Molecular Ecology最新文献

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Local Selection Shaped the Diversity of European Maize Landraces. 地方选择塑造了欧洲玉米地方品种的多样性。
IF 4.5 1区 生物学
Molecular Ecology Pub Date : 2025-03-17 DOI: 10.1111/mec.17720
Margarita Takou, Kerstin Schulz, Markus G Stetter
{"title":"Local Selection Shaped the Diversity of European Maize Landraces.","authors":"Margarita Takou, Kerstin Schulz, Markus G Stetter","doi":"10.1111/mec.17720","DOIUrl":"https://doi.org/10.1111/mec.17720","url":null,"abstract":"<p><p>The introduction of populations to novel environments can lead to a loss of genetic diversity and the accumulation of deleterious mutations due to selection and demographic changes. We investigate how the recent introduction of maize to Europe shaped the genetic diversity and differentiation of European traditional maize populations and quantify the impact of its recent range expansion and consecutive breeding on the accumulation of genetic load. We use genome-wide genetic markers of almost 2000 individuals from 38 landraces, 155 elite breeding lines, and a large set of doubled haploid lines derived from two landraces to find extensive population structure within European maize, with landraces being highly differentiated even over short geographic distances. Yet, diversity change does not follow the continuous pattern of range expansions. Landraces maintain high genetic diversity that is distinct between populations and does not decrease along the possible expansion routes. Signals of positive selection in European landraces that overlap with selection in Asian maize suggest convergent selection during maize introductions. At the same time, environmental factors partially explain genetic differences across Europe. Consistent with the maintenance of high diversity, we find no evidence of genetic load accumulating along the maize introduction route in European maize. However, modern breeding likely purged highly deleterious alleles but accumulated genetic load in elite germplasm. Our results reconstruct the history of maize in Europe and show that landraces have maintained high genetic diversity that could reduce genetic load in the European maize breeding pools.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17720"},"PeriodicalIF":4.5,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143646633","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}
引用次数: 0
The Distribution and Dispersal of Large Haploblocks in a Superspecies. 一个超种中大单倍体的分布和扩散。
IF 4.5 1区 生物学
Molecular Ecology Pub Date : 2025-03-17 DOI: 10.1111/mec.17731
Darren Irwin, Staffan Bensch, Caleigh Charlebois, Gabriel David, Armando Geraldes, Sandeep Kumar Gupta, Bettina Harr, Paul Holt, Jessica H Irwin, Vladimir V Ivanitskii, Irina M Marova, Yongchao Niu, Sampath Seneviratne, Ashutosh Singh, Yongjie Wu, Shangmingyu Zhang, Trevor D Price
{"title":"The Distribution and Dispersal of Large Haploblocks in a Superspecies.","authors":"Darren Irwin, Staffan Bensch, Caleigh Charlebois, Gabriel David, Armando Geraldes, Sandeep Kumar Gupta, Bettina Harr, Paul Holt, Jessica H Irwin, Vladimir V Ivanitskii, Irina M Marova, Yongchao Niu, Sampath Seneviratne, Ashutosh Singh, Yongjie Wu, Shangmingyu Zhang, Trevor D Price","doi":"10.1111/mec.17731","DOIUrl":"https://doi.org/10.1111/mec.17731","url":null,"abstract":"<p><p>Haploblocks are regions of the genome that coalesce to an ancestor as a single unit. Differentiated haplotypes in these regions can result from the accumulation of mutational differences in low-recombination chromosomal regions, especially when selective sweeps occur within geographically structured populations. We introduce a method to identify large well-differentiated haploblock regions (LHBRs), based on the variance in standardised heterozygosity (ViSHet) of single nucleotide polymorphism (SNP) genotypes among individuals, calculated across a genomic region (500 SNPs in our case). We apply this method to the greenish warbler (Phylloscopus trochiloides) ring species, using a newly assembled reference genome and genotypes at more than 1 million SNPs among 257 individuals. Most chromosomes carry a single distinctive LHBR, containing 4-6 distinct haplotypes that are associated with geography, enabling detection of hybridisation events and transition zones between differentiated populations. LHBRs have exceptionally low within-haplotype nucleotide variation and moderately low between-haplotype nucleotide distance, suggesting their establishment through recurrent selective sweeps at varying geographic scales. Meiotic drive is potentially a powerful mechanism of producing such selective sweeps, and the LHBRs are likely to often represent centromeric regions where recombination is restricted. Links between populations enable introgression of favoured haplotypes and we identify one haploblock showing a highly discordant distribution compared to most of the genome, being present in two distantly separated geographic regions that are at similar latitudes in both east and central Asia. Our results set the stage for detailed studies of haploblocks, including their genomic location, gene content and contribution to reproductive isolation.