Molecular Ecology最新文献

{"title":"Fire Frequency Driven Increases in Burn Heterogeneity Promote Microbial Beta Diversity: A Test of the Pyrodiversity-Biodiversity Hypothesis","authors":"Jacob R. Hopkins,&nbsp;Alison E. Bennett,&nbsp;Thomas P. McKenna","doi":"10.1111/mec.17756","DOIUrl":"10.1111/mec.17756","url":null,"abstract":"<p>Fire is a common ecological disturbance that structures terrestrial ecosystems and biological communities. The ability of fires to contribute to ecosystem heterogeneity has been termed pyrodiversity and has been directly linked to biodiversity (i.e., the pyrodiversity–biodiversity hypothesis). Since climate change models predict increases in fire frequency, understanding how fire pyrodiversity influences soil microbes is important for predicting how ecosystems will respond to fire regime changes. Here we tested how fire frequency-driven changes in burn patterns (i.e., pyrodiversity) influenced soil microbial communities and diversity. We assessed pyrodiversity effects on soil microbes by manipulating fire frequency (annual vs. biennial fires) in a tallgrass prairie restoration and evaluating how changes in burn patterns influenced microbial communities (bacteria and fungi). Annual burns produced more heterogeneous burn patterns (higher pyrodiversity) that were linked to shifts in fungal and bacterial community composition. While fire frequency did not influence microbial (bacteria and fungi) alpha diversity, beta diversity did increase with pyrodiversity. Changes in fungal community composition were not linked to burn patterns, suggesting that pyrodiversity effects on other ecosystem components (e.g., plants and soil characteristics) influenced fungal community dynamics and the greater beta diversity observed in the annually burned plots. Shifts in bacterial community composition were linked to variation in higher severity burn pattern components (grey and white ash), suggesting that thermotolerance contributed to the observed changes in bacterial community composition and lower beta diversity in the biennially burned plots. This demonstrates that fire frequency-driven increases in pyrodiversity augment biodiversity and may influence productivity in fire-prone ecosystems.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 10","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17756","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143787422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic Insights Into Introgression Between Quercus aquifolioides and Its Sympatric Relatives Across Elevational Gradients.","authors":"Yue-Bo Ren, Shu-Liang Yu, Hang Sun, Xiang-Guang Ma","doi":"10.1111/mec.17747","DOIUrl":"https://doi.org/10.1111/mec.17747","url":null,"abstract":"<p><p>Geographically widespread species tend to have more opportunities to hybridise with different related species. However, the evolutionary consequences of such multi-species hybridisation are still poorly understood. In the Hengduan Mountains of southwest China, Quercus aquifolioides and its closely related species form two types of elevational hybrid zone in different geographical areas (i.e., Q. aquifolioides-Q. guyavaefolia-Q. longispica and Q. aquifolioides-Q. spinosa). Here, we investigated genome-wide patterns of introgression between Q. aquifolioides and its sympatric relatives to assess the evolutionary consequences of multi-species hybridisation. A new assembled genome of Q. longispica as a reference genome and whole-genome resequencing data of these focal oaks were used in this study. Our results showed that bidirectional gene flow occurred between Q. aquifolioides and its sympatric relatives, and candidate genomic regions derived from introgression were broadly distributed across the oak genome. Local introgression with different sympatric relatives has fuelled the intraspecific divergence of Q. aquifolioides between two regions with different species compositions. We found genomic signatures of positive selection in some candidate introgressed regions. Putative adaptation signals were detected in candidate introgressed genes with diverse functions, including stress response and organism development and growth. In addition, we identified the genomic targets of environment-associated selection in Q. aquifolioides, some of which were located in candidate introgressed regions. In sum, this study demonstrates that local introgression with relatives is a non-negligible mechanism facilitating intraspecific divergence and reveals putative adaptive introgression between Q. aquifolioides and its sympatric relatives.