Mutation rate is a fundamental parameter in population genetics. Apart from being an important scaling parameter for demographic and phylogenetic inference, it allows one to understand at what rate new genetic diversity is generated and what the expected level of genetic diversity is in a population at equilibrium. However, except for well-established model organisms, accurate estimates of de novo mutation rates are available for a very limited number of organisms from the wild. We estimated mutation rates (µ) in two marine populations of the nine-spined stickleback (Pungitius pungitius) with the aid of several 2- and 3-generational family pedigrees, deep (>50×) whole-genome resequences and a high-quality reference genome. After stringent filtering, we discovered 308 germline mutations in 106 offspring translating to µ = 4.83 × 10⁻⁹ and µ = 4.29 × 10⁻⁹ per base per generation in the two populations, respectively. Up to 20% of the mutations were shared by full-sibs showing that the level of parental mosaicism was relatively high. Since the estimated µ was 3.1 times smaller than the commonly used substitution rate, recalibration with µ led to substantial increase in estimated divergence times between different stickleback species. Our estimates of the de novo mutation rate should provide a useful resource for research focused on fish population genetics and that of sticklebacks in particular.

The Colorado potato beetle (Leptinotarsa decemlineata) is one of the most notorious insect pests of potatoes globally. Here, we generated a high-quality chromosome-level genome assembly of L. decemlineata using a combination of the PacBio HiFi sequencing and Hi-C scaffolding technologies. The genome assembly (−1,008 Mb) is anchored to 18 chromosomes (17 + XO), with a scaffold N50 of 58.32 Mb. It contains 676 Mb repeat sequences and 29,606 protein-coding genes. The chromosome-level genome assembly of L. decemlineata provides in-depth knowledge and will be a helpful resource for the beetle and invasive biology research communities.

The genomic consequences of prolonged population decline and isolation are increasingly recognized, but quantitative assessments of mutation loads have been limited by low population-level replication in individual studies. Moreover, how inbreeding and purifying selection shape the genomic landscape of deleterious variation remains poorly understood. We evaluated the abundance and frequency of putative deleterious mutations, characterized the landscape of deleterious variation, and measured the efficacy of purifying selection in 17 wild nine-spined stickleback (Pungitius pungitius) populations covering varying levels of inbreeding (FROH = 0.015 to 0.912) and histories of isolation. We found significantly more deleterious homozygous mutations and a greater frequency of mildly deleterious variants in long-term small, isolated, and inbred populations than in larger outbred populations. Deleterious homozygotes were enriched in runs of homozygosity regions across all study populations, but the extent of enrichment was more pronounced in larger outbred populations than in small inbred populations. Historical effective population sizes serve as an indicator of the strength of purifying selection for mildly deleterious alleles but not for strongly deleterious alleles. The results demonstrate that the accumulation and purging of deleterious variants can occur simultaneously and that a large fraction of segregating strongly deleterious variants are recessive lethals. These findings, which are based on analyses of highly replicated samples of populations, suggest that the level of inbreeding is a good predictor of realized loads of deleterious mutations and that the genomic consequences of prolonged isolation in small populations are predictable.

As a fundamentally important genetic parameter and evolutionary force, germline mutation rates have many applications in evolutionary biology. However, accurate estimates of de novo mutation (DNM) rates are still relatively scarce, even for extensively studied evolutionary biology models. We estimated DNM rates for the three-spined stickleback (Gasterosteus aculeatus), the ‘supermodel’ of ecology and evolutionary biology. Using a large number of family trios sequenced to 45x coverage, we identified 115 unique mutations genome-wide and estimated the DNM rate at µ = 5.11 × 10⁻⁹/bp/gen without any detectable sex bias. The localised DNM rate was found to be positively correlated with the recombination rate, supporting the notion that recombination is a mutagenic process. Correlations between µ and genomic characteristics of studied species and the related nine-spined stickleback (Pungitius pungitius) revealed a high degree of similarity, suggesting that despite 17.5 million years of independent evolution, the mutational processes in the two species appear to have been conserved.

Population genetic theory predicts that natural selection will be more efficient in large than small populations because genetic drift reduces the efficiency of selection in small populations. Small populations adapting to new environments can also be expected to evolve higher recombination rates to facilitate adaptation as well as to dissociate and purge harmful mutations. We tested these hypotheses (1) by investigating differences in the strength of association between nucleotide diversity ( π ) and recombination rate across the genomes of nine-spined sticklebacks ( Pungitius pungitius ) from four small freshwater (mean N _e ≈ 2 578) and four large marine (mean N _e = 86 742) populations, as well as (2) by comparing recombination rates between small and large populations using population specific linkage maps. We found the predicted positive correlation of π with recombination rate from all but the smallest freshwater populations, suggesting prevalent linked selection even after accounting for variation in GC/CpG content, and gene density. Mean recombination rates did not differ between freshwater and marine populations, except that the smallest N _e freshwater population exhibited significantly elevated recombination rate. GWAS analyses suggested a polygenic basis for recombination rates. These results suggest an important role for linked selection in reducing π in low recombination regions especially in large populations. Moreover, as predicted by theory, at least one of the small freshwater populations appears to have evolved a higher recombination rate than its marine ancestors.

Availability of de novo mutation rate ( µ ) estimates based on approaches that rely on bioinformatic validations has increased tremendously during the past few years, but the accuracy and precision of these estimates often remain unclear as Sanger sequencing validation of the mutations is often lacking. We used both long- and short-read sequencing data and different bioinformatic pipelines to estimate µ , as well as false positive (FPR) and negative (FNR) rates, for family trios of flat-headed loaches ( Oreonectes platycephalus ). By comparing estimates against PCR-verified mutations, we observed that the top-performing approach (as ranked by the F1 score of seven approaches at the same depth) still exhibited a 4% false positive rate (FPR) alongside a 12% false-negative rate (FNR). Across the remaining methods, FPR values ranged from 4–12%, and FNRs from 8–19%. Irrespective of the bioinformatic approach used, long-read data yielded consistently lower µ estimates than short-read data because of the larger callable genome sizes. In addition, a higher mapping depth resulted in a lower FNR. These results call for caution regarding de novo mutations without Sanger sequencing validation in non-model organisms and raise the possibility that many published µ -estimates, especially those based on low mapping depths, might be biased.