What is systematics and what is taxonomy?

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Over the past few years there have been increasing numbers of calls for governments to properly fund systematics and taxonomy (and a number of largely molecular-focused biologists insisting they can do the requisite tasks with magic molecule detectors, so don't fund old-school, fund new-fangled-tech). But I think that there is considerable confusion about what systematics and taxonomy are.

Now the usual way a philosopher resolves such questions, apart from interrogating their intuitions relying upon what they learned in grade school, is to go find a textbook or some other authoritative source and quote that. If it is someone they already know, all the better, like Mayr or Dawkins. This is problematic, so I thought I'd do a slightly better job at reviewing what people think. And then I will of course give my own view.

Randall Schuh, in his Biological systematics: principles and applications (2000) says that systematics and taxonomy are the same thing, and consist of three activities: recognition of species, classification into a hierarchical scheme, and placing this in a broader context. Gurcharan Singh, in his Plant systematics: An integrated approach (2004) also treats them as identical activities. Richard Mayden in his Systematics, historical ecology, and North American freshwater fishes (1992) does not discuss taxonomy, but defines systematics as "the field of science concerned with reconstructing the evolutionary or ancestor-descendant relationships of groups of organisms, whether fossil or recent, on the basis of heritable traits". Kevin de Quieroz defined it as "the branch of science devoted to the study of the different kinds of organisms (biological diversity, in contemporary terms)".

Overall, there is much confusion, as summarised by Peter F. Stevens in his classic work The development of biological systematics: Antoine-Laurent de Jussieu, nature, and the natural system (1994):
Words like "method," "system," and "systematics" are perhaps the key words used by [his subjects for the book], and I must clear up some of the ambiguities surrounding their use. First, as to the distinction between taxonomy and systematics, Simpson offered a much-quoted definition of systematics: "the scientific study of the kinds and diversity of organisms and any and all relationships among them." Classification was the grouping of organisms into the hierarchy of a classification; taxonomy was the theoretical study of classification [in his 1961: 7-11]. For Frans Stafleu, on the other hand, taxonomy was represented by keys, systematics by interpretive relationships. Recently, a different distinction has been drawn between systematization and classification, the former being an ordering according to element/system or part/whole relationships, the latter of categories based on common properties.

Ornduff (1969) proposed same view as Simpson:

Taxonomy: classification of taxa (units of classification) in a system that expresses their relationships

Systematics: comparative studies of a systematic unit (i.e., a group of organisms or species and higher), the fact-finding field of taxonomy

However, most systematists today would invert this. What in the sam hell is going on?

The terms were defined independently of each other, by A. P. de Candolle for taxonomy, 1813, Lindley for systematics, 1830. De Candolle defined classification as having three components in his Thorie lmentaire de la bontanique ( second edition, page 19): Glossologie (we would call it nomenclature now), Taxonomie (the theory of classifications), and Phytographie (the rules of describing plants). Lindley, an adherent of the Jussieu scheme of multiple lines of evidence rather than single keys in the Linnaean system, used the term "systematic botany" for this approach, which he thought was a natural classification system in contrast to the artificiality of Linnaeus. So far as I can find he did not use the term "systematics" directly.

What is significant with de Candolle's scheme is that he includes arbitrary and natural facets under the single heading of "classification". Rules of description, or phytography, are roughly the same thing as what a modern systematist would mean by "taxonomy": the description of species from specimens, and what he would mean by taxonomy is what we would now mean by systematics - the arrangement of the species into schemes of relationships.

A student of both de Candolle's approach and of Lindley's in botany, was the very influential Asa Gray. His influence is threefold. One, he was American, and hence influenced the later generations of American botanists and their theoretical ruminations. I found him being quoted as late as 1935 as an authority on just this matter in the Proceedings of the Linnean Society of London. Second, he was a botanist, and the botanical discussions ran rather parallel to and in some cases in contradiction to the zoological ones. And third, he was a Darwinian, and so his strictures were regarded as modern enough to accept.

