Population genetic diversity and structure are known to influence successful colonisation and establishment of a population in a novel habitat. However, our understanding of actual population genetic changes in the early stage of colonisation and detailed time-series of genetic changes during the establishment of a new population is still limited due to the difficulty of making long-term direct observations of a colonising population. Using a paleolimnological approach, we revealed the long-term genetic dynamics of an obligate parthenogenetic panarctic Daphnia pulex population during the early stage of colonisation and subsequent establishment in Lake Fukami-ike of Nagano, Japan. We collected diapausing eggs in ephippia of D. pulex from layers of sediment core samples (c. 370 cm long; dated 1662–2017) and then the mitochondrial DNA was sequenced using the markers designed for the NADH dehydrogenase 5 (ND5) gene and the control region. Daphnia pulex colonised and established a population in the early 2000s. Population genetic analysis showed that one colonising haplotype predominated in the population throughout the study period. Genetic diversity was consistently limited and there was no recovery of genetic diversity after colonisation. Clearly limited genetic diversity did not hamper population growth, possibly because phenotypic plasticity was used to cope with changes in predation pressure. Analysis using multivariate auto-regressive models showed that responses to environmental and ecological factors varied depending on the haplotype, which may have contributed to successful colonisation of the lake by the different haplotypes. The present results suggest that an obligate parthenogenetic population can establish in a new habitat and be maintained for generations even though it has limited genetic diversity. We found that two independent lineages (JPN1 and JPN2) successfully established and coexisted toward the end of the study period. Although limited genetic diversity did not impede colonisation success, how the later colonising JPN1 lineage has successfully invaded a population consisting solely of the early colonising JPN2 deserves future attention to understand the population genetic dynamics revealed in this study.
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