کد مقاله کد نشریه سال انتشار مقاله انگلیسی نسخه تمام متن
4498169 1318967 2009 6 صفحه PDF دانلود رایگان
عنوان انگلیسی مقاله ISI
A basic limitation on inferring phylogenies by pairwise sequence comparisons
موضوعات مرتبط
علوم زیستی و بیوفناوری علوم کشاورزی و بیولوژیک علوم کشاورزی و بیولوژیک (عمومی)
پیش نمایش صفحه اول مقاله
A basic limitation on inferring phylogenies by pairwise sequence comparisons
چکیده انگلیسی
Distance-based approaches in phylogenetics such as Neighbor-Joining are a fast and popular approach for building trees. These methods take pairs of sequences, and from them construct a value that, in expectation, is additive under a stochastic model of site substitution. Most models assume a distribution of rates across sites, often based on a gamma distribution. Provided the (shape) parameter of this distribution is known, the method can correctly reconstruct the tree. However, if the shape parameter is not known then we show that topologically different trees, with different shape parameters and associated positive branch lengths, can lead to exactly matching distributions on pairwise site patterns between all pairs of taxa. Thus, one could not distinguish between the two trees using pairs of sequences without some prior knowledge of the shape parameter. More surprisingly, this can happen for any choice of distinct shape parameters on the two trees, and thus the result is not peculiar to a particular or contrived selection of the shape parameters. On a positive note, we point out known conditions where identifiability can be restored (namely, when the branch lengths are clocklike, or if methods such as maximum likelihood are used).
ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Journal of Theoretical Biology - Volume 256, Issue 3, 7 February 2009, Pages 467-472
نویسندگان
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