Gray adopts de Candolle's overall view, despite the fact that classification is now thought to be explained by evolution. Gray, in his Structural Botany (1879: 3) distinguishes between

Taxonomy, or the principles of classification, as derived from the facts and ideas upon which species, genera, &c., rest; Classification or the System of Plants, the actual arrangement of known plants in systematic order according to their relationships ...

as well as several other aspects of "Systematic Botany" such as Phytography (rules for description), Glossology or Terminology, and Nomenclature (the methods and rules adopted for the formation of botanical names"). Here, Systematics includes both taxonomy and classification. This can be shown as a diagram:

Systematics Gray.png

Gray thought, as most systematists did at the time, that the taxonomic and classificatory aspects were in fact dealing with natural truths, the former from a theoretical or methodological point of view, the latter from an empirical or epistemological point of view. The communicative and conventional aspects of nomenclature and phytography, respectively, were not natural. We might generalise this for all scientific classificatory activities thus:

Systematics.png

This is eminently sensible, so why is it not currently the default view? A lot happened in the twentieth century, and not all of it was to do with Julian Huxley's New Systematics (1940). In a symposium in 1935, held by the Linnean Society of London, Walter B. Turrill introduced the terms "alpha" and "omega" taxonomy, and it caught on. As he defined it (Turrill 1935),

... the time has come when the student of floras whose taxonomy on the old lines is relatively well known should attempt to investigate species by much more complete analyses of a wider range of characters than is now the rule. There is thus distinguished an alpha taxonomy and an omega taxonomy, the latter being an ideal which will probably never be completely realized. ... The aim of the alpha taxonomist must be to complete the preliminary and mainly morphological survey of plant-life ... Some of the criteria which those who aim at an omega taxonomy are ... ecological, genetical, cytological, and biometrical.

So, alpha taxonomy replaced taxonomy in general, conflating the older term for all of systematic biology. But the way Turrill introduced this term indicates that he saw the omega taxonomy as the final form of all classification, along some continuum of completeness and naturalness (cf. his 1940 and 1942).

As the field changed under the influence of Simpson and Mayr's insistence that taxonomy/systematics were the same, and that they were aimed solely at the reconstruction of evolutionary history (the view that Mayden evinces), two further developments arose. One was the numerical taxonomy movement started by Sneath and Sokal (1963, Sokal and Sneath 1973). Here several issues were in play. They wished to make classification nonsubjective (that is, objective) and take the decisions out of the hands of biased observers. To do this they introduced mathematical algorithms that could be implemented in computer programs or done by hand. They relied upon any data whatsoever, without prior filtering, in order to achieve naturalness. Another issue was that they wished to make the process of classification purely operational, following Percy Bridgman's philosophy that all that counted in science was how things were measured (operations of measurement, hence the name operationalism). The problem here that arose was that depending upon the principal components chosen, different taxa fell out. While numerical taxonomy, which came to be known as "phenetics" (from the Greek phaneros, to seem) found structure in the data, it seemed it was not always, or even often, taxonomic structure.

But Sneath and Sokal's books were extremely clear and coherent, and they set up the contrasts in modern taxonomy, which was that taxonomy and systematics were the same thing. Around this time also, Hennig's Phylogenetic Systematics (1966) was published in English, along with Lars Brundin's classification of midges using these techniques (1966, 1972a, 1972b, attacked by Darlington 1970), leading to the school[s] of thought now called (following an insult of Mayr's) cladistics. On this view, initially, classification was solely aimed at reconstructing evolutionary history (which was something Hennig appealed to Simpson and Mayr in support of). Later, critics argued that classification did not give the history but that the history was an inference or hypothesis based upon and tested by the classification, which was independent (Nelson 1972, Nelson and Platnick 1981, Patterson 1982). The history view was confirmed for philosophers by Elliot Sober's very influential Reconstructing the Past (1988).

