Lifemap

Methylation-associated mutagenesis underlies variation in the mutation spectrum across eukaryotes

Mutation spectra vary across genetic and environmental contexts, leading to differences between and within species. Most research on mutation spectrum has focused on the trinucleotide (3-mer) mutation types in mammals, limiting the breadth and depth of variation surveyed. In this study, we use whole-genome resequencing data across 108 eukaryotic species - including mammals, fish, plants, and invertebrates - to characterize pentanucleotide (5-mer) non-coding mutation spectra using a Bayesian approach. Our findings reveal cytosine transition mutability at CpG and (among plants) at CHG sites as the main drivers of variation in mutation spectra across eukaryotes, correlating strongly with genomic CpG and CHG depletion. However, despite the influence of methylation on CpG mutability, genome-wide average CpG methylation levels do not predict CpG transition rates across species and CHG methylation does not predict CHG transition rate, indicating unknown genetic or environmental factors influencing mutation rates at methylated cytosines. Together, our results illustrate the pivotal role of mutagenesis in shaping genome composition across eukaryotes and highlight a gap in knowledge about the mechanisms governing mutation rates. ### Competing Interest Statement The authors have declared no competing interest. NIGMS, R35GM133708, R35GM133708 Alfred P. Sloan Foundation, FG-2021-15702

Minimal overlaps in responses to insecticides between pollinator species

Insecticides are important for protecting crops from agricultural pests, yet their use inadvertently drives global declines in beneficial insects, including pollinators. Insecticide regulation relies on the assumption that model bee species adequately represent responses to exposure across the diversity of insect taxa, despite over 479 million years of evolutionary divergence and a limited understanding of how exposure effects vary across insect orders. Here, using comparative whole-brain transcriptomics, we show differences in molecular responses to modern insecticides across evolutionary distant pollinator lineages: butterflies, flies, and bees. Within each of the four species studied, different insecticides (sulfoxaflor and clothianidin) triggered broadly similar gene regulatory responses. In surprising contrast, exposure impacts differed sharply among species, with no genes or pathways being consistently affected. Strikingly, we found that sulfoxaflor, approved based on its supposed safety for bees, causes more disruptions in non-bee pollinators than the restricted neonicotinoid clothianidin, revealing a critical blind spot in current assessment protocols. Our findings demonstrate that over large evolutionary timescales, species‐level differences can outweigh variations in insecticide chemical structures in shaping the effects of insecticide exposure. These interspecific differences likely reflect distinct physiological and metabolic traits shaped over tens to hundreds of millions of years. Together, our findings highlight the urgent need to reevaluate insecticide safety assessments to incorporate phylogenetic diversity, potentially explaining why regulatory efforts have failed to halt pollinator declines despite stricter testing requirements. ### Competing Interest Statement The authors have declared no competing interest.

Tspecies, Rapid Optimization for Estimating Species Divergence Time Using Ks Distribution

Ks distribution, the distribution of the synonymous substitutions, has been widely used to estimate the species divergence using orthologous genes. However, conventional approaches often ignore the underlying bias that species divergence is delayed to average gene divergence by 2Ne generations, where Ne represents the ancestral effective population size, due to the lack of scalable methods for Ne inference. Here, we demonstrate through simulations that Ks distribution variance correlates with Ne, enabling direct estimation of ancestral population parameters from standard Ks data. Leveraging this relationship, we present Tspecies, an R package that corrects divergence time estimates using only substitution rates and Ks distributions, without requiring additional genomic data. Our practical application of Tspecies in Liriodendron has inferred a divergence time between North American and East Asian lineages (3.49 Ma) that align with late Pliocene cooling, and a large ancestral Ne (~5 * 105) consistent with fossil evidence. By incorporating a readily estimated Ne, our tool resolves a long-standing bias in Ks-based dating while maintaining computational efficiency and broad applicability. Tspecies is freely available under an MIT license at https://github.com/limj0987/Tspecies.git. ### Competing Interest Statement The authors have declared no competing interest.

Sequence diversity lost in early pregnancy - Nature

Around 1 in 136 pregnancies is lost due to a pathogenic small sequence variant genotype in the fetus.

