S J Lehnert, T Kess, P Bentzen, N Barson, S Lien, J B Dempson, I R Bradbury
{"title":"Large Haplotypes Linked to Climate and Life History Variation in Divergent Lineages of Atlantic Salmon (Salmo salar).","authors":"S J Lehnert, T Kess, P Bentzen, N Barson, S Lien, J B Dempson, I R Bradbury","doi":"10.1111/mec.70107","DOIUrl":"https://doi.org/10.1111/mec.70107","url":null,"abstract":"<p><p>Advances in sequencing are revealing that linked genomic architectures, enabling the evolution of co-adapted alleles at multiple loci, often shape complex phenotypes. Several recent studies have identified such architectures (e.g., chromosomal rearrangements and supergenes) contributing to adaptation or divergence across diverse species, from plants to mammals. Specifically, within Atlantic salmon (Salmo salar ), genomic studies are revealing large haplotypes and structural variants that may underpin local adaptation in the species. Using data from > 4000 individuals from 134 locations spanning the North Atlantic Ocean, we identify a large (~3 Mbp) genomic region on Ssa18 showing patterns of differentiation and linkage disequilibrium (LD) indicative of a large haplotype block containing three divergent haplotypes (herein A, B and C haplotypes). In Europe, haplotypes A and B were common, whereas A and C were more common within North America, suggesting a shared 'ancestral' A haplotype, with different continent-specific alternative haplotypes. Data support independent origins of divergent haplotypes in each continent, as well as signals of trans-oceanic introgression of haplotypes. Haplotype frequency is strongly associated with latitude, climate and life history (smolt age); however, the strength and direction of these relationships vary across continents. Overall, our analyses were consistent with other studies that identify chromosomal rearrangements; however, long-read sequence data did not find evidence of a structural variant, and instead an ancestral fusion may explain the formation and maintenance of the observed haplotypes. Our study contributes to ongoing efforts to understand the evolutionary role of linked genomic architecture in Atlantic salmon and its significance in salmonid diversification.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70107"},"PeriodicalIF":3.9,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145224830","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}
Bonnie T Derne, Stephanie S Godfrey, Mark N Hutchinson, Philip Weinstein, Michael G Gardner
{"title":"Mixing in Moderation: Slow Transmission of Non-Local Macroparasites Following a Population Augmentation of an Endangered Australian Skink.","authors":"Bonnie T Derne, Stephanie S Godfrey, Mark N Hutchinson, Philip Weinstein, Michael G Gardner","doi":"10.1111/mec.70121","DOIUrl":"https://doi.org/10.1111/mec.70121","url":null,"abstract":"<p><p>Translocating threatened wildlife to more suitable habitat is increasingly necessary for conserving biodiversity. However, parasite dynamics in such translocations are poorly characterised, despite their potential importance for influencing translocation success and contributing to biodiversity and ecosystem function. We used single nucleotide polymorphism (SNP) genotyping to evaluate the transmission of parasites with different population origins following a population augmentation of the endangered pygmy bluetongue lizard (Tiliqua adelaidensis) involving three isolated, wild populations in South Australia. We examined inter-population genetic variation for source and recipient host populations in the ecotoparasitic mite Ophiomegistus michaeli and the nematode pinworm Pharyngodon wandillahensis. Ordination and STRUCTURE analyses of SNP markers revealed population-based genetic structure, particularly for P. wandillahensis. For 2 years following the population augmentation, hosts mostly retained parasite genotypes congruent with their origin, though cluster exceptions suggested some inter-population transmission over time. Modelling of parasite pairwise relatedness over time supported different P. wandillahensis lineages gradually infecting hosts from different sources, as relatedness increased between nematodes collected from different hosts, particularly those from different source populations, and conversely decreased between nematodes collected from the same host. In contrast, O. michaeli pairwise relatedness changed little over time, suggesting minimal inter-host movement. The apparently minimal and slow nature of transmission of non-local mites and nematodes between translocated and resident host lizards is likely driven by the non-social nature of T. adelaidensis and as yet uncharacterised aspects of the parasites' life histories, highlighting the importance of considering these during conservation management.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70121"},"PeriodicalIF":3.9,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145190522","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}