Finally, a fourth approach arose, one which as yet has no simple name. On this view, classification is dispensed with entirely, and systematics is only about phylogenetic reconstruction, usually employing statistical methods of analysis of very large and mostly molecular data sets. The champion of this view, both theoretically and practically, is Joe Felsenstein, whose recent book Inferring Phylogenies (2004) is now the standard bible for methods and algorithms, as well as espousing what he calls the "It Doesn't Matter Very Much" school of classification. Joe, who is one of the most personable folk you'll ever meet in a field that tends towards the fractious, also maintains a site from which you can download nearly every computer program used in systematics these days. I am going to baptise this view statistical phylogenetics. Joe holds that classification and the philosophy that underpins it, is a matter of personal preference, and nothing much hangs on what one chooses:

A phylogenetic systematist and an evolutionary systematist may make very different classifications, while inferring much the same phylogeny. If it is the phylogeny that gets used by other biologists, their differences about how to classify may not be important. I have consequently announced that I have founded the fourth great school of classification, the It-Doesn't-Matter-Very-Much school. [2004: 145]

With this, the assimilation of systematics into phylogenetics is complete. All is now subordinated to the finding out of historical pathways that explain our present biodiversity. Evolution ber alles!

I reject this for several reasons, some of which I have previously given on this blog; basically it is that classification is a separate activity in science from theory and history. By all means we should try to reconstruct the past, but we do this not by subordinating classification to phylogeny, but by doing phylogeny on the basis of classificatory information. I am not here taking the pattern cladist line: I do think we can, to some degree of confidence, reconstruct past sequences. But this is always hypothetical, and requires that we have empirical foundations for our reconstructions independent of our prior assumptions about how biological history unfolds, because biology is a bitch, and she won't be tamed by simplistic schemes, not even of common descent and models of speciation.

So I would urge that we take the generalised version of Gray's "taxonomy" of classification and adopt it in general, and not just for the biological sciences either.

Originally published at Evolving Thoughts

References

Brundin, Lars Zakarias. 1966. Transantartic relationships and their significance, as evidenced by chironomid midges. With a monograph of the subfamilies Podonominae and Aphroteniinae and the austral Heptagyiae, etc.: Almqvist & Wiksell: Stockholm.

Brundin, Lars Zakarias. 1972. Evolution, Causal Biology, and Classification. Zoologica Scripta 1 (3):107-120.

Brundin, Lars Zakarias. 1972. Phylogenetics and Biogeography. Systematic Zoology 21 (1):69-79.

Candolle, Augustine-Pyramus de. 1819. Thorie lementaire de la botanique, ou exposition des principes de la classification naturelle et de l'art de dcrire et d'tudier les vgtaux. 2nd ed. Paris.

Darlington, P. J., Jr. 1970. A Practical Criticism of Hennig-Brundin "Phylogentic Systematics" and Antarctic Biogeography. Systematic Zoology 19 (1):1-18.

Felsenstein, Joseph. 2004. Inferring phylogenies. Sunderland, Mass.: Sinauer Associates.

Gray, Asa. 1879. Structural botany, or Organography on the basis of morphology. To which is added the principles of taxonomy and phytography, and a glossary of botanical terms. New York, Chicago: Ivison, Blakeman, Taylor.

Huxley, Julian, ed. 1940. The new systematics. London: Oxford University Press.

Lindley, John. 1830. An introduction to the natural system of botany: or, A systematic view of the organisation, natural affinities, and geographical distribution, of the whole vegetable kingdom: together with the uses of the most important species in medicine, the arts, and rural or domestic economy. London: Longman, Rees, Orme, Brown, and Green.

Mayden, Richard L. 1992. Systematics, historical ecology, and North American freshwater fishes. Stanford, Calif.: Stanford University Press.

Nelson, Gareth J. 1972. Phylogenetic Relationship and Classification. Systematic Zoology 21 (2):227-231.