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17731"},"PeriodicalIF":4.5,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143646652","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}
引用次数: 0
Symbiont-Mediated Metabolic Shift in the Sea Anemone Anthopleura elegantissima 共生体介导的海葵代谢转变。
IF 4.5 1区 生物学
Molecular Ecology Pub Date : 2025-03-17 DOI: 10.1111/mec.17722
Tyler J. Carrier, Holland Elder, Jason Macrander, James L. Dimond, Brian L. Bingham, Adam M. Reitzel
{"title":"Symbiont-Mediated Metabolic Shift in the Sea Anemone Anthopleura elegantissima","authors":"Tyler J. Carrier,&nbsp;Holland Elder,&nbsp;Jason Macrander,&nbsp;James L. Dimond,&nbsp;Brian L. Bingham,&nbsp;Adam M. Reitzel","doi":"10.1111/mec.17722","DOIUrl":"10.1111/mec.17722","url":null,"abstract":"<p>Coral reefs and their photosynthetic algae form one of the most ecologically and economically impactful symbioses in the animal kingdom. The stability of this nutritional mutualism and this ecosystem is, however, at risk due to increasing sea surface temperatures that cause corals to expel their symbionts. Symbioses with these microeukaryotes have independently evolved multiple times, and non-coral cnidarians (e.g., sea anemones) serve as a valuable and insightful comparative system due to their ease of husbandry in the laboratory and their ability to shuffle different strains of their photosymbionts to acclimate to thermal conditions. This breadth of symbiont shuffling is exemplified by the sea anemone \u0000 <i>Anthopleura elegantissima</i>\u0000 , which naturally occurs in symbiosis with the dinoflagellate <i>Breviolum muscatinei</i> (formerly <i>Symbiodinium</i>) or the chlorophyte <i>Elliptochloris marina</i> as well as being aposymbiotic. Here, we assembled a draft genome and used multi-omics to characterise multiple physiological levels of each phenotype. We find that \u0000 <i>A. elegantissima</i>\u0000 has symbiont-specific transcriptional and metabolomic signatures, but a similar bacterial community dominated by a single <i>Sphingomonas</i> species that is commonly found in the cnidarian microbiome. Symbiosis with either eukaryotic symbiont resulted in differential gene expression and metabolic abundance for diverse processes spanning metabolism and immunity to reproduction and development, with some of these processes being unique to either symbiont. The ability to culture \u0000 <i>A. elegantissima</i>\u0000 with its phylogenetically divergent photosymbionts and perform experimental manipulations makes \u0000 <i>A. elegantissima</i>\u0000 another tractable sea anemone system to decode the symbiotic conversations of coral reef ecosystems and aid in wider conservation efforts.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 8","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17722","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143646650","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}
引用次数: 0
Tailocin-Mediated Interactions Among Soft Rot Pectobacteriaceae 软腐乳酸菌科中tailocin介导的相互作用。
IF 4.5 1区 生物学
Molecular Ecology Pub Date : 2025-03-15 DOI: 10.1111/mec.17728
Marcin Borowicz, Dorota M. Krzyżanowska, Marta Sobolewska, Magdalena Narajczyk, Inez Mruk, Paulina Czaplewska, Jacques Pédron, Marie-Anne Barny, Pierre Yves Canto, Joanna Dziadkowiec, Robert Czajkowski