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17747"},"PeriodicalIF":4.5,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143778647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Large Inversions Shape Diversification and Genome Evolution in Common Quails","authors":"Sara Ravagni,&nbsp;Santiago Montero-Mendieta,&nbsp;Jennifer A. Leonard,&nbsp;Matthew T. Webster,&nbsp;Matthew J. Christmas,&nbsp;Ignas Bunikis,&nbsp;José Domingo Rodríguez-Teijeiro,&nbsp;Ines Sanchez-Donoso,&nbsp;Carles Vilà","doi":"10.1111/mec.17740","DOIUrl":"10.1111/mec.17740","url":null,"abstract":"<div>\u0000 \u0000 <p>Chromosomal inversions, by suppressing recombination, can profoundly shape genome evolution and drive adaptation. In the common quail (<i>Coturnix coturnix</i>), a highly mobile bird with a vast Palearctic breeding range, we previously identified a massive inversion on chromosome 1 associated with distinct phenotypes and restricted geographic distribution. Here, using a new <i>de novo</i> genome assembly, we characterise this inversion and uncover additional, ancient structural variation on chromosome 2 that segregates across the species' range: either two putatively linked inversions or a single, large inversion that appears as two due to scaffolding limitations. Together, the inversions encompass a remarkable 15.6% of the quail genome (153.6 Mbp), creating highly divergent haplotypes that diverged over a million years ago. While the chromosome 1 inversion is linked to phenotypic differences, including morphology and migratory behaviour, the chromosome 2 inversion(s) show no such association. Notably, all inversion regions exhibit reduced effective population size and a relaxation of purifying selection, evidenced by elevated nonsynonymous-to-synonymous substitution ratios (N/S). This suggests that inversions, particularly the geographically restricted one on chromosome 1, may act as engines of diversification, accelerating the accumulation of functional variation and potentially contributing to local adaptation, especially within isolated island populations. Our findings demonstrate how large-scale chromosomal rearrangements can compartmentalise a genome, fostering distinct evolutionary trajectories within a single, highly mobile species.</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 9","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143778650","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Submerged Corridors of Ancient Gene Flow in an Island Amphibian","authors":"Miranda B. Sherlock,&nbsp;Mark Wilkinson,&nbsp;Simon T. Maddock,&nbsp;Ronald A. Nussbaum,&nbsp;Julia J. Day,&nbsp;Jeffrey W. Streicher","doi":"10.1111/mec.17742","DOIUrl":"10.1111/mec.17742","url":null,"abstract":"<p>Many island archipelagos sit on shallow continental shelves, and during the Pleistocene, these islands were often connected as global sea levels dropped following glaciation. Given a continental shelf only 30–60 m below sea level, the terrestrial biota of the Seychelles Archipelago likely dispersed amongst now isolated islands during the Pleistocene. <i>Hypogeophis rostratus</i> is an egg-laying, direct-developing caecilian amphibian found on 10 islands in the granitic Seychelles. Despite the seemingly limited dispersal abilities of this salt-intolerant amphibian, its distribution on multiple islands suggests likely historic dispersal across now submerged continental shelf corridors. We tested for the genetic signature of these historic corridors using fine-scale genomic data (ddRADseq). We found that genomic clusters often did not correspond to islands in the archipelago and that isolation-by-distance patterns were more consistent with gene flow across a continuous landscape than with isolated island populations. Using effective migration surfaces and ancestral range expansion prediction, we found support for contemporary populations originating near the large southern island of Mahé and dispersing to northern islands via the isolated Frégate island, with additional historic migration across the flat expanse of the Seychelles bank. Collectively, our results suggest that biogeographic patterns can retain signals from Pleistocene ‘palaeo-islands’ and that present-day islands can be thought of as hosting bottlenecks or transient refugia rather than discrete genetic units. Thus, the signatures of gene flow associated with palaeo-islands may be stronger than the isolating effects of contemporary islands in terrestrial species distributed on continental shelf islands.