Nelson, Gareth J., and Norman I. Platnick. 1981. Systematics and biogeography: cladistics and vicariance. New York: Columbia University Press.

Ornduff, Robert. 1969. The systematics of populations in plants, Systematic Biology Pubn 1692. Washington DC: NAS.

Patterson, Colin. 1982. Classes and cladists or individuals and evolution. Systematic Zoology 31:284-286.

de Queiroz, Kevin. 2005. Ernst Mayr and the modern concept of species. PNAS 102 (Supp. 1):6600-6607.

Schuh, Randall T. 2000. Biological systematics: principles and applications. Ithaca, NY: Cornell University Press.

Simpson, George Gaylord. 1961. Principles of animal taxonomy. New York: Columbia University Press.

Singh, Gurcharan. 2004. Plant systematics: an integrated approach. Enfield, NH: Science Publishers.

Sneath, P. H. A., and Robert R. Sokal. 1973. Numerical taxonomy: the principles and practice of numerical classification, A Series of books in biology. San Francisco: W. H. Freeman.

Sober, Elliott. 1988. Reconstructing the past: parsimony, evolution, and inference. Cambridge, Mass.: MIT Press.

Sokal, Robert R., and P. H. A. Sneath. 1963. Principles of numerical taxonomy, A Series of books in biology. San Francisco,: W. H. Freeman.

Stevens, Peter F. 1994. The development of biological systematics: Antoine-Laurent de Jussieu, nature, and the natural system. New York: Columbia University Press.

Turrill, Walter B. 1935. The investigation of plant species. Proceedings of the Linnean Society of London 147:104-105.

Turrill, Walter B. 1940. Experimental and synthetic plant taxonomy. In The new systematics, edited by J. Huxley. London: Oxford University Press:47-72.

Turrill, Walter B. 1942. Taxonomy and Phylogeny. Botanical Review 8 (4):247-270.

29 Comments

John Wilkins said (of my It Doesn’t Matter Very Much position):

I reject this for several reasons, some of which I have previously given on this blog; basically it is that classification is a separate activity in science from theory and history. By all means we should try to reconstruct the past, but we do this not by subordinating classification to phylogeny, but by doing phylogeny on the basis of classificatory information.

I don’t see that we are using classification except for “alpha” classification, in delimiting species. It is higher level classification that Doesn’t Matter Very Much, and I stand by that. Sure, it is a separate activity, but still, for phylogeny and for inferring biological processes and history it Doesn’t Matter Very Much.

Considering taxonomy/systematics is the direction I want my research to go in… this is something I wonder about. What I’ve gathered through my schooling so far is that taxonomy is mostly concerned with the describing and naming of species, while systematics is organizing them by evolutionary history. Though the semantics does not concern me as much as the next part of your post, which is *how* we should conduct systematics. I think any approach that attempts to overly simplify the problem (let’s just use numbers or make a computer do it!) is bound to run into difficulties. I agree, biology is a bitch, and I expect to have to use a lot of different tools to do my own research.

With this, the assimilation of systematics into phylogenetics is complete. All is now subordinated to the finding out of historical pathways that explain our present biodiversity. Evolution über alles!

Yay! Everyone agrees! Wait, there’s more? :)

Ruh-ro!

I reject this for several reasons, some of which I have previously given on this blog; basically it is that classification is a separate activity in science from theory and history. By all means we should try to reconstruct the past, but we do this not by subordinating classification to phylogeny, but by doing phylogeny on the basis of classificatory information.

It’s hard to know what it would even mean to do phylogeny “on the basis of classificatory information”. Phylogeny is done on the basis of character information. The characters are sometimes those that someone has assigned to an OTU (operational taxonomic unit) we are calling a species (or, more rarely, a genus or whatever). But, it’s pretty dang common for the characters to just be those of individual specimens, and the decisions about what the “species” are, are made after the analysis, rather than before. See every paper ever on “cryptic species.”

