the biofixer

Not just another genome

” Sequence analysis of the Daphnia pulex genome holds some surprises that could not have been anticipated from what was learned so far from other arthropod genomes. It establishes Daphnia as an eco-genetical model organism par excellence.”

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Genome of an aquatic sensor

               In a typical lake, Daphnia lives in paradise with food in the form of algae swimming around it ready to be collected at will. But no paradise lasts for ever. As the Daphnia population grows, algae become increasingly rare to the point of almost complete disappearance, leading to a short phase in the yearly cycle of a lake in which the water becomes crystal clear. Daphnia itself increasingly becomes a victim of predators during the yearly cycle and, although it starts to develop defenses, its population shrinks such that the algae can become more abundant again. The nutrient flux that is involved in this cycle is enormous and drives the whole ecology of the lake. But how can a genome sequence help to learn more about this ecology? The Daphnia genome turns out to hold a large number of genes which were previously not known and which, excitingly, are likely to have a specific role in the interaction with its environment. The Daphnia genome may thus become a Rosetta stone for studying the genetic repertoire of fresh water ecology

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Life cycle plasticity may facilitate rapid evolution

             Why is Daphnia so particularly amenable to developing an eco-responsive gene repertoire? On the one hand it is known that positive selection is much more efficient in large populations, since even genes or alleles that provide only a very small advantage are retained in the population rather than being lost by drift. However, large population sizes are also found in the insects for which full genome sequences are available - and they show no indication of a particularly strong genomic response to the environment. The explanation may lie with some additional peculiarities of population genetics shown by Daphnia.                        

              It can switch between parthenogenetic and sexual reproduction and it can produce resting stages that can survive for decades. Since parthenogenetic reproduction is numerically twice as efficient as sexual reproduction, Daphnia takes advantage of this in spring when a particularly fast population expansion is possible. This leads to a rapid amplification of clones that may have only a minimal advantage over their conspecifics. Of course, once the environment changes, the advantage of such clones may falter quickly, but this is the point where they can go into a sexual cycle and can produce special eggs that are protected by a cuticular structure that allows them to survive in the mud. Thus, all lakes harbor a genetic reservoir of resting eggs derived from animals that had a particular advantage at a previous time. Genes or alleles that were once successful can thus be preserved, even if the environmental conditions are temporarily changed. An explicit evolutionary theory that models the long-term adaptive consequences of such complex life cycles is still missing but, at least intuitively, it would seem that this adds to the evolutionary dynamics that have led to the special gene repertoire of Daphnia.

              Because of these peculiarities, Daphnia should now also become a prime model for studying the evolution and the role of sex. One of the companion papers has indeed already specifically addressed such issues by looking at the evolutionary dynamics of transposons in Daphnia [8]. These authors identified the major transposon families in the Daphnia genome and found active copies for most of them. Six of these were then studied in lines where sex was either promoted or inhibited. The data indicate that sexual reproduction is indeed a major factor to keep the elements under control. This effect could at least partially compensate for the short-term cost of sex and thus explain why sexual reproduction is maintained. Intriguingly, a previous study had suggested that sexual and parthenogenetic reproduction makes use of the same set of meiosis related genes and that an expansion of this gene complement may have helped to develop the parthenogenetic life cycle.

            Thus, both the ecological relevance and the evolutionary dynamics of Daphnia populations are bound to attract general attention to Daphnia as a new model system in genetics. The current genome paper focuses on D. pulex but another species of the genus, Daphnia magna, has an equally long history in ecological research and efforts to elucidate its genome are underway as well. These developments are bound to fuel the newly emerging discipline of ecological genomics, which has so far been one of the last black boxes of genetic research.