Tokyo Inst Technol, Grad Sch Biosci & Biotechnol, Yokohama, Kanagawa 2268501, Japan; Univ Otago, Dept Geol, Dunedin, New Zealand; Chinese Acad Sci, Inst Hydrobiol, Wuhan 430072, Peoples R China; Inst Stat Math, Tokyo 1068569, Japan; NOAA, SW Fisheries Sci Ctr, La Jolla, CA 92037 USA; Univ Calif Berkeley, Museum Paleontol, Berkeley, CA 94720 USA
SINE (short interspersed element) insertion analysis elucidates contentious aspects in the phylogeny of toothed whales and dolphins (Odontoceti), especially river dolphins. Here, we characterize 25 informative SINEs inserted into unique genomic loci during evolution of odontocetes to construct a cladogram. and determine a total of 2.8 kb per taxon of the flanking sequences of these SINE loci to estimate divergence times among lineages. We demonstrate that: (i) Odontocetes are monophyletic; (ii) Ganges River dolphins, beaked whales, and ocean dolphins diverged (in this order) after sperm whales; (iii) three other river dolphin taxa, namely the Amazon, La Plata, and Yangtze river dolphins, form a monophyletic group with Yangtze River dolphins being the most basal; and (iv) the rapid radiation of extant cetacean lineages occurred some 28-33 million years B.P., in strong accord with the fossil record. The combination of SINE and flanking sequence analysis suggests a topology and set of divergence times for odontocete relationships, offering alternative explanations for several long-standing problems in cetacean evolution.
Masato Nikaido; Fumio Matsuno; Healy Hamilton; Robert L. Brownell, Jr.; Ying Cao; Wang Ding; Zhu Zuoyan; Andrew M. Shedlock; R. Ewan Fordyce; Masami Hasegawa and Norihiro Okada.Retroposon analysis of major cetacean lineages: The monophyly of toothed whales and the paraphyly of river dolphins,PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA,2001,98(13):7384-7389