robust time estimation reconciles views of the antiquity of placental mammals健壮的时间估计和解的古代胎盘类哺乳动物的观点.pdfVIP

Robust Time Estimation Reconciles Views of the Antiquity of Placental Mammals 1 2 2,3 1 1 1 1 Yasuhiro Kitazoe *, Hirohisa Kishino , Peter J. Waddell , Noriaki Nakajima , Takahisa Okabayashi , Teruaki Watabe , Yoshiyasu Okuhara 1 Center of Medical Information Science, Kochi Medical School, Nankoku, Kochi, Japan, 2 Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan, 3 South Carolina Cancer Center (SCCC), University of South Carolina, Columbia, South Carolina, United States of America Background. Molecular studies have reported divergence times of modern placental orders long before the Cretaceous– Tertiary boundary and far older than paleontological data. However, this discrepancy may not be real, but rather appear because of the violation of implicit assumptions in the estimation procedures, such as non-gradual change of evolutionary rate and failure to correct for convergent evolution. Methodology/Principal Findings. New procedures for divergence-time estimation robust to abrupt changes in the rate of molecular evolution are described. We used a variant of the multidimensional vector space (MVS) procedure to take account of possible convergent evolution. Numerical simulations of abrupt rate change and convergent evolution showed good performance of the new procedures in contrast to current methods. Application to complete mitochondrial genomes identified marked rate accelerations and decelerations, which are not obtained with current methods. The root of placental mammals is estimated to be ,18 million years more recent than when assuming a log Brownian motion model. Correcting the pairwise distances for convergent evolution using MVS lo