Zooplankton study challenges traditional views of evolution

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

Their findings, reported in the current issue of the journal Proceedings of the National Academy of Sciencesbuild 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 considerably from year to year, maintaining variation and potentially improving the ability to adapt to changing environmental conditions in the future by providing raw material on which natural selection can act.

In seemingly stable environments, the frequency of genetic variants called alleles in specific chromosomal regions fluctuates significantly over time, even though 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 changes.

“This study has given us, for the first time, insight into the kinds of temporal changes in gene frequencies that occur even in seemingly constant environments, a kind of continuous shuffling of genetic variation distributed across the genome,” said Michael Lynch, lead author of the new study.

Lynch is director of the Biodesign Center for Mechanisms of Evolution and a professor in ASU’s School of Life Sciences. Other researchers involved 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 their 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 reproduction cycle and are sensitive to various environmental pollutants.

These tiny creatures are a vital food source for fish and help limit algae growth. Their ability to adapt quickly to environmental changes could give us clues about how other species, including those that play an important role in the human food supply, might respond to pollution, climate change and other human-induced stressors.

Most sites examined on the Daphnia genome were subject to changing selection pressures over 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. Rather, the genetic advantages or disadvantages of specific traits change from one period to another.

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

Rethinking genetic variation

The study breaks new ground by identifying precisely when and where selection pressures occur within the genome. Aside from traits known to be strongly influenced by natural selection, there is little information on how allele frequencies change over time in natural populations.

Multi-year genome-wide analysis of nearly 1,000 genetic samples from a Daphnia pulex population shows that most genetic sites are subject to variable selection, with an average effect close to zero, indicating low selection pressure consistent over different time periods and selection distributed across many genomic regions.

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

Variation and survival

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

This effect could help explain why species sometimes adapt faster than scientists normally expect. On the other hand, the same phenomenon can cause deleterious alleles to shift to higher frequencies in favor of linked beneficial alleles, reducing the overall effectiveness of selection in some cases.

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

Although the study focused on Daphnia pulex, the results could have implications for understanding how other species might respond to rapid environmental changes, including those caused by human activities, such as pollution and climate change. Assessing the stability of allele frequencies in more stable environments is an important first step. Such studies are essential because laboratory experiments alone cannot reproduce the complexity of environmental influences acting on wild populations.

Furthermore, understanding the evolution of daphnia could provide insights into the resilience of entire ecosystems. This knowledge could help researchers predict and potentially mitigate the impacts of environmental change on biodiversity and food webs.

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