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, forma 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.
Nikaido, M., Graduate School of Bioscience and Biotechlogy, Tokyo Institute of Techlogy, 4259 Nagatsuta-cho, Yokohama, Kanagawa 226-8501, Japan; Matsuno, F., Graduate School of Bioscience and Biotechlogy, Tokyo Institute of Techlogy, 4259 Nagatsuta-cho, Yokohama, Kanagawa 226-8501, Japan; Hamilton, H., Museum of Paleontology, University of California, Berkeley, CA 94720, United States; Brownell Jr., R.L., NOAA, Southwest Fisheries Science Center, San Diego, CA 92037, United States; Cao, Y., Graduate School of Bioscience and Biotechlogy, Tokyo Institute of Techlogy, 4259 Nagatsuta-cho, Yokohama, Kanagawa 226-8501, Japan, Institute of Statistical Mathematics, Tokyo 106-8569, Japan; Ding, W., Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; Zuoyan, Z., Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; Shedlock, A.M., Graduate School of Bioscience and Biotechlogy, Tokyo Institute of Techlogy, 4259 Nagatsuta-cho, Yokohama, Kanagawa 226-8501, Japan, Institute of Statistical Mathematics, Tokyo 106-8569, Japan; Fordyce, R.E., Department of Geology, University of Otago, P.O. Box 56, Dunedin, New Zealand; Hasegawa, M., Institute of Statistical Mathematics, Tokyo 106-8569, Japan; Okada, R., Graduate School of Bioscience and Biotechlogy, Tokyo Institute of Techlogy, 4259 Nagatsuta-cho, Yokohama, Kanagawa 226-8501, Japan
Recommended Citation:
Nikaido M.,Matsuno F.,Hamilton H.,et al. Retroposon analysis of major cetacean lineages: The monophyly of toothed whales and the paraphyly of river dolphins[J]. Proceedings of the National Academy of Sciences of the United States of America,2001-01-01,98(13)