Huelsenbeck et al.
Abstract.Many questions in evolutionary biology are best addressed by comparing traits in different species. Often such studies involve mapping characters on phylogenetic trees. Mapping characters on trees allows the nature of the transformations, their number, and timing to be identified. The parsimony method is the only method available for mapping morphological characters on phylogenies. Although the parsimony method often makes reasonable reconstructions of the history of a character, it has a number of limitations. These limitations include the inability to consider more than a single change along a branch on a tree and the uncoupling of evolutionary time from amount of character change. Here we extend a method described by Nielsen (2002) to the mapping of morphological characters under continuous-time Markov models. We demonstrate the utility of the method for mapping characters on trees and also for identifying character correlation.
Morando et al.
Abstract.Recovery of evolutionary history and delimiting species boundaries in widely distributed, poorly-known groups requires extensive geographic sampling, but this is difficult to design a priori because evolutionary diversity is often "hidden" by an inadequate taxonomy. Large data sets are needed, and these provide unique challenges for analysis when they span intra and inter-specific levels of divergence. Protocols have been designed to combine methods of analysis for DNA sequences that exhibit both very shallow and relatively deeper divergences (Crandall and Fitzpatrick, 1996). In this study we combine several tree-based phylogeny reconstruction methods with nested clade analysis, to extract maximum historical signal at various levels, in the poorly-known Liolaemus elongatus-kriegi complex in temperate South America. We implement the basic protocol of Wiens and Penkrot (2002) to test for species boundaries, and propose modifications to accommodate large data sets and gene regions with heterogeneous substitution rates. Combining haplotype trees with nested-clade analyses allowed testing of species boundaries on the basis of a priori defined criteria, and this approach suggests that the number of putative species could be doubled. We discuss these findings in the context of the advantages and limitations of a combined approach for retrieval of maximum historical information in large data sets, in the context of the yet formidable unresolved issues of sampling strategies.
Abstract.Marmots have a prominent role in the study of mammalian social evolution, but only recently has their systematics received the attention it deserves if sociobiological studies are to be placed in a phylogenetic context. Moreover, sciurid morphology offers a fascinating model to test the congruence between morphological change and phylogeny as sciurid skeletal characters are considered to be inclined to convergence. In spite of this, no morphological study involving all marmot species has ever been undertaken. Therefore, geometric morphometric techniques were applied in a comparative study of the marmot mandible. The adults of all 14 living marmot species were compared and mean shapes of their mandible used to investigate the morphological evolution of the genus Marmota. Three major trends can be outlined. 1) The phylogenetic signal in the variation of landmark geometry, which describes mandible morphology, seems to account for the shape differences at intermediate taxonomic levels. The subgenera Marmota and Petromarmota, recently proposed on the basis of mitochondrial cyt b sequence, receive support from mandible morphology. Moreover, when other sciurid genera are included in the analysis, the monophyly of the genus Marmota and that of the tribe Marmotini (i.e., marmots, prairie dogs and ground squirrels) are strengthened by the morphological data. 2) The marmotine mandible may have evolved as a mosaic of characters and does not show convergence determined by size similarities. 3) Allopatric speciation in peripheral isolates may have acted as a powerful force for modelling shape. This is strongly suggested by the peculiar mandible of M. vancouverensis and, to a lesser degree, by that of M. olympus, both thought to have originated as isolated populations in Pleistocene ice-free refugia.
Hassanin and Douzery
Abstract.The ruminants constitute the largest group of ungulates with more than 190 species and its distribution is widespread throughout all continents but Australia and Antarctica. Six families are traditionally recognized within the suborder Ruminantia: Antilocapridae (pronghorns), Bovidae (cattle, sheep, and antelopes), Cervidae (deers), Giraffidae (giraffes and okapis), Moschidae (musk deers) and Tragulidae (chevrotains). The interrelationships of the families have been an area of controversy among morphology, palaeontology and molecular studies, and almost all possible evolutionary scenarios have been proposed in the literature. We analyzed a large DNA data set (5,322 nucleotides) including both mitochondrial (cytochrome b, 12S rRNA, and 16S rRNA) and nuclear (k-casein, cytochrome P 450, lactoferrin and α-lactalbumin) markers for 23 species. Our results show that the family Tragulidae occupies a basal position with respect to all other ruminant families, confirming the traditional view that separates Tragulina and Pecora. Within the pecorans, Antilocap ridae and Giraffidae emerge first and the families Bovidae, Moschidae, and Cervidae are allied with the unexpected placement of Moschus close to bovids rather than cervids. These molecular results are used for assessing the homoplastic evolution of morphological characters within the Ruminantia. A Bayesian relaxed molecular clock approach based on the continuous autocorrelation of evolutionary rates along branches is applied to estimate the divergence ages between the major clades of ruminants. The evolutionary radiation of Pecora occurred at the Early / Late Oligocene transition, and Pecoran families diversified and dispersed rapidly during the Early and Middle Miocene epoch. We then propose a biogeographic scenario to explain the extraordinary expansion of this group during the Cenozoic era.
Holland et al.
Abstract.We conducted a simulation study of the phylogenetic methods UPGMA, neighbor joining, maximum parsimony, and maximum likelihood for a five-taxon tree under a molecular clock. The parameter space included a small region where maximum parsimony is inconsistent, so we tested inconsistency correction for parsimony and distance correction for neighbor joining. As expected, corrected parsimony was consistent. For these data, maximum likelihood with the clock assumption outperformed each of the other methods tested. The distance-based methods performed marginally better than did maximum parsimony and maximum likelihood without the clock assumption. Data correction was generally detrimental to accuracy, especially for short sequence lengths. We identified another region of the parameter space where, although consistent for a given method, some incorrect trees were each selected with up to twice the frequency of the correct (generating) tree for sequences of bounded length. These incorrect trees are those where the outgroup has been incorrectly placed. In addition to this problem, the placement of the outgroup sequence can have a confounding effect on the ingroup tree, whereby the ingroup is correct when using the ingroup sequences alone, but with the inclusion of the outgroup the ingroup tree becomes incorrect.
Harris et al.
Abstract.Character construction, the methods by which characters and character states are produced from observations of variation, is a crucial but poorly understood step in phylogenetic analysis. Alternative approaches are used in practice, but there has been relatively little investigation of their theoretical bases and analytical consequences. Three published numerical analyses of the phylogenetic relationships within the Triassic Aetosauria are reviewed. Combined data from these studies were used to explore the impact of alternative approaches to character construction. Some previous aetosaurian characters represent parallel variations in the morphology of osteoderms from different body regions, and their independence is questionable, leading us to propose more composite alternative constructions. Phylogenetic analyses reveal that inferred relationships within the Aetosauria are in general poorly resolved and weakly supported by the available data, and are sensitive to alternative approaches to character construction. Thus the results from this and previous studies should not, for the most part, be accepted as robust hypotheses of aetosaurian interrelationships. The treatment of systems of intraorganismal (e.g. serial, antimeric) homologues, such as osteoderms, in character construction is discussed. Applied to parallel variations in systems of intraorganismal homologues, previous advice on choosing among alternative character constructions and Hennig's auxiliary principle agree in favoring a more composite approach, in accordance with common practice.