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Biology subjects

McEnany, J. D.

Publications and source records attributed to McEnany, J. D..

4 recordsLinked to original sources

Rapid evolution can select for fitness tradeoffs in fluctuating environments

In fluctuating environments, the fates of new mutations depend on the fitness tradeoffs they experience across multiple environmental conditions. Selection on these tradeoffs is well-understood when mutations compete in isolation, but much less is known in the empirically relevant case where multiple mutations compete at the same time. Here, we develop a theory to predict how rapidly adapting populations select on fitness tradeoffs at many linked genetic loci. We derive analytical expressions showing how the fixation probabilities of these mutations depend on their underlying fitness tradeoffs, the timescales of environmental variation, and the future mutations they produce over time. We find that in large populations, competition between linked mutations can strongly favor mutations that carry larger fitness tradeoffs, even when they have a lower geometric mean fitness. We show that this "specialist advantage" arises because transient benefits enhance the rate of producing future mutations -- an effect that continues to compound over time even when local conditions shift. We also demonstrate that successful lineages acquire well-timed mutations that appear to anticipate future environments, which can boost the rate of adaptation. These results show how large populations balance competing demands in temporally fluctuating environments, and provide a baseline for interpreting fitness tradeoffs in many natural and experimental settings.

evolutionary biology↗

Dynamics of local B cell migration during affinity maturation in the human tonsil

Affinity maturation enhances B cell binding within germinal centers, where spatial structure preserves sequence diversity by restricting cell movement. While recent studies show that some B cell lineages span multiple germinal centers, the sources, rates and consequences of this spreading process remain unknown. Here, we show that the spatial arrangement of B cells in the human tonsil is driven by local migration during affinity maturation. Through an evolutionary re-analysis of spatial transcriptomics data, we demonstrate that these local migrations follow a clock-like process, in which cells migrate at an average rate of [~]1/50 cell divisions that is consistent across lineages and time. Migrating cells continue to evolve and diversify in their new germinal centers at similar rates, such that the largest lineages in each germinal center often originate from another. These results suggest that affinity maturation operates in a regime of pervasive but intermediate migration, balancing diversity and selection.

immunology↗

Predicting the First Steps of Evolution in Randomly Assembled Communities

Microbial communities can self-assemble into highly diverse states with predictable statistical properties. However, these initial states can be disrupted by rapid evolution of the resident strains. When a new mutation arises, it competes for resources with its parent strain and with the other species in the community. This interplay between ecology and evolution is difficult to capture with existing community assembly theory. Here, we introduce a mathematical framework for predicting the first steps of evolution in large randomly assembled communities that compete for substitutable resources. We show how the fitness effects of new mutations and the probability that they coexist with their parent depends on the size of the community, the saturation of its niches, and the metabolic overlap between its members. We find that successful mutations are often able to coexist with their parent strains, even in saturated communities with low niche availability. At the same time, these invading mutants often cause extinctions of metabolically distant species. Our results suggest that even small amounts of evolution can produce distinct genetic signatures in natural microbial communities.

evolutionary biology↗

piRNAs of Caenorhabditis elegans broadly silence nonself sequences through functionally random targeting

Small non-coding RNAs such as piRNAs serve as guides for Argonaute proteins, enabling sequence-specific, post-transcriptional regulation of gene expression. The piRNAs of Caenorhabditis elegans have been observed to bind targets with high mismatch tolerance, and appear to lack specific transposon targets, unlike piRNAs in Drosophila melanogaster and other organisms. These observations support a model in which C. elegans piRNAs provide a broad, indiscriminate net of silencing, acting in competition with siRNAs associated with the CSR-1 Argonaute that specifically protect self genes from silencing. However, the breadth of piRNA targeting has not been subject to in-depth quantitative analysis, nor has it been explained how piRNAs are distributed across sequence space to achieve complete coverage. Through a bioinformatic analysis of piRNA sequences, incorporating an original metric of piRNA-target distance, we demonstrate that C. elegans piRNAs are functionally random, in that their coverage of sequence space is comparable to that of random sequences. By possessing a sufficient number of distinct, essentially random piRNAs, C. elegans is able to target arbitrary nonself sequences with high probability. This result elucidates the mechanism by which newly transcribed mRNAs in C. elegans are classified as self or nonself, and has implications for piRNA evolution and biogenesis.

bioinformatics↗