MBE Advance Access published online on April 2, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn074
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Research Article |
Parallel Rate Heterogeneity in Chloroplast and Mitochondrial Genomes of Brazil Nut Trees (Lecythidaceae) is Consistent with Lineage Effects.
* Department of Biology, Georgetown University
Biological Dynamics of Forest Fragments Project, National Institute for Research in the Amazon, Manaus, Brazil
Corresponding author: David F. Soria-Hernanz, e-mail: dsoria{at}ngs.org
Received for publication January 11, 2008. Accepted for publication March 11, 2008.
We investigated whether relative rates of divergence were correlated between the mitochondrial and chloroplast genomes as expected under lineage effects or were genome-specific as expected with locus-specific effects. Five mitochondrial non-coding regions (nad1B_C, nad4exon1_2, nad7exon2_3, nad7exon3_4, and rps14-cob) for 21 samples from Lecythidaceae were sequenced. Three chloroplast regions (rpl20-5’rps12, trnS-trnG and psbA-trnH) were sequenced to expand the taxa in an existing data set. Absolute rates of nucleotide and indel change were thirteen times faster in the chloroplast genome than in the mitochondrial genome. Similar indel length frequency distributions for both organelles suggested that common mechanisms were responsible for generating indels. Molecular clock tests applied to phylogenetic trees estimated from mitochondrial and chloroplast sequences revealed global rate heterogeneity of nucleotide substitution. Maximum-likelihood and Tajima's 1D relative rates tests show that Lecythis zabucajo exhibited a rate acceleration for both the mitochondrial and chloroplast sequences. While Escheweilera romeu-cardosoi showed a significant rate slowdown for chloroplast sequences, the mitochondrial sequences for three Escheweilera taxa showed evidence for a rate slowdown only when compared to Lecythis zabucajo. Significant rate heterogeneity was also observed for indel changes in the mitochondrial genome but not for the chloroplast. The lack of mitochondrial nucleotide changes for some taxa as well as chloroplast indel homoplasy may have limited the power of relative rate tests to detect rate variation. Relative ratio tests consistently indicated rate proportionality among branch lengths between the mitochondrial and chloroplast phylogenetic trees. The relative ratio tests showed that taxa possessing rate heterogeneity had parallel relative divergence rates in both mitochondrial and chloroplast sequences as expected under lineage effects. A neutral replication-dependent model of rate heterogeneity for both nucleotide and indel changes provides a simple explanation for common patterns of rate heterogeneity across the two organelle genomes in Lecythidaceae. The lineage effects observed here were uncoupled from annual/perennial habit since all the species from this study are perennial.
Key Words: chloroplast DNA • lineage effect • mitochondrial DNA • rate heterogeneity • relative rate test • relative ratio test
1 Present address: The Genographic Project, National Geographic Society, Washington, DC
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