Molecular Ecology最新文献

{"title":"Genetic Adaptation to Brackish Water and Spawning Season in European Cisco.","authors":"Qiaoling Deng, Jake Goodall, Mikaela Bergenius Nord, Ignas Bunikis, Arianna Cocco, Bo Delling, Elisabet Einarsdottir, Julia Heintz, Henrik Lantz, Kerstin Lindblad-Toh, Mai-Britt Mosbech, Remi-Andre Olsen, Stefan Palm, Mats E Pettersson, Martin Pippel, Lucile Soler, Anti Vasemägi, Olga Vinnere Pettersson, Leif Andersson","doi":"10.1111/mec.70094","DOIUrl":"https://doi.org/10.1111/mec.70094","url":null,"abstract":"<p><p>How species adapt to diverse environmental conditions is essential for understanding evolution and the maintenance of biodiversity. The European cisco (Coregonus albula) is a salmonid that occurs in both fresh and brackish water, and this together with the presence of sympatric spring- and autumn-spawning lacustrine populations provides an opportunity for studying the genetics of adaptation in relation to salinity and timing of reproduction. Here, we present a high-quality reference genome of the European cisco based on PacBio HiFi long read sequencing and HiC-directed scaffolding. We generated low-coverage whole-genome sequencing data from 336 individuals across 12 population samples to explore population structure and genetics of ecological adaptation. We found a major subdivision between two groups of populations most likely reflecting colonisation from different glacial refugia. Within the two major groups, we detected further genetic differentiation between spring- and autumn-spawning populations and between populations from freshwater lakes, rivers and brackish water (Bothnian Bay). A genome-wide screen for genetic differentiation among populations identified a set of outlier SNPs strongly correlated with spawning timing and salinity. Several of the genes associated with spawning time, including BHLHE40, TIMELESS and CPT1A, have previously been shown to have a role in circadian rhythm biology. As many as 17 loci were associated with genetic differentiation between populations reproducing in fresh and brackish water. This study provides insights into the genomic basis of ecological adaptation in European cisco with implications for sustainable fishery management.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70094"},"PeriodicalIF":3.9,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144991024","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":"Molecular Footprints of Quaternary Climate Fluctuations in the Circumpolar Tundra Shrub Dwarf Birch","authors":"Maria Dance,&nbsp;Erin E. Saupe,&nbsp;James Borrell,&nbsp;Pernille Bronken Eidesen,&nbsp;Daniel Ackerman,&nbsp;Jakob Assmann,&nbsp;Bruce C. Forbes,&nbsp;Marina Gurskaya,&nbsp;Toke T. Høye,&nbsp;Stein R. Karlsen,&nbsp;Timo Kumpula,&nbsp;Mariusz Lamentowicz,&nbsp;Michael M. Loranty,&nbsp;Isla Myers-Smith,&nbsp;Janet Prevéy,&nbsp;Christian Rixen,&nbsp;Gabriela Schaepman-Strub,&nbsp;Michał Słowiński,&nbsp;Sandra Słowińska,&nbsp;Aleksandr Sokolov,&nbsp;James D. M. Speed,&nbsp;Marcus Spiegel,&nbsp;Martin Wilmking,&nbsp;Marc Macias-Fauria","doi":"10.1111/mec.70082","DOIUrl":"10.1111/mec.70082","url":null,"abstract":"<p>The Arctic tundra biome is undergoing rapid shrub expansion (‘shrubification’) in response to anthropogenic climate change. During the previous ~2.6 million years, glacial cycles caused substantial shifts in Arctic vegetation, leading to changes in species' distributions, abundance and connectivity, which have left lasting impacts on the genetic structure of modern populations. Examining how shrubs responded to past climate change through genetic data reveals the demographic dynamics that shaped their current diversity and distribution and sheds light on the resilience of Arctic shrubs. Here we test scenarios of Quaternary demographic history of dwarf birch species (<i>Betula nana</i> L. and <i>Betula Glandulosa</i> Michx.) using Single Nucleotide Polymorphism (SNP) markers obtained from RAD sequencing and approximate Bayesian computation. We compare the timings of modelled population events with ice sheet reconstructions and other paleoenvironmental information to untangle the impacts of alternating cold and warm periods on dwarf birch. Our best supported model suggested that the species diverged in the Mid-Pleistocene Transition as glaciations intensified. We found support for a complex history of inter- and intraspecific divergences and gene flow, and secondary contact occurred during both ice sheet expansion and retreat. Our spatiotemporal analysis suggests that the modern genetic structure of dwarf birch results from transitions in climate between glacials and interglacials, with ice sheets acting alternatively as a barrier or an enabler of population mixing. Tundra shrubs may have had more nuanced responses to past climatic changes than phylogeographic analyses have often suggested, with implications for future eco-evolutionary responses to anthropogenic climate change.