MBE Advance Access originally published online on July 31, 2009
Molecular Biology and Evolution 2009 26(11):2427-2440; doi:10.1093/molbev/msp169
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Research Articles |
Big and Slow: Phylogenetic Estimates of Molecular Evolution in Baleen Whales (Suborder Mysticeti)
* Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University
School of Biological Sciences, Auckland University, Auckland, New Zealand
Facultad de Ciencias, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, México, Mexico
Department of Biological Sciences, Hopkins Marine Station, Stanford University, Pacific Grove, CA
E-mail: jacksonjennifera{at}gmail.com.
Accepted for publication July 4, 2009.
Baleen whales are the largest animals that have ever lived. To develop an improved estimation of substitution rate for nuclear and mitochondrial DNA for this taxon, we implemented a relaxed-clock phylogenetic approach using three fossil calibration dates: the divergence between odontocetes and mysticetes 
34 million years ago (Ma), between the balaenids and balaenopterids 28 Ma, and the time to most recent common ancestor within the Balaenopteridae 12 Ma. We examined seven mitochondrial genomes, a large number of mitochondrial control region sequences (219 haplotypes for 465 bp) and nine nuclear introns representing five species of whales, within which multiple species-specific alleles were sequenced to account for within-species diversity (1–15 for each locus). The total data set represents >1.65 Mbp of mitogenome and nuclear genomic sequence. The estimated substitution rate for the humpback whale control region (3.9%/million years, My) was higher than previous estimates for baleen whales but slow relative to other mammal species with similar generation times (e.g., human–chimp mean rate > 20%/My). The mitogenomic third codon position rate was also slow relative to other mammals (mean estimate 1%/My compared with a mammalian average of 9.8%/My for the cytochrome b gene). The mean nuclear genomic substitution rate (0.05%/My) was substantially slower than average synonymous estimates for other mammals (0.21–0.37%/My across a range of studies). The nuclear and mitogenome rate estimates for baleen whales were thus roughly consistent with an 8- to 10-fold slowing due to a combination of large body size and long generation times. Surprisingly, despite the large data set of nuclear intron sequences, there was only weak and conflicting support for alternate hypotheses about the phylogeny of balaenopterid whales, suggesting that interspecies introgressions or a rapid radiation has obscured species relationships in the nuclear genome.
Key Words: mutation rate • genomic • mitochondrial • whale • cetacean
Koichiro Tamura, Associate Editor