TY - CHAP
T1 - Tangled trees
T2 - The challenge of inferring species trees from coalescent and noncoalescent genes
AU - Anderson, Christian N.K.
AU - Liu, Liang
AU - Pearl, Dennis
AU - Edwards, Scott V.
PY - 2012
Y1 - 2012
N2 - Phylogenies based on different genes can produce conflicting phylogenies; methods that resolve such ambiguities are becoming more popular, and offer a number of advantages for phylogenetic analysis. We review so-called species tree methods and the biological forces that can undermine them by violating important aspects of the underlying models. Such forces include horizontal gene transfer, gene duplication, and natural selection. We review ways of detecting loci influenced by such forces and offer suggestions for identifying or accommodating them. The way forward involves identifying outlier loci, as is done in population genetic analysis of neutral and selected loci, and removing them from further analysis, or developing more complex species tree models that can accommodate such loci.
AB - Phylogenies based on different genes can produce conflicting phylogenies; methods that resolve such ambiguities are becoming more popular, and offer a number of advantages for phylogenetic analysis. We review so-called species tree methods and the biological forces that can undermine them by violating important aspects of the underlying models. Such forces include horizontal gene transfer, gene duplication, and natural selection. We review ways of detecting loci influenced by such forces and offer suggestions for identifying or accommodating them. The way forward involves identifying outlier loci, as is done in population genetic analysis of neutral and selected loci, and removing them from further analysis, or developing more complex species tree models that can accommodate such loci.
UR - http://www.scopus.com/inward/record.url?scp=84860189879&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84860189879&partnerID=8YFLogxK
U2 - 10.1007/978-1-61779-585-5_1
DO - 10.1007/978-1-61779-585-5_1
M3 - Chapter
C2 - 22399453
AN - SCOPUS:84860189879
SN - 9781617795848
T3 - Methods in Molecular Biology
SP - 3
EP - 28
BT - Evolutionary Genomics
A2 - Anisimova, Maria
A2 - Anisimova, Maria
ER -