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Assessing substitution patterns, rates and homoplasy at HVRI of Steller sea lions, Eumetopias jubatus
Author(s) -
PHILLIPS C. D.,
TRUJILLO R. G.,
GELATT T. S.,
SMOLEN M. J.,
MATSON C. W.,
HONEYCUTT R. L.,
PATTON J. C.,
BICKHAM J. W.
Publication year - 2009
Publication title -
molecular ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.619
H-Index - 225
eISSN - 1365-294X
pISSN - 0962-1083
DOI - 10.1111/j.1365-294x.2009.04283.x
Subject(s) - biology , biological dispersal , phylogeography , range (aeronautics) , evolutionary biology , population , genetic variation , mtdna control region , zoology , haplotype , phylogenetics , genetics , allele , gene , demography , materials science , sociology , composite material
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.