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Conflict amongst chloroplast DNA sequences obscures the phylogeny of a group of Aspenium ferns


Shepherd, LD and Holland, BR and Perrie, LR, Conflict amongst chloroplast DNA sequences obscures the phylogeny of a group of Aspenium ferns , Molecular Phylogenetics and Evolution, 48, (1) pp. 176-187. ISSN 1055-7903 (2008) [Refereed Article]

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DOI: doi:10.1016/j.ympev.2008.02.023


A previous study of the relationships amongst three subgroups of the Austral Asplenium ferns found conflicting signal between the two chloroplast loci investigated. Because organelle genomes like those of chloroplasts and mitochondria are thought to be non-recombining, with a single evolutionary history, we sequenced four additional chloroplast loci with the expectation that this would resolve these relationships. Instead, the conflict was only magnified. Although tree-building analyses favoured one of the three possible trees, one of the alternative trees actually had one more supporting site (six versus five) and received greater support in spectral and neighbor-net analyses. Simulations suggested that chance alone was unlikely to produce strong support for two of the possible trees and none for the third. Likelihood permutation tests indicated that the concatenated chloroplast sequence data appeared to have experienced recombination. However, recombination between the chloroplast genomes of different species would be highly atypical, and corollary supporting observations, like chloroplast heteroplasmy, are lacking. Wider taxon sampling clarified the composition of the Austral group, but the conflicting signal meant analyses (e.g., morphological evolution, biogeographic) conditional on a well-supported phylogeny could not be performed.

Item Details

Item Type:Refereed Article
Keywords:Asplenium; Chloroplast DNA; Conflict; Homoplasy; Recombination
Research Division:Biological Sciences
Research Group:Evolutionary biology
Research Field:Phylogeny and comparative analysis
Objective Division:Expanding Knowledge
Objective Group:Expanding knowledge
Objective Field:Expanding knowledge in the biological sciences
UTAS Author:Holland, BR (Professor Barbara Holland)
ID Code:62984
Year Published:2008
Web of Science® Times Cited:20
Deposited By:Mathematics
Deposited On:2010-03-31
Last Modified:2010-04-30

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