Phylogeny of the Carnivora – molecules, fossils, and total evidence
Fossil taxa are inherently at a disadvantage in resolving phylogenetic relationships, relative to living forms, as soft anatomy, DNA, physiology, and most life-history attributes are not readily available for the vast majority of these taxa, other than some fascinating new sequences available for Pleistocene fossil taxa (e.g. Smilodon, Homotherium, Miracinonyx, Ursus spelaeus, etc.; Loreille et al., 2001; Barnett et al., 2005). Nevertheless, fossil data possess several key advantages in phylogenetic analyses, including the ability to break-up ‘long branches’ in phylogenies, where the divergence between modern-day clades occurred deep in geological time. Fossils preserve morphologies that can become obscured along these long branches, and also provide temporal context for the evolution of living clades that may be crucial for accurately reconstructing ancestral conditions and partitioning synapomorphic versus homoplasious resemblances among modern-day taxa. Some workers feel that molecular data are inherently superior for reconstructing phylogeny than morphological characters (see for example: Scotland et al., 2003; but see Jenner, 2004), and as a consequence, phylogenies for many clades, particularly those that are not well represented in the fossil record, often are based solely on molecular sequence data. Within Carnivora, for example, the most recent studies reconstructing phylogenetic relationships among living taxa have relied principally on molecular sequences (e.g. Flynn et al., 2000, 2005).