something about positive selection on amino acids substitutions

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• ?????????? ?????????? (distance-based methods),
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• ?????????? ???????? (parsimony-based methods)
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1 2 3 4 5
???? A 1 0 0 0 0
???? B 0 0 0 1 0
???? C 1 1 0 0 0
???? D 1 1 0 0 1
???? E 0 0 0 1 0
???? F 0 0 0 0 0
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• ?????????? ?????????? (distance-based methods),
  ?????????????
• ??????
• ??????, ???? ???????? ??????? (?????. ????)
• ?????????? ???????? (parsimony-based methods)
• ???? ??? ?????????? ??? ?????????? ??????
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• maximum likelihood (ML) ????????? ????????
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Models of nucleotide substitutions
Jukes-Cantor model
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Models of nucleotide substitutions
Jukes-Cantor model
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Models of nucleotide substitutions
Jukes-Cantor model
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Models of nucleotide substitutions
Jukes-Cantor model
Haubold and Wiehe 2006Introduction to
Computational Biology an Evolutionary
Approach p.176
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Models of nucleotide substitutions
Jukes-Cantor model
Kimura 2-parameter model
Haubold and Wiehe 2006Introduction to
Computational Biology an Evolutionary
Approach p.176
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Nikaido et al. PNAS 1999
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Aguinaldo et al. Nature 1997
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Aguinaldo et al. Nature 1997Wolf et al. 2004
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Aguinaldo et al. Nature 1997Wolf et al.
2004 Irimia et al. 2007
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Aguinaldo et al. Nature 1997Wolf et al.
2004 Irimia et al. 2007 Rogozin et al. 2007
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Aguinaldo et al. Nature 1997Wolf et al.
2004 Irimia et al. 2007 Rogozin et al. 2007
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Example of phylogenetic reconstructions mammals.
Phylogeny of mammals - red stars indicate clades
that are still ambiguous
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Nikaido et al. PNAS 1999
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W.F.Doolittle 2000Sci Am
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W.F.Doolittle 2000Sci Am
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2001Nature
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Mitochondrial genes are subject to evolutionarily
frequent horizontal transfer between distantly
related flowering plants. A phylogeny of 280
angiosperms is marked according to the presence
(red) or absence (blue) of rps2 (a) and rps11 (b)
in mitochondrial DNA. Blue and red bullets mark
inferred losses and regains, respectively, of
these genes. Names of taxa with gene regain are
shown in red lettering, selected taxa with gene
loss are in blue. There must be mechanisms for
the delivery of DNA between unrelated plants.
This is unusual for multicellular organisms.
Nature 424, 197-201, 2003.
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