An Interview with Mr. Darwin

On Friday afternoon Dave and Malte step into the Hoop and Toy for their regular ‘end-of-the-week’ pint (or three).

At the bar they are approached by a dark and mysterious man with a cockney accent and an unlit cigarette hanging precariously from his lips. “’Ere, interest’d in a time machine?” David chokes on his beer. “‘Ow much den?” (David is also a cockney, so it’s going to be a bit complicated). Anyway, they buy it for a fiver (5 British Pounds Sterling).

It takes six pints and a Japanese translator (an unwitting tourist) to work out how the thing turns on. Within two hours and a spectacular light display, too complex to describe here, Malte and Dave make it to 19th century England. Due to the Earth’s orbit, and other dreary time-space continuum explanations privy only to Doctor Who fans, they end up in the village of Downe in Kent, 1862.

“Sh*t, where are we?”
“Dunno. Fancy a pint?”

After several hours in the George and Dragon Inn – David and Malte discover that they are only 20 minutes away by horse-and-cart from Down House, home of Charles Darwin.

“Hang on. What if we interviewed Chuck for our blog, eh?” The pints were taking their toll.
“That’ll show them who's wrong!”

An Interview with Mr. Darwin

[Loud banging on door - followed by intermittent singing and shushing. A distinguished, but slight nervous looking, gentleman opens the door a crack. A brass chain can be seen securing it to the rest of Down House]

“Chucky!”
“I do not wish to purchase excessive merriment from two louts! Please be off with you!
“Hey, Chuck … sorry Mr. Darwin. We are schistema … cystmena … nat … naturists …?”
“I am ill. Please go away!”
“… Naturalists!”
“I am very sick. Please let leave me in peace!”
“… from the futu… er … Australia …”
“I’m not talking to you. I am too ill. Please remove your foot from my door!”
“Look, in the future people are all fighting over your ideas and your work. Evolution has become an explanation for almost everything and you seem to be considered the originator of all modern ideas in biological classification, as well as, plant and animal geography!”

[Darwin paused for a moment and seemed to relax].

“But why? Ideas are developed through time. Evolution is an idea to which I had been introduced. Most of it made no sense. Some of it was simply nonsensical. I make no excuse for my ideas, but surely a good rational explanation makes for a better understanding of the processes at work?”
“… er… What?”
“Where do you think I got my ideas from? I didn’t just invent them there and then! They evolved from other ideas.”

[Dave and Malte think this is a pun and giggle]

But people in the future think 1859 and your Origin was a turning point for biology!”
“Please make no such assumption! I, Monsieur Lamarck and probably others, have provided ways with which to explain the biological world. It is not the answer but simply an explanation that I am convinced is good and rational …”
“But ..”
“I am ill. Goodbye to you sir!”

[David and Malte look at each other].

“He called me sir!”
“Want to interview Agassiz?”

Classification and Non-Trees

In spite its role as a ‘central metaphor’ and two decades of effort to promote ‘tree-thinking’, evolutionary relationships are now being portrayed in ways other than the simple bifurcating tree, recent examples being the ‘ring of life’ (Rivera & Lake 2004), the interlinking, anastomosing networks of major eukaryote groups (Doolittle 1999, 2000, Doolittle & Bapteste 2007, for commentary see Arnold 2007, Lane & Archibald 2008, McInerney et al. 2008, Dagan & Martin 2006), interconnecting networks relating various taxa (Hertel et al. 2006), and so on, the idea being summarised in a recent New Scientist article “Why Darwin was wrong about the tree of life”.

