M. Lynch

Quantifying the evolutionary paths to endomembranes

The paper quantifies evolutionary fitness gains of endomembrane systems through two models: pinocytosis and proto-endoplasmic reticulum, finding the latter provides net fitness gains.

Trade-offs, trade-ups, and high mutational parallelism underlie microbial adaptation to extreme feast/famine

This study experimentally evolved E. coli populations under feast/famine cycles, finding high mutational parallelism and trade-offs between growth and survival traits.

Consideration of a liquid mutation accumulation experiment to measure mutation rates by successive serial dilution.

The paper proposes a liquid-phase mutation-accumulation experiment to measure mutation rates and spectra, demonstrating it can replicate results from plate-based experiments and detect a modified mutation spectrum.

Evolutionary Genomics of Sister Species Differing in Effective Population Sizes and Recombination Rates

This study compares population-genomics data between two sister species, D. pulex and D. pulicaria, to understand genetic mechanisms of ecological speciation and identify genes under positive selection.

Evolutionary Insights from a Large-scale Survey of Population-genomic Variation

This study analyzes population-genomic variation in Daphnia pulex to reveal evolutionary-genomic features and identify genes under selection.

A Narrow Range of Transcript-error Rates Across the Tree of Life

The paper analyzes transcript-error rates across diverse species, finding a narrow range and suggesting mechanisms for error purging, but the model explains only 20% of the variation.

The Genome-wide Signature of Short-term Temporal Selection

This study analyzes genome-wide selection patterns in Daphnia pulex over nine years, finding fluctuating selection with near-zero mean coefficients and weak negative selection on minor alleles.

Molecular Coevolutionary Drive

The paper introduces a general model to evaluate how coevolutionary rates between interacting molecules depend on population genetics factors like Ne, mutation rates, and selection strength.

The Divergence of Mean Phenotypes Under Persistent Directional Selection

The paper extends theoretical models of directional selection to account for varying mutational effects on traits, showing how variance in effects influences the relationship between mean phenotypes and population size.

Flagellar energy costs across the Tree of Life

The paper estimates flagellar construction costs across different organisms and shows that only larger cells could evolve eukaryotic flagella due to their higher energy costs.

Microfluidic system-based time-course tracking of physical proximity between cells and its effect on gene expression for elucidating live single cancer-immune cell interactions

This study tracks physical proximity between NK and TNBC cells over time using a microfluidic system and links it to gene expression changes, revealing transcriptional memory in immune-cancer interactions.

Recommendations for improving statistical inference in population genomics

The paper discusses challenges in population genomics due to data abundance and highlights best practices for statistical inference and model fitting.

Chromosomal rearrangements preserve adaptive divergence in ecological speciation

The paper analyzes chromosomal rearrangements in Daphnia species to show their role in preserving adaptive divergence during ecological speciation.

Evolutionary dynamics of asexual hypermutators adapting to a novel environment

This study evolves E. coli populations with different mutation rates in a complex medium for 900 days and finds that higher mutation rates do not significantly increase fitness improvement despite faster genome evolution.

Evolution of a minimal cell

This study compares the evolutionary adaptation of a minimal synthetic cell to its non-minimized counterpart, finding equivalent adaptation rates despite fitness loss from genome streamlining.

Revisiting the notion of deleterious sweeps

The paper examines how fixation of mildly deleterious mutations affects polymorphism patterns and divergence between populations, finding minor but measurable impacts on private variants and FST.

Poised cell circuits in human skin are activated in disease

The paper creates a single-cell atlas of human skin, showing how cell circuits change in inflammatory diseases like atopic dermatitis and psoriasis.

Evolutionary Response to Resource Deprivation: Parallelism and Nonmonotonicity

This study shows that intermediate starvation periods in E. coli lead to distinct phenotypes not predicted by extremes, suggesting non-monotonic evolutionary forces.

Enhanced nutrient uptake is sufficient to drive emergent cross-feeding between bacteria

The paper shows that enhanced nutrient uptake by recipient bacteria, not increased excretion by producers, drives emergent cross-feeding in microbial communities.

The recombinational landscape in Daphnia pulex

This study reveals the recombinational landscape in Daphnia pulex using linkage disequilibrium analysis, showing uniform recombination and rejecting existing population-genetic models.

Genomic analyses of population structure reveal metabolism as a primary driver of local adaptation in Daphnia pulex.

This study uses genomic analyses to show that metabolism-related genes drive local adaptation in Daphnia pulex populations.

Defining the Energetic Costs of Cellular Structures

The paper defines and separates energetic costs of molecular building blocks from opportunity costs to improve accuracy in estimating cellular structure energy requirements.

Universal trends of post-duplication evolution revealed by the genomes of 13 Paramecium species sharing an ancestral whole-genome duplication.

This study analyzes 13 Paramecium species with a shared ancestral whole-genome duplication to reveal trends in post-duplication gene retention and selective pressures.

Population genetics of Paramecium mitochondrial genomes: recombination, mutation spectrum, and efficacy of selection.

This study analyzes mitochondrial genome variation in Paramecium species, finding high conservation of gene order, variable tRNA content, increased GC content in the P. aurelia complex, and no evidence of recombination.

An Escherichia coli nitrogen starvation response is important for mutualistic coexistence with Rhodopseudomonas palustris

The paper identifies an E. coli nitrogen starvation response as critical for stable mutualism with R. palustris through cross-feeding.

Variation in the microbiome of the urogenital tract of koalas (Phascolarctos cinereus) with and without "wet bottom"

This study analyzes the urogenital tract microbiome of koalas with and without wet bottom using 16S rRNA sequencing to identify potential causative agents beyond Chlamydia pecorum.

Catalytic properties of RNA polymerases IV and V: accuracy, nucleotide incorporation and rNTP/dNTP discrimination

This study compares the catalytic properties of RNA polymerases IV and V with Pol II, finding differences in nucleotide incorporation rate, accuracy, and rNTP/dNTP discrimination.