Symbiotic interactions can leave long-term imprints on the genomes of participating organisms. Traditionally, studies emphasize adaptive changes driven by new niches and selection pressures; however, nonadaptive processes — particularly those associated with altered demography — can also strongly influence genomic evolution. One frequently discussed nonadaptive outcome is a reduction in effective population size (Ne) for symbionts, which can weaken the efficacy of natural selection and elevate the role of genetic drift. This bundle of genomic consequences is sometimes called a genomic syndrome, and evidence for such syndrome has been most thoroughly documented in bacterial symbionts.
Whether a comparable, genome-wide reduction in selection efficacy occurs in eukaryotic symbionts with more complex life histories and demography remains unresolved. Lichen symbioses, which pair fungi with photosynthetic algal partners, provide a test case for whether a transition to a lichen-associated lifestyle consistently reshapes algal genomes in predictable ways.
The study aimed to detect signatures of reduced efficacy of selection associated with lichen symbiosis in algae. To do this, the author compared four lichen-forming algal taxa to their closest free-living relatives. The design used complementary genomic metrics to capture different aspects of molecular evolution and codon-level patterns that can reflect changes in selective efficacy and mutational or compositional biases.
Details on sampling, taxon identities, sequencing depth, genome assembly quality, and precise phylogenetic distances were cited in the full manuscript and supplementary materials but are not reproduced in this summary.
Three complementary classes of measures were used to evaluate changes in molecular evolution expected under reduced selection efficacy:
These measures together aim to distinguish whether lichenization is associated with a genome-wide relaxation of selection, altered mutational/compositional regimes, or lineage-specific outcomes.
Comparisons of dN/dS ratios and K between lichen-forming algae and their closest free-living relatives produced heterogeneous outcomes. The effect of the lichen-forming lifestyle on dN/dS was not uniform across the four studied lineages: some lineages showed changes consistent with altered selection efficacy, whereas others did not. The study reports that the influence of lifestyle on these substitution-based metrics was lineage specific rather than globally consistent.
Analyses of codon use bias using ENC' likewise revealed lineage-specific patterns. The impact of lichen association on codon bias varied among the four algal taxa, indicating that a universal reduction in codon-level selection was not observed across all lichen-forming lineages.
GC3 was consistently reduced in the lichen-forming taxa examined relative to their free-living counterparts. However, the authors note that the underlying causes of GC3 reduction differed among lineages. Thus, while a uniform pattern in GC3 content was detected, its drivers appear to be heterogeneous and not attributable to a single common mechanism reported across all taxa.
When the authors searched for genes that showed uniformly intensified or relaxed selection across all four lichen-forming taxa, none were identified. This absence of a set of genes responding in the same direction across lineages supports the interpretation that selection changes are not globally uniform across lichenized algae.
Taken together, the findings indicate that lichen symbiosis does not impose a single, predictable genomic syndrome on algal symbionts. While symbiosis can reshape population-genetic parameters and often elevates the role of genetic drift in symbionts, lichen-forming algae respond in lineage-specific ways. Differences in demographic histories, ecological contexts, and functional demands of particular lichen partnerships likely determine the genomic signatures observed in each lineage.
The article is a preprint and has not undergone peer review. Specific methodological details (for example, precise taxon names, sampling numbers, and statistical tests) and extended results are provided in the manuscript and supplementary files; those details are not reproduced here. The author shared data and code via a public repository referenced in the manuscript footnotes.
This comparative genomic study of four lichen-forming algal taxa versus close free-living relatives finds heterogeneous effects of lichenization on molecular-evolution metrics. GC3 is consistently reduced in lichen-forming taxa, but dN/dS and codon bias outcomes vary by lineage, and no genes showed uniform selection shifts across all taxa. The results support a model in which symbiosis alters symbiont population genetics in ways that can increase drift, but the ultimate genomic consequences are shaped by lineage-specific demography and ecological-functional context rather than by a single, universal genomic syndrome.