Pierre Methou, Shannon B Johnson, John Sherrin, Timothy M Shank, Chong Chen, Verena Tunnicliffe
{"title":"A Tale of Two Shrimps-Speciation and Demography of Two Sympatric Shrimp Species From Hydrothermal Vents.","authors":"Pierre Methou, Shannon B Johnson, John Sherrin, Timothy M Shank, Chong Chen, Verena Tunnicliffe","doi":"10.1111/mec.70119","DOIUrl":"https://doi.org/10.1111/mec.70119","url":null,"abstract":"<p><p>Hydrothermal vents can serve as natural laboratories to study speciation processes due to their fragmented distribution, often with geographic barriers between habitats. Two sympatric species of Rimicaris shrimps occur at vents on the Izu-Bonin-Mariana volcanic arc: Rimicaris loihi also occurs near Hawai'i and R. cambonae is present on the Tonga Arc. These two species biogeographically co-occur and are genetically similar, raising questions about their speciation mechanisms, how they maintain distinct species, and whether interbreeding occurs. Here, we used barcoding and shotgun sequencing to test their genetic isolation and investigate their speciation process. We also evaluated population demography over 10 years to assess population densities and sex ratios at vents. Our results supported R. cambonae and R. loihi as two distinct species despite sympatry throughout part of their range. We also observed regional-scale genetic structure among R. loihi populations from the Izu-Bonin-Mariana volcanic arc, despite high dispersal potential. Finally, we found concomitant variations of shrimp densities and genetic diversity following fluctuations in geological and venting activities over a decade. A combination of geological instability, ocean currents dynamics and sea-level changes might drive temporary isolation among these local populations. We suggest that similar factors, with longer isolation periods, may also have promoted speciation between the two Rimicaris species, whereas distinct life-history traits could strengthen and maintain reproductive barriers. Overall, we found that the two species with large geographic distributions had significant patterns of genetic partitioning on a volcanic arc; this scenario contrasts with those observed previously at vents from mid-ocean ridges or back-arc basin systems.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70119"},"PeriodicalIF":3.9,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145184417","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}
Jill Ashey, Federica Scucchia, Ariana S Huffmyer, Hollie M Putnam, Tali Mass
{"title":"Thermal and Acidification Gradients Reveal Tolerance Thresholds in Pocillopora acuta Recruits.","authors":"Jill Ashey, Federica Scucchia, Ariana S Huffmyer, Hollie M Putnam, Tali Mass","doi":"10.1111/mec.70116","DOIUrl":"https://doi.org/10.1111/mec.70116","url":null,"abstract":"<p><p>Ocean warming and acidification are among the biggest threats to the persistence of coral reefs. Organismal stress tolerance thresholds are life stage specific, can vary across levels of biological organisation and also depend on natural environmental variability. Here, we exposed the early life stages of Pocillopora acuta in Kāne'ohe Bay, Hawai'i, USA, a common reef-building coral throughout the Pacific, to projected ocean warming and acidification scenarios. We measured ecological, physiological, biomineralisation and molecular responses across the critical transition from larvae to newly settled recruits following 6 days of exposure to diel fluctuations in temperature and pH in Control (26.8°C-27.9°C, 7.82-7.96 pH<sub>Total</sub>), Mid (28.4°C-29.5°C, 7.65-7.79 pH<sub>Total</sub>) and High conditions (30.2°C-31.5°C, 7.44-7.59 pH<sub>Total</sub>). We found that P. acuta early life stages are capable of survival, settlement and calcification under all scenarios. The High conditions, however, caused a significant reduction in survival and settlement capacity, with changes in the skeletal fibre deposition patterns. Although there was limited impact on the expression of biomineralisation genes, exposure to High conditions resulted in strong transcriptomic responses including depressed metabolism, reduced ATP production and increased activity of DNA damage-repair processes, indicative of a compromised metabolic state. Collectively, our findings demonstrate that coral juveniles living in environments with large diurnal fluctuations in seawater temperature and pH, such as Kāne'ohe Bay, can tolerate exposure to moderate projected increased temperature and reduced pH. However, under more severe environmental conditions, significant negative effects on coral cellular metabolism and overall organismal survival jeopardise species fitness and recruitment.