K. E. Lohmueller

The impact of non-neutral synonymous mutations when inferring selection on non-synonymous mutations

This study shows that selection on synonymous mutations can bias inferences of the DFE for nonsynonymous mutations when using demographic parameters estimated from synonymous variants.

Inference of the demographic histories and selective effects of human gut commensal microbiota over the course of human history

The paper infers demographic histories and distribution of fitness effects of gut commensal microbes in North Americans compared to African rural populations, revealing population size changes and varying selective pressures across species.

The influence of gene flow on population viability in an isolated urban caracal population

The paper examines the genomic effects of isolation and low gene flow in an urban caracal population and models the impact of migration on population viability.

Using computational simulations to quantify genetic load and predict extinction risk

This paper advocates for using computational simulations to better quantify genetic load and predict extinction risk in small wildlife populations by addressing limitations in current genomic approaches.

MaLAdapt reveals novel targets of adaptive introgression from Neanderthals and Denisovans in worldwide human populations

MaLAdapt identifies novel adaptive introgression loci from Neanderthals and Denisovans in non-African populations using machine learning.

Quantifying the fraction of new mutations that are recessive lethal

The paper quantifies the fraction of new mutations that are recessive lethal using simulations and genomic data, finding that less than 1% of nonsynonymous mutations are recessive lethal in humans and Drosophila.

Genomic underpinnings of population persistence in Isle Royale moose

This study examines the genomic factors contributing to population persistence in Isle Royale moose despite low genetic diversity and inbreeding, finding evidence of purging and reduced fitness.

A signature of Neanderthal introgression on molecular mechanisms of environmental responses

The paper identifies Neanderthal introgression variants that influence gene expression in response to environmental perturbations and validates their regulatory function.

Strongly deleterious mutations are a primary determinant of extinction risk due to inbreeding depression

This study shows that strongly deleterious mutations, not just genetic diversity, are key to extinction risk in small populations due to inbreeding depression.

Greater strength of selection and higher proportion of beneficial amino acid changing mutations in humans compared to mice and Drosophila melanogaster

The paper estimates higher proportions of beneficial mutations and stronger selection in humans compared to mice and Drosophila melanogaster, suggesting organismal complexity influences adaptive evolution.

Negative linkage disequilibrium between amino acid changing variants reveals interference among deleterious mutations in the human genome

The paper examines negative linkage disequilibrium between amino acid changing variants and finds that deleterious mutations tend to be on different haplotypes, suggesting interference or negative epistasis.

Recessive deleterious variation has a limited impact on signals of adaptive introgression in human populations

This study shows that recessive deleterious variants can increase false positives in detecting adaptive introgression, but most signals remain robust, with HYAL2 and HLA being particularly affected.

Haplotype-based inference of the distribution of fitness effects

The paper develops a likelihood-based method to infer selection intensity on low-frequency variants using haplotype data and applies it to the UK10K dataset, finding similar proportions of neutral and deleterious variants as previous estimates.

Genomic signatures of extensive inbreeding in Isle Royale wolves, a population on the threshold of extinction

The paper analyzes genomic data from Isle Royale wolves to assess the effects of inbreeding and finds that homozygosity of deleterious mutations, not heterozygosity or variant count, correlates with inbreeding depression.

Complex patterns of sex-biased demography in canines

The paper analyzes genetic variation in canines to investigate sex-biased demography, finding evidence of both male- and female-biased mating patterns across different canine populations.

Comparison of single genome and allele frequency data reveals discordant demographic histories

The paper compares whole genome and allele frequency data to show discordant demographic histories inferred by different methods.