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John Gatesy

Publications and source records attributed to John Gatesy.

8 recordsLinked to original sources
PubMed2006

The supermatrix approach to systematics.

Recent reviews of the construction of large phylogenies have focused on supertree methods that involve separate analyses of data sets and subsequent integration of the resulting trees. Here, we consider the alternative method of analyzing all character data simultaneously. Such 'supermatrix' analyses use information from each character directly and enable straightforward incorporation of diverse kinds of data, including characters from fossils. The approach has been extended by the development of new methods, including model-based techniques for analyzing heterogeneous data and hierarchical methods for constructing extremely large trees. Recent work also suggests that the problem of missing data in supermatrix analyses has been overstated. Although the supermatrix approach is not suited for all cases, we suggest that its inherent strengths will ensure that it will continue to have a central role in inferring large phylogenetic trees from diverse data.

Animals↗
PubMed2005

Hidden likelihood support in genomic data: can forty-five wrongs make a right?

Combined analysis of multiple phylogenetic data sets can reveal emergent character support that is not evident in separate analyses of individual data sets. Previous parsimony analyses have shown that this hidden support often accounts for a large percentage of the overall phylogenetic signal in cladistic studies. Here, reanalysis of a large comparative genomic data set for yeast (genus Saccharomyces) demonstrates that hidden support can be an important factor in maximum likelihood analyses of multiple data sets as well. Emergent signal in a concatenation of 106 genes was responsible for up to 64% of the likelihood support at a particular node (the difference in log likelihood scores between optimal topologies that included and excluded a supported clade). A grouping of four yeast species (S. cerevisiae, S. paradoxus, S. mikatae, and S. kudriavzevii) was robustly supported by combined analysis of all 106 genes, but separate analyses of individual genes suggested numerous conflicts. Forty-eight genes strictly contradicted S. cerevisiae + S. paradoxus + S. mikatae + S. kudriavzevii in separate analyses, but combined likelihood analyses that included up to 45 of the "wrong" data sets supported this group. Extensive hidden support also emerged in a combined likelihood analysis of 41 genes that each recovered the exact same topology in separate analyses of the individual genes. These results show that isolated analyses of individual data sets can mask congruence and distort interpretations of clade stability, even in strictly model-based phylogenetic methods. Consensus and supertree procedures that ignore hidden phylogenetic signals are, at best, incomplete.

Classification↗
PubMed2003

Combined support for wholesale taxic atavism in gavialine crocodylians.

Morphological and molecular data sets favor robustly supported, contradictory interpretations of crocodylian phylogeny. A longstanding perception in the field of systematics is that such significantly conflicting data sets should be analyzed separately. Here we utilize a combined approach, simultaneous analyses of all relevant character data, to summarize common support and to reconcile discrepancies among data sets. By conjoining rather than separating incongruent classes of data, secondary phylogenetic signals emerge from both molecular and morphological character sets and provide solid evidence for a unified hypothesis of crocodylian phylogeny. Simultaneous analyses of four gene sequences and paleontological data suggest that putative adaptive convergences in the jaws of gavialines (gavials) and tomistomines (false gavials) offer character support for a grouping of these taxa, making Gavialinae an atavistic taxon. Simple new methods for measuring the influence of extinct taxa on topological support indicate that in this vertebrate order fossils generally stabilize relationships and accentuate hidden phylogenetic signals. Remaining inconsistencies in minimum length trees, including concentrated hierarchical patterns of homoplasy and extensive gaps in the fossil record, indicate where future work in crocodylian systematics should be directed.

Adaptation, Biological↗
PubMed2002

Is morphology still relevant?

The utility of morphological data in modern systematics has recently been challenged because strong selection pressures are thought to create widespread patterns of convergent evolution at this level. This concern has led to suggestions that morphological data should be excluded either from all analyses or at least from analyses where there is conflict with molecular data. These concerns, however, are generally unwarranted and excluding data is not a defensible strategy for dealing with problems that do exist. We emphasize the importance of empirical responses, such as collecting additional and diverse data and exploring taxa and data set interactions, rather than the implementation of a priori assumptions, to overcoming many of the concerns associated with combining morphological and molecular data. Numerous factors may create biases in both molecules and morphology. While these biases are prevalent enough to cause widespread incongruence, they highlight the importance of combining, rather than separating, data. Morphological data also offer distinct advantages over molecular data, such as the inclusion of fossil taxa, cost-effectiveness and presence of biases different from those in molecular data.

Animals↗
PubMed2002

Relative quality of different systematic datasets for cetartiodactyl mammals: assessments within a combined analysis framework.

High congruence, support, stability, resolution and decisiveness are seen as positive attributes by many systematists. Within a cladistic context, the consistency index, the retention index, branch support, data decisiveness, the number of nodes resolved in a strict consensus tree and the incongruence length difference are direct measures of these qualities. Phylogenetic analyses of 29 datasets for cetartiodactyl mammals show that for a particular character partition, these indices can vary radically in separate versus combined analysis of datasets. The quality of any single dataset is of little importance in comparison to a thorough sampling of the available character space.

Animals↗