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 19","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.70082","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144937394","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":"Recent Adaptation in a Threatened Salmonid Revealed by Museum Genomics","authors":"Andrew G. Sharo,&nbsp;Megan A. Supple,&nbsp;Randy Cabrera,&nbsp;William E. Seligmann,&nbsp;Samuel Sacco,&nbsp;Cassondra D. Columbus,&nbsp;Devon E. Pearse,&nbsp;Beth Shapiro,&nbsp;John Carlos Garza","doi":"10.1111/mec.70063","DOIUrl":"10.1111/mec.70063","url":null,"abstract":"<p>Steelhead/rainbow trout (<i>Oncorhynchus mykiss</i>) is an imperilled salmonid with two main life history strategies: migrate to the ocean or remain in freshwater. Domesticated hatchery forms of this species have been stocked into almost all California waterways, possibly resulting in introgression into natural populations and altered population structure. We compared whole-genome sequence data from contemporary populations against a set of museum population samples of steelhead from the same locations that were collected prior to most hatchery stocking. We observed minimal introgression and few steelhead-hatchery trout hybrids despite a century of extensive stocking. Our historical data show signals of introgression with a sister species and indications of an early hatchery facility. Finally, we found that migration-associated haplotypes have become less frequent over time, a likely adaptation to decreased opportunities for migration. Since contemporary migration-associated haplotype frequencies have been used to guide species management, we consider this to be a rare example of shifting baseline syndrome that has been validated with historical data. We suggest cautious optimism that a century of hatchery stocking has had minimal impact on California steelhead population genetic structure, but we note that continued shifts in life history may lead to further declines in the ocean-going form of the species.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 18","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.70063","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144937385","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":"Ecological and Mutation-Order Speciation in Senecio.","authors":"Maddie E James, Maria C Melo, Federico Roda, Diana Bernal-Franco, Melanie J Wilkinson, Gregory M Walter, Huanle Liu, Jan Engelstädter, Daniel Ortiz-Barrientos","doi":"10.1111/mec.70090","DOIUrl":"https://doi.org/10.1111/mec.70090","url":null,"abstract":"<p><p>Natural selection shapes how new species arise, yet the mechanisms that generate reproductive barriers remain actively debated. Although ecological divergence in contrasting environments and mutation-order processes in similar environments are often viewed as distinct speciation mechanisms, we show they can occur simultaneously and act as part of a continuum of selective pressures. In the Senecio lautus species complex, Dune and Headland ecotypes have evolved repeatedly along the Australian coastline. Through crossing experiments and field studies, we find that divergent natural selection promotes strong reproductive isolation between the Dune and Headland ecotypes. While uniform selection maintains reproductive compatibility among ecologically similar Dune populations, geographically distant Headland populations have evolved reproductive barriers despite their convergent prostrate phenotypes, likely driven by adaptation to subtle environmental differences between each Headland location. To understand how this habitat heterogeneity contributes to patterns of reproductive isolation, we extend previous theoretical work on the accumulation of hybrid incompatibilities to account for environmental gradients and polygenic adaptation. We show that the probability of reproductive isolation depends on three factors: how similar the environments are, how complex the genetic architecture is and how selection coefficients are distributed among beneficial mutations. These theoretical findings explain how reproductive isolation arises in systems like Senecio, where multiple forms of selection jointly drive speciation.