{"title":"Collapsing landmasses and secondary contacts: introgression and the evolution of adaptive diversity in Caucasian rock lizards.","authors":"David Tarkhnishvili, Mariami Todua, Giorgi Iankoshvili, Ortaç Çetintaş, Marine Murtskhvaladze, Alexey Yanchukov","doi":"10.1093/evolut/qpaf147","DOIUrl":"https://doi.org/10.1093/evolut/qpaf147","url":null,"abstract":"<p><p>Caucasian rock lizards (Darevskia) are known for high species diversity, adaptation to a broad range of habitats, and widespread hybridization patterns and gene introgression between the species. We explored the speciation history within a highly diverse \"caucasica\" clade of this genus by analyzing phylogenies based on the mitochondrial cytochrome b gene in representative samples of 16 described species, and the genome-wide SNP data genotyped using ddRAD-seq in six ingroup taxa. We also inferred geographic expansion pathways, which led to secondary contacts among the evolutionary lineages after periods of isolation. The analyses showed multiple introgression patterns in the secondary contact areas, evident from D-statistics and TreeMix analyses and the discordance between the mitochondrial and nuclear phylogenies. These processes may have shaped ecological niches and phenotypes in the incipient species, particularly in the rock-dwelling, ground-dwelling, and intermediate adaptive phenotypes. The role of introgression during a period between establishing secondary contacts among the diverging lineages and the development of effective prezygotic isolation in the speciation process is discussed.</p>","PeriodicalId":12082,"journal":{"name":"Evolution","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144599847","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EvolutionPub Date : 2025-07-09DOI: 10.1093/evolut/qpaf144
Sean Buckley
{"title":"Digest: A mosaic of genomic ancestries paints Iberian broom hare genomes.","authors":"Sean Buckley","doi":"10.1093/evolut/qpaf144","DOIUrl":"https://doi.org/10.1093/evolut/qpaf144","url":null,"abstract":"<p><p>The dynamic nature of evolutionary lineages means it is often challenging to disentangle historical patterns of diversification and hybridisation. Souto et al. (2025) use whole genome approaches to demonstrate the genomic legacy of demographic history and historical introgression on European hare species, including potentially functional changes in the broom hare genome. These findings highlight the pervasive nature of introgression in phylogeographic studies, with implications for biogeography and conservation management.</p>","PeriodicalId":12082,"journal":{"name":"Evolution","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144590752","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EvolutionPub Date : 2025-07-08DOI: 10.1093/evolut/qpaf146
Kevin F P Bennett, Peri E Bolton, Robb T Brumfield, Gerald S Wilkinson, Michael J Braun
{"title":"Impact of a putative riverine barrier on genomic population structure and gene flow in the presence of sexual selection.","authors":"Kevin F P Bennett, Peri E Bolton, Robb T Brumfield, Gerald S Wilkinson, Michael J Braun","doi":"10.1093/evolut/qpaf146","DOIUrl":"https://doi.org/10.1093/evolut/qpaf146","url":null,"abstract":"<p><p>Gene flow connects populations and facilitates the exchange of alleles, impacting speciation and adaptation. In western Panama, lekking golden-collared and white-collared manakins (Manacus vitellinus and M. candei, respectively) interbreed in a narrow hybrid zone across which males' brilliant yellow collar plumage, principally controlled by the carotenoid metabolism gene BCO2, has introgressed from vitellinus into candei under sexual selection. Plumage introgression is sharply limited across the lower reaches of the widest river in the region, but both color morphs occur on both riverbanks at its headwaters. Previous authors have speculated that the river may be a strong barrier to gene flow, preventing further plumage color introgression, but this hypothesis has never been tested. In this study, we used between ∼10,000 and 14,000 single nucleotide polymorphisms (SNPs) to test this hypothesis by assessing genetic differentiation and estimating gene flow across the river. We found that, while the river did show a clear effect of structuring genetic variation, particularly along its wide lower reaches, it was not sufficient to prevent extensive gene flow at its narrow headwaters. This result mirrors observed patterns at some of the world's larges rivers, albeit on a much smaller scale. It also implicates several possible alternatives to the strong barrier hypothesis, including that introgression is still ongoing or that selection for plumage color varies across the river. Either scenario is rare to capture in nature, and we recommend behavioral studies to further untangle this intriguing case of evolution in action.</p>","PeriodicalId":12082,"journal":{"name":"Evolution","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144583473","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EvolutionPub Date : 2025-07-08DOI: 10.1093/evolut/qpaf145
Tanner Lee
{"title":"Digest: The impact of egg and sperm proteins on sea urchin reproductive compatibility.","authors":"Tanner Lee","doi":"10.1093/evolut/qpaf145","DOIUrl":"https://doi.org/10.1093/evolut/qpaf145","url":null,"abstract":"<p><p>Levitan and Hao (2025) investigate reproductive isolation in sea urchins using fertilization assays, pinpointing amino acid substitutions that may cause isolation between species. Genotyping wild urchins showed that a single substitution in an egg protein could limit hybridization where two species coexist. Their findings shed light on how interspecific isolation can evolve and manifest in the wild, with eggs potentially under stronger selection to reduce hybridization due to higher costs.</p>","PeriodicalId":12082,"journal":{"name":"Evolution","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144583472","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EvolutionPub Date : 2025-07-08DOI: 10.1093/evolut/qpaf142
