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Methods and theory of phylogenetic inference

Doyle, Jeff J. [1].

Incongruence around the species level: Is the glass half full or half empty?.

For many years now, systematists have been aware of the gene tree/species tree issue, and it is often discussed as a potential problem or trotted out as a convenient ad hoc explanation for unexpected or unpalatable topologies. But is it really taken seriously? And how should it be dealt with? The acquisition of multiple molecular data sets brings the problem into sharper focus, pitting one gene tree against another, in contrast to the less tractable situation of a gene tree hypothesis in competition with a (species) tree hypothesized from multiple, putatively independent characters, or, more nebulously, an intuitive scheme based on taxonomy. Incongruence is expected to be a particular problem around the species level, where the recency of evolutionary events and the low levels of variation often preclude explanations that may be tenable for higher-level taxa with highly diverged sequences. At the same time, the fact that the events leading to incongruence did not take place tens of millions of years ago makes finding concrete biological explanations for incongruence seem within reach, and makes incongruent patterns a tantalizing "window on molecular evolution." In dealing with species complexes, the boundary between tokogenetic and phylogenetic relationships is often poorly developed, and there simply may be no "right" phylogenetic answers, or rather, as has been stated by various authors over the years, each conflicting gene tree answer reveals a different facet of evolutionary history. To expect a simple answer, represented by a dichotomizing combined analysis tree, is often unrealistic and is a recipe for frustration. The problems with species level incongruence will be illustrated with examples from ongoing work, particularly the A-genome diploid species complex of Glycine (Leguminosae).

1 - Cornell University, L.H. Bailey Hortorium, Department of Plant Biology, Ithaca, New York, 14853, U.S.A.

gene tree/species tree

Presentation Type: Symposium
Session: 31-2
Location: Alpine A (Snowbird Center)
Date: Tuesday, August 3rd, 2004
Time: 9:00 AM
Abstract ID:123

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