IMHO we are rapidly moving towards the point where every specimen anyone collects will have its DNA sequenced. At that point, the way you will do analyses e.g. of a series of forest diversity plots in an ecological study will be to suck in all your DNA data from all the plots, estimate the phylogeny and the relative degree of relationship within and between plots – independently for each gene sequenced – and you may not ever bother to even input the species names into the analysis, because the different species names mean different things (different degrees of relationship within each species, etc.).

What’ll you do then, Wilkins!?! Bwa ha ha…

(still, fun post)

PS I may be biased, having just sat through Dave Lindberg’s lecture on this: http://ib.berkeley.edu/courses/ib20[…]ndouts.shtml

…Jan. 25.

(Note also that Wilkins is cited in recommended readings on the lecture, on the essentialism issue.)

It seems to me that any natural system of classification must be based on evolutionary relationships. You can indeed classify organism using other criteria, but as Joe says, who cares? It also seems to me that the best approach to determine evolutionary relationships utilizes molecular characters. This field is known as molecular systematics and it has proven to be very successful.

When birds and mammals are classified as separate subsets of a larger ancestral group containing reptiles, then progress will be made. Until then, no one cares about the biases of those who developed the classification scheme without knowledge of evolutionary relationships.

As for molecular approaches, there are several good reasons why they can provide a more reliable basis for reconstruction of evolutionary relationships than many other types of data. The Barcode of Life project is gaining momentum and will probably be widely accepted in the near future. Hopefully, it will provide important information to be used in classification and systematics. Just as hopefully, it will not be seen as infallible, or relied on as the only source of information.

If the goal is to understand evolution and the history of life on earth, a reliable phylogeny is only the first step in the process. It would be wise for those in molecular systematics to remember this.

(and a number of largely molecular-focused biologists insisting they can do the requisite tasks with magic molecule detectors, so don’t fund old-school, fund new-fangled-tech).

Can you support this rather extreme statement with some citations? In particular, it’s the part where they claim that they use “magic molecule detectors” that I want to see some documentation of.

It’s unequivocal that different aspects of biology attract more attention at different times, due to background advances.

Charles Darwin’s career took place at a time when field biology and description of new lineages occupied the highest percentage of biologists and enjoyed the highest relative prestige.

Light microscopy, medical microbiology, and non-genetic biochemistry dominated the latter half of the nineteenth century, due to major advances in those fields. Paleontology also began exploding at that time, due to finds in the American west.

Mendelian genetics began to be taken seriously around the beginning of the twentieth century.

That was pretty much the mix until the mid-twentieth century. Although everyone knows that DNA was identified as the genetic material and the double helix structure worked out at that time, the equal if not dominant development was electron microscopy. (Classical light microscopy remains dominant in the medical field of pathology, with specialized exceptions, because the field of view and resolution are better for that purpose.)

Electron microscopy has become something of a routine technique, and biology entered the molecular genetics era in a hard core way some time around the 1970’s, with that trend accelerated by the development of PCR.

At the same time, some trends are emerging that may be unhealthy for US biomedical research in the future, including but not limited to difficulty of obtaining grants, high debt levels of graduating US students (but not most international students), imbalance of opportunity to study or research abroad in the US (from elsewhere, easy) versus from the US (going elsewhere for part of studies/training, not as easy), exaggeratedly low training time/income ratio for scientists (itself related to social factors like massive relative pay increase for corporate executives over the last few decades, making other career choices look silly in comparison), and the increasing outright hostility to science that is mainly but by no means exclusively emanating from the political right. The latter may reflect all of the former; as scientists become perceived as relatively lower paid (compared to other educated people) and less likely to succeed in their own field, they lose prestige, and attacks on science gain credibility.

I do think that, for all the incredible progress made during the “molecular” era, the trends I discuss may be negative in both the sense of discouraging choice of biomedical science as a career, and in the sense of discouraging any deviation from current paradigms by those who do make that choice.