Efficient Estimation of Nucleotide Diversity and Divergence using Depth Information

The increasing scale of population genomic datasets presents computational challenges in estimating summary statistics such as nucleotide diversity (π) and divergence (dxy). Unbiased estimates of diversity require knowledge of missing data and existing tools require all-sites VCFs. However, generating these files is computationally expensive for large datasets. Here, we introduce Callable Loci And More (clam), a tool that leverages callable loci -- determined from depth information -- to estimate population genetic statistics using a variant-only VCF. This approach offers improvements in storage footprint and computational performance compared to contemporary methods. We benchmark clam using a large muskox dataset and demonstrate that it produces unbiased estimates of π while reducing runtime and storage requirements, compared to an existing approach. clam provides an efficient and scalable alternative for population genomic analyses, facilitating the study of increasingly large and diverse datasets. clam is available as a standalone program and integrated into snpArcher for efficient reproducible population genomic analysis. ### Competing Interest Statement The authors have declared no competing interest. National Science Foundation, DEB-1754397

The landscape of fitness effects of putatively functional noncoding mutations in humans

​​While annotations of noncoding regions in the human genome are increasing, the fitness effects of mutations in these regions remain unclear. Here, we leverage these functional genomic annotations and human polymorphism data to infer the distributions of fitness effects of new noncoding mutations in humans. Our novel approach controls for mutation rate variation and linked selection along the genome. We find distinct patterns of selection in putative enhancers, promoters, and conserved noncoding regions. While mutations in enhancers are often neutral, approximately 30% of mutations in promoters are deleterious. The most conserved noncoding regions, showing reduced divergence across mammals and primates, have the highest proportion of deleterious mutations. Notably, while we infer the most conserved sites across mammals and primates are enriched for deleterious mutations, such conserved sites only account for a minority of the deleterious mutations in noncoding regions. For example, the top 5% of conserved noncoding sites encompass fewer than 20% of deleterious mutations, indicating that functional noncoding regions vary widely in the distribution of their evolutionary constraint. Our findings highlight the dynamic evolution of gene regulation and shifting selection pressures over deep evolutionary timescales. Consistent with this finding, we infer mutations in ~7-9% of the noncoding genome are deleterious. These insights have broad implications for using comparative genomics to identify non-neutrally evolving sequences in the human genome. ### Competing Interest Statement The authors have declared no competing interest. National Institute of General Medical Sciences, R35GM119856

The distribution of fitness effects varies phylogenetically across animals

The distribution of fitness effects (DFE) describes the selection coefficients ( s ) of newly arising mutations and fundamentally influences population genetic processes. However, the extent and mechanisms of DFE variation have not been systematically investigated across species with divergent phylogenetic histories and ecological functions. Here, we inferred the DFE in natural populations of eleven animal (sub)species, including humans, mice, fin whales, vaquitas, wolves, collared flycatchers, pied flycatchers, halictid bees, drosophila, and mosquitoes. We find that the DFE co-varies with phylogeny, where the expected mutation effects are more similar in closely related species (Pagel's λ = 0.84, P = 0.01). Additionally, mammals have a higher proportion of strongly deleterious mutations (22% to 47% in mammals; 0.0% to 5.4% in insects and birds) and a lower proportion of weakly deleterious mutations than insects and birds. Population size is significantly negatively correlated with the expected impact of new deleterious mutations (PGLSλ, P = 0.03), and the proportion of new beneficial mutations ( r 2 = 0.73, P < 0.001). These findings align with Fisher's Geometric Model (FGM), which defines organismal complexity as the number of phenotypes under selection. Consistent with the FGM's predictions, we observe that mutations are more deleterious in complex organisms, while beneficial mutations occur more frequently in smaller populations to compensate for the drift load. Our study demonstrates strong phylogenetic constraints in the evolution of a fundamental population genetics parameter, and proposes that, through mechanisms of global epistasis, long-term population size and organismal complexity drive variation in the DFE across animals. ### Competing Interest Statement The authors have declared no competing interest. National Institute of General Medical Sciences, https://ror.org/04q48ey07, R35GM142939, R35GM119856