Molecular Biology and Evolution, Vol 5, 568-583, Copyright © 1988 by Society for Molecular Biology and Evolution
P Pamilo and M Nei
It is well known that a phylogenetic tree (gene tree) constructed from DNA
sequences for a genetic locus does not necessarily agree with the tree that
represents the actual evolutionary pathway of the species involved (species
tree). One of the important factors that cause this difference is genetic
polymorphism in the ancestral species. Under the assumption of neutral
mutations, this problem can be studied by evaluating the probability (P)
that a gene tree has the same topology as that of the species tree. When
one gene (allele) is used from each of the species involved, the
probability can be expressed as a simple function of Ti = ti/(2N), where ti
is the evolutionary time measured in generations for the ith internodal
branch of the species tree and N is the effective population size. When any
of the Ti's is less than 1, the probability P becomes considerably less
than 1.0. This probability cannot be substantially increased by increasing
the number of alleles sampled from a locus. To increase the probability,
one has to use DNA sequences from many different loci that have evolved
independently of each other.
ORIGINAL ARTICLE
Relationships between gene trees and species trees
Center for Demographic and Population Genetics, University of Texas Health Science Center, Houston 77225.
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|
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|
|
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|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
V. Albert, S. Williams, and M. Chase Carnivorous plants: phylogeny and structural evolution Science, September 11, 1992; 257(5076): 1491 - 1495. [Abstract] [PDF]
|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
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|
|
|
|
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|
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|
|
|
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