This study investigates the population structure of the Tucunaré (Cichla pleiozona) in the Bolivian Amazon (Upper Madera) by using nuclear (EPIC-PCR, 67 individuals) and mitochondrial (Control Region, 41 published and 76 new sequences) DNA analyses, in relation with ecological (water quality: muddy, clear and mix) and geographic factors. Our analyses of both markers showed the highest diversity in clear waters (Yata, Middle and Upper Iténez), and the existence of two populations in muddy waters (Sécure and Ichilo) and one in mix waters (Manuripi). On the other hand, mitochondrial analyses identified three populations in clear waters where nuclear analyses identified a panmictic population. The highest diversity observed in the Yata-Iténez system suggests that an aquatic refuge occurred during the past in this area. The possible explanations for the observed discrepancy between nuclear and mitochondrial markers are discussed, and a sex-biased dispersal seems to be the most plausible hypothesis in the light of the available information and field observations.
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