Elijah Reyes, Ailene MacPherson, Leithen K M'Gonigle
{"title":"It's better to be choosy in small populations: drift promotes the evolution of weak female preference for rare phenotypes.","authors":"Elijah Reyes, Ailene MacPherson, Leithen K M'Gonigle","doi":"10.1093/evolut/qpaf142","DOIUrl":"https://doi.org/10.1093/evolut/qpaf142","url":null,"abstract":"<p><p>Evidence from lab and field studies suggest that females sometimes prefer males bearing rare phenotypes. Such a finding poses a theoretical challenge, because preference for a rare phenotype makes that phenotype less rare, thereby lowering the fitness of sons bearing it. Further, a preference for rarity creates negative frequency-dependent selection which leads to equal representation of male types. This then eliminates any benefit to a preference for rarity. It seems paradoxical, then, that preference for rarity has been observed across so many taxa. Genetic drift, by promoting stochastic fixation or loss of alleles, is a source of constant rarity. Here we ask whether finite population sizes might provide the necessary conditions that favour a preference for rarity. Indeed, we find that drift, by constantly perturbing male display allele frequencies, provides the fuel required to favour a choosy female preference allele. Once this preference allele spreads, resultant negative frequency-dependent selection at the male display locus can act to maintain diversity in male display ornaments. Thus, drift plays an atypical role by helping maintain diversity. Further, we show that this finding is stronger in multi-patch landscapes. This work provides a novel potential explanation for the repeated evolution of female preference for rarity.</p>","PeriodicalId":12082,"journal":{"name":"Evolution","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144583474","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EvolutionPub Date : 2025-07-07DOI: 10.1093/evolut/qpaf138
James S Santangelo, Marc T J Johnson, Rob W Ness
{"title":"Signatures of selective sweeps in urban and rural white clover populations.","authors":"James S Santangelo, Marc T J Johnson, Rob W Ness","doi":"10.1093/evolut/qpaf138","DOIUrl":"https://doi.org/10.1093/evolut/qpaf138","url":null,"abstract":"<p><p>Urbanization is increasingly recognized as a powerful force of evolutionary change. However, anthropogenic sources of selection can often be similarly strong and multifarious in rural habitats, and whether selection differs in either strength or its targets between habitats is rarely considered. Despite numerous examples of phenotypic differentiation between urban and rural populations, we still lack an understanding of the genes enabling adaptation to these contrasting habitats. In this study, we conducted whole genome sequencing of 120 urban, suburban, and rural white clover plants from Toronto, Canada and used these data to identify urban and rural signatures of positive selection. We found evidence for selection in genomic regions involved in abiotic stress tolerance and growth/development in both urban and rural populations, and clinal change in allele frequencies at SNPs within these regions. Patterns of allele frequency and haplotype differentiation suggest that most sweeps are incomplete and our strongest signals of selective sweeps overlap known large-effect structural variants. These results highlight how both urban and rural habitats are driving ongoing selection in Toronto white clover populations, and motivate future work disentangling the genetic architecture of ecologically important phenotypes underlying adaptation to contemporary anthropogenic habitats.</p>","PeriodicalId":12082,"journal":{"name":"Evolution","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144583475","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EvolutionPub Date : 2025-07-07DOI: 10.1093/evolut/qpaf141
Dan Kehila, Alireza G Tafreshi, Nobuhiko Tokuriki
{"title":"Stability of multi-species consortia during microbial metabolic evolution.","authors":"Dan Kehila, Alireza G Tafreshi, Nobuhiko Tokuriki","doi":"10.1093/evolut/qpaf141","DOIUrl":"https://doi.org/10.1093/evolut/qpaf141","url":null,"abstract":"<p><p>Explaining multi-genic adaptations is a major objective of evolutionary theory. Metabolic pathways require multiple functional enzymes to generate a phenotype, and their evolution in microbes remains underexplored. In particular, sites polluted with manmade chemicals or \"xenobiotics\", like plastic or pesticides, provide evidence for the rapid adaptation of novel metabolic pathways in microbes, which degrade these xenobiotics into utilizable nutrients. Decades of microbiological studies revealed that these pathways often are not consolidated within a single microbial species but are rather distributed across several different species cooperatively degrading xenobiotics. These diverse consortia are remarkably stable in the laboratory, but the determinants of this stability have not been hereto addressed. In this study, we predict barriers to stable co-existence arising from the metabolic roles each species plays in the novel metabolic pathway. Then, we show that ecological variation in microbial life history overcomes these barriers and explains stable co-existence in mathematical models of exemplary consortia growing on a xenobiotic as the sole source of a limiting nutrient. Stability hinges on an \"ecological matching\" between a species' metabolic role and its nutrient utilization strategy which, if satisfied, can greatly accelerate the evolution of metabolic pathways in both field and laboratory.</p>","PeriodicalId":12082,"journal":{"name":"Evolution","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144583476","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EvolutionPub Date : 2025-07-04DOI: 10.1093/evolut/qpaf139
