Assessing substitution patterns, rates and homoplasy at HVRI of Steller sea lions, Eumetopias jubatus


  • Caleb Phillips' research interests include mtDNA molecular evolution, phylogeography, speciation, hybridization, and systematics. Robert Trujillo's research interests focus on molecular systematics, phylogeography, and population genetics of mammals. Tom Gelatt and his research group are responsible for investigating various questions pertaining to the declining populations of Steller sea lions contributing a wide assortment of projects involving animal foraging behaviors, demographics, and abundance estimation to collectively address these questions and provide fisheries management direction. Mike Smolen is interested in conservation and Alaskan community involvement in regional science studies. Cole Matson's research focuses on aquatic and evolutionary toxicology. He also has additional interests in phylogeography and conservation genetics. Rodney Honeycutt is a University Professor, whose research interests include population genetics, molecular evolution, and molecular phylogenetics. John Patton's major interests involve the processes of genomic differentiation among intraspecific and interspecific populations and how reticulate evolution affects these processes of differentiation. To achieve this in mammals his investigations focus on the evolutionary patterns of clonally inherited mtDNA, Y, and effectively haplodiploid X chromosomes and the subsequent contrasts of those patterns with patterns observed among autosomally inherited genes both above and below the level of species. John Bickham's research interests focus on genetic mutations and how they are produced and transmitted in individuals, populations, species and the evolutionary processes that affect genetic change. His current sponsored research projects include population genetics of Steller sea lions and bowhead whales, biodiversity studies in bats and ecotoxicological studies in contaminated environments in Azerbaijan. This paper is one in a series resulting from a long-term study (since 1992) on the population genetics and systematics of Steller sea lions sponsored mainly by NMFS. The genetic studies are part of an overall program studying the population trends, basic biology, and conservation status of this endangered species.

Caleb D. Phillips, Fax: 765-496-1369;


Despite the widely recognized incidence of homoplasy characterizing this region, the hypervariable region I (HVRI) of the mitochondrial control region is one of the most frequently used genetic markers for population genetic and phylogeographic studies. We present an evolutionary analysis of HVRI and cytochrome b sequences from a range-wide survey of 1031 Steller sea lions, Eumetopias jubatus, to quantify homoplasy and substitution rate at HVRI. Variation in HVRI was distributed across 41 variable sites in the 238-bp segment examined. All variants at HVR1 were found to be transitions. However, our analyses suggest that a minimum of 101 changes have actually occurred within HVRI with as many as 18 substitutions occurring at a single site. By including this hidden variation into our analyses, several instances of apparent long-range dispersal were resolved to be homoplasies and 8.5–12% of observed HVRI haplotypes were found to have geographic distributions descriptive of convergent molecular evolution rather than identity by descent. We estimate the rate of substitution at HVRI in Steller sea lions to be ∼24 times that of cytochrome b with an absolute rate of HVRI substitution estimated at 27.45% per million years. These findings have direct implications regarding the utility of HVRI data to generate a variety of evolutionary genetic hypotheses.