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70090"},"PeriodicalIF":3.9,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144937411","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":"Beet Chlorosis Virus Infection Mitigates Aphid-Induced Plant Defences and Improves Plant Acceptability to Aphid Vectors.","authors":"Thomas Armand, Sylvaine Boissinot, Alessandra Maia-Grondard, Philippe Hugueney, Véronique Brault, Quentin Chesnais","doi":"10.1111/mec.70092","DOIUrl":"https://doi.org/10.1111/mec.70092","url":null,"abstract":"<p><p>Plant viruses often alter host traits in ways that affect interactions with herbivores, potentially facilitating their own acquisition and transmission by insect vectors. However, little is known about the molecular mechanisms underlying this phenomenon. This is particularly true for agronomically important pathosystems, such as the viruses responsible for sugar beet yellowing. Among them is the beet chlorosis virus (BChV), whose effects on aphid vector behaviour and plant defence mechanisms have not been fully characterised. In this study, we demonstrate that BChV infection suppresses sugar beet defences induced by aphid pre-infestation, enhancing plant acceptability for aphids. Specifically, gene expression analyses revealed a downregulation of the aphid-induced ethylene pathway in infected plants, along with alterations in the salicylic acid pathway that may benefit aphids. Metabolic profiling highlighted reduced levels of phenolic acids, including cinnamic and coumaric acids, in virus-infected plants which likely contribute to increased plant acceptability by aphids. By integrating gene expression, metabolic profiling, and behavioural assays, our findings illustrate how BChV manipulates host-plant defences to potentially increase its transmission by aphids, underscoring the broad ecological and evolutionary significance of virus-mediated plant-vector interactions.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70092"},"PeriodicalIF":3.9,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144937435","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":"Whole Genome Sequencing Reveals How Plasticity and Genetic Differentiation Underlie Sympatric Morphs of Arctic Charr","authors":"Khrystyna Kurta,&nbsp;Mariano Olivera Fedi,&nbsp;Kendall Baker,&nbsp;Tom Barker,&nbsp;Leah Catchpole,&nbsp;Claudio Ciofi,&nbsp;Arianna Cocco,&nbsp;Joanna Collins,&nbsp;Genevieve Diedericks,&nbsp;Maria Angela Diroma,&nbsp;Alex Durrant,&nbsp;Kjetil Hindar,&nbsp;Alessio Iannucci,&nbsp;Naomi Irish,&nbsp;Vanda Knitlhoffer,&nbsp;Linda Laikre,&nbsp;Henrique G. Leitão,&nbsp;Sacha Lucchini,&nbsp;Seanna McTaggart,&nbsp;Arnar Pálsson,&nbsp;Mats E. Pettersson,&nbsp;Nils Ryman,&nbsp;Sigurður S. Snorrason,&nbsp;Hannes Svardal,&nbsp;David Swarbreck,&nbsp;Robert M. Waterhouse,&nbsp;Christopher Watkins,&nbsp;Jonathan M. D. Wood,&nbsp;Han Xiao,&nbsp;Karim Gharbi,&nbsp;Zophonías O. Jónsson,&nbsp;Leif Andersson","doi":"10.1111/mec.70085","DOIUrl":"10.1111/mec.70085","url":null,"abstract":"<p>Salmonids have a remarkable ability to form sympatric morphs after postglacial colonisation of freshwater lakes. These morphs often differ in morphology, feeding and spawning behaviour. Here, we explored the genetic basis of morph differentiation in Arctic charr (<i>n</i> = 283) by first establishing a high-quality reference genome and then using this in whole genome sequencing of distinct morphs present in two Norwegian and two Icelandic lakes. The four lakes represent the spectrum of genetic differentiation between morphs from one lake with no genetic differentiation between morphs, implying phenotypic plasticity, to two lakes with locus-specific genetic differentiation, implying incomplete reproductive isolation, and one lake with strong genome-wide divergence consistent with complete reproductive isolation. As many as 12 putative inversions ranging from 0.45 to 3.25 Mbp in size segregated among the four morphs present in one lake, Thingvallavatn, and these contributed significantly to the genetic differentiation among morphs. None of the putative inversions were found in any of the other lakes, but there were cases of partial haplotype sharing in similar morph contrasts in other lakes. Our findings are consistent with a highly polygenic basis of morph differentiation with population-specific selection on alleles linked to the development of similar morph phenotypes. The results support a model where morph differentiation is first established through phenotypic plasticity, leading to niche expansion and separation. This may be followed by gradual development of reproductive isolation, locus-specific differentiation and eventually complete reproductive isolation and genome-wide divergence.