Submitted to: Systematic Biology
Publication Type: Peer reviewed journal
Publication Acceptance Date: 12/22/2004
Publication Date: 6/3/2005
Citation: Pfeil, B., Schlueter, J., Shoemaker, R.C., Doyle, J. 2005. Placing palepolyploidy in relation to taxon divergence: a phylogenetic analysis in legumes using 39 gene families. Systematic Biology. 54(3):441-454. Interpretive Summary: Many plants have undergone a complete duplication of all hereditary material at sometime in their past. Knowledge of this event, if it took place, is important to geneticists who are trying to make genetic comparisons. It is difficult to determine if a duplication event ocurred using small, individual pieces of DNA. In this study the authors used 39 families of genes in soybean, and compared the hereditary code of each member of the family to other members of the family and to related genes in another plant. They showed that the two plants, although not seemingly related, shared a common duplication event at some time in their past. These findings demonstrated that previous methods used to estimate duplication of genes may be misleading. This information is important to geneticists and evolutionary biologists who study relatedness of diverse organisms.
Technical Abstract: Young polyploid events are easily diagnosable by various methods, but older polyploid events become increasingly difficult to identify as chromosomal rearrangements, tandem gene or partial chromosome duplications, changes in substitution rates among duplicated genes and inter-locus interactions complicate the means of inferring past genetic events. Genomic data have provided valuable information about the polyploid history of numerous species, but fail to show whether related species, each with a polyploid past, share a particular polyploid event. A phylogenetic approach, however, provides a powerful method to determine this. Although many processes can affect individual gene trees and potentially mislead investigators, the processes that may affect any one gene most likely will not affect all genes, and almost certainly will not affect genes in the same way. Thus a multigene approach, which combines the large-scale aspect of genomics with the resolution of phylogenetics, has the power to overcome these difficulties and allow us to infer genomic events further into the past than has been previously possible. We present a case study using 39 gene families with three or four members in Glycine max and the putative orthologues in Medicago truncatula to show that these taxa, along with approximately 7,000 other legume species from the same clade, actually share an ancient polyploid event. Individual gene trees were also subjected to analysis of the synonymous rates between sequence pairs. This analysis revealed that some of the gene trees can be misleading despite having topological support for either of the two hypotheses considered here. Only c. 41% of genes examined support either hypothesis, which strongly suggests that single-gene approaches may be insufficient when studying ancient events with nuclear DNA.