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 9","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17742","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143778654","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Understanding Dynamic Molecular Responses Is Key to Designing Environmental Stress Experiments: A Review of Gene and Protein Expression in Cnidaria Under Stress","authors":"Clarissa G. Molinari,&nbsp;Carmel McDougall,&nbsp;Kylie A. Pitt","doi":"10.1111/mec.17753","DOIUrl":"10.1111/mec.17753","url":null,"abstract":"<p>Gene and protein expression analyses are powerful tools to investigate the responses of cnidarians to stress, providing information on both genetic and functional variation and capturing dynamic shifts in organismal physiology. As the use of high throughput sequencing to understand responses of cnidarians to stressors is still relatively new, standard experimental protocols have not yet been established, which limits the ability to compare studies. We (1) systematically reviewed the literature of cnidarian gene and protein expression studies related to environmental stressors to determine how the laboratory experiments were designed and (2) investigated the consistency in responses of genes commonly used as biomarkers within stress experiments conducted on the five most-studied cnidarian genera. Duration of exposure to the stressor, acclimation period and intensity of stress varied greatly among experiments, and most studies did not sample during acclimation and recovery. Before designing experiments that aim to characterise molecular responses to a specific environmental stress, research efforts need to focus on understanding the plasticity of whole transcriptome responses, as gene expression can vary under different stress intensities and durations of exposure. Additionally, only seven genes that were tested in at least two different genera showed a consistent response under heat stress (CuZn-SOD, c-type lectin, FGFR1, MMP, Zn-MP, NF-κB and SLC26). These genes have the potential to standardise evaluations of temperature stress across experiments on cnidarians, and we suggest exploring their use as general cnidarian biomarkers of temperature stress (cBATS).</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 9","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17753","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143762523","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multiple Pathways to Red Carotenoid Coloration: House Finches (Haemorhous mexicanus) Do Not Use CYP2J19 to Produce Red Plumage","authors":"Rebecca E. Koch,&nbsp;Christy N. Truong,&nbsp;Hannah R. Reeb,&nbsp;Brooke H. Joski,&nbsp;Geoffrey E. Hill,&nbsp;Yufeng Zhang,&nbsp;Matthew B. Toomey","doi":"10.1111/mec.17744","DOIUrl":"10.1111/mec.17744","url":null,"abstract":"<p>The carotenoid-based colours of birds are a celebrated example of biological diversity and an important system for the study of evolution. Recently, a two-step mechanism, with the enzymes cytochrome P450 2J19 (CYP2J19) and 3-hydroxybutyrate dehydrogenase 1-like (BDH1L), was described for the biosynthesis of red ketocarotenoids from yellow dietary carotenoids in the retina and plumage of birds. A common assumption has been that all birds with ketocarotenoid-based plumage coloration used this CYP2J19/BDH1L mechanism to produce red feathers. We tested this assumption in house finches (<i>Haemorhous mexicanus</i>) by examining the catalytic function of the house finch homologues of these enzymes and tracking their expression in birds growing new feathers. We found that CYP2J19 and BDH1L did not catalyse the production of 3-hydroxy-echinenone (3-OH-echinenone), the primary red plumage pigment of house finches, when provided with common dietary carotenoid substrates. Moreover, gene expression analyses revealed little to no expression of <i>CYP2J19</i> in liver tissue or growing feather follicles, the putative sites of pigment metabolism in moulting house finches. Finally, although the hepatic mitochondria of house finches have high concentrations of 3-OH-echinenone, observations using fluorescent markers suggest that both CYP2J19 and BDH1L localise to the endomembrane system rather than the mitochondria. We propose that house finches and other birds that deposit 3-OH-echinenone as their primary red plumage pigment use an alternative enzymatic pathway to produce their characteristic red ketocarotenoid-based coloration.