. However daunting the process, researchers have made breathtaking progress in the last 20 years, thanks to gene sequencing. According to University of Georgia systematist David Giannasi, "it was a case of technology catching up with theory." By comparing DNA sequences such as those encoding ribosomal RNA and chloroplast proteins, systematists redrew large chunks of the plant taxonomic map.

A good example of the redefining process is found in the milkweeds, which taxonomists traditionally placed in a family called the Asclepiadaceae. They also thought the milkweeds were allied with a second family, the Apocynaceae. But based on molecular data, "the Asclepiadaceae nests within the Apocynaceae," says Giannasi, "so we now know they should be lumped together." The same is true for the mints, thought to be in their own family just a few years ago but now grouped with the verbenas.

Researchers have also clarified some of the most basal groups in the plant family tree. They now know that a previously obscure New Caledonian shrub called Amborella is sister to all other flowering plants, or Angiosperms, with water lilies branching off the evolutionary trunk at the same level or just above.1 They also think the gnetales, previously considered flowering plant allies, are probably more closely related to pines, in the Gymnosperms.2 And horsetails and whisk ferns, once thought to relic descendents of early land plants, now seem more closely tied to the true ferns.3


Feds Fertilize Interactions

One of the key ingredients in systematists' recipe for success was cooperation and communication. Thanks to joint funding starting in 1994 from the U.S. Department of Agriculture, Department of Energy, and National Science Foundation, a consortium of researchers called the Green Plant Phylogeny Research Coordination Group, or Deep Green, pooled ideas and resources in a joint plan of attack. Machi Dilworth, head of NSF's Division of Biological Infrastructure, thinks, "Deep Green was one of the very visible success stories" of the three agency effort. "With a little support they were able to come together and accomplish major scientific achievements."

NSF was so impressed with the collaborative approach, it decided to fund "Research Coordination Networks" (RCNs) serving all areas of the biological sciences. Like Deep Green, the grants foster communication and collaboration between scientists, but don't directly cover research costs funded by other programs. Two of the RCNs are scions of Deep Green.


Systematists Dip Into Genomics

In one of the team projects, called Deep Gene, systematists join forces with molecular biologists working on entire genomes like those of Arabidopsis and rice.4,5 By tracing suites of genes that govern processes such as flower development, they hope to clarify mechanisms governing major evolutionary changes, including new biochemical pathways and the appearance of complex morphological characters. Sequencing also uncovers large-scale genomic changes including chromosomal rearrangements, which can be invaluable in defining plant relationships. Likewise, evolution depends on alteration in spatial and temporal controls governing gene activity--when and where genes turn on and off. The new RCN hopes to discover how gene regulation changed in the evolution of various plant groups.

Tolerance toward desiccation is a good example of how traits may have appeared and disappeared during evolution. The first plants to occupy dry land faced a big problem compared to their aquatic ancestors: an uncertain supply of water. Mosses, for example, grow in moist environments but also suffer periodic drying. That's why they require biochemical mechanisms that allow them to survive dry periods. When larger vascular plants arose, with roots and a plumbing system to extract water from the soil and move it long distances, desiccation tolerance became less important. But it reappeared later on in seed plants, which remove water from tissues surrounding young embryos in preparation for dormancy.

According to Deep Gene principal investigator Brent Mishler of the University of California at Berkeley--and a veteran of Deep Green--"around 80 genes are involved in desiccation tolerance in mosses. When desiccation re-evolved in seeds, some of these genes were reused." Mishler would like to know how such changes in gene regulation arose during major evolutionary events. Mishler chaired a symposium on Deep Green at the annual meeting of the American Association for the Advancement of Science, February 15-20, in San Francisco.

Daphne Preuss, molecular biologist at the University of Chicago and Deep Gene co-PI, says she brings to the table "the tools and techniques of high throughput, big scale biology." Still, in a true collaboration everybody benefits. With Deep Gene, genomicists like Preuss want to advance their own projects. In her case, that means figuring out how centromeres work. Centromeres are DNA sequences located where chromosomes attach to spindle fibers during mitosis and meiosis. Preuss has dissected centromeric DNA in Arabidopsis but knows that "the sequences are very diverse from organism to organism." The question is, "how did these differences evolve, and what key components are important for centromere function?" Adds Preuss," I want insight from looking at conservation through evolution."

