Abstract Asexual organisms are ubiquitous. While being members of a single species with the same ecological requirements, multiple asexual genotypes within a species are often found in a single habitat. Niche partitioning in time and space among genotypes has been proposed to explain this phenomenon. However, it is not clear whether these different genotypes co‐occur in the long term. Therefore, we examined the population dynamics of two asexual Daphnia cf. pulex genotypes (JPN1 and JPN2) over 9 years in a small mountain lake. These two genotypes consistently occurred in the same seasons and layers, suggesting that niche partitioning cannot explain their long‐term co‐occurrence. The abundance of JPN1 was typically higher in most years. However, the abundance of dormant eggs in lake sediments was at the same level between the genotypes. Results of a laboratory experiment showed that JPN1 competitively excluded JPN2. However, many JPN2 individuals produced dormant eggs before JPN1 competitively excluded them from the experiment. Furthermore, the competitively inferior JPN2 produced dormant eggs abundantly in the medium containing a crowding cue from JPN1 while no such trend was observed for JPN1. These results showed that a competitively inferior asexual genotype could maintain a population with a competitively superior genotype for a long period of time because it had the ability to detect an increase in competitors and produce dormant eggs each year before being competitively eliminated. Based on these results, we suggest that the variation in genotype‐specific response in dormant egg production to environmental change plays a key role in the long‐term co‐occurrence of different asexual genotypes in single habitats. Read the free Plain Language Summary for this article on the Journal blog.
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