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 9","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17744","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750344","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Temporal Dynamics of Genetic Diversity in Protected and Unprotected Wild Rice (Oryza rufipogon) Populations: Implications for Conservation","authors":"Zhi-Zhou He,&nbsp;Wen-Wen Shao,&nbsp;Olivier Honnay,&nbsp;Hui Liao,&nbsp;Hao Chen,&nbsp;Jing Liu,&nbsp;Shan-Shan Dong,&nbsp;Ding Li,&nbsp;Guo-Zhen Fan,&nbsp;Yao Zhao,&nbsp;Jun Rong,&nbsp;Yan Liu,&nbsp;Fan Lu,&nbsp;Xin-Hong Cui,&nbsp;Wen-Ju Zhang,&nbsp;Yu-Guo Wang,&nbsp;Lin-Feng Li,&nbsp;Ji Yang,&nbsp;Zhi-Ping Song","doi":"10.1111/mec.17750","DOIUrl":"10.1111/mec.17750","url":null,"abstract":"<div>\u0000 \u0000 <p>Genetic diversity is vital for population survival, yet there is a paucity of studies focusing on the effectiveness of establishing protected areas for maintaining the population genetic diversity of threatened plant species. To evaluate the effectiveness of in situ conservation measures, we used simple sequence repeats (SSR) and single nucleotide polymorphisms (SNP) markers to monitor temporal dynamics in genetic diversity of the threatened wild rice <i>Oryza rufipogon</i> in both protected and unprotected populations in China between 2001 and 2020. Unprotected populations tended to have decreased census population sizes (<i>Nc</i>) compared to protected populations, although they both showed a reduction in effective population size (<i>Ne</i>). While allele diversity and expected heterozygosity remained stable, several populations, especially those without protection, exhibited a significant decrease in observed heterozygosity (<i>Ho</i>) and an increase in inbreeding (<i>F</i>_IS). The level of genetic differentiation between populations did not change over time, but the number of private alleles increased and <i>Ne</i> varied in several populations, indicating the effects of genetic drift. Indicators for temporal trends in <i>Ho</i>, <i>F</i>_IS, and <i>Ne</i> revealed that both protected and unprotected populations are facing warnings of declining genetic diversity, although some protected populations remain resilient, reflecting the genetic lag behind <i>Nc</i> change. Overall, these findings highlight the effectiveness of in situ conservation efforts in maintaining population size and genetic diversity, yet we also show the necessity of lasting population dynamics monitoring, using different genetic indicators.</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 9","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143741932","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Geographic Variation in Epigenetic Responses to Hypoxia in Deer Mice (Peromyscus maniculatus) Distributed Along an Elevational Gradient","authors":"Dhriti Tandon,&nbsp;Shane Campbell-Staton,&nbsp;Zachary Cheviron,&nbsp;Bridgett M. von Holdt","doi":"10.1111/mec.17752","DOIUrl":"10.1111/mec.17752","url":null,"abstract":"<p>Lowland and highland <i>Peromyscus maniculatus</i> populations display divergent, locally adapted physiological phenotypes shaped by altitudinal differences in oxygen availability. Many physiological responses to hypoxia seem to have evolved in lowland ancestors to offset episodic and localised bouts of low internal oxygen availability. However, upon chronic hypoxia exposure at high elevation, these responses can lead to physiological complications. Therefore, highland ancestry is often associated with evolved hypoxia responses, particularly traits promoting tolerance of constant hypoxia. Environmentally induced DNA methylation can dynamically alter gene expression patterns, providing a proximate basis for phenotypic plasticity. Given each population's differential reliance on plasticity for hypoxia tolerance, we hypothesised that lowland mice have a more robust epigenetic response to hypoxia exposure, driving trait plasticity, than highland mice. Using DNA methylation data of tissues from the heart's left ventricle, we show that upon hypoxia exposure, lowland mice chemically modulate the epigenetic landscape to a greater extent than highland mice, especially at key hypoxia-relevant genes such as <i>Egln3</i>. This gene is a regulator of the gene <i>Epas1</i> that is frequently targeted for positive selection at high elevation. We find higher methylation among wild highland mice at gene <i>Egln3</i> compared to wild lowland mice, suggesting a shared epigenetic ancestral response to episodic and chronic hypoxia. These findings highlight each population's distinct reliance on molecular plasticity driven by their unique evolutionary histories.