Having said all that, I can’t really decide from your article whether taxonomy and/or systematics are underfunded.

I look at it kind of like the NCAA Football championship game. If you vote for who is number one and two, and then let them have a month off before the game, no one will care who wins. Now when they get a national championship tournament, not some commercialized bowl nonsense, then maybe I will care, but not before.

Likewise with systematics. You can base classification on anything you want. But unless you have a means of determining evolutionary relationships and determining the reliability of those conclusions, no one will care.

I didn’t comment at Wilken’s site because I don’t have much to say. I am mostly alpha taxonomist with later forays into DNA based or assisted phylogeny’s. I think systematics is the study of relationships, and taxonomy is naming things as best we can to reflect our understanding of their relationships.

Taxonomy and Systematics have converged basically due to the biological reality of the species. Taxonomy is a classification of taxa. Those taxa only make sense in a systematic manner if they are constant in time, as well as morphospace. So any objection to this convergence is likely to be based on a lack of confidence in the reality of the stasis of species. If you believe instead in species as evolving lineages then you must suspect that taxonomy in effect places a dividing line between a mother and a daughter and wonder at its objectivity of its approach. Instead, a modern understanding of speciation events validates the systematic approach to taxonomy.

(and a number of largely molecular-focused biologists insisting they can do the requisite tasks with magic molecule detectors, so don’t fund old-school, fund new-fangled-tech).

Was that largely veiled snark aimed at bar-coding? If so, go ahead. Several of the main bar-coding advocates make ridiculously overblown claims. And one of the selling points is supposed to be a Star Trek tricorder (actual words). But if you’re talking about molecular methods in general, I don’t see any problem with that. Nobody is saying they can substitute for morphological study; they just change the reasons for doing it.

Perhaps it is worth noting that of all of the many published trees based on molecular phylogeny/cladistics, very few of the tissued specimens have been compared directly to a holotype, and no mention of reference even to the original description is mentioned in the methods section. Yet species names are given to the specimens in the tree, and clades usually, or at least often, carry higher category names. This means that the specimens were named based on the morphological examination by someone, either using a key or personal familiarity with the taxon. Very few of these specimens are even topotypes, much less holotypes (in my field, herpetology, preservation techniques have denatured the nucleic acids of most types). As morphological taxonomists know, even syntypes, cotypes, and paratypes have smetimes turned out to be a different species from the holotype. Thus the subjective identifications of molecular specimens are a further step removed from the subjective, if informed, judgements of morphological taxonomists. This is not to say that such taxonomic techniques haven’t been extremely revealing and useful, particularly as they have revealed new and previously unrecognized taxa. However, before devoting all funding to molecular techniques at the expense of morphological studies, it should be noted that molecular characters are among the least interesting characters, as they tell us nothing (at least at our current state of knowledge) about adaptation, behavior, or ecological relations among species. It is morphology where the rubber meets the road.

Steve Anderson said:

However, before devoting all funding to molecular techniques at the expense of morphological studies, it should be noted that molecular characters are among the least interesting characters, as they tell us nothing (at least at our current state of knowledge) about adaptation, behavior, or ecological relations among species. It is morphology where the rubber meets the road.

First, I don’t know of anyone who advocates for all funding to be committed to molecular techniques. Second, molecular characters can be very interesting in and of themselves because of what they can tell us about the mechanisms of evolution. THird, molecular characters can tell us a great deal about adaptation, behavior and ecological relationships among species, as well as the mechanism by which such features arose. Fourth, as I already stated:

“If the goal is to understand evolution and the history of life on earth, a reliable phylogeny is only the first step in the process. It would be wise for those in molecular systematics to remember this.”

We will always need trained taxonomists in order to define species characteristics and propose hypotheses about higher level groups. We will always need trained morphologists and developmental biologists in order to determine how traits evolved. But, unless we can test phylogenetic hypotheses and build phylogenies with confidence, none of that is going to happen in any meaningful way. Molecular characters provide the best opportunity for accomplishing that first step.

