Correlation of functional domains and rates of nucleotide substitution in cytochrome b

被引:103
作者
Griffiths, CS
机构
[1] Department of Ornithology, American Museum of Natural History, New York
基金
美国国家科学基金会;
关键词
D O I
10.1006/mpev.1997.0404
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Distinguishing noise from signal presents a problem when DNA sequences are used for phylogeny reconstruction. Multiple substitutions at sites are a primary cause of noise and this is compounded by variation in substitution rates among sites. For protein-coding genes, one method used to determine if data are noisy is to assess levels of saturation of substitutions by codon position. However, this procedure may not be a fine enough filter for assessing noise. Variation in substitution rates may also be caused by constraints on change imposed by the function of the protein product. Using a structural model of the cytochrome b protein as a template, I divided cyt b sequence data for species within the avian family Falconidae (falcons and caracaras) into three functional domains. Saturation of substitutions of sequences within these regions was assessed graphically. This qualitative determination of saturation was then used to differentially weight phylogenetic analysis, resulting in an hypothesis congruent with existing cladistic analyses and traditional morphology. These results demonstrate that saturation of substitutions is correlated with functional regions of cytochrome b and that using this information improves phylogenetic inference. (C) 1997 Academic Press.
引用
收藏
页码:352 / 365
页数:14
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