Such expressions as that famous one of Linnæus, and which we often meet with in a more or less concealed form, that the characters do not make the genus, but that the genus gives the characters, seem to imply that something more is included in our classification, than mere resemblance. I believe that something more is included; and that propinquity of descent,—the only known cause of the similarity of organic beings,—is the bond, hidden as it is by various degrees of modification, which is partially revealed to us by our classifications (Darwin, 1859, p. 413f).

Wednesday, 7 January 2009

Paraphyly Watch 2009

ResearchBlogging.org
Welcome to the New Year and the start of a new campaign: Paraphyly Watch 2009

The aim is to document, as comprehensively as possible, all the misuses and abuses of paraphyly in the scientific and popular literature for 2009.
    By paraphyly we mean non-monophyletic groups or taxa (e.g., grades).
    By misuse, we mean accepting paraphyletic groups* as informative (e.g., using them in analysis).
    By abuse we mean treating paraphyly as being evolutionary or evidence for evolution (e.g., accepting non-monophyletic groups in taxonomy and evolutionary biology).
If you wish to read up more about paraphyly and it's role in classification, see our previous post here.

In December we will award the Pewter Leprechaun to the most outrageous misuse and/or abuse of Paraphyly for 2009.

To start off our watch we have picked up two exemplary cases of paraphyly misuse and abuse in last 2008 issue of Taxon 57(4) by R.K. Brummitt and R.A. Zander.

Brummitt's Evolution in taxonomic perspective consists of several abuses of paraphyly:
    "... emphasis has been increasingly placed on the need for a classification which recognises evolution" (Brummitt, 2008:1050).
This is what monophyly is all about. Once you discover monophyly you have discovered evolution within your group. Unfortunately, this is contrary to Brummitt (and his followers) who believe that their taxonomies alone (without any need for testing, it seems) are evolutionary. This runs counter to empiricism in science, which makes hypotheses of relationships (e.g., taxonomies) and uses cladistics to test them. It seems that Brummitt's taxonomy is the yardstick that cladistics has to abide. If it doesn't (i.e., the taxon is paraphyletic) cladistics is wrong, not Brummitt. Therefore paraphyly is evidence and empiricism politely excused.
    "To overcome these objections to cladistic taxonomy, its proponents argue that we are dealing only with present day taxa and must ignore ancestors because we do not have them and so cannot name them. So at the same time as they define paraphyly in terms of ancestry, they insist on ignoring ancestors (Brummitt, 2008:1050)."
Wrong again! Ancestors exist, we just have no empirical way of finding out who they were. Just because we cannot discover ancestors does not mean we only include 'present day taxa' and exclude fossil taxa in cladistics. This is another major flaw in Brummitt's thinking. Fossils can be used along side extant taxa in any cladistic analysis.

Possibly Brummitt's most incredulous slogan is
    "One cannot avoid paraphyletic groups. Again, 'Evolution is paraphyly all the way'..."
Paraphyly means evolution is not present in a group. Evolution is absent in paraphyletic groups, this is why they are paraphyletic. No matter how many times this is stated, Brummitt simply doesn't seem to get it - perhaps this is why he ignores the literature that has made these calls in the first place. Ignorance for some must really be bliss.

Zander's Evolutionary inferences from non-monophyly on molecular trees starts off promisingly:
    "I here suggest that not only is paraphyly acceptable, but non-monophyly in general may be evolutionarily informative. Non-monophyly of taxa is satisfied by either a paraphyletic" (Zander, 2008:1182).
Not surprisingly, Zander's argument falls apart in the next paragraph:
    "Two different species of the same non-monophyletic genus imply an ancestor with phenotype resolvable only at the genus level" (Zander, 2008:1182).
The sentence is in need of some explanation. Two different taxa with a non-monophyletic taxon may not belong there as they may be more closely related to something else. Relationship after all is what evolution is about. Whether this implies an ancestor is truly hearsay. Paraphyly is not a test for ancestors. It never has been. Such a test is non-empirical as it is based on something not being there - in this case a natural grouping. There is nothing to be resolved other than revising the taxonomy. Using a explanation that can not be tested is purely subjective. This leads on to:
    "Classifications based on phylogeny should be changed to accommodate non-monophyly-based taxon trees" (Zander, 2008: 1183).
Zander makes the same mistake as Brummitt. The cladistic analysis is the test, not the original taxonomy. If cladistics shows that the taxonomy (in this case a genus) is non-monophyletic, then it is the taxonomy that needs to be changed. Current taxonomies made by taxonomists are there to be tested by cladistic analysis, not the other way around! This mistake keeps coming up time and time again. Taxonomies are not evolutionary unless we are able to test them and discover monophyletic groups. If they are not monophyeltic, they are not evolutionary. Zander and Brummitt however see this the other way around.

The blight of paraphyly abuse and misuse is one commonly associated with other mistakes such as confusing taxa as species:
    "The exemplars A1 and A2 are paraphyletic, and if A is a species, then the ancestor of A1, A2 and species B is species A" (Zander, 2008: 1184).
and confusing supporters of the Phylocode as a cladistic movement and cladistics in general
    "The cladistic movement of the late 20th century has now split into two. Some can see the impossibility of classification into ranked taxa without any being paraphyletic, and have moved on to the PhyloCode with all its practical disadvantages arising from the abandonment of ranks" (Brummitt, 2008:1050).
We suggest that Zander and Brummitt actual read the cladistic literature in order to resolve their inherent misuses and abuses of paraphyly, cladistics and systematics.

* Hennig (1966: 146) defines paraphyletic groups as " ... distinguished from the monophyletic ones essentially by the fact that they have no independent history and thus possess neither reality nor individuality".

References

Brummitt, R.K. (2008). Evolution in taxonomic perspective Taxon 57:1049–1050.

Hennig, W. 1966. Phylogenetic systematics. The University of Illinois Press, Urbana.

Zander, R.H. (2008). Evolutionary inferences from non-monophyly on molecular trees Taxon 57:1182-1188.

5 comments:

Deborah said...

Hi, Does anyone know who first coined the term "paraphyletic"? Was in Haekel? Thanks!

Malte C. Ebach and David M. Williams said...

Paraphyly was first used by Hennig (1962) in a footnote:

"Diese handliche Bezeichnung habe ich kürzlich für die auf Symplesiomorphie begründeten
Gruppenbildungen . . . eingeführt". (Hennig 1962: 35, footnote 1; Translated as :'This handy designation I use for groups based by symplesiomorphy') (see Williams & Ebach, 2008: 17).

Hennig, W. 1962. Veränderungen am phylogenetischen System der Insekten seit 1953. Tagungsberichte Deutsche Akademie der Landwirthschaftswissenschaften 45. In Bericht über die 9. Wanderversammlung Deutscher Entomologen, 6.–8. Juni 1961 in Berlin, Zusammengestellt von Hans Sachtleben. pp. 29–42 Deutsche Akademie der Landwirtschaftswissenschaften,
Berlin.

Deborah said...

Thank you so much! Deborah

Anonymous said...

I am sorry to disagree completely with you. You yourself state that ancestors exist. This automatically makes them paraphyletic at a given level (at least species level). It does not matter whether they can be empirically detected or not.

Malte C. Ebach said...

"You yourself state that ancestors exist".

"This automatically makes them paraphyletic at a given level (at least species level)."

So because ancestors 'exist' they are paraphyletic. But paraphyletic groups don't exist. What a conundrum. Something that exists and may or may not be discovered. "It does not matter whether they can be empirically detected or not". Something that may or may not be discovered is an ancestor and that notion is still central to the question of ancestors. Seems you know something we don't. Or is this evolution by definition.