Most of this recent batch of non-trees have resulted from analysis of molecular data, although the general argument – if biological classification is hierarchical, then it prevents the representation of ‘real’ reticulate patterns – was explored in a cladistic context some three decades ago (Bremer & Wanntorp 1979).
Significance (or explanation) for many of these molecular diagrams is offered via the process of Lateral (or Horizontal) Gene Transfer (LGT, HGT), the horizontal transfer of a gene or genetic material from one organism to another, distantly related organism (Dagan & Martin 2006), first outlined some years ago to support the theory of serial endosymbiosis (Margulis 1998) to explain the origin of chloroplasts and mitochrondria (see Journal of Phycology 44 (1) and Lane & Archibald 2008). LGT is a mechanism to explain instances of xenology (“foreign genes”, Gray and Fitch 1983, p. 64), “a form of homology (inferred common ancestry) in which the sequence (gene) homology is incongruent with that of the organisms carrying the gene, and horizontal gene transfer or transfection is the assumed cause” (Patterson 1988, p. 612). Xenology finds its closest morphological equivalent in parallelism, a term which remains hard to define but can be simplified by associating it with incongruent homologies (similarities); xenology finds its biogeographical equivalent in dispersal, a term equally hard to define but simply suggests incongruent distributions (Williams & Embley 1996, pp. 581—582). Parallelism (Arendt & Reznick 2008) and dispersal (Queiroz 2005) are being discussed again, within the fresh gloss provided by molecular data, although interpretations of parallelism never really disappeared (Roth 1984:14; Sluys 1989; Wagner 1989:55, 66; Brooks 1996; DeSalle et al. 1996; Gould 2002), with suggestions being made such as “the significance of this similarity [parallelism] is thus dependent on the existence of a relevant underlying process” (Sanderson and Hufford 1996:328). Even earlier, Simpson wrote:

“In the most restricted sense virtually all evolution involves parallelism. Homologous genes tend to mutate in the same way (p. 9)… Homology is always valid evidence of affinity. Parallelism is less direct and reliable, but it is also valid evidence within somewhat broader limits. It may lead to overestimates of degree of affinity, but it is not likely to induce belief in wholly false affinity (p. 10)” (Simpson 1945, pp. 9—10).

Simpson’s words turned out not to be so, for the parallelisms he noted simply mislead determination of exact relationships among mammals (McKenna & Bell 1997): those similarities identified as parallelisms (like xenology and dispersal) are simply incongruent characters.
All the same, it has been argued that reticulate networks allow incongruent ‘homologies’ to be accommodated on the same diagram relative to congruent homologies (Huson & Bryant 2006). The general idea seems similar to that explored by William Sharp Macleay and his circular systems: an attempt to represent what he called analogies and affinities (homologies) in one system (Macleay 1819, Fig. 6).

Yet if even orthologous (homologous) genes do not support ‘tree-thinking’ (Bapteste et al. 2005), incongruence among gene-trees presents problems for the effectiveness of these data, rather than provide alternative explanations for incongruence (LGT = parallelism=dispersal). Simply put: Cladograms deal with character distributions and their implications for taxon relationships (classifications), rather than vehicles for explaining incongruence.