A wise man once said that knowledge of pattern informs knowledge of process and also the other way around. Once again, I was right.

Steve Anderson said: Perhaps it is worth noting that of all of the many published trees based on molecular phylogeny/cladistics, very few of the tissued specimens have been compared directly to a holotype, and no mention of reference even to the original description is mentioned in the methods section.

Yes, I would say it isn’t worth noting. Very few specimens of any sort have been compared directly to a holotype, and very few systematists of any sort try to use the type specimen when conducting any sort of analysis, unless the identification of specimens to species is somehow in doubt. Now if you doubt the identifications of any species in a molecular analysis, all you have to do is look up the individual the tissue was taken from, which is generally a museum specimen connected to that tissue by a record. Both the specimen and the record should be freely available for your perusal. And this differs in no way from a morphological study. Now, if you were talking about someone erecting a new species based solely on molecular data, then we might talk, and mention of types might be nice.

I’ve examined a considerable number of type specimens, and the same is true of my colleagues in alpha taxonomy of fishes. I feel better about a molecular phylogeny of a group of fishes when one of the authors is an alpha taxonomist who is a recognized authority on the group.

Jim Thomerson said:

I’ve examined a considerable number of type specimens, and the same is true of my colleagues in alpha taxonomy of fishes. I feel better about a molecular phylogeny of a group of fishes when one of the authors is an alpha taxonomist who is a recognized authority on the group.

I also would like to have a type specimens available and an expert in alpha taxonomy on hand to boot. However, both are sometimes useless in the case of groups where there is a paucity of morphological characteristics, such in some parasitic nematodes. In this case molecular data is useful but may also be insufficient and other “characteristics” are now being recognized as useful (i.e., pathology, location in host, population ecology, and transmission dynamics, etc.)in delineating groups. That is, while much of the discussion on this thread thus far has centered on morphology and molecules, there are parameters/characteristics that are useful as well and should now be considered in the discussion of taxonomy.

Jim Thomerson said:

I’ve examined a considerable number of type specimens, and the same is true of my colleagues in alpha taxonomy of fishes. I feel better about a molecular phylogeny of a group of fishes when one of the authors is an alpha taxonomist who is a recognized authority on the group.

Really? Do we really need type specimens to tell a seahorse from a goby, which is the sort of thing most molecular phylogenies would require? Even among closely related species, it doesn’t take a careful comparison of specimens to distinguish a mallard from a shoveler. And you should also consider trusting colleagues that came before you. If a specimen has been previously determined by some competent worker to belong to Mergus serrator, are you really going to demand that someone compare it to the holotype, wherever that may be, before you will believe it isn’t M. merganser?

It is true that type specimens might not always be required for every molecular phylogenetic project. However, it is always desirable to have them if possible. In fact, that is one of the requirements for the Barcode of Life project. In order to be granted barcode designation:

“Gene sequences must derive from a designated gene region, they must meet quality standards and they must derive from a specimen whose taxonomic assignment can be reviewed, ordinarily through linkage to a specimen that is held in a major collection (Hanner et al. 2007).”

Molecular Ecology Notes (2007)

The project has the advantage of being able to provide easy access to type specimen information. This can be important when making species identifications.

Molecular systematics and morphological cladistics are problematic because they are based on structuralism. They use lemmas and theorems not hypotheses and theories, and test the fact of the nested results of clustering by similarity against theories of descent with modification. A fact always wins against a theory unless one notices that these cannot be compared; the theory should subsume the fact or be changed. Most theories of descent of taxa (stem-group macroevolution) do subsume the facts of morphological and molecular nesting. Check out the Modern Evolutionary Systematics Web site, particularly the Manifesto: http://www.mobot.org/plantscience/r[…]t/21EvSy.htm

Most of my alpha taxonomic work, as well as the molecular phylogeny work, has involved South and Central American rivulid killifishes. This is a group still not very well known, with a number of species and genera described in the 1800’s and early 1900’s. The literature varies in accuracy of description and illustration. I’ve seen published illustrations of holotypes which were somewhat fanciful. So I have visited most of the Museums in USA and Europe which house type material. I would think anyone serious about describing new species, revising genera, etc. would do the same. As a result, I have been able to supply specimens, identified to my satisfaction, at least, for molecular phylogenetic studies.

