Molecules Under the Microscope
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Molecules under the microscope Clive Stace looks at how DNA has altered the way we classify plants and argues it is a change for the better HE DESIRE TO CLASSIFY, whether people alphabetically in a telephone directory, elements according to atomic T RHS LINDLEY LIBRARY number in a periodic table, or living organisms in some taxonomic system, is universal, and a Plate, dated 1793, from Linnaeus’s System of Botany fundamental feature of human nature. The process by William Curtis showing groups of related plants. is fully justified because it ensures retrieval of components and information far more easily and a plant belongs to the Diandria tells one nothing quickly than can random searching. It achieves more about it – an artificial classification is not order out of chaos. With regard to plants, ancient predictive of further characters. man probably employed primitive systems of Linnaeus realized his system was artificial, as classification in order to communicate, since plants had others before him and everyone after him, and were (and are) vital as sources of food and medicine, in 1764 he listed 58 ‘natural orders’ (what we now but the earliest written examples are those of the call families), many of which are recognisable as Greeks, dating back at least 2300 years. This can families that we still accept, e.g. Umbellatae are be seen as the start of the first of the three great largely our Apiaceae. These taxa (natural orders) phases of plant classification: phenetic or artificial; are far more predictive than the classes in his phyletic or natural; and molecular. sexual system; learning that a plant belongs to the The earliest attempts that we know of used the Umbellatae immediately tells one a lot about that most obvious features to classify plants, such as plant, without one ever having seen it let alone growth habit and gross features of flower structure having investigated those characters in it. The and fruit types. More characters were utilized as main aim of taxonomists in the nineteenth and finer distinctions were required, but even in the twentieth centuries has been to construct ever sixteenth century these same characteristics still more predictive classifications, and in my view this held pride of place. The trend to increase the range sole criterion should be the primary judge of how of characters employed was bucked in the seventeenth good (useful) a particular system of classification is. century by Linnaeus, whose ‘sexual system’ can be Once the more obvious (exomorphic) structural considered the culmination of the artificial features of plants had been investigated, botanists systems. It was based mainly on the number of increasingly turned their attention to cryptic (less stamens and pistils. Such systems are considered obvious or even invisible) characters in order to artificial because the most similar species or achieve greater predictivity. These included genera are not necessarily classified together. For vegetative, floral and fruit anatomy (often example, Linnaeus’ class Diandria (t wo stamens) concentrating on particular aspects such as included Anthoxanthum (Poaceae), Syringa (Oleaceae), epidermis, trichomes, pollen, timber or leaf Salvia (Lamiaceae) and Circaea (Onagraceae). vasculature), phytochemistry, chromosomes and These all share two stamens, but have scarcely patterns of hybridization. All of these fields of anything else in common. In other words, saying investigation have provided many new insights 57 The Plant Review Molecular taxonomy into plant relationships, and have therefore led to These assertions are surely incontrovertible. improved (more predictive) classifications. And we The main advantages and disadvantages of the must not forget that these data are still of enormous molecular approach are listed in Table 1. importance in botanical investigation, and should Examples of major taxonomic changes in the not be abandoned just because a newer or more British flora demanded by adopting a molecular fashionable field of study has emerged. If taxonomists classification are the amalgamation of Anagallis, of that generation dared to believe that one day Centunculus, Glaux and Trientalis into Lysimachia they would hit upon the magic data-set that (loosestrifes), and the splitting of Gnaphalium revealed the ultimate über-predictive classification, (cudweeds) and Chenopodium (goosefoots) each they would have been frustrated. Such a revelation into five segregate genera. Such radical changes to came only with the advent of molecular classifications. our system of classification are not welcome, but are inescapable. Even greater consternation arises The molecular revolution in those (so far rather few) cases where genera Even before Darwin’s time it was realized that must be considered separate on molecular grounds, patterns of past evolution must bear an intimate but are not distinguishable on morphological correlation with present similarity. Taxa that characters. Examples, again from the British flora, separated relatively recently will be more similar are the