Systematics Section / ASPT
Edwards, Christine E. , Lefkowitz, David , Soltis, Douglas E. , Soltis, Pamela S. .
Combined phylogenetic analysis of heterozygous nuclear loci: an example using Conradina and related mints (Lamiaceae).
Although low-copy nuclear genes can be useful for elucidating phylogenetic relationships among closely related species because of their high substitution rates, a single locus alone may not contain enough information to resolve phylogenetic relationships. To increase resolution and support, multiple gene sequences from each individual are often concatenated into a single, multigene “sequence” for combined phylogenetic analysis. However, single- or low-copy nuclear genes are frequently heterozygous, complicating concatenation because each individual is represented by two alleles at a locus. We investigated methods of concatenation for combined analyses of multiple heterozygous nuclear genes in Conradina and related mints (Lamiaceae) using gene sequences from: 1) two copies of the GapC gene family that demonstrate moderate to high levels of heterozygosity, 2) ITS, and 3) plastid regions. We considered all available methods of concatenating data from more than one heterozygous nuclear gene, evaluated the utility of these methods, and used six approaches to combine our data matrices. The six concatenation methods produced congruent topologies in some regions of the tree; however, in other regions of the tree, topologies resulting from consensus and distance-based methods were generally much more resolved than the other concatenation approaches, probably because they ignore the conflict among the data sets caused by heterozygosity. If trees resulting from all concatenation methods agree, then any of the methods will yield an equally adequate representation of phylogenetic relationships. However, if topologies resulting from consensus and distance approaches are more resolved than the other methods, this is likely because consensus methods ignore conflict among data sets due to heterozygosity, and in these cases, the most suitable approach to represent this conflict is to use concatenation methods that allow for multiple placements of heterozygous individuals in a single tree and that cause nodes to collapse in the presence of conflict among the data matrices.
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1 - University of Florida, Department of Botany, Florida Museum of Natural History, P.O. Box 117800, Gainesville, Florida, 32611-7800, USA
2 - University of Florida, College of Medicine, Gainesville, Florida, 32601, USA
3 - University of Florida, Department of Botany, 220 Bartram Hall, P.O. Box 118526, Gainesville, Florida, 32611-8526, USA
4 - University of Florida, Florida Museum of Natural History, PO Box 117800, Gainesville, FL, 32611-7800, USA
combined phylogenetic analysis
Presentation Type: Oral Paper:Papers for Sections
Location: Stevens 2/Hilton
Date: Tuesday, July 10th, 2007
Time: 9:00 AM