@article{19438, abstract = {Polymorphic short insertions and deletions (INDELs 50 bp) are abundant, although less common than single nucleotide polymorphisms (SNPs). Evidence from model organisms shows INDELs to be more strongly influenced by purifying selection than SNPs. Partly for this reason, INDELs are rarely used as markers for demographic processes or to detect divergent selection. Here, we compared INDELs and SNPs in the intertidal snail Littorina saxatilis, focussing on hybrid zones between ecotypes, in order to test the utility of INDELs in the detection of divergent selection. We computed INDEL and SNP site frequency spectra using capture sequencing data. We assessed the impact of divergent selection by analyzing allele frequency clines across habitat boundaries. We also examined the influence of GC-biased gene conversion because it may be confounded with signatures of selection. We show evidence that short INDELs are affected more by purifying selection than SNPs, but part of the observed site frequency spectra difference can be attributed to GC-biased gene conversion. We did not find a difference in the impact of divergent selection between short INDELs and SNPs. Short INDELs and SNPs were similarly distributed across the genome and so are likely to respond to indirect selection in the same way. A few regions likely affected by divergent selection were revealed by INDELs and not by SNPs. Short INDELs can be useful (additional) genetic markers helping to identify genomic regions important for adaptation and population divergence.}, author = {Perini, Samuel and Johannesson, Kerstin and Butlin, Roger K. and Westram, Anja M}, issn = {1420-9101}, journal = {Journal of Evolutionary Biology}, number = {3}, pages = {367--378}, publisher = {Oxford University Press}, title = {{Short INDELs and SNPs as markers of evolutionary processes in hybrid zones}}, doi = {10.1093/jeb/voaf002}, volume = {38}, year = {2025}, } @article{17207, author = {Fouqueau, Louise and Polechova, Jitka}, issn = {1420-9101}, journal = {Journal of evolutionary biology}, number = {6}, pages = {579--587}, publisher = {Oxford University Press}, title = {{Eco-evolutionary dynamics in changing environments: Integrating theory with data}}, doi = {10.1093/jeb/voae067}, volume = {37}, year = {2024}, } @article{17237, abstract = {The impact of climate change on populations will be contingent upon their contemporary adaptive evolution. In this study, we investigated the contemporary evolution of 4 populations of the cold-water kelp Laminaria digitata by analyzing their spatial and temporal genomic variations using ddRAD-sequencing. These populations were sampled from the center to the southern margin of its north-eastern Atlantic distribution at 2 time points, spanning at least 2 generations. Through genome scans for local adaptation at a single time point, we identified candidate loci that showed clinal variation correlated with changes in sea surface temperature (SST) along latitudinal gradients. This finding suggests that SST may drive the adaptive response of these kelp populations, although factors such as species’ demographic history should also be considered. Additionally, we performed a simulation approach to distinguish the effect of selection from genetic drift in allele frequency changes over time. This enabled the detection of loci in the southernmost population that exhibited temporal differentiation beyond what would be expected from genetic drift alone: these are candidate loci which could have evolved under selection over time. In contrast, we did not detect any outlier locus based on temporal differentiation in the population from the North Sea, which also displayed low and decreasing levels of genetic diversity. The diverse evolutionary scenarios observed among populations can be attributed to variations in the prevalence of selection relative to genetic drift across different environments. Therefore, our study highlights the potential of temporal genomics to offer valuable insights into the contemporary evolution of marine foundation species facing climate change.