Rooting the eutherian tree: the power and pitfalls of phylogenomics (2007)
Nishihara, Hidenori, Okada, Norihiro, Hasegawa, Masami
Abstract Background Ongoing genome sequencing projects have led to a phylogenetic approach based on genome-scale data (phylogenomics), which is beginning to shed light on longstanding unresolved...
Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions
Nishihara, Hidenori, Hasegawa, Masami, Okada, Norihiro
Despite the recent large-scale efforts dedicated to comprehensive phylogenetic analyses using mitochondrial and nuclear DNA sequences, several relationships among mammalian orders remain...
Functional noncoding sequences derived from SINEs in the mammalian genome
Nishihara, Hidenori, Smit, Arian F.A., Okada, Norihiro
Recent comparative analyses of mammalian sequences have revealed that a large number of nonprotein-coding genomic regions are under strong selective constraint. Here, we report that some of these...
Rooting the eutherian tree: the power and pitfalls of phylogenomics
Nishihara, Hidenori, Okada, Norihiro, Hasegawa, Masami
In an attempt to root the eutherian tree using genome-scale data with the maximum likelihood method, a concatenate analysis supports a putatively wrong tree, whereas separate analyses of different...