Japanese eels (Anguilla japonica) are commercially important species, harvested extensively for food. Currently, this and related species (American and European eels) are challenging to breed on a commercial basis. As a result, the wild stock is used for aquaculture. Moreover, climate change, habitat loss, water pollution, and altered ocean currents affect eel populations negatively. Accordingly, the International Union for Conservation of Nature lists Japanese eels as endangered and on its red list. Here we presented a high-quality genome assembly for Japanese eels and demonstrated that large chromosome reorganizations occurred in the events of third-round whole-genome duplications (3R-WRDs). Several chromosomal fusions and fissions have reduced the ancestral protochromosomal number of 25 to 19 in the Anguilla lineage. A phylogenetic analysis of the expanded gene families showed that the olfactory receptors (group δ and ζ genes) and voltage-gated Ca²⁺ channels expanded significantly. Both gene families are crucial for olfaction and neurophysiology. Additional tandem and proximal duplications occurred following 3R-WGD to acquire immune-related genes for an adaptive advantage against various pathogens. The Japanese eel assembly presented here can be used to study other Anguilla species relating to evolution and conservation.

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.

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 ≈ 7 096) and four large marine (mean N _e = 376 828) 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. Exploratory GWAS analyses suggested a possible polygenic basis for recombination rate. 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.

The Poitevin stickleback (Pungitius vulgaris) is a Near Threatened freshwater fish endemic to France. Using PacBio HiFi long reads and Hi-C scaffolding, we generated the first chromosome-level reference genome for this species. The assembly spans 489.65 Mb across 21 chromosomes, with a scaffold N50 of 21.77 Mb and 99.5% BUSCO completeness. A total of 21,656 protein-coding genes were predicted, and approximately 25.65% of the genome was identified as repetitive sequences. Based on the enrichment of male-specific k-mers on chromosome 12 (chr12), we identified this chromosome as the putative sex chromosome, is consistent with an XY sex-determination system. A short male-specific region (~4 kb; chr12: 24,419,000-24,423,000 bp) was identified that is located in a highly repetitive region and contains one protein-coding gene (gata1a-like). Although the exact boundary of the sex-determining region (SDR) can not be determined, this short male-specific region embedded in highly repetitive elements suggests a sex-determining architecture distinct from that reported in other sticklebacks. This reference genome provides a foundational resource for population genomics and for studies of sex chromosome evolution in the Poitevin stickleback.