}, author = {Reynes, Lauric and Fouqueau, Louise and Aurelle, Didier and Mauger, Stephane and Destombe, Christophe and Valero, Myriam}, issn = {1420-9101}, journal = {Journal of Evolutionary Biology}, number = {6}, pages = {677--692}, publisher = {Oxford University Press}, title = {{Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary evolution of kelp populations}}, doi = {10.1093/jeb/voae048}, volume = {37}, year = {2024}, } @article{17238, abstract = {We know that heritable variation is abundant, and that selection causes all but the smallest populations to rapidly shift beyond their original trait distribution. So then, what limits the range of a species? There are physical constraints and also population genetic limits to the effectiveness of selection, ultimately set by population size. Global adaptation, where the same genotype is favoured over the whole range, is most efficient when based on a multitude of weakly selected alleles and is effective even when local demes are small, provided that there is some gene flow. In contrast, local adaptation is sensitive to gene flow and may require alleles with substantial effect. How can populations combine the advantages of large effective size with the ability to specialise into local niches? To what extent does reproductive isolation help resolve this tension? I address these questions using eco-evolutionary models of polygenic adaptation, contrasting discrete demes with continuousspace.}, author = {Barton, Nicholas H}, issn = {1420-9101}, journal = {Journal of Evolutionary Biology}, number = {6}, pages = {605--615}, publisher = {Oxford University Press}, title = {{Limits to species' range: The tension between local and global adaptation}}, doi = {10.1093/jeb/voae052}, volume = {37}, year = {2024}, } @article{14556, abstract = {Inversions are structural mutations that reverse the sequence of a chromosome segment and reduce the effective rate of recombination in the heterozygous state. They play a major role in adaptation, as well as in other evolutionary processes such as speciation. Although inversions have been studied since the 1920s, they remain difficult to investigate because the reduced recombination conferred by them strengthens the effects of drift and hitchhiking, which in turn can obscure signatures of selection. Nonetheless, numerous inversions have been found to be under selection. Given recent advances in population genetic theory and empirical study, here we review how different mechanisms of selection affect the evolution of inversions. A key difference between inversions and other mutations, such as single nucleotide variants, is that the fitness of an inversion may be affected by a larger number of frequently interacting processes. This considerably complicates the analysis of the causes underlying the evolution of inversions. We discuss the extent to which these mechanisms can be disentangled, and by which approach.}, author = {Berdan, Emma L. and Barton, Nicholas H and Butlin, Roger and Charlesworth, Brian and Faria, Rui and Fragata, Inês and Gilbert, Kimberly J. and Jay, Paul and Kapun, Martin and Lotterhos, Katie E. and Mérot, Claire and Durmaz Mitchell, Esra and Pascual, Marta and Peichel, Catherine L. and Rafajlović, Marina and Westram, Anja M and Schaeffer, Stephen W. and Johannesson, Kerstin and Flatt, Thomas}, issn = {1420-9101}, journal = {Journal of Evolutionary Biology}, number = {12}, publisher = {Wiley}, title = {{How chromosomal inversions reorient the evolutionary process}}, doi = {10.1111/jeb.14242}, volume = {36}, year = {2023}, } @article{12264, abstract = {Reproductive isolation (RI) is a core concept in evolutionary biology. It has been the central focus of speciation research since the modern synthesis and is the basis by which biological species are defined. Despite this, the term is used in seemingly different ways, and attempts to quantify RI have used very different approaches. After showing that the field lacks a clear definition of the term, we attempt to clarify key issues, including what RI is, how it can be quantified in principle, and how it can be measured in practice. Following other definitions with a genetic focus, we propose that RI is a quantitative measure of the effect that genetic differences between populations have on gene flow. Specifically, RI compares the flow of neutral alleles in the presence of these genetic differences to the flow without any such differences. RI is thus greater than zero when genetic differences between populations reduce the flow of neutral alleles between populations. We show how RI can be quantified in a range of scenarios. A key conclusion is that RI depends strongly on circumstances—including the spatial, temporal and genomic context—making it difficult to compare across systems. After reviewing methods for estimating RI from data, we conclude that it is difficult to measure in practice. We discuss our findings in light of the goals of speciation research and encourage the use of methods for estimating RI that integrate organismal and genetic approaches.