Evolution最新文献

Variation of recombination rate along the genome is of crucial importance to rapid adaptation and organismal diversification. Many unknowns remain regarding how and why recombination landscapes evolve in nature. Here, we reconstruct recombination maps based on linkage disequilibrium and use subsampling and simulations to derive a new measure of recombination landscape evolution: the Population Recombination Divergence Index (PRDI). Using PRDI, we show that fine-scale recombination landscapes differ substantially between two cichlid fish ecotypes of Astatotilapia calliptera that diverged only ~2,500 generations ago. Perhaps surprisingly, recombination landscape differences are not driven by divergence in terms of allele frequency (FST) and nucleotide diversity (Δ(π)): although there is some association, we observe positive PRDI in regions where FST and Δ(π) are zero. We found a stronger association between the evolution of recombination and 47 large haplotype blocks that are polymorphic in Lake Masoko, cover 21% of the genome, and appear to include multiple inversions. Among haplotype blocks, there is a strong and clear association between the degree of recombination divergence and differences between ecotypes in heterozygosity, consistent with recombination suppression in heterozygotes. Overall, our work provides a holistic view of changes in population recombination landscapes during the early stages of speciation with gene flow.

An important goal of comparative and functional genomics is to connect genetic polymorphisms to phenotypic variation. Leopards (Panthera pardus) from northern South Africa are particularly diverse, as here a unique color morph occurs, as well as two deeply diverged southern (SA) and central African (CA) mitochondrial clades, stemming from Pleistocene refugia. Here, we present the first whole genomes of a red leopard and a black (captive) leopard, and wildtypes belonging to the CA and SA mitochondrial clades, to evaluate genome-wide diversity, divergence, and high-impact mutations that may relate to their phenotype. In the black leopard, we found long runs of homozygosity (ROHs), low nucleotide diversity across the genome, and a large number of homozygous structural variants, likely resulting from inbreeding to maintain this color morph in captivity. In red leopards, runs of homozygosity were slightly longer compared to wildtype leopards, with potential deleterious mutations relating to its phenotype, including impaired vision. When assessing population structure, we found no divergence between CA and SA leopards and the rest of Africa, whether comparing single nucleotide or structural variants. This illustrates the homogenizing effect of introgression, and highlights that although leopards in northern South Africa may be phenotypically unique, they are not genetically different.

Variability in warning signals is common but remains puzzling since deviations from the most common form should result in a higher number of predator attacks. One explanation may lie in constraints due to genetic correlations between warning color and other traits under selection. To explore the relationship between variation in warning color and different life-history traits, we used an extensive data set comprising 64,741 individuals from a Finnish and an Estonian population of the wood tiger moths, Arctia plantaginis, that have been maintained in captivity over 25 generations. This species exhibits variable warning coloration in larval and adult stages. Measuring these traits alongside several fitness components allowed us to set color variation into context and obtain a better understanding of selection and constraints. Complete pedigree information enabled us to estimate genetic variances and covariances, which revealed several complex interplays between fitness components: Selection for faster development led to a significantly reduced fecundity. Fecundity was also constrained by negative correlations between direct genetic and maternal effects. However, we found no evidence that genetic associations with life-history traits constrain the efficiency of warning colors.

Reciprocal selection between extended and somatic phenotypes is an active area of investigation. Recent research on the influence of web-building on somatic evolution in spiders has produced conflicting results, with some finding no effect of web use on somatic evolution and others showing significant effects. These studies differed in focus, with the former surveying general anatomical traits and the latter concentrating on somatic systems with significant functional roles in prey capture. Here we propose and test the hypothesis that prey immobilization by webs is broadly synergistic with cheliceral biting force and that web builders have lower cheliceral forces compared to free hunters. Our analysis focused on the intercheliceral (IC) sclerite and muscles, a newly characterized system that is synapomorphic and ubiquitously distributed in spiders. Using µCT scans, we quantify IC sclerite shape and model IC muscle function. Statistical analyses show that inferred size-corrected isometric muscle force is lower in web-builders than in free hunters. No such association was found for IC sclerite shape. In the investigation of reciprocal selective effects between extended and somatic phenotypes, our results highlight the importance that these traits be functionally linked and adaptive.

