期刊
MOLECULAR PHYLOGENETICS AND EVOLUTION
卷 98, 期 -, 页码 176-183出版社
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.ympev.2016.01.022
关键词
Algae; Plastid; Phylogenetic conflict; Codon bias
资金
- NSF [DEB-1036448, DEB-1354146]
- Division Of Environmental Biology
- Direct For Biological Sciences [1354146, 1036448] Funding Source: National Science Foundation
Chloroplast sequence data are widely used to infer phylogenies of plants and algae. With the increasing availability of complete chloroplast genome sequences, the opportunity arises to resolve ancient divergences that were heretofore problematic. On the flip side, properly analyzing large multi-gene data sets can be a major challenge, as these data may be riddled with systematic biases and conflicting signals. Our study contributes new data from nine complete and four fragmentary chloroplast genome sequences across the green algal order Sphaeropleales. Our phylogenetic analyses of a 56-gene data set show that analyzing these data on a nucleotide level yields a well-supported phylogeny - yet one that is quite different from a corresponding amino acid analysis. We offer some possible explanations for this conflict through a range of analyses of modified data sets. In addition, we characterize the newly sequenced genomes in terms of their structure and content, thereby further contributing to the knowledge of chloroplast genome evolution. (C) 2016 Elsevier Inc. All rights reserved.
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