}, author = {Westram, Anja M and Stankowski, Sean and Surendranadh, Parvathy and Barton, Nicholas H}, issn = {1420-9101}, journal = {Journal of Evolutionary Biology}, keywords = {Ecology, Evolution, Behavior and Systematics}, number = {9}, pages = {1143--1164}, publisher = {Wiley}, title = {{What is reproductive isolation?}}, doi = {10.1111/jeb.14005}, volume = {35}, year = {2022}, } @article{12265, author = {Westram, Anja M and Stankowski, Sean and Surendranadh, Parvathy and Barton, Nicholas H}, issn = {1420-9101}, journal = {Journal of Evolutionary Biology}, keywords = {Ecology, Evolution, Behavior and Systematics}, number = {9}, pages = {1200--1205}, publisher = {Wiley}, title = {{Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’}}, doi = {10.1111/jeb.14082}, volume = {35}, year = {2022}, } @article{8708, abstract = {The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study ‘replicated’ instances of secondary contact between closely related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry‐informative panel of such SNPs. We then compared their frequencies in newly sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi‐stable variants (Dobzhansky‐Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact.}, author = {Simon, Alexis and Fraisse, Christelle and El Ayari, Tahani and Liautard‐Haag, Cathy and Strelkov, Petr and Welch, John J and Bierne, Nicolas}, issn = {1420-9101}, journal = {Journal of Evolutionary Biology}, number = {1}, pages = {208--223}, publisher = {Wiley}, title = {{How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels}}, doi = {10.1111/jeb.13709}, volume = {34}, year = {2021}, } @article{8928, abstract = {Domestication is a human‐induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species‐specific demographic processes between species. A convergent history of domestication with gene flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species‐specific and supported by the few historical records available.}, author = {Arnoux, Stéphanie and Fraisse, Christelle and Sauvage, Christopher}, issn = {1420-9101}, journal = {Journal of Evolutionary Biology}, number = {2}, pages = {270--283}, publisher = {Wiley}, title = {{Genomic inference of complex domestication histories in three Solanaceae species}}, doi = {10.1111/jeb.13723}, volume = {34}, year = {2021}, } @article{9100, abstract = {Marine environments are inhabited by a broad representation of the tree of life, yet our understanding of speciation in marine ecosystems is extremely limited compared with terrestrial and freshwater environments. Developing a more comprehensive picture of speciation in marine environments requires that we 'dive under the surface' by studying a wider range of taxa and ecosystems is necessary for a more comprehensive picture of speciation. Although studying marine evolutionary processes is often challenging, recent technological advances in different fields, from maritime engineering to genomics, are making it increasingly possible to study speciation of marine life forms across diverse ecosystems and taxa. Motivated by recent research in the field, including the 14 contributions in this issue, we highlight and discuss six axes of research that we think will deepen our understanding of speciation in the marine realm: (a) study a broader range of marine environments and organisms; (b) identify the reproductive barriers driving speciation between marine taxa; (c) understand the role of different genomic architectures underlying reproductive isolation; (d) infer the evolutionary history of divergence using model‐based approaches; (e) study patterns of hybridization and introgression between marine taxa; and (f) implement highly interdisciplinary, collaborative research programmes. In outlining these goals, we hope to inspire researchers to continue filling this critical knowledge gap surrounding the origins of marine biodiversity.}, author = {Faria, Rui and Johannesson, Kerstin and Stankowski, Sean}, issn = {1420-9101}, journal = {Journal of Evolutionary Biology}, number = {1}, pages = {4--15}, publisher = {Wiley}, title = {{Speciation in marine environments: Diving under the surface}}, doi = {10.1111/jeb.13756}, volume = {34}, year = {2021}, } @article{7205, abstract = {Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the "Crab" and "Wave" ecotypes of the snail Littorina saxatilis, divergent selection forms strong barriers to gene flow, while the role of post‐zygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Post‐zygotic barriers might include genetic incompatibilities (e.g. Dobzhansky–Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of >500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1,011 embryos (mean 130 ± 123), and abortion rates varied between 0% and 100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterized female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index, and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant post‐zygotic barriers contributing to ecotype divergence, and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females.