Retroposon analysis of major cetacean lineages: the monophyly of toothed whales and the paraphyly of river dolphins.
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.
Nikaido
M
M
Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Yokohama, Kanagawa 226-8501, Japan.
Matsuno
F
F
Hamilton
H
H
Brownell
R L
RL
Cao
Y
Y
Ding
W
W
Zuoyan
Z
Z
Shedlock
A M
AM
Fordyce
R E
RE
Hasegawa
M
M
Okada
N
N
D000818:Animals; D001483:Base Sequence; D002591:Cetacea / Q000145:classification* / Q000235:genetics*; D004289:Dolphins / Q000145:classification* / Q000235:genetics*; D019143:Evolution, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D018626:Retroelements; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D020086:Short Interspersed Nucleotide Elements / Q000235:genetics
D018626:Retroelements