Biology subjects

Bright, L.

Publications and source records attributed to Bright, L..

3 recordsLinked to original sources

bioRxiv2026

Evolutionary Dynamics of Paramecium Mitochondrial Genomes

Ciliates are a diverse group of single-celled eukaryotes that can exhibit a wide range of genetic diversity within morphologically indistinguishable species. However, they are still not well studied as their mechanisms of speciation and the extent of diversification remain unknown. Mitochondrial genomes offer an effective framework for resolving species relationships and evolutionary changes. Here, we analyzed a globally sampled dataset of Paramecium to understand the evolution of mitochondrial genomes in ciliates. Phylogenetic analysis of linear mitochondrial genomes shows the presence of cryptic diversity beyond the P. aurelia complex, with P. bursaria lineage appearing as a deeply diverging out-group. Protein-coding genes are largely conserved, with limited rearrangements, and some ciliate-specific genes appear to be missing in P. bursaria. Population genetic analysis show little to no evidence of recombination along with substantial differences in effective population size across species. Patterns of molecular evolution also indicate purifying selection as the predominant force, the strength of which is at least as strong as in the nucleus and consistent with mitochondrial effective population sizes that are similar or larger than those of the nucleus. Across the functional groups, the electron transport chain and ribosomal genes are highly constrained, while ciliate-specific ymf genes show reduced efficacy of selection compared to the others. These findings offer a basis for connecting mitochondrial variation to evolutionary divergence, functional constraint, and speciation in microbial eukaryotes.

genomics↗

bioRxiv2026

Shifts in the population-genetic landscape of the ciliate genus Paramecium

Ciliates are one of the most ecologically diverse and morphologically intricate unicellular organisms. Despite their evolutionary significance and their prominence in cell-biological research, the population-genetic processes governing their diversification have received remarkably little attention. A fundamental unresolved problem is the existence of geographic isolation among free-living protists and its consequences for species richness. We addressed this issue in the model ciliate Paramecium by sequencing genomes of hundreds of isolates collected worldwide, capturing multiple morphological and cryptic species, with multiple populations each. Contrary to previous reports, we found evidence of geographic differentiation in the majority of species. In a few cases, geographic structure became evident when deeply diverging clades in a species were treated separately. This suggests that the biogeographical patterns of Paramecium have been shaped by periods of genetic isolation leading to speciation, with rare events of global dispersal realized over its long evolutionary history. Despite being largely isolated, populations were remarkably similar in their effective population size, recombination rate, and efficacy of natural selection. Across species, selection appears to be least effective in Paramecium aurelia lineages, and most effective in P. bursaria, presumably due to differences in their breeding characteristics. Despite differences among species in the population-genetic environment, patterns of variation across the genome remained consistent. Selective constraints on a core set of genes seemed to have gradually diverged across the species phylogeny. Genes with multiple copies retained from whole-genome duplication events in P. aurelia were found to be under relatively relaxed purifying selection. Moving forward, this dataset will serve to test hypotheses on the ecological and cellular complexity of Paramecium and beyond.

evolutionary biology↗

bioRxiv2020

Heritable variation in resistance to the endonuclear parasite Holospora undulata across clades of Paramecium caudatum

Resistance is a key determinant in interactions between hosts and their parasites. Understanding the amount and distribution of genetic variation in this trait can provide insights into (co)evolutionary processes and their potential to shape patterns of diversity in natural populations. Using controlled inoculation in experimental mass cultures, we investigated the quantitative genetic variation in resistance to the bacterial parasite Holospora undulata across a worldwide collection of strains of its ciliate host Paramecium caudatum. We combined the observed variation with available information on the phylogeny and biogeography of the strains. We found substantial variation in resistance among strains (with broad-sense heritability > 0.5), repeatable between laboratories and ranging from total resistance to near-complete susceptibility. Early (one week post inoculation) measurements provided higher estimates of resistance heritability than did later measurements (2-3 weeks), possibly due to diverging epidemiological dynamics in replicate cultures of the same strains. Genetic distance (based on a neutral marker) was positively correlated with the difference in resistance phenotype between strains (r = 0.45), essentially reflecting differences between highly divergent clades (haplogroups) within the host species. Haplogroup A strains, mostly European, were less resistant to the parasite (49% infection prevalence) than non-European haplogroup B strains (28%). At a smaller geographical scale (within Europe), strains that are geographically closer to the parasite origin (Southern Germany) were more susceptible to infection than those from further away. These patterns are consistent with a picture of local parasite adaptation. Our study demonstrates ample natural genetic variation in resistance on which selection can act and hints at symbiont adaptation producing signatures in geographic and lineage-specific patterns of resistance in this model system.

genetics↗