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 19","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.70085","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144937404","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":"Heat-Induced Secondary Dormancy Contributes to Local Adaptation in Arabidopsis thaliana","authors":"Nhu Loc Thuy Tran,&nbsp;Tahir Ali,&nbsp;Gregor Schmitz,&nbsp;Juliette de Meaux","doi":"10.1111/mec.70086","DOIUrl":"10.1111/mec.70086","url":null,"abstract":"<p>Seeds should not germinate in conditions unsuitable for seedling growth. Dormancy, which allows seeds to remain inactive in an environment that would otherwise enable germination, helps optimise the timing of germination. Primary dormancy, developed during seed maturation on the parent plant, prevents immediate germination post-dispersal, regardless of external conditions. Secondary dormancy, however, is triggered post-dispersal when seeds face unfavourable conditions, enabling them to re-enter dormancy even if initially non-dormant. This mechanism allows seeds to fine-tune germination according to environmental conditions. In this study, we examined the role of heat-induced secondary dormancy in local adaptation by analysing natural variations within 361 <i>Arabidopsis thaliana</i> accessions from across Europe. We discovered that secondary dormancy acquisition varies with primary dormancy levels and after-ripening. Both primary and heat-induced secondary dormancy exhibited adaptive clines along temperature and precipitation gradients, with secondary dormancy showing a steeper cline, indicating its significant role in local adaptation. Using species distribution models, we predicted that genotypes with high secondary dormancy would show greater resilience to future climate changes. Additionally, we identified specific genomic regions controlling secondary dormancy levels including a novel candidate gene for secondary dormancy variation. Our findings show that secondary dormancy is a complex adaptive mechanism and a predominant contributor to the dormancy trait syndrome that favours plant survival in habitats exposed to harsh summers.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 19","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.70086","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144937452","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":"Persistent Genomic Erosion in Whooping Cranes Despite Demographic Recovery.","authors":"Claudia Fontsere, Samuel A Speak, Andrew J Caven, Juan Antonio Rodríguez, Xuejing Wang, Carolina Pacheco, Molly Cassatt-Johnstone, Georgette Femerling, Brigid Maloney, Jennifer Balacco, Joanna Collins, Ying Sims, Linelle Abueg, Olivier Fedrigo, Erich D Jarvis, Barry K Hartup, Beth Shapiro, M Thomas P Gilbert, Cock van Oosterhout, Hernán E Morales","doi":"10.1111/mec.70088","DOIUrl":"https://doi.org/10.1111/mec.70088","url":null,"abstract":"<p><p>Integrating in-situ (wild) and ex-situ (captive) conservation efforts can mitigate genetic diversity loss and help prevent extinction of endangered wild populations. The whooping crane (Grus americana) experienced severe population declines in the 18th century, culminating in a collapse to ~20 individuals by 1944. Legal protections and conservation actions have since increased the census population from a stock of 16 individuals to approximately 840 individuals, yet the impact on genomic diversity remains unclear. We analysed the temporal dynamics of genomic erosion by sequencing a high-quality reference genome, and re-sequencing 16 historical (years 1867-1893) and 37 modern (2007-2020) genomes, including wild individuals and four generations of captive-bred individuals. Genomic demographic reconstructions reveal a steady decline, accelerating over the past 300 years with the European settlement of North America. Temporal genomic analyses show that despite demographic recovery, the species has lost 70% of its historical genetic diversity and has increased its inbreeding. Although the modern population bottleneck reduced the ancestral genetic load, modern populations possess more realised load than masked load, possibly resulting in a chronic loss of fitness. Integrating pedigree and genomic data, we underscore the role of breeding management in reducing recent inbreeding. Yet ongoing heterozygosity loss, load accumulation, and persistent effects of historical inbreeding (i.e., background inbreeding) argue against the species' downlisting from its current Endangered status on the IUCN Red List and the Endangered Species Act. The presence of private genetic variation in wild and captive populations suggests that wild-captive crosses could enhance genetic diversity and reduce the realised load. Our findings emphasise the role of genomics in informing conservation management and policy.