DOES DNA PROVIDE ALL THE ANSWERS?

The impact of molecular systematics, especially DNA sequences, on plant taxonomy and biosystematics has been fundamental and era-splitting. It has led to reactions by researchers ranging from advocating that it is now the only kind of research worth pursuing in considering molecular data as merely another body of evidence to be utilised equally with all the others. Can DNA "lie"? What reasons might there be to question the veracity of what appears to tell us about plant evolution? This [Taxon] paper is an attempted discussion on the extent to which we can afford to rely solely upon DNA sequences to unravel the evolution of and relationships between plants, and on the principles underlying our utilization of DNA data in making taxonomic decisions.

The main topics visited [in the original article] are: interpretation of chloroplast DNA and rDNA ITS sequences in polyploids in the light of maternal inheritance and concerted evolution; importance of "traditional" characters such as crossability and chromosomal homology as revealed by DNA evidence; desirability of insisting on a monophyletic classification; effect of sample-size on phylogenetic ananlyses; and the suitability for evolutionary studies of a molecule composed of only four different elements in terms of likely levels of homoplasy. Special reference was made to recent phylogenetic analyses of festucoid grasses, especially the genus Vulpia, where it is proposed that the obvious "misplacement" of certain poplyploid species can actually be used to infer their parentage.

The caveats and misgivings [the author outlined in his Taxon article] do not question the value of DNA data, but emphasise the need to treat them more critically than is often the case, with the following in mind:

1. DNA data are invaluable and in the future must become universally accepted as an integral part of the process of classification at all levels from phylum to ecotype.
2. Since something like 50% of angiosperms are polyploids (see Stebbins 1971, Stace 1989), sequencing just rDNA ITS and chloroplast DNA regions is unwise, because they are not reliable cross-checks, but rather tend to demonstrate the same bias. Alvarez & Wendel (2003) have recently catalogued problems involved with the use of ITS sequences for phylogenetic analysis, which led to the question of their suitability. If ITS sequences are used their results need to be confirmed by other sequences, not chloroplast DNA but single- or few-copy sequences. A general rule of thumb has developed (M. Chase, pers.com.) which states that if three genes show the same results they can be taken as reliable. But, since these three sequences are in the great majority of studies ITS and two chloroplast regions, this is not a good reassurance. The recent "addition" to the evidence from a third chloroplast region (Hilu et al. 2003) doe not help per se.
3. DNA data should not be regarded as inevitably of paramount importance, nor to be used at the expense of other ("traditional") data. Morphology, chemistry, cytology and breeding relationships will remain as important as ever, and the use of DNA carries as many caveats as any other data sets. Taxonomic, phylogenetic and biossystematic studies msust still be tackled by a multivariate approach.
4. Since the main problems relating to chloroplast and ITS DNA apply to polyploids, whenever possible during studies at the species level it seems advisable to investigate only the diploids (at least at first), with the possibility of adding in the polyploids later once the main features of the phylogeny are clear. This is not a novel suggestion. Seberg & Frederiksen (2001) made a cladistic analysis (using morphological characters) of just the diploid members of Triticeae (Poaceae), an approach worthy of emulation.
5. Much effort is still needed in improving our methods of anaylysis, particularly in the knowledge that fuller account needs to be taken of reticulation and homoplasy, which are widespread and abundant features of plant evolution.
6. In practical terms, taxonomic investigations should be taxon-based, not technique-based, i.e., it is essential to gain a deep knowledge of the group before new techniques are applied, preferably including an extensive field study. The attitude "I have this new technique; to shich taxon can I apply it?" is not likely to achieve best results.

References [cited in this excerpt]

Alvarez, I. & J.F. Wendel. 2003.

Ribosomal ITS sequences and plant phylogenetic inference. Mol. Phylog. Evol. 29: 417- 434.

Hilu, K.W. & al. [15 co-authors]. 2003.

Angiosperm phylogeny based on matK sequence information. Amer. J. Bot. 90: 1758- 1776.

Seberg, O. & S. Fredericksen. 2001.

A phylogenetic analysis of the monogenomic Triticeae (Poaceae) based on morphology. Bot. J. Linn. Soc. 136: 75-97.

Stace, C.A. 1989.

Plant taxonomy and biosystematics. 2nd edition. Edward Arnold, London.

Stebbins, G.L. 1971.

Chromosomal evolution in higher plants. Edward Arnold, London.

THE END OF THE JOURNAL OF THE HATTORI BOTANICAL LABORATORY?

The year 2006 saw the publication of No. 100 (centennial issue) of the Journal of the Hattori Botanical Laboratory. Fifty-five original research papers (886 pages) were published in this issue. Contents are available at the journal home page http://www7.ocn.ne.jp/~hattorib/journal.html

The Board of Administration of the Hattori Botanical Laboratory have recently decided that it was too difficult to continue publishing the Journal of the Hattori Botanical Laboratory because of financial and other reasons. It was with deep sadness that the announcement was made recently that issue number 100 will mark the final one for the journal.

When Dr. Hattori passed away in 1992, Dr. Zen Iwatsuki succeeded the editorship of this journal. Fortunately, supported by many bryologists, the journal was published for many more years until it reached No. 100.

As the editor, Dr. Zen Iwatsuki on this occasion expressed in BRYONET his great appreciation to all bryologists who had submitted their manuscripts for publication in the journal, and also to those who helped review the manuscripts. He also thanked all members of the Editorial Board who sent him much useful advice and many suggestions over the years.

The Hattori Botanical Laboratory, however, will continue to support its bryological research activities. Publications, including many back issues of the Journal of the Hattori Botanical Laboratory are still available through the journal homepage: http://www7.ocn.ne.jp/~hattorib/journal.html

A CD-Rom which contains much useful information about the Hattori Journal is attached at the end of the centennial issue.

When the sad news broke out in the BRYONET, many people openly expressed concern over the cessation of publication of the Journal of the Hattori Botanical Laboratory. In response to the strong reactions to the news shown by the bryological community worldwide, the Family of the Hattori and the editorial board of the journal are now examining various ways to continue to publish the Journal.

In order to explore all possible solutions to the problem and to look for a way forward, a small committee has been formed to address this possibility. The group is made up of the following: Benito Tan, Zen Iwatsuki, Rod Seppelt, Wilf Schofield, and Janice Glime.

The group will examine all possible ways of continuing publication of the "Hattori Journal". While the bryologist community understands that the cessation of publication of the journal is a hard business decision made by the Hattori Family, there are always solutions if there is a will and a way forward.

The ad hoc committee formed to help save the journal from meeting its final fate would welcome all and any comments and suggestions regarding the (hopeful) continuation of publication of the Journal, even in a modified form.

Ben Tan has agreed to coordinate comments; meanwhile, please send all comments to him for collation at dbsbct@nus.edu.sg

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