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).

Thursday, 22 January 2009

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.


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