1 The technical term for evolutionary genealogy is "phylogeny." Phylogeny is the pattern of descent relationships which links, eventually, all life into a single tree.
2 Johnston, R.F. 1992. Evolution in the Rock Dove: Skeletal Morphology. Auk 109: 530-542.
2a A very valuable series of recent discussions of the topic of homology may be found in Hall, B.K. (ed.) 1994. Homology: the hierarchical basis of comparative biology. Academic Press.
In the first pages of Hall's introduction to the volume, he presents some "unanswered questions" including the following, which effectively convey the difficulty of the concept:
3 Essentially, the parsimony principle in phylogenetics amounts to the view that the most likely explanation of a taxonomic data set (an array of taxa and their character-values) is the one which requires the smallest number of character state transitions. This amounts to saying that a pattern of evolutionary diversification is as simple as it can possibly be, consistent with the facts of any given case, and it involves the assumption that character state transitions are unlikely events, and that character reversals and convergence are relatively rare. The appropriateness of this criterion to the demands of phylogenetic research is a much debated issue, and the issues have been reviewed and criticised by Elliott Sober (1988. Reconstructing the Past. Parsimony, Evolution & Inference. MIT Press, Cambridge, Massachussetts. .
4 Carrol, R. & Z-M Dong. 1991. Hupehsuchus, an enigmatic aquatic reptile from the Triassic of China, and the problem of establishing relationships. Phil. Trans. Roy. Soc. Lond. B. 331: 131-153.
5 Kollar and Fisher, 1980. Tooth induction in chick epithelium: Expression of quiescent genes for enamel synthesis. Science 207: 993-995. .
6 This fascinating topic is discussed extensively in Raff, R. 1996. The shape of life : genes, development, and the evolution of animal form . Chicago : University of Chicago Press. .
7 See for example Givnish, T. & K. Sytsma. 1997. Homoplasy in molecular vs. morphological data: the liklihood of correct phylogenetic inference. Chapter 2 in: Givnish, T. & K. Sytsma (eds.) Molecular Evolution and Adaptive Radiation. Cambridge University Press. .
8 Here I am distinguishing taxonomy, as the naming of taxa, from classification, as their grouping into higher taxonomic categories. .
9 The importance of contingency in affecting the trajectory of evolutionary diversification on this planet is a highly contentious issue. Some (notably Stephen Jay Gould - see S.J. Gould 1989. Wonderful Life. W.W. Norton.) hold the view that chance and history are the primary dictators of much of the evolutionary story, dramatizing this view by suggesting that if we could run the experiment "World" many times again under similar cosmological conditions, the outcome after 3.8 billion years would be different every time. On this view, extinction of taxonomic groups is more a matter of bad luck than bad adaptation, and contingencies have a major impact on what else develops thereafter. Thus, for example, there is nothing inevitable about vertebrate animals, still less about humans - maybe there's nothing inevitable about animals, or even eukaryotes, at all - perhaps the world might have continued happily for ever with a prokaryote biota. Others are persuaded that, although chance events are indeed greatly influential over many historical details (such as the obliteration of the dinosaur lineages, perhaps), many prominent features of life on earth would reappear with each re-run of the "World" experiment, albeit in different phylogenetic guises (again, provided that the earth's physical environments showed similar trends in each re-run.) Thus, for example, they would say: such characteristics as photosynthesis, morphological complexity, heterotrophy, homeothermy and behavioural complexity would reliably evolve, no matter which lineages would actually be involved in giving rise to them. .
10 Poospiza is one of several seed-eater genera that have been proposed by Sibley & Ahlquist (see footnote 11) to have their closest evolutionary affinities among the tanagers (Thraupinae), rather than with the sparrows and finches (Emberizinae). Thus, it is their view that some large part of the neotropical sead-eater assemblage represents an autochthonous radiation convergent on the emberizines (which probably find their origins in n. America.) As part of an extensive investigation into this matter, Stephen Lougheed of Queen's University, Canada, and I have made an analysis of the phylogentic relationships among members of the genus Poospiza. We hope that these results will be published within the year; interested readers may contact us for information about this work at: firstname.lastname@example.org or email@example.com. .
11 Fjeldså, J. 1992. Biogeographic patterns and evolution of the avifauna of relict high-altitude woodlands of the Andes. Steenstrupia 18: 9-62.
12 Ellsworth, D.A. et al. 1995. Phylogenetic relationships among N. American grouse inferred from Restriction Endonuclease analysis of Mitochondrial DNA. Condor 97: 492-502. .
13 Lanyon, S.M. 1994. Polyphyly of the balckbird genus Agelaius and the importance of assumptions of monophyly in comparative studies. Evolution. 48: 679-693. Though these analyses show that Agelaius is not a natural group, the other genera used in the analyses are supported. Thus, the cytochrome-B gene does provide substantial phylogenetic information, and the conclusion of paraphyly in Agelaius must be taken seriously..
14 Sibley, C. & J. Ahlquist. 1990. Phyloeny and Classification of Birds. Yale University Press. New Haven.
15 See for example Bledsoe, A.H. 1988 Nuclear DNA evolution and phylogeny of the New World nine-primaried oscines. Auk 105: 504-515.; Bleiweiss, R. et al. 1994. DNA-DNA hybridization evidence for subfalily structure among hummingbirds. Auk 111: 8-19..; Harshman, J. 1994. Reweaving the tapestry: what can we learn from Sibley & Ahlquist? Auk 111: 377-388. ; Lanyon, S. and J. Hall 1994. Re-examination of barbet monophyly using mitochondrial DNA sequence data. Auk 111: 389-397.; Mooers, A. and P. Cotgreave. 1994 Sibley & Ahlquist's tapestry dusted off. Trends in Ecology & Evolution. 9: 458-459.; Bleiweiss, R. et al. 1995. Confirmation of a portion of the Sibley-Ahlquist "tapestry." Auk 112: 87-97.
16 Losos, J., T. Jackman, A. Larson, K. de Queiroz, L. Rodriguez-Schettino 1998. Contingency and Determinism in Replicated Adaptive Radiations of Island Lizards. Science 279: 2115-2118. Very similar phenomena have been reported recently in stickleback fish (Gasterosteus aculeatus) in western Canada: the species has repeatedly invaded freshwater habitats from its ancestral inshore marine range, and many times, lake populations have independently generated near-identical parallel species pairs in benthic & limnetic microhabitats (see Chapter 18 in Ref. 18).
17 See, for example, the classic discussion of this matter in Cain, A. J. 1964 The perfection of animals. pp. 36-63 in: J.D. Carthy and C.L. Duddington (eds.) Viewpoints in Biology, vol. 3. London: Butterworth.
18 Givnish, T. & K. Sytsma (eds.) 1997.
Molecular Evolution and Adaptive Radiation. Cambridge University Press.