“Multivariate Divergence in Wild Microbes: No Evidence for Evolution along a Genetic Line of Least Resistance”
Emile Gluck-Thaler, Muhammad Arsam Shaikh, and Corlett W. Wood: Read the article
Wild Microbes Take the Evolutionary Road Less Traveled
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Understanding how the correlation of multiple traits shapes evolutionary trajectories of organisms has been the key focus of evolutionary biology research for over 40 years. While studies on higher eukaryotes have shown that correlations between certain traits remain consistent across long evolutionary periods, whether this holds for microorganisms remains an open question. In contrast to higher eukaryotes, trait correlation might not be as stable in microbial evolution and might have a weaker impact on the trajectory of evolution due to different modes of inheritance of genetic material (i.e., asexual reproduction and acquisition of genetic material through horizontal gene transfer). Emile Gluck-Thaler, Muhammad Shaikh, and Corlett W. Wood test this hypothesis using two fungal lineages from the same family sampled from the same plant host species. These fungal species are facultative symbionts, which can have distinct host-associated and free-living stages.
Their work addresses three main questions using growth rates on different substrates as traits: (1) Have the two lineages diverged in response to different substrates? (2) Are there trade-offs between growth on different chemical classes of carbon sources, and are these trade-offs conserved across lineages? Trade-offs were expected when grown on diverse carbon sources since some were growth-inhibiting (components of plant defense mechanisms) and others were growth-promoting compounds. (3) Did divergence in response to growth source occur along a genetic line of least resistance (linear combination having maximum genetic variance within a population) to evolutionary change by natural selection? The researchers compared divergence in growth rate under specific substrate concentrations (carbon sources) between two fungal lineages, summarized in a G matrix. The concept of G matrix has been used to study the inheritance of multiple traits. In this study, the diagonals represent variance across each isolate for substrate-specific growth rate, and off-diagonals represent covariances of isolate growth rate between pairs of substrates. The largest eigenvector of this matrix denotes the combination of traits that represent the most variation in growth. This largest eigenvector represents a direction with maximum genetic variance, which can influence the direction of evolutionary change under selection. G matrices were constructed for each lineage, and their eigenvectors can be compared to check if there is a difference in genetic variation between lineages, if growth on different substrates is correlated in a lineage-specific manner, and if lineages differ in their direction of trait correlations.
The researchers show that the lineages differed in their amount of genetic variation, implying that the lineages have different evolutionary capacities to respond to selection imposed by substrates. Although there was no trade-off between different chemical classes of carbon sources within each lineage, lineages differed in the relative growth rates on growth-inhibiting vs. growth-promoting substrates, demonstrating lineage-specific trade-offs. This suggests specialization of these lineages to different growth strategies. The authors also show that trait divergence does not occur along a genetic line of least resistance in these two fungal lineages. This could possibly be due to the lifestyle of these fungi; selection pressures may differ between host-associated and free-living life stages of these facultative symbionts. If important fitness-related traits in either life stage are not accounted for, the missing correlated trait could dictate the direction of trait divergence, overriding the genetic line of least resistance. Another possibility is that acquisition of genetic material through horizontal gene transfer can affect multiple phenotypes.
In conclusion, the authors demonstrate functional divergence in closely related lineages. This divergence could result from both small differences across multiple traits and large differences across specific traits. Such divergence may have broad consequences, especially in the context of plant microbiome composition, structure and function of plant-associated fungal communities, and variation in host phenotypes. Further studies into trait divergence of microorganisms will give us a better understanding of the stability of multiple trait correlation over time, how trade-offs between traits shape the ecological strategies of microorganisms, and the role of trait correlations in determining adaptation to ecological niches.
Deepika Gunasekaran is a Postdoctoral Scholar at University of California, Merced, in Dr. Clarissa Nobile’s lab. She is a computational biologist, and her work focuses on developing computational methods to study gene expression and epigenomics, aiming to understand the mechanisms and evolution of fungal pathogenesis. In her spare time, she enjoys reading historical fiction, painting, and traveling.