}, author = {Johannesson, Kerstin and Zagrodzka, Zuzanna and Faria, Rui and Westram, Anja M and Butlin, Roger K.}, issn = {1420-9101}, journal = {Journal of Evolutionary Biology}, number = {3}, pages = {342--351}, publisher = {Wiley}, title = {{Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes?}}, doi = {10.1111/jeb.13570}, volume = {33}, year = {2020}, } @article{617, abstract = {Insects are exposed to a variety of potential pathogens in their environment, many of which can severely impact fitness and health. Consequently, hosts have evolved resistance and tolerance strategies to suppress or cope with infections. Hosts utilizing resistance improve fitness by clearing or reducing pathogen loads, and hosts utilizing tolerance reduce harmful fitness effects per pathogen load. To understand variation in, and selective pressures on, resistance and tolerance, we asked to what degree they are shaped by host genetic background, whether plasticity in these responses depends upon dietary environment, and whether there are interactions between these two factors. Females from ten wild-type Drosophila melanogaster genotypes were kept on high- or low-protein (yeast) diets and infected with one of two opportunistic bacterial pathogens, Lactococcus lactis or Pseudomonas entomophila. We measured host resistance as the inverse of bacterial load in the early infection phase. The relationship (slope) between fly fecundity and individual-level bacteria load provided our fecundity tolerance measure. Genotype and dietary yeast determined host fecundity and strongly affected survival after infection with pathogenic P. entomophila. There was considerable genetic variation in host resistance, a commonly found phenomenon resulting from for example varying resistance costs or frequency-dependent selection. Despite this variation and the reproductive cost of higher P. entomophila loads, fecundity tolerance did not vary across genotypes. The absence of genetic variation in tolerance may suggest that at this early infection stage, fecundity tolerance is fixed or that any evolved tolerance mechanisms are not expressed under these infection conditions.}, author = {Kutzer, Megan and Kurtz, Joachim and Armitage, Sophie}, issn = {1420-9101}, journal = {Journal of Evolutionary Biology}, number = {1}, pages = {159 -- 171}, publisher = {Wiley}, title = {{Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance}}, doi = {10.1111/jeb.13211}, volume = {31}, year = {2018}, } @article{1905, abstract = {The unprecedented polymorphism in the major histocompatibility complex (MHC) genes is thought to be maintained by balancing selection from parasites. However, do parasites also drive divergence at MHC loci between host populations, or do the effects of balancing selection maintain similarities among populations? We examined MHC variation in populations of the livebearing fish Poecilia mexicana and characterized their parasite communities. Poecilia mexicana populations in the Cueva del Azufre system are locally adapted to darkness and the presence of toxic hydrogen sulphide, representing highly divergent ecotypes or incipient species. Parasite communities differed significantly across populations, and populations with higher parasite loads had higher levels of diversity at class II MHC genes. However, despite different parasite communities, marked divergence in adaptive traits and in neutral genetic markers, we found MHC alleles to be remarkably similar among host populations. Our findings indicate that balancing selection from parasites maintains immunogenetic diversity of hosts, but this process does not promote MHC divergence in this system. On the contrary, we suggest that balancing selection on immunogenetic loci may outweigh divergent selection causing divergence, thereby hindering host divergence and speciation. Our findings support the hypothesis that balancing selection maintains MHC similarities among lineages during and after speciation (trans-species evolution).}, author = {Tobler, Michael and Plath, Martin and Riesch, Rüdiger and Schlupp, Ingo and Grasse, Anna V and Munimanda, Gopi and Setzer, C and Penn, Dustin and Moodley, Yoshan}, issn = {1420-9101}, journal = {Journal of Evolutionary Biology}, number = {5}, pages = {960 -- 974}, publisher = {Wiley}, title = {{Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations}}, doi = {10.1111/jeb.12370}, volume = {27}, year = {2014}, }