And, yes, I trust colleagues who came before me, but I have a lot more study material available than they had, so it is trust but verify. I expect the same attitude from my future colleagues.

Ah; classification is easy. Even a young child just learning to speak can do it.

I remember a young kid who was just learning to talk pointing to the grate in a fireplace and saying, “goggie!” (doggie)

DS said:

It is true that type specimens might not always be required for every molecular phylogenetic project. However, it is always desirable to have them if possible. In fact, that is one of the requirements for the Barcode of Life project. In order to be granted barcode designation:

“Gene sequences must derive from a designated gene region, they must meet quality standards and they must derive from a specimen whose taxonomic assignment can be reviewed, ordinarily through linkage to a specimen that is held in a major collection (Hanner et al. 2007).”

Molecular Ecology Notes (2007)

The project has the advantage of being able to provide easy access to type specimen information. This can be important when making species identifications.

Notice that there is nothing about types in that first passage. The requirement is that the sequence be traceable to a museum specimen, which need not be the type. Fortunately, since museums are generally not anxious to have types snipped up for DNA, and even mitochondrial sequencing can be iffy for older specimens.

I admit I’m not sure what the second paragraph means. Unless they intend to have a database of type specimens linked to the barcodes?

Mike Elzinga said: Ah; classification is easy.

Ellen Degeneres had a routine talking about classifying her CD collection while stoned.

The next day she noticed The Carpenters, The Doors, and Nine-Inch Nails neatly arranged together.

John Harshman said:

Notice that there is nothing about types in that first passage. The requirement is that the sequence be traceable to a museum specimen, which need not be the type. Fortunately, since museums are generally not anxious to have types snipped up for DNA, and even mitochondrial sequencing can be iffy for older specimens.

I admit I’m not sure what the second paragraph means. Unless they intend to have a database of type specimens linked to the barcodes?

You are correct, type specimens are not mentioned. But then again, as you point out, there is no need to destroy or mutilate the actual type specimen in order to get a DNA sample of the species.

You are also correct in that they have a specimen database linked to the barcode information, including collection data and photographs. The web site has instructions for submissions:

http://www.boldsystems.org/views/login.php

Of course none of this negates the need for trained taxonomists and real type specimens but it does make it easier for lowly molecular biologists to do experiments.

mrg said:

Mike Elzinga said: Ah; classification is easy.

Ellen Degeneres had a routine talking about classifying her CD collection while stoned.

The next day she noticed The Carpenters, The Doors, and Nine-Inch Nails neatly arranged together.

:-)

Makes perfectly good sense to me.

Mike Elzinga said: Makes perfectly good sense to me.

Hmm. I bet you smoke the same stuff.

mrg said:

Mike Elzinga said: Makes perfectly good sense to me.

Hmm. I bet you smoke the same stuff.

Actually a carpenter made a display hook on a door using a nine-inch nail.

I saw it through the haze.

Mike Elzinga said:

“I saw it through the haze.”

Two-way purple haze?

From a strictly cladistic viewpoint, I guess the Beatles, Adam Ant, Super Fly and the Bee Gees should all be grouped together. Or would that be an insectuous relationship?

IMHO we are rapidly moving towards the point where every specimen anyone collects will have its DNA sequenced.

Obviously, you are not a taxonomic entomologist.

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This page contains a single entry by John S. Wilkins published on February 5, 2011 9:50 PM.

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