L Winkler, K B McNamara, M Lovegrove, J L Fitzpatrick, L W Simmons
{"title":"How resource acquisition influences the detection of trade-offs.","authors":"L Winkler, K B McNamara, M Lovegrove, J L Fitzpatrick, L W Simmons","doi":"10.1093/evolut/qpaf139","DOIUrl":"https://doi.org/10.1093/evolut/qpaf139","url":null,"abstract":"<p><p>Trade-offs should be ubiquitous in nature. Yet, direct trade-offs between traits essential for fitness are challenging to detect. Recent theory suggests that population level variation in resource acquisition could play an important role in our ability to detect trade-offs. Here, we test experimentally the hypothesis that the detection of trade-offs depends on the underlying distribution of individuals with different resource acquisition in a population. Specifically, we re-sampled ecologically and experimentally relevant resource acquisition distributions from a population of male Australian field crickets (Teleogryllus oceanicus) subjected to a continuous range of diet manipulation. While we found evidence for trade-offs between different male fitness traits, the distribution of resource acquisition in the population had no systematic effect on the strength of these trade-offs. Interestingly, trade-offs were most pronounced between post-copulatory traits and immune function, but trade-offs involving pre-copulatory traits were relatively weak. Overall, our findings question the hypothesis that resource acquisition may influence our ability to detect trade-offs and instead suggest that other factors, like the hierarchical complexity of resource allocation, make detecting trade-offs so elusive.</p>","PeriodicalId":12082,"journal":{"name":"Evolution","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144559552","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Phenotypic plasticity drives the development of laterality in the scale-eating cichlid fish Perissodus microlepis.","authors":"Nanako Marubayashi, Masaki Yasugi, Yuichi Takeuchi","doi":"10.1093/evolut/qpaf131","DOIUrl":"https://doi.org/10.1093/evolut/qpaf131","url":null,"abstract":"<p><p>Phenotypic plasticity, in which traits change in response to environmental conditions, is closely related to predator-prey interactions and speciation. The scale-eating cichlid fish Perissodus microlepis exhibits marked left-right differences in predatory behavior and mouth morphology. While phenotypic plasticity is hypothesized to contribute to the formation of laterality, direct evidence remains scarce. We examined how plasticity shapes laterality by analyzing the predatory behavior and mandibular changes under different foraging conditions: picking granulated feed (non-scale-eating) and tearing scales from prey fish. During the predation experiment, the number of attacks increased over time. Behavioral analysis revealed the mean inter-individual distance from scale-eater to prey gradually decreased, whereas mean swimming activity increased. Morphological analysis of the mandible showed elongation of the dentary bone along the anterior-posterior axis in the scale-eating groups compared to the non-scale-eating group. Furthermore, mandible height was significantly greater on the dominant side, with the degree of asymmetry increasing with scale-eating experience. This strongly suggests that phenotypic plasticity contributes to the enhancement of laterality and promotes disruptive selection of lateral morphs. This study advances our understanding of the unique adaptation in P. microlepis and highlights the importance of feeding experience in shaping adaptive traits within the cichlid lineage.</p>","PeriodicalId":12082,"journal":{"name":"Evolution","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144559553","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EvolutionPub Date : 2025-07-04DOI: 10.1093/evolut/qpaf137
Sarah Britton, Goggy Davidowitz
{"title":"Dietary constraints and costs of melanin pigmentation plasticity.","authors":"Sarah Britton, Goggy Davidowitz","doi":"10.1093/evolut/qpaf137","DOIUrl":"https://doi.org/10.1093/evolut/qpaf137","url":null,"abstract":"<p><p>Understanding the evolution of adaptive plasticity requires considering the costs of producing a plastic trait. We test the hypothesis that diet can act as a constraint on melanin pigmentation and lead to costly resource allocation trade-offs in Hyles lineata, the white-lined sphinx moth. In a diet manipulation experiment, we found that two aspects of melanin pigmentation, % melanic area and darkness, are relatively robust in the face of diet variation in environments where they are prioritized. Next, we tested whether larval melanin pigmentation is involved in resource allocation trade-offs with traits sharing the same dietary precursors: larval immune response, adult flight muscle mass, and adult wing pigmentation. Larval pigmentation trades off with both immunity and adult pigmentation. Contrary to many patterns reported in the literature, these trade-offs existed on the high resource diet, but not the low resource diet, indicating that certain traits may have a minimum threshold of expression. Larvae can plastically increase melanin pigmentation in contexts where melanin benefits outweigh costs, but otherwise reduce melanin pigmentation so that limited dietary precursors can be allocated to immunity and adult pigmentation. These context specific costs and benefits of melanin can help explain the adaptive value of melanin plasticity in this species.</p>","PeriodicalId":12082,"journal":{"name":"Evolution","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144559551","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}