References

Arnold, M. 2007. Evolution through Genetic Exchange, Oxford University Press, Oxford.
Arendt, J. & Resnick, D. 2008. Convergence and parallelism reconsidered: what have we learned about the genetics of adaptation? Trends in Ecology & Evolution 23: 26—32.
Bapteste, E., Susko, E., Leigh, J., MacLeod, D., Charlebois, R.L. & Doolittle, W.F. 2005. Do orthologous gene phylogenies really support tree-thinking? BMC Evolutionary Biology, 5:33; doi:10.1186/1471-2148-5-33.
Bremer, K. & Wanntorp, H.-E. 1979. Hierarchy and reticulation in systematics. Systematic Zoology 28: 624—627.
Brooks, D. R. 1996. Explanation of homoplasy at different levels of biological organisation. In M.J. Sanderson and L. Hufford (eds) Homoplasy. The Recurrence of Similarity in Evolution, pp. 3—36. San Diego: Academic Press.
Dagan, T. & Martin, W. 2006. The tree of one percent. Genome Biology 7: 118.1—118.7.
DeSalle, R., Agosti, D., Whiting, M., Perez-Sweeney, B., Renson, J., Baker, R., Bonacum, J. & Bang, R. 1996. Cross-roads, milestones, and landmarks in insect development and evolution: Implications for systematics. Aliso 14:305—21.
Doolittle, W.F. 1999. Phylogenetic classification and the universal tree. Science 284: 2124—2128.
Doolittle, W.F. 2000. Uprooting the tree of life. Scientific American, Feb. 2000: 90—95.
Doolittle, W. F. & Bapteste, E. 2007. Pattern pluralism and the Tree of Life hypothesis. PNAS 104:2043—2049.
Gould, S.J. 2002. The Structure of Evolutionary Theory. Cambridge MA: Harvard Univ. Press.
Gray G.S. & Fitch, W.M. 1983. Evolution of antibiotic resistance genes: the DNA sequence of a kanamycin resistance gene from Staphylococcus aureus. Mol. Biol.Evol. 1: 57–66.
Hertel, J., Lindemeyer, M., Missal, K., Fried, C., Tanzer, A., Flamm, C., Hofacker, I.L., Stadler, P.F. and the Students of Bioinformatics Computer Labs 2004 and 2005. 2006. The expansion of the metazoan microRNA repertoire. BMC Genomics 2006, 7:25.
Huson D.H. & Bryant D. 2006. Application of phylogenetic networks in evolutionary studies. Molecular Biology & Evolution 23:254—67.
Lane, C.E. & Archibald, J.M. 2008. The eukaryotic tree of life: Endosymbiosis takes its TOL. Trends in Ecology and Evolution 23: 268—275.
Margulis, Lynn. 1998. Symbiotic Planet: A New Look at Evolution. New York: Basic Books.
McInerney, J.O., Cotton, J.A. & Pisani, D. 2008. The prokaryotic tree of life: Past, present...and future? Trends in Ecology and Evolution 23: 276—281.
McKenna, M.C. & Bell, S.K. 1997. [with contributions from G. G. Simpson et al.]. Classification of mammals above the species level. New York: Columbia University Press.
MacLeay, W.S. 1819—1821. Horae entomologicae: or Essays on the Annulose Animals, &c. Vol. 1, Pt. 1 & 2. S. Bagster, London.
Patterson, C. 1988. Homology in classical and molecular biology. Molecular Biology and Evolution 5: 603—625.
Rivera, M.C. & Lake, J.A. 2004. The ring of life provides evidence for a genome fusion origin of eukaryotes. Nature (9th September 2004) 431: 152—155.
Roth, V. 1984. On homology. Biological Journal of the Linnean Society 22:13—29.
Sanderson, M.J. and Hufford, L. (eds) 1996. Homoplasy. The Recurrence of Similarity in Evolution, San Diego: Academic Press.
Simpson, G. G. 1945. The principles of classification and a classification of mammals. Bulletin of the American Museum of Natural History 85:1-350.
Sluys, R. 1989. Rampant parallelism: An appraisal of the use of nonuniversal derived character states in phylogenetic reconstruction. Systematic Zoology 38:350—70.
Wagner, G.P. 1989. The Biological Homology Concept. Annual Review of Ecology and Systematics 20: 51—69; doi:10.1146/annurev.es.20.110189.000411
Williams, DM. & Embley, TM. 1996. Microbial Diversity. Annual Review of Ecology and Systematics 27: 569-595.

Paraphyly Watch 1: Fossil Fish & Missing Links

There are many ways to say "Oh #!@*! My group is paraphyletic! The following is perhaps the most eloquent:

"These recent fossils [Palaeozoic ‘acanthodians’] started to make us question: are these a natural group or are we looking at a bunch of organisms closely related to the common ancestor of all jawed vertebrates?" says Brazeau. "It's tempting to put them all into one group; however, they might come from different groups but all look very similar." This, Brazeau adds, is a common problem" (Nature 2009, 457:234).

Paraphyly sure is a 'common problem'. But what has lead to this devastating discovery?

"Ptomacanthus is placed as a basal stem chondrichthyan, but this result should be viewed with caution. A large part of the acanthodians, including Acanthodes, form a cohesive monophyletic group on the osteichthyan stem. However, the position of Ptomacanthus is problematical" (Brazeau 2009:307).

It certainly is! According to cladistic and phenetic (Bayesian) analysis Palaeozoic ‘acanthodians’ are paraphyletic. Why is this problematic?

"Current conceptions of gnathostome phylogeny depict a rather simplistic arrangement of nominally monophyletic and, apparently, morphologically disparate groups. The emerging picture of acanthodian (and perhaps placoderm) paraphyly does not overturn a general consensus about gnathostome interrelationships. Instead, it populates the long, naked internal branches, revealing a much richer picture of character evolution in early gnathostomes" (Brazeau 2009:307).

