Author:
Yamamoto Yuki,Takanashi Airi,Yokosawa Yuji,Ikeda Minoru
Abstract
AbstractThe hypervariable region (HVR) in the control region of the mitochondrial DNA has frequently been used for population genetics and phylogeographic studies because of its highly variable nature. Although the HVR is beneficial for evaluating recent evolutionary history, including population demography, recent studies have implied the incidence of homoplasy in this region. To assess the accuracy of relying solely on the HVR for population genetics studies, molecular evolutionary analysis of the HVR, NADH-dehydrogenase subunit 2 (ND2), and cytochrome b genes were performed using 120 individuals of marbled flounder Pseudopleuronectes yokohamae. The HVR exhibited the highest genetic variability among the three regions, with sites showing high site-specific substitution rates. Considering the reticulate haplotype network structure and evolutionary linkages between regions, homoplastic mutations were indicated in the HVR in addition to ND2, underestimating genetic diversity. We found that homoplasy was less likely to affect coalescent-based demographic inferences in the population; however, there is still a potential risk of misinterpretation of population demography when solely using the HVR owing to its hypervariable nature. Collectively, we suggest analyzing other regions in addition to the HVR in fish population genetic research to improve accuracy and eliminate biases caused by homoplasy.
Funder
Japan Society for the Promotion of Science
Publisher
Springer Science and Business Media LLC
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