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70088"},"PeriodicalIF":3.9,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144937481","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":"Quaternary Glaciation Accelerates Speciation in Aquatic Snakes Through Recent Bottlenecks.","authors":"Jin-Long Ren, Rui-Han Li, Ru-Wan Jia, Zhi-Tong Lyu, Chaochao Yan, Dechun Jiang, Ying-Yong Wang, Jia-Tang Li","doi":"10.1111/mec.70071","DOIUrl":"https://doi.org/10.1111/mec.70071","url":null,"abstract":"<p><p>Climatic fluctuations during glacial periods have profoundly shaped the demographic history and gene flow dynamics of many taxa. This study integrated high-throughput sequencing of 67 individuals with comprehensive genomic analyses to investigate biogeographic patterns, genetic divergence and demographic trajectories in the Opisthotropis latouchii species complex, a group of mountain stream snakes distributed across Central China. Our analyses revealed substantial genetic divergence, identifying four distinct lineages, each confined to one of the four major mountain ranges in Central China, including one previously unrecognised species. These lineages exhibited distinct demographic signatures, with population bottlenecks occurring during Quaternary glaciations. Initial isolation in the glacial refugia of the southern regions of these mountains during the Late Pliocene was followed by postglacial expansions along a northward trajectory, with further divergence along a latitudinal gradient associated with mountain distribution. Notably, the mountain ranges of Central China acted as critical refugia during glacial periods, promoting rapid speciation, and as dispersal corridors during interglacial periods, facilitating range expansion and enabling recent gene flow. These findings highlight the profound impact of Quaternary climatic oscillations on genetic structure, demographic history and gene flow patterns of these endemic taxa.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e70071"},"PeriodicalIF":3.9,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144937438","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":"Contrasting Patterns of Connectivity Between Populations of Euphotic and Mesophotic Hydroids in Reunion Island Support the Deep Reef Refuge Hypothesis","authors":"David Ory,&nbsp;Nicole Gravier-Bonnet,&nbsp;Pascale Chabanet,&nbsp;Chloé A.- F. Bourmaud,&nbsp;Emilie Boissin","doi":"10.1111/mec.70089","DOIUrl":"10.1111/mec.70089","url":null,"abstract":"<div>\u0000 \u0000 <p>In the context of coral reef decline, mesophotic coral ecosystems (MCEs, 30–150 m) offer hope for the recovery of degraded euphotic reefs. The Deep Reef Refuge Hypothesis (DRRH) postulates the potential of mesophotic reefs to reseed euphotic reefs. This hypothesis needs to be further tested by estimating connectivity along the depth gradient. Mesophotic data are lacking worldwide, particularly in the southwestern Indian Ocean (SWIO). Here, using a total of 2218 samples collected at depths ranging from 10 to 103 m, we estimated the connectivity of 7 hydroid species sampled at euphotic, upper, and lower mesophotic depths around Reunion Island using a multi-species comparative framework. Population genetic analyses using 8–17 microsatellite markers per species (80 markers in total) as well as Bayesian inference were performed to estimate population structure and contemporary migration rates to highlight connectivity patterns and directionality of gene flow between depths. The results revealed three main genetic patterns depending on the species: a horizontal stepping stone pattern between areas around the island, a vertical stepping stone pattern between adjacent depths, and a quasi-panmictic pattern. Each species showed some specificity within these patterns, but overall, at least 4 of the 7 species support the assumption of vertical connectivity from the Deep Reef Refuge Hypothesis, highlighting the importance of studying multiple species. The existence of vertical connectivity between euphotic and mesophotic depths in the southwestern Indian Ocean confirms the importance of mesophotic coral ecosystems for conservation efforts and our global understanding of coral reef ecosystem dynamics.</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 19","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144937406","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}