What Brazeau had found is analogous to the platypus - an organism that has characteristics of two different groups, in this case, osteichthyans and chondrichthyans. Like the platypus, Brazeau (or at least the media) are tempted to state that a 'missing link' has been found, but to their surprise, this missing link (read 'ancestor') turns out to be nested within the chondrichthyans. Whoops! Not only is the missing link gone, but so too is the assumed monophyly of acanthodians. What to do?

What any systemtist should do - re-classify the osteichthyans and chondrichthyans in light of this new evidence. Brazeau is naive to suggest that this discovery will "...not overturn a general consensus about gnathostome interrelationships" If Ptomacanthus is more closely related to chondrichthyans then bang goes the acanthodians. They need to be reclassified along with the chondrichthyans. But rather than saying the obvious, Brazeau descends into evolutionary explanation "... populates the long, naked internal branches, revealing a much richer picture of character evolution in early gnathostomes". No it does not reveal anything other than that Ptomacanthus is a chondrichthyan and that acanthodians are paraphyletic! And this is exactly what the media has picked on:

"The study also suggests that some acanthodians are ancestors to all modern jawed vertebrates" (BBC Online, 19 January 2009).

This is false and misleading - the study shows quite the opposite.

I place Brazeau (2009) as the first Paraphyly Watch entry for 2009 (and the first in the race for the Pewter Leprechaun) for mis-using paraphyly. Rather than reclassifying the gnathasomes, Brazeau (2009) as alluded to a missing link (which admittedly could have been done without the cladistic and phenetic analyses).

References

Martin D. Brazeau (2009). The braincase and jaws of a Devonian ‘acanthodian’ and modern gnathostome origins Nature, 457 (7227), 305-308 DOI: 10.1038/nature07436

The Absence of Evolution (Homology)

We almost labeled the paper entitled Bringing Homologies Into Focus by Anastasia Thanukos as 'Paraphyly Watch'. Here is why.

The paper is part of a new journal called Evolution: Education and Outreach - aimed at science school teachers rather than academia in general. The paper is a rather typical guide to homology - for instance:

"Homologies are traits present in two or more organisms that were inherited from the common ancestor of those organisms. The human five-fingered hand and the five-toed foot of a lizard, for example, were both inherited from our common ancestor that lived more than 300 Mya" (p. 498).

Almost right. Homologies, as a concept, existed in the literature before 'ancestors' were accepted in an evolutionary context - so it would be technically incorrect to associate them with ancestors per se - in the same way Alexander von Humboldt wasn't a biogeographer (the concept may have existed but not as we understand it today; and the term was coined much later to refer to something else). Is this a case of whiggish history? Possibly. Homologies are the only evidence we have of a common history, that is evolution. We may be splitting hairs but explanations as to how things originate does rather detract from the meaning (as we will show later). A clearer definition is "Homologies are relationships and occur when the same structure exists in two organisms but as different manifestations (in this case forearm and wing)". What this implies (and how it got there) is another matter that detracts from the homologies themselves. And this is exactly what happens with the rest of the paper.

Why would a paper titled 'Bringing Homologies Into Focus' give more space to explaining analogies and homoplasies? Is the absence of homology really more interesting? If so, we would assume non-evolution is of greater interest. This is a typical trend in evolutionary biology - attempting to explain why evolution is not present by invoking other assumed 'evolutionary' mechanisms. This is contradictory and send out the wrong message. What is important is when evolution is present - namely homologies. When it is not present it should really be of little or no interest. Then why probe into the absence of evolution?

There is a misconception in science that everything needs to be explained. This is the underlying premise of paraphyly 'enthusiasts'. When a group turns out to be non-monophyletic, that is non-evolutionary, people insist that evolution has gone on anyway. Apart from flying in the face of empiricism, explaining the absence of evolution by using other explanatory 'evolution' mechanisms is meaningless. Convergent evolution is not evolutionary. It does not result in homologies, only in analogies, that is non-homologies. Why this is even taught as 'evolution' mystifies us. We wonder if this happens in other fields? When volcanic rocks are absent from an area, do geologists explain it through volcanism? They could, but it would be very silly indeed.

References
Anastasia Thanukos (2008). Bringing Homologies Into Focus. Evolution: Education and Outreach, 1 (4), 498-504 DOI: 10.1007/s12052-008-0080-5

Paraphyly Watch 2009

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.