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70116"},"PeriodicalIF":3.9,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145184338","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":"Doubled Genomes, Divergent Fates: Genomic Insights Into Diversification in an Allotetraploid Cavefish.","authors":"Santiago Montero-Mendieta, Yuwei Wang, Chongnv Wang, Fanwei Meng, Yahui Zhao, Xinxin Li, Baocheng Guo","doi":"10.1111/mec.70118","DOIUrl":"https://doi.org/10.1111/mec.70118","url":null,"abstract":"<p><p>Cave environments impose unique challenges that drive remarkable genetic and phenotypic changes in cave-dwelling organisms. In this study, we investigated the genomic basis of adaptation in the small eye golden-line fish (Sinocyclocheilus microphthalmus), an allotetraploid cavefish endemic to Guangxi, China. Using whole-genome resequencing data from 47 individuals across six cave locations, we examined how neutral and selective forces influence diversification. Our analyses uncovered significant population structure indicative of allopatric divergence, along with evidence of locus-specific selection contributing to genomic differentiation. We identified seven single outlier clusters (SOCs), each tied to the divergence of specific populations, underscoring the role of local processes in driving diversity. Genes associated with vision showed relaxed selection, likely reflecting adaptation to darkness, while positive selection on other loci revealed additional functional shifts. Notably, allopolyploidy was found to fuel divergence through subgenome-specific patterns and asymmetric evolution within SOCs and among homoeologs. Taken together, these findings provide valuable insights into mechanisms of cave evolution and illustrate how allotetraploid genomes can facilitate diversification, potentially contributing to speciation in extreme environments.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70118"},"PeriodicalIF":3.9,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145147152","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}
Kurt Villsen, Gaït Archambaud-Suard, Emese Meglécz, Simon Blanchet, Jean-Pierre Balmain, Mathilde Bertrand, Rémi Chappaz, Vincent Dubut, Emmanuel Corse
{"title":"Disentangling the Effects of Biotic and Abiotic Dimensions of Ecological Opportunity on Individual Trophic Trait Variation.","authors":"Kurt Villsen, Gaït Archambaud-Suard, Emese Meglécz, Simon Blanchet, Jean-Pierre Balmain, Mathilde Bertrand, Rémi Chappaz, Vincent Dubut, Emmanuel Corse","doi":"10.1111/mec.70115","DOIUrl":"https://doi.org/10.1111/mec.70115","url":null,"abstract":"<p><p>Within-species individual trait variation (ITV) plays a critical role in ecological and evolutionary dynamics by influencing community structure, ecosystem functioning, and individual fitness. While the role of the biotic dimension of ecological opportunity (e.g., interspecific competition, prey availability) in shaping trophic ITV is now well established, the role of the abiotic dimension, and its interactions with biotic factors, remains critically overlooked, limiting our understanding of how individuals cope with changes in ecological opportunity. To address this knowledge gap, we investigated trophic ITV in the endangered riverine fish Zingel asper using a multi-faceted approach: (i) precise quantification of trophic ITV via faecal metabarcoding, (ii) fine-scale mapping of prey availability and habitat structure across seasons, and (iii) path analysis to assess the direct and indirect effects of prey, habitat, and their spatial heterogeneity in driving ITV. The individual niche width (INW) in Z. asper was largely determined by preferred prey availability, while between-individual variation (BIC) was largely determined by a combination of prey and habitat factors, with habitat exerting a direct effect (i.e., not mediated via prey) on trophic ITV. This study provides a mechanistic explanation of the processes underlying the shift from selective to opportunistic foraging strategies. Notably, we demonstrated that trophic ITV is altered by the interaction between predator life-history traits (in the present study, size) and four distinct dimensions of ecological opportunity: prey availability and their spatial distribution, habitat structure and seasonality.