This paper addresses the general problem of how to rationally choose an algorithm for phylogenetic inference. Specifically, the controversy between maximum likelihood (ML) and maximum parsimony (MP) perspectives is reframed within the philosophical issue of theory choice. A Kuhnian approach in which rationality is bounded and value-laden is offered and construed through the notion of a Style of...

Despite impressive technical and theoretical developments, reconstruction of phylogenetic trees for enormous quantities of molecular data is still a challenging task. A key tool in analyses of large data sets has been the construction of separate trees for subsets (e.g., quartets) of sequences, and subsequent combination of these subtrees into a single tree for the full set (i.e., supertree ana...

This thesis develops and expands upon known techniques of mathematical physics relevant to the analysis of the popular Markov model of phylogenetic trees required in biology to reconstruct the evolutionary relationships of taxonomic units from biomolecular sequence data. The techniques of mathematical physics are plethora and have been developed for some time. The Markov model of phylogenetics ...

The freshwater mussel family Hyriidae (Mollusca: Bivalvia: Unionida) has a disjunct trans-Pacific distribution in Australasia and South America. Previous phylogenetic analyses have estimated the evolutionary relationships of the family and the major infra-familial taxa (Velesunioninae and Hyriinae: Hyridellini in Australia; Hyriinae: Hyriini, Castaliini, and Rhipidodontini in South America), bu...

A phylogeny is a set of relationships among groups of genes or organisms that reflects their evolutionary history. Inferring a phylogeny is an estimation procedure, a statistical inference of a true phylogenetic tree that is unknown. However, the aim of the phylogenetic analysis is not merely the reconstruction of a tree topology; the phylogeny provides a powerful framework in which several hyp...

We can place more than just organisms into trees: individual genes from the genomes of various organisms can also be placed into trees, and from these gene phylogenies, we can often infer the species phylogenies. Often, this is done with the geological record in mind: not all branches of the tree of life terminate in the present – there are many that end in the various mass extinctions that hav...

This study unravels the evolution and biogeographic history of the globally distributed ant genus Crematogaster on the basis of a molecular phylogeny, reconstructed from five nuclear protein-coding genes and a total of 3384 bp of sequence data. A particular emphasis is placed on the evolutionary history of these ants in the Malagasy region. Bayesian and likelihood analyses performed on a datase...

1055-7903/$ see front matter 2008 Elsevier Inc. A doi:10.1016/j.ympev.2008.05.006 * Corresponding author. Fax: +1 515 294 1337. E-mail address: [email protected] (J.M. Serb). Evolutionary relationships of the Pectinidae were examined using two mitochondrial genes (12S rRNA, 16S rRNA) and one nuclear gene (Histone H3) for 46 species. Outgroup taxa from Propeamussidae, Spondylidae and Limidae were...

Molecular data have converged on a consensus about the genus-level phylogeny of extant platyrrhine monkeys, but for most extinct taxa and certainly for those older than the Pleistocene we must rely upon morphological evidence from fossils. This raises the question as to how well anatomical data mirror molecular phylogenies and how best to deal with discrepancies between the molecular and morpho...

Starting with articles by Bock (1973) and Wiley (1975) in this journal, the field of systematic biology has a history, reviewed by Helfenbein and DeSalle (2005), of examining its methods in the context of the philosophy of science articulated by Karl R. Popper (e.g., 1959, 1962, 1983). Two main categories of debates have emerged in this literature. In one, Popper’s philosophy is assumed to be r...