FUNCTIONAL CONSTRAINTS AND RBCL EVIDENCE FOR LAND PLANT PHYLOGENY
FUNCTIONAL CONSTRAINTS AND RBCL EVIDENCE FOR LAND PLANT PHYLOGENY
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DOI：
10.2307/2399902
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发表时间：
1994-01-01
影响因子：
1.9
通讯作者：
NIXON, KC
中科院分区：
文献类型：
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作者：
ALBERT, VA;BACKLUND, A;NIXON, KC
尽管真核生物基因组中“功能性”DNA的比例存在争议，但大多数为系统发育目的收集的序列无疑是功能性的。例如，核糖体rna的变异模式可能受到强烈限制，因为它们在蛋白质翻译中的结构和催化作用，而在蛋白质编码基因中，由于蛋白质本身的功能。尽管这些担忧看似显而易见，但生产基因树的工人通常会忽略它们。我们研究了陆生植物rbcL序列的功能限制程度。rbcL序列的变化不仅具有时钟规律，而且基于核苷酸的进化图表明，内部分支上大约97.5%的密码子变化是功能中性的（即同义或功能不稳定）。从这个角度来看，rbcL的进化似乎受到功能的强烈约束。将核苷酸数据转换为特殊的字符串识别，足以改变单位字符的大小，以突出显示可能或可能不受功能约束的保守信息的“块”。同时对所有可用证据的分支分析将突出一致信息的比例，尽管所分析的字符之间存在不同的功能约束。我们结合Nixon等人的种子植物数据，使用不同形式的相同rbcL证据（即核苷酸、序列或氨基酸）来证明这种方法的强度。
Although the proportion of ''functional'' DNA in eukaryotic genomes is both debatable and subject to definition, most sequences gathered for phylogenetic purposes are indisputably functional. For example, patterns of variation are likely to be strongly constrained in ribosomal RNAs because of their structural and catalytic roles in protein translation, and in protein-coding genes, because of protein function itself. Although seemingly obvious, these concerns are usually ignored by workers producing gene trees. We have examined the extent of functional constraints in land-plant rbcL sequences. Not only do rbcL sequences appear to change with essentially clocklike regularity, but nucleotide-based cladograms imply that approximately 97.5% of codon changes on internal branches are functionally neutral (i.e., synonymous or functionally labile). From this perspective, rbcL evolution appears to be strongly constrained by function. Transforming nucleotide data into ad hoc string recognitions alters the size of the unit character sufficiently to highlight ''blocks'' of conservative information that may or may not be functionally constrained. Simultaneous cladistic analysis of all available evidence will highlight the proportion of congruent information, despite diverse functional constraints among the characters analyzed. We demonstrate the strength of this approach using different forms of the same rbcL evidence (i.e., nucleotides, strings, or amino acids) in combination with the seed-plant data of Nixon et al.