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70115"},"PeriodicalIF":3.9,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145129738","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":"Patterns of Genomic Divergence and Introgression in Two Primulina Hybrid Zones.","authors":"Huiqin Yi, Lihua Yang, Ming Kang","doi":"10.1111/mec.70117","DOIUrl":"https://doi.org/10.1111/mec.70117","url":null,"abstract":"<p><p>Hybrid zones have long been promoted as natural laboratories for understanding the mechanisms of speciation. Multiple or replicated hybrid zones are particularly informative, as they allow for assessing the consistency of genomic divergence and introgression across different environmental contexts and demographic histories, thereby improving our understanding of the factors that drive or hinder speciation on a broader scale. Here, using whole-genome resequencing data, we compare the patterns of genomic divergence and introgression in two Primulina hybrid zones. We found that genomic divergence in both hybrid zones is largely shaped by neutral processes, with only a few genomic regions showing signatures of balancing or lineage-specific selection. Genomic cline analyses identified numerous SNPs that showed significantly steeper clines and biased centres than the genome-wide expectation in both hybrid zones, consistent with the existence of reproductive barriers. Within regions of restricted gene flow, we identified 21 genes shared between the two hybrid zones. Annotation of gene function revealed that several genes are involved in reproductive processes. In addition, many zone-specific outlier loci were linked to genes associated with pollen and flower development, suggesting that these barriers may contribute to reproductive isolation under localised ecological conditions. Overall, these findings suggest that while certain reproductive barriers remain consistent across independent hybrid zones, others may be contingent on local environmental contexts. Our results demonstrate that both general and zone-specific mechanisms contribute to reproductive isolation in Primulina, providing empirical evidence that some genomic barriers recur across independent hybrid zones while others arise through localised adaptation.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70117"},"PeriodicalIF":3.9,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145129759","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}
Emily C Giles, Romuald Laso-Jadart, Daniel Ortiz-Barrientos, Paulina Carimán Soto, Erwan Delrieu-Trottin, Marie Laure Guillemin, Stefano Mona, Xavier Pochon, Pablo Saenz-Agudelo
{"title":"Mapping Species Birth Across the Recombination Landscapes of Marine Snails.","authors":"Emily C Giles, Romuald Laso-Jadart, Daniel Ortiz-Barrientos, Paulina Carimán Soto, Erwan Delrieu-Trottin, Marie Laure Guillemin, Stefano Mona, Xavier Pochon, Pablo Saenz-Agudelo","doi":"10.1111/mec.70108","DOIUrl":"https://doi.org/10.1111/mec.70108","url":null,"abstract":"<p><p>Understanding the drivers of heterogeneous genomic divergence is essential for uncovering the mechanisms that generate and constrain biodiversity. The extent to which adaptation and speciation are facilitated by reorganisation of the recombination landscape remains untested in many systems. Marine ecosystems, with their dynamic and fluid habitats, offer a compelling context to investigate genomic divergence. In this study, we mapped genomic divergence and selection across recombination landscapes of parapatric marine snail sister species that we show have recently undergone secondary contact. Regions of reduced recombination were enriched for genes exhibiting signatures of negative selection, whereas regions of high recombination were associated with genes under putative positive selection. Notably, the recombination landscape of the population in parapatry of one species (Scurria viridula) differs markedly from that of the other population within this same species, highlighting the role of introgression in reshaping recombination landscapes. In the other species (Scurria zebrina), conservation of the recombination landscape and divergent selection among populations suggest trapping of beneficial allele combinations in regions of low recombination maintains the identity of this species. Among species, signals of divergence with gene flow consistently cluster within specific genomic regions characterised by high recombination rate variation among the populations of S. viridula. These results challenge traditional theoretical expectations of recombination evolution by showing that the causes of genomic divergence can be population-specific. This study demonstrates that recombination landscapes are key modulators of genomic divergence, with contemporary evolutionary shifts that could enable populations to adapt to distinct environments. Our findings provide new insights into the interplay between recombination, selection, and gene flow during speciation, underscoring the complexity of evolutionary trajectories in marine systems.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70108"},"PeriodicalIF":3.9,"publicationDate":"2025-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145111593","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}