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 9","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17752","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143741925","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metagenomic Insights Into the Dietary Diversity of the Adaptive Radiation of Cichlid Fishes in Lake Tanganyika","authors":"Charlotte E. T. Huyghe,&nbsp;Antoine Fages,&nbsp;Fabrizia Ronco,&nbsp;Adrian Indermaur,&nbsp;Frederic D. B. Schedel,&nbsp;Ismael Kimirei,&nbsp;Lawrence Makasa,&nbsp;Patrick Tschopp,&nbsp;Walter Salzburger","doi":"10.1111/mec.17743","DOIUrl":"10.1111/mec.17743","url":null,"abstract":"<div>\u0000 \u0000 <p>Diet specialisation is a main driver of diversification in many adaptive radiations. Therefore, identifying diet items is essential to characterise trophic specialisations and to understand the dynamics of dietary adaptations. In this study, we explored the trophic niches of 56 species from the adaptive radiation of cichlid fishes in Lake Tanganyika, encompassing all major phylogenetic lineages and feeding specialisations. We employed a metagenomic sequencing approach to identify the food sources of the investigated species at high taxonomic resolution, sequencing over 400 digestive content samples from wild-caught individuals at around 50 million paired-end read depth per sample. Our analyses revealed Arthropoda, Chordata (fishes), Bacillariophyta and Streptophyta as the primary diet phyla of the Tanganyikan cichlids. Moreover, we confirmed the presence of other food sources and identified taxa not previously documented to be part of the cichlids' diet. Based on their dietary compositions, the Tanganyikan cichlids can be grouped into herbivores, invertivores, piscivores and mixed feeders. Further, we showed that trophic disparity in the radiation is shaped by rapid divergence and documented cases of dietary niche convergence. Diet composition correlated with carbon and nitrogen stable isotope values, gut length, and body morphology. Differences in diet—such as the consumption of diatoms, streptophytes and chlorophytes versus fish and arthropods—were associated with changes in body, upper oral jaw and lower pharyngeal jaw shape. Collectively, this study presents a comprehensive and detailed diet classification of the Tanganyikan cichlids, highlighting the power of metagenomic approaches in delineating dietary adaptations.</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 9","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143741928","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic, Phenotypic and Environmental Correlates of Speciation in the Midwife Toads (Alytes)","authors":"Johanna Ambu,&nbsp;Spartak N. Litvinchuk,&nbsp;Carlos Caballero-Díaz,&nbsp;Alfredo Nicieza,&nbsp;Guillermo Velo-Antón,&nbsp;Helena Gonçalves,&nbsp;Fernando Martínez-Freiría,&nbsp;Helena Martínez-Gil,&nbsp;Juan Francisco Beltrán,&nbsp;David Donaire-Barroso,&nbsp;Axel Hernandez,&nbsp;Tomasz Suchan,&nbsp;Pierre-André Crochet,&nbsp;ĺñigo Martínez-Solano,&nbsp;Christophe Dufresnes","doi":"10.1111/mec.17736","DOIUrl":"10.1111/mec.17736","url":null,"abstract":"<p>Speciation, i.e., the formation of new species, implies that diverging populations evolve genetic, phenotypic or ecological factors that promote reproductive isolation (RI), but the relative contributions of these factors remain elusive. Here we test which of genomic, bioacoustic, morphological, and environmental differences best predicts RI across a continuum of divergence in the midwife toads (genus <i>Alytes</i>), a group of Western Mediterranean amphibians, using a total evidence approach. We found that, without strong geographic barriers to dispersal, the extent of introgression across hybrid zones between phylogeographic lineages, which should reflect the strength of RI, predominantly covaries with genomic divergence. Overall phenotypic differentiation becomes substantial only between well established, fully isolated species. These results suggest that speciation in midwife toads initially involve cryptic lineages, which probably evolve RI through intrinsic (genetic) hybrid incompatibilities. As they continue to diverge, these nascent species eventually differentiate externally, which potentially enforces pre-mating barriers and facilitates sympatry. This speciation scenario has practical implications for species delimitation, notably when using hybrid zones and divergence thresholds as proxies for reproductive isolation.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 8","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17736","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699271","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}