Preuss admits that "this is expensive work, so every decision counts. We're now making key decisions as to which species to look at next. We're looking to people in phylogenetics to help." Mishler sees other practical benefits from Deep Gene. "Can we use the information for agriculturally important plants that aren't desiccation tolerant?" he asks. By guiding researchers to promising sources, Deep Gene can also "predict useful chemicals for pharmacology," says Mishler. That makes University of Georgia's Giannasi smile because older studies comparing the chemical composition of plants--including substances such as terpenoids--predicted changes cemented by more recent gene sequencing projects. "The secondary chemistry was there, but nobody trusted it," comments Giannasi.


Fossils and Morphology Join the Fray

Doug and Pamela Soltis of Washington State University in Pullman lead another RCN called "Deep Time." Having done much of the gene sequencing for Deep Green, the Soltis' want to superimpose other kinds of information on their phylogenetic trees, and in the process add the dimension of time to key points in plant evolution.

Years before systematists accessed gene sequences, they relied on other information in the form of morphological, anatomical and chemical characters. While valuable, such characters can be misleading. For example, a structural trait shared by two groups could have arisen by convergent evolution rather than common ancestry (though the same applies to DNA sequences). Moreover, the number of structural characters applicable to phylogenetic analysis is limited; DNA sequences, on the other hand, are far more useful since the average protein encoding sequence contains 1,000-2,000 characters, or nucleotides. That's why they turned to genes.

But the tide may be changing again, at least a little. The Deep Time RCN will arrange plants according to a "morphological matrix" of characters, but "constrain the taxa to conform to the DNA-based topology already available, and in which we have good confidence at this point," say Pam and Doug Soltis. They'll then "conduct a phylogenetic analysis of the morphological matrix with fossils included." The trick will be to pick characters from existing plants that also apply to fossils. Despite the fact that "fossils have rarely been integrated in a phylogenetic context for any group," the Soltis' are hopeful. Since dates are available for many of the fossils, their inclusion adds a time factor to the phylogenetic tree--systematists can assign dates to key branch points. They'll also integrate data from molecular clocks governed by mutations. "It's sort of like the movie Back to the Future,'' note the Soltis', "Having the timing of a key event in the past nailed down is critical in understanding what has occurred to produce what we see in the present."

The Soltis' also wax philosophical about the collaboration: "We spent a decade in the area of systematics largely focused on molecules. There is a wealth of information in nonDNA characters such as morphology and anatomy, and we can't lose expertise in these areas."


Problems? Cooperation is the Key

Deep Gene and Deep Time researchers realize that reaching their goals may not be easy. According to the Soltis', "two big issues are missing data and the combinability of molecular and morphological data sets." Mishler agrees: "We don't know entirely how to do it. Theory hasn't kept pace--it's dealt mostly with sequence data." Researchers hope the latest collaborations will foster development of new methods to tackle such problems. Mishler sees promise. "The RCN will help us. Even a small amount of data from these other sources can improve phylogenetic trees" and eventually "lead to more research funding." The depth of cooperation is all the more impressive because deep Gene and Deep Time will interact.

The "Deep" projects testify to the importance of collaboration in modern research. According to Doug Soltis, "the cooperative nature of botanists has really turned the tide in the past decade." Mishler agrees that "research would have gone on, but it would not have made the progress it did." Preuss taps federal agencies for greasing the skids. "Some of these things are initiated by granting incentives, so I think it's wise. It's good to stir the pot and mix people together." Adds Machi Dilworth of NSF, "we would like to foster communication among scientists, to advance science through collaboration and coordination."


Barry A. Palevitz ( is a contributing editor to The Scientist.



1. B.A. Palevitz, "Discovering relatives in the flowering plant family tree," The Scientist, 13[24]:12, Dec. 6, 1999.

2. L.M. Bowe et al., "Phylogeny of seed plants based on all three genomic compartments: extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers," Proceedings of the National Academy of Sciences, 97:4092-97, April 11, 2000.

3. K.M. Pryer et al., "Horsetails and ferns are a monophyletic group and the closest living relatives to seed plants," Nature, 409:618-22, Feb. 2, 2001.

4. B.A. Palevitz, "Arabidopsis genome. Completed project opens new doors for plant biologists," The Scientist, 15[1]:1, Jan. 8, 2001.

5. B.A. Palevitz, "Rice genome gets a boost," The Scientist, 14[9]:1, May 1, 2000.


Copyright 2001, The Scientist, Inc. All rights reserved. Copied with permission.




Deep Time Home | Projects | Meetings | News and Info | Goals | Links | Site Map | FLMNH