Filippo Nicolini, Sergey V Nuzhdin, Fabrizio Ghiselli, Andrea Luchetti, Liliana Milani
{"title":"Comparative Genomics of Sex-Determination-Related Genes Reveals Shared Evolutionary Patterns Between Bivalves and Mammals, but Not Fruit Flies.","authors":"Filippo Nicolini, Sergey V Nuzhdin, Fabrizio Ghiselli, Andrea Luchetti, Liliana Milani","doi":"10.1111/mec.70103","DOIUrl":"https://doi.org/10.1111/mec.70103","url":null,"abstract":"<p><p>The molecular basis of sex determination (SD), while being extensively studied in model organisms, remains poorly understood in many animal groups. Bivalves, a diverse class of molluscs with a variety of reproductive modes, represent an ideal yet challenging clade for investigating SD and the evolution of sexual systems. However, the absence of a comprehensive framework has limited progress in this field, particularly regarding the study of sex-determination-related genes (SRGs). In this study, we performed a genome-wide sequence evolutionary analysis of the Dmrt, Sox and Fox gene families in more than 40 bivalve species. For the first time, we provide an extensive and phylogenetically aware dataset of these SRGs, and we find support for the hypothesis that Dmrt-1L and Sox-H may act as primary sex-determining genes by showing their high levels of sequence diversity within the bivalve genomic context. To validate our findings, we studied the same gene families in two well-characterised systems, mammals and fruit flies (genus Drosophila). In the former, we found that the male sex-determining gene Sry exhibits a pattern of amino acid sequence diversity similar to that of Dmrt-1L and Sox-H in bivalves, consistent with its role as master SD regulator. In contrast, no such pattern was observed among genes of the fruit fly SD cascade, which is controlled by a chromosomic mechanism. Overall, our findings highlight similarities in the sequence evolution of some mammal and bivalve SRGs, possibly driven by a comparable architecture of SD cascades. This work underscores once again the importance of employing a comparative approach when investigating understudied and non-model systems.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70103"},"PeriodicalIF":3.9,"publicationDate":"2025-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145111608","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}
Nozomu Muto, Yong-Chao Su, Harutaka Hata, Nguyen Van Quan, Veera Vilasri, Mazlan Abd Ghaffar, Ricardo P Babaran
{"title":"Homoploid Hybrid Speciation in a Marine Pelagic Fish.","authors":"Nozomu Muto, Yong-Chao Su, Harutaka Hata, Nguyen Van Quan, Veera Vilasri, Mazlan Abd Ghaffar, Ricardo P Babaran","doi":"10.1111/mec.70112","DOIUrl":"https://doi.org/10.1111/mec.70112","url":null,"abstract":"<p><p>Homoploid hybrid speciation (HHS) is an enigmatic evolutionary process where new species arise through hybridisation of divergent lineages without changes in chromosome number. Although increasingly documented in various taxa and ecosystems, convincing cases of HHS in marine fishes have been lacking. This study presents a possible case of HHS in a pelagic marine fish based on comprehensive genomic, morphological, and ecological analyses. Population genomics, species tree estimation, and tests of introgression and admixture identified three sympatric clusters in Megalaspis cordyla in the western Pacific and the admixed nature of one cluster between the others. Moreover, model-based demographic inference favoured a hybrid speciation scenario over introgression for the origin of the admixed cluster. While contemporary gene flow suggested partial reproductive isolation, examination of occurrence data and ecologically relevant morphological characters suggested ecological differences between the clusters, potentially contributing to the reproductive isolation and niche partitioning in sympatry. The clusters are also morphologically distinguishable and thus can be taxonomically recognised as separate species. The hybrid cluster is restricted to the coasts of Taiwan and Japan, where all three clusters coexist. The parental clusters are additionally found in lower latitudes, where they display non-overlapping distributions. Given the geographical distributions, estimated times of species formation, and patterns of historical demographic changes, we propose that the Pleistocene glacial cycles were the primary driver of HHS in this system. We also develop an ecogeographic model of HHS in marine coastal ecosystems, including a novel hypothesis to explain the initial stages of HHS.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70112"},"PeriodicalIF":3.9,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145084723","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}