The study of zooplankton challenges traditional views of evolution

In the new research, Arizona State University scientists and their colleagues investigated the genetic changes that occur in a naturally isolated population of the water flea, Daphnia pulex. This tiny crustacean, barely visible to the naked eye, plays a crucial role in freshwater ecosystems and provides a unique window into natural selection and evolution.

Their findings, reported in the current issue of the journal Proceedings of the National Academy of Sciences, draw on a decade of research. Using advanced genomic techniques, the research team analyzed DNA samples from nearly 1,000 Daphnia.

They found that the strength of natural selection on individual genes varies significantly from year to year, maintaining variation and potentially increasing the ability to adapt to future changing environmental conditions by providing raw material for natural selection to act on.

In apparently stable environments, there are significant fluctuations in the frequency of gene variants known as alleles in specific chromosomal regions over time, even if the overall strength of selection remains close to zero on average over many years. This suggests that such genetic variation allows populations to remain adaptable to environmental change.

“This study has given us, for the first time, a glimpse of the kinds of temporary changes in gene frequencies that occur even in seemingly constant environments, a kind of continuous genetic change distributed throughout the genome,” says Michael Lynch, manager. author of the new study.

Lynch is the director of the Biodesign Center for Mechanisms of Evolution and a professor in the School of Life Sciences at ASU. Additional researchers in the study include colleagues from ASU, Central China Normal University and the University of Notre Dame.

The power of selection

Daphnia, a form of zooplankton, have fascinated biologists for centuries because of their crucial role in aquatic ecosystems and ability to adapt to environmental stressors. In addition to their value for multigenerational genetic research, Daphnia are widely used model organisms for freshwater toxicity testing because they have a rapid asexual reproductive cycle and are sensitive to various environmental pollutants.

The tiny creatures are a vital food source for fish and help control algae growth. Their ability to quickly adapt to environmental changes may hold clues to how other species—including those important to the human food supply—might respond to pollution, climate change, and other stressors caused by the man.

Most of the sites examined in the Daphnia genome were shown to experience shifting selection pressures during the study period. On average, these pressures tend to balance out to have little overall effect, meaning that no single direction of selection consistently dominates over time. Instead, the genetic advantages or disadvantages of specific traits vary from period to period.

These findings challenge the traditional belief that measuring genetic diversity (the range of different traits in a population) and genetic divergence (differences between populations) can easily show how natural selection works consistently. Instead, natural selection appears to operate with greater subtlety and complexity than previously thought.

Rethinking genetic variation

The study breaks new ground by determining when and where selection pressures occur within the genome. Apart from traits known to be strongly influenced by natural selection, little is known about how allele frequencies change over time in natural populations.

Multiyear genome-wide analysis of nearly 1,000 genetic samples from a Daphnia pulex population shows that most genetic loci experience divergent selection, with an average effect close to zero, indicating little consistent selection pressure at different times and widespread selection in many genomic regions.

These findings challenge the common understanding of genetic diversity and divergence as indicators of random genetic drift and the intensity of selection.

Variation and survival

The observed patterns of selection at different gene loci provide a mechanism for maintaining genetic diversity, which is essential for rapid adaptation. The study also found that genes located next to each other on chromosomes tend to evolve in a coordinated manner. This linkage allows beneficial combinations of gene variants to be inherited together, potentially speeding up the adaptation process.

This effect may help explain how species sometimes adapt faster than scientists would normally expect. On the other hand, the same phenomenon can result in the distribution of deleterious alleles at higher frequencies than associated beneficial alleles, reducing the overall efficiency of selection in some cases.

The study shows that evolution is more dynamic and complex than previously appreciated. The influence of environment on genes changes frequently, perhaps helping species maintain the genetic variety needed to adapt to future conditions. This new understanding may prompt scientists to rethink how they study evolution in nature.

While the study focused on Daphnia pulex, the findings may have implications for understanding how other species may respond to rapid environmental changes, including those driven by human activities, such as pollution and climate change. Assessing the stability of allele frequencies in more stable environments is an important preliminary step. Such studies are critical, as laboratory experiments alone cannot duplicate the complexity of environmental influences acting on wild populations.

Further, understanding how Daphnia evolves can provide insights into the resilience of entire ecosystems. This knowledge can help researchers predict and potentially mitigate the impacts of environmental change on biodiversity and food webs.

As the world faces an accelerating environmental crisis, studies like this provide crucial insights into nature’s capacity for resilience and adaptation. By continuing to study these tiny creatures, scientists hope to better understand the underlying mechanisms of evolution and apply these lessons to broader ecological and conservation efforts.