ragworts Senecio and Jacobaea, the orchids than those whose divergence was more ancient. Orchis and Anacamptis, and the vetches Vicia and The rise in popularity of phylogenetic systems can Ervilia. In such cases the generic attribution of a be seen as an obvious extension of the concept of new species could not be made without a DNA natural classifications. But the problem was how analysis. The previous classification (e.g. Jacobaea to deduce the past evolutionary patterns and, with included in Senecio) arose because the gross reliance on the same data-sets as earlier workers, features of these plants over-rode the less obvious no certain solution was reached. But once DNA but vastly more numerous characters indicating was utilized, nowadays usually via the base the true relationships. Unfortunately, we simply sequence of very small portions of DNA, the have to learn to live with these problem taxa. ultimate goal, so eagerly sought by previous generations, had been attained. There can be no Limitations of molecular data doubt about this. DNA sequences are indisputably Despite the above assertions, which are based a true measure of the course of evolution, and on the overwhelming reliability of molecular data, therefore of relationships. If our ‘traditional and on the illogicality of ignoring the latter when methodology’ (phenetics, phyletics) were an the going gets tough, DNA does not provide all accurate predictor of relationships, the molecular the answers in every case. Molecular data cannot methodology would simply confirm it. Where the be applied in a mechanical, inflexible way, but molecular system contradicts the traditional one taxonomic judgement is still important, and is vital the phenetic characters have misled us, or we have in many cases. I want to mention five situations. misinterpreted them, or we have misconstrued the molecular evidence. The Angiosperm Phylogenetic Incongruity Group (APG) system (based on DNA sequences) This is actually simply a euphemism for ‘something’s of family classification, now universally adopted, gone wrong’. It is a term used when two analyses, is certain to endure for centuries to come, as it using different parts of DNA, produce different will prove to be the most highly predictive system. data sets leading to different classifications. It is Table 1. Positive GOOD IDEA BAD IDEA and negative aspects of the Not affected by environment Characters are cryptic adoption of a DNA-based Not affected by gene expression Very expensive classification. Constant across all life-forms Dependent on high level of expertise Will not change with time Some radical taxonomic changes, unless faulty data-collection or some of which are ‘unacceptable’ -manipulation has occurred by some users March 2020 58 Z X Y X Y Z X Y Z Q Q Q P P P X and Y X and Y X and Y are monophyletic are polyphyletic are paraphyletic Fig. 1 Patterns of relationship revealed by DNA analysis. most commonly encountered when nuclear and well-known emergent aquatics Typha (bulrush) chloroplast DNA data are compared. However, and Sparganium (bur-reed). These two genera have various reasons for such differences are well no close relatives and are often placed in two understood, and there can be little doubt that after separate monogeneric families, Typhaceae and investigation in each case these will be ascertained Sparganiaceae. Molecular data confirm that they and the true classification will be revealed. This is have a common ancestor, which is shared by no our experience so far. Apparent incongruity can other genera. Hence in the derived cladogram they also emerge when the facts have been misrepresented; are separated by a simple bifurcation. Whether one perhaps the sampling was inadequate, or the data- places these two genera in one or two families (or, analysis was faulty. The remedy in these situations indeed, in one or two genera) is a matter of is obvious, and it is a warning to taxonomists that subjective judgement. In other words, the concept they should not adopt new classifications until of splitters and lumpers is as relevant today as it their molecular basis has been fully investigated ever was. The authors of the APG system state that and understood. they have opted for the lumping approach, and so recognise the Typhaceae with two genera, but the ‘No difference’ two-family alternative is equally valid as it is There are several cases in the literature where equally supported by the molecular evidence. DNA analyses have not revealed any difference in Another example in the British flora is the the base sequences of two similar species. But the amalgamation or separation of Lamium conclusion that such pairs of species are (deadnettles) and Lamiastrum (yellow archangel), molecularly identical and must be amalgamated, and on a world scale the splitting or not of the which has been expressed by some taxonomists in Boraginaceae into 12 separate families. the past, is surely erroneous. Only a tiny fraction of the DNA has ever been sequenced, so we have The paraphyly conundrum no idea of the total level of difference between the This topic remains the most controversial area of two species.