Phylogeny reconstruction

Hancock, J.M. and Vogler, A.P. (2000) How slippage-derived sequences are incorporated into rRNA variable-region secondary structure implications for phylogeny reconstruction. Molecular Phylogenetics and Evolution 14, 366-374. 

There are two evolutionary questions relevant to the clonal inheritance of the Y chromosome. First, do haploid nuclear sequences that do not recombine in meiosis evolve in a different manner and at a different rate than autosomal or X chromosomal sequences which do recombine Second, are clonally inherited nuclear sequences useful for phylogeny reconstruction ... 

Swofford, D. L., Olsen, G. J. (1990) Phylogeny Reconstruction. In Molecular Systematics. Eds. Hillis, D. M., Moritz, C., Sinauer Associates, Sunderlang, Massachusetts. 411-501. 

Weston, P. H. (1994). Methods for rooting cladistic trees. In Models in Phylogeny Reconstruction R. W. Scotland, D. J. Siebert, and D. M. Williams, Eds. (Oxford Systematics Association), p. 125-155. 

Page RDM (1994) Parallel phylogenies reconstructing the history of host-parasite assemblages. Cladistics 10(2) 155-173... 

Swofford DL, Olsen GJ (1990) Phylogeny reconstruction. In Hillis DM, Moritz C (eds) Molecular Systematics. Sinauer, Sunderland, Mass, p 411... 

Donoghue MJ, Doyle JA, Gauthier JA, Kluge AG, Rowe T (1989) The importance of fossils In phylogeny reconstruction. Annu Rev Ecol Syst 20 431 -460. 

The central tenets of the falsificationist philosophy of Karl R. Popper are reviewed in detail, and the way they do or do not apply to systematics and phylogeny reconstruction is analyzed. Cladistic analysis, cast in either maximum parsimony or in maximum likelihood approaches, is not compatible with Popperian falsificationism. The main reasons are the absence of a deductive link between a hypothesis of phylogenetic relationships and character distribution on a tree, which translates into the absence of the basic asymmetry of falsification versus verification. This sets Popper s philosophy of science apart from inductive systems. In cladistic analysis, falsification (disconfirmation) is symmetrical to verification (confirmation), which reveals an inductive and hence probabilistic background. The basic problem of systematics as an empirical science resides in character conceptualization and its critical evaluation. 

Fit of data to a hypothesis invokes methods of maximum-likelihood inference. Indeed, Popper s philosophy of science has recently been appealed to in support of likelihood approaches to phylogeny reconstruction (DeQneiroz and Poe, 2001), but this is possible only if Popper is taken out of context (Kluge, 2001a). 

Having said all of this, it is important to remember, however (Popper, 1976 Appendix IX), ... that non-statistical theories have as a rule a form totally different from that of the h here described, that is, they are of the form of a universal proposition. The question thus becomes whether systematics, or phylogeny reconstruction, can be construed in terms of a statistical theory that satisfies the rejection criteria formulated by Popper (see footnote 1) and that, in case of favorable evidence, allows the comparison of degree of corroboration versus Fisher s likelihood function. As far as phylogenetic analysis is concerned, I found no indication in Popper s writing that history is subject to the same logic as the test of random samples of statistical data. As far as a metric for degree of corroboration relative to a nonstatistical hypothesis is concerned. Popper (1973 58-59 see also footnote 1) clarified. 

Gaffney, E.S., An introduction to the logic of phylogeny reconstruction, in Phylogenetic Analysis and Paleontology, Cracraft, J. and Eldredge, N., Eds., Columbia University Press, New York, 1979, pp. 79-111. 

Conclusion With regard to Darwin s theory of evolution (Darwin, 1859) and phylogenetic parsimony as the method of choice for phylogeny reconstruction, it needs to be shown what exactly the theoretical components of descent, with modification are that mandate parsimony analysis and how the cladogram generated by parsimony analysis connects to decent, with modification. In a Popperian context, this coimection would have to be a deductive one, that is, one rooted in logic. 

Wagele, J.W. and Misof, B., On quality of evidence in phylogeny reconstruction a reply to Zrzavy s defence of the Ecdysozoa hypothesis,/. Zool. Syst. Evol. Res., 39,165-176,2001. 

Schoch, R.M., Phylogeny Reconstruction in Paleontology, Van Nostrand Reinhold, New York, 1986. 

It is worthwhile to pause and briefly consider what approaches to phylogeny reconstruction and classification were being pursued by invertebrate paleontologists. Early twentieth century invertebrate paleontologists were, with some exceptions (e.g., Rowe, 1899), either... 

This is more serious because if one can impose a model of evolution onto phylogeny reconstruction then the phylogeny becomes disengaged from observation. In this case the fact that brachiopods all share a particular type of shell — the observation — has been dismissed as irrelevant because a model of an adaptive pathway proclaims this observation to be misleading. Such methods of reconstructing phylogeny also mean that choice between competing hypotheses are choices between the models. 

Paleontology has the additional and unique information of time, measured either as absolute age or as relative stratigraphic position. The assumption that time imparts a key role to fossils in phylogeny reconstruction has been with us since the nineteenth century. However, it is only within the last quarter of the twentieth century that the strengths and limitations of time have been discussed in detail. There is an ongoing debate about the impact that consideration of time should have on our ability to reconstruct phylogeny. 

I mention both stratolikelihood and stratocladistics because these are the current developments influencing theoretical paleontological research into phylogeny reconstruction. In many ways, these methods reflect a desire to put stratigraphy, ancestor-descendent relationships and evolutionary models back into phylogeny reconstruction. We must await the reaction of those practicing paleontologists. 

Alroy, J., Stratigraphy in phylogeny reconstruction — reply to Smith (2000),/. PaleontoL, 76, 587-589, 2002. 

Patterson, C., Null or minimal models, in Models in Phylogeny Reconstruction, Scotland, R.W., Siebert, D.J., and Williams, D.M., Eds., Clarendon Press, Oxford, 1994, pp. 173-192. 

---