arXiv subjects

Elisa Heinrich-Mora

Publications and source records attributed to Elisa Heinrich-Mora.

4 recordsLinked to original sources

arXiv2026

How recombination rates affect escape from low-fitness states

Adaptation often requires the assembly of favorable combinations of mutations that are individually deleterious. As a result, populations may remain trapped in low-fitness genetic states even when higher-fitness genotypes exist. Recombination plays a dual role in this process because it can both generate and disrupt advantageous multilocus combinations. Previous work showed that the balance between selection and recombination determines whether populations cross fitness valleys or persist in low-fitness states associated with demographic decline. We study this problem in a three-locus model consisting of two selected loci and a recombination modifier locus. The modifier has no direct effect on fitness but alters the recombination rate between the selected loci, allowing recombination itself to evolve. We characterize the fixation states of the system and derive explicit conditions for the local stability of the low-fitness fixation set. Stability depends on selection strength, recombination among selected loci, recombination between the modifier and selected loci, and modifier composition. In the classical two-locus model, stability depends on a single recombination parameter. By contrast, the modifier model generates a continuum of fixation states whose stability varies with modifier frequency. Populations with identical selected-haplotype frequencies can therefore differ in stability solely because they differ in modifier composition. We further show that modifier polymorphism can either stabilize or destabilize the low-fitness state, depending on the relative magnitudes of modifier-dependent recombination rates. These results demonstrate that genetic variation affecting recombination alters evolutionary outcomes not only by changing the formation of favorable multilocus combinations but also by changing the stability of alternative evolutionary states.

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arXiv2026

Recombination Rate Modifiers under Stochastic Transmission

The Reduction Principle states that, near a stable equilibrium under fixed viability selection, a selectively neutral modifier allele that reduces recombination rate among selected loci is favored, whereas one that increases recombination rate is eliminated. This result assumes constant transmission parameters across generations, so that invasion is determined by the dominant eigenvalue of a single transmission-selection matrix. Here we analyze a minimal departure from this framework. In a diploid model, two loci experience symmetric multiplicative viability selection and a third, neutral locus modifies their recombination rate. All parameters are fixed except that recombination in modifier heterozygotes varies randomly across generations according to a stochastic process. When the recombination rate in modifier heterozygotes is constant, the Reduction Principle holds exactly: invasion occurs if the rare modifier allele reduces recombination relative to the resident rate. When recombination varies randomly across generations, invasion is governed by the top Lyapunov exponent of a product of random matrices. We show that temporal variation in recombination rate alone, in the absence of fluctuating viability selection, can reverse the direction of selection on the modifier locus predicted by the deterministic model. The mean recombination rate is insufficient to determine invasion of $M_2$; instead, outcomes depend on the full distribution of recombination rates and their ordered accumulation across generations. Parameters that affect only the magnitude of selection under constant transmission - including resident recombination, selection strength, and background linkage - can alter its sign under stochastic transmission. These results demonstrate that temporal variability in transmission constitutes an independent and qualitatively distinct force in the evolution of recombination rates.

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arXiv2026

Mutation Rate Variation Across Genomic Regions in \textit{Arabidopsis thaliana}

In population genetics, mutation rate is often treated as a homogeneous parameter across the genome. Empirical evidence, however, shows systematic variation across genomic contexts associated with chromatin organization and epigenomic features. Using gene-level de novo mutation data from Arabidopsis thaliana, we test whether chromatin features predict not only the mean per-base mutation rate but also its variability across genes. To reduce heterogeneity in selective regime, we restrict analysis to essential and lethal loci subject to strong purifying selection. Across complementary multivariable models including heteroskedasticity-robust linear regression, length-weighted regression, and Poisson generalized linear models with exposure offsets, histone marks associated with active transcription (H3K4me1, H3K4me3, H3K36ac) are consistently associated with lower mean mutation rates and substantially reduced between-gene variance. GC content shows little association with the mean once chromatin predictors are controlled but is positively associated with mutation-rate variability. Estimates of skewness and kurtosis reveal no significant higher-order structure attributable to epigenomic predictors. A standardized Tajima's $D$ statistic yields directionally consistent but statistically underpowered associations with both the mean and variance of gene-level mutation rates. These results indicate that mutation rate is systematically structured by chromatin state within functionally constrained genes and suggest that evolutionary processes may act not only on expected mutation rate but also on its variability across loci.

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arXiv2026

Evolution under Stochastic Transmission: Mutation-Rate Modifiers

Evolutionary analyses of large populations commonly incorporate stochasticity through temporal variation in selection while treating genetic transmission as fixed. Much less attention has been given to stochasticity in transmission itself. We study a selected locus with alleles $A$ and $a$ under constant selection, linked to a neutral modifier locus whose alleles $M_1$ and $M_2$ control the mutation rate from $A$ to $a$. Under constant transmission, the Reduction Principle applies: near a mutation--selection balance where $M_1$ is fixed with mutation rate $u_1$, a rare allele $M_2$ invades if its associated rate $u_2$ is smaller than $u_1$, but cannot invade if $u_2$ is larger than $u_1$. This result holds for both haploid and diploid populations and is independent of recombination, which affects only the rate, not the direction, of evolutionary change. We extend this framework by allowing the mutation rate associated with the invading modifier to fluctuate randomly across generations. In this stochastic setting, invasion is no longer determined by mean mutation rates alone. Instead, it depends on the temporal distribution of mutation rates, the strength of selection at the selected locus, and the recombination rate between modifier and target. Stochastic transmission and recombination therefore do not merely rescale deterministic predictions based on the Reduction Principle; they can alter the direction of selection on modifier alleles.

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