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

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 approximately 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.

Contrasting patterns of genetic diversity at three different genetic markers in a marine mammal metapopulation.

Many studies use genetic markers to explore population structure and variability within species. However, only a minority use more than one type of marker and, despite increasing evidence of a link between heterozygosity and individual fitness, few ask whether diversity correlates with population trajectory. To address these issues, we analysed data from the Steller's sea lion, Eumetiopias jubatus, where three stocks are distributed over a vast geographical range and where both genetic samples and detailed demographic data have been collected from many diverse breeding colonies. To previously published mitochondrial DNA (mtDNA) and microsatellite data sets, we have added new data for amplified fragment length polymorphism (AFLP) markers, comprising 238 loci scored in 285 sea lions sampled from 23 natal rookeries. Genotypic diversity was low relative to most vertebrates, with only 37 loci (15.5%) being polymorphic. Moreover, contrasting geographical patterns of genetic diversity were found at the three markers, with Nei's gene diversity tending to be higher for AFLPs and microsatellites in rookeries of the western and Asian stocks, while the highest mtDNA values were found in the eastern stock. Overall, and despite strongly contrasting demographic histories, after applying phylogenetic correction we found little correlation between genetic diversity and either colony size or demography. In contrast, we were able to show a highly significant positive relationship between AFLP diversity and current population size across a range of pinniped species, even though equivalent analyses did not reveal significant trends for either microsatellites or mtDNA.

Fetus in fetu in a harbor seal (Phoca vitulina richardi): histopathologic, genetic, and toxicologic analysis.

A young harbor seal (Phoca vitulina richardi), stranded on the coast of California, was found to have a 20-cm-diameter cranial cervical mass. Surgical excision revealed the subcutaneous mass to be covered in haired skin with multiple glabrous areas and structures resembling a jaw with tooth buds, eyelids, and a tail. The mass deformed the host pup's skull. Histologic examination revealed a complete vertebra in the tail, teeth in the jaw, and areas resembling tongue and larynx. Class 1 MHC sequences amplified by polymerase chain reaction from the mass and the host twin were identical. The mass was diagnosed as a fetus in fetu, a rare congenital anomaly in which 1 conjoined twin is completely enclosed in the body of the other twin. The host pup died, and no additional defects were found; however, blubber levels of persistent organic pollutants were high. The cause of the congenital anomaly in this pup is uncertain.