The accurate estimation of the distribution of fitness effects (DFE) of new mutations is critical for population genetic inference but remains a challenging task. While various methods have been developed for DFE inference using the site frequency spectrum of putatively neutral and selected sites, their applicability in species with diverse life history traits and complex demographic scenarios is not well understood. Selfing is common among eukaryotic species and can lead to decreased effective recombination rates, increasing the effects of selection at linked sites, including interference between selected alleles. We employ forward simulations to investigate the limitations of current DFE estimation approaches in the presence of selfing and other model violations, such as linkage, departures from semidominance, population structure, and uneven sampling. We find that distortions of the site frequency spectrum due to Hill-Robertson interference in highly selfing populations lead to mis-inference of the deleterious DFE of new mutations. Specifically, when inferring the distribution of selection coefficients, there is an overestimation of nearly neutral and strongly deleterious mutations and an underestimation of mildly deleterious mutations when interference between selected alleles is pervasive. In addition, the presence of cryptic population structure with low rates of migration and uneven sampling across subpopulations leads to the false inference of a deleterious DFE skewed towards effectively neutral/mildly deleterious mutations. Finally, the proportion of adaptive substitutions estimated at high rates of selfing is substantially overestimated. Our observations apply broadly to species and genomic regions with little/no recombination and where interference might be pervasive.

Baker's law is the observation that recently dispersed populations are more likely to be self-fertilizing than populations at the range core. The explanatory hypothesis is that dispersal favors self-fertilization due to reproductive assurance. Caenorhabditis elegans nematodes reproduce via either self-fertilization or outcrossing and frequently disperse in small numbers to new bacterial food sources. While C. elegans males facilitate outcrossing, males and outcrossing are rare in natural C. elegans populations. Here, we use experimental evolution to test if frequent dispersal selects for the invasion of self-fertilization into predominantly outcrossing populations. C. elegans dispersal often occurs in the dauer alternative life stage. Therefore, we tested the effects of dispersal on rates of self-fertilization in populations exposed to dauer-inducing conditions and populations maintained under standard lab conditions. Overall, we found that populations required to disperse to new food sources rapidly evolved substantially elevated rates of self-fertilization compared to populations that were not required to disperse in both dauer and non-dauer populations. Our results demonstrate that frequent dispersal can readily favor the evolution of increased selfing rates in C. elegans populations, regardless of life stage. These data provide a potential mechanism to explain the dearth of outcrossing in natural populations of C. elegans.

Utilizing whole genome sequencing and multiple species delimitation models, Gaughran et al. (2025) show support for up to 13 distinct living Galapagos giant tortoise species, in contrast to the current classification of a single species. This result highlights the potential for rapidly radiating organisms on islands to act as model systems for investigating species boundaries, helping to settle taxonomic debates.

When broods fail, parents may assist neighbors' offspring, a behavior called redirected helping that is observed in many species. Flatrès and Wild (2025) used inclusive fitness models to study this behavior. They showed that redirected helping can evolve in viscous populations, where individuals stay near their birthplace, increasing relatedness and competition among neighbors, especially when helping costs are low. Life-history traits like survival, dispersal, and brood-failure rates shape this behavior. Interestingly, survival benefits from helping can outweigh reproductive gains, challenging assumptions and providing fresh insights into cooperative breeding dynamics.

The evolution of placentation is predicted to intensify intergenomic conflicts between mothers and offspring over optimal levels of maternal investment by providing offspring opportunities to manipulate mothers into allocating more resources. Parent-offspring conflicts can result in the evolution of reproductive isolation among populations when conflicts resolve in different ways. Postzygotic reproductive isolation is hypothesized to evolve more rapidly following the evolution of placentation due to the predicted increase in conflict. We tested this hypothesis by performing interpopulation crosses within placental and nonplacental species of Poeciliopsis to determine if the relationship between genetic distance and measures of postzygotic reproductive success differed as function of reproductive mode. We did not observe any differences in offspring viability or sterility among crosses. Offspring size declined rapidly as a function of interpopulation genetic distance within the placental species, but not among our nonplacental species. The decrease in offspring size in the placental species was beyond normal variation, likely representing a major fitness cost, consistent with the prediction that negative epistatic interactions are evolving more quickly among populations in our placental species than the nonplacental species. We discuss how our results support the role parent-offspring conflicts play in the evolution of reproductive isolation and reproductive mode.