{"title":"Tailocin-Mediated Interactions Among Soft Rot Pectobacteriaceae","authors":"Marcin Borowicz,&nbsp;Dorota M. Krzyżanowska,&nbsp;Marta Sobolewska,&nbsp;Magdalena Narajczyk,&nbsp;Inez Mruk,&nbsp;Paulina Czaplewska,&nbsp;Jacques Pédron,&nbsp;Marie-Anne Barny,&nbsp;Pierre Yves Canto,&nbsp;Joanna Dziadkowiec,&nbsp;Robert Czajkowski","doi":"10.1111/mec.17728","DOIUrl":"10.1111/mec.17728","url":null,"abstract":"<p>Bacteria carry phage-derived elements within their genomes, some of which can produce phage-like particles (tailocins) used as weapons to kill kin strains in response to environmental conditions. This study investigates the production and activity of tailocins by plant-pathogenic bacteria: <i>Pectobacterium</i>, <i>Dickeya,</i> and <i>Musicola</i> genera, which compete for niche, providing an attractive model to study the ecological role of tailocins. Microscopy revealed that most analysed strains (88%) produced tailocins. Tailocin-mediated killing interactions were assessed across 351 strain pairs, showing that <i>Dickeya</i> spp. had a higher likelihood of killing neighbours (57.1%) than <i>Pectobacterium</i> spp. (21.6%). Additionally, <i>Dickeya</i> spp. strains exhibited broader phylogenetic killing, targeting both <i>Pectobacterium</i> spp. and <i>Musicola</i> sp., while <i>Pectobacterium</i> spp. tailocins were genus-specific. The mutual (bilateral) killing was observed in 33.9% of interactions, predominantly within <i>Dickeya</i> spp. Although tailocins were morphologically indistinguishable between producers, genomic analyses identified conserved clusters having diverse structural and organisational differences between <i>Pectobacterium</i> spp. and <i>Dickeya</i> spp. tailocins. This suggests different origins of these particles. Induction experiments demonstrated that tailocin production was boosted by hydrogen peroxide, supporting the role of these particles in bacteria–bacteria competition during plant infection when plants produce ROS to protect themselves from pathogens. Tailocins were detectable in infected potato tissue but not in river water, highlighting the particular ecological relevance of tailocins in these studied environments.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 8","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17728","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143633286","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}
引用次数: 0
The Same Source of Microbes has a Divergent Assembly Trajectory Along a Hot Spring Flowing Path 同一来源的微生物在温泉流动路径上有不同的装配轨迹。
IF 4.5 1区 生物学
Molecular Ecology Pub Date : 2025-03-15 DOI: 10.1111/mec.17727
Qing He, Shang Wang, Kai Feng, Weiguo Hou, Wenhui Zhang, Fangru Li, Yidi Zhang, Wanming Hai, Yuxuan Sun, Ye Deng
{"title":"The Same Source of Microbes has a Divergent Assembly Trajectory Along a Hot Spring Flowing Path","authors":"Qing He,&nbsp;Shang Wang,&nbsp;Kai Feng,&nbsp;Weiguo Hou,&nbsp;Wenhui Zhang,&nbsp;Fangru Li,&nbsp;Yidi Zhang,&nbsp;Wanming Hai,&nbsp;Yuxuan Sun,&nbsp;Ye Deng","doi":"10.1111/mec.17727","DOIUrl":"10.1111/mec.17727","url":null,"abstract":"<div>\u0000 \u0000 <p>Hot spring microbial mats represent intricate biofilms that establish self-sustaining ecosystems, hosting diverse microbial communities which facilitate a range of biochemical processes and contribute to the structural and functional complexity of these systems. While community structuring across mat depth has received substantial attention, mechanisms shaping horizontal spatial composition and functional structure of these communities remain understudied. Here, we explored the contributions of species source, local environment and species interaction to microbial community assembly processes in six microbial mat regions following a flow direction with a temperature decreasing from 73.3°C to 52.8°C. Surprisingly, we found that despite divergent community structures and potential functions across different microbial mats, large proportions of the community members (45.50%–80.29%) in the recipient mat communities originated from the same source community at the upper limit of temperature for photosynthetic life. This finding indicated that the source species were dispersed with water and subsequently filtered and shaped by local environmental factors. Furthermore, critical species with specific functional attributes played a pivotal role in community assembly by influencing potential interactions with other microorganisms. Therefore, species dispersal via water flow, environmental variables, and local species interaction jointly governed microbial assembly, elucidating assembly processes in the horizontal dimension of hot spring microbial mats and providing insights into microbial community assembly within extreme biospheres.</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 8","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143633287","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}
引用次数: 0
Assessing Microsatellite Variations in Plasmodium falciparum Following a Decade-Long Antimalaria Campaign in Kenya 在肯尼亚长达十年的抗疟疾运动后评估恶性疟原虫微卫星变异。
IF 4.5 1区 生物学
Molecular Ecology Pub Date : 2025-03-14 DOI: 10.1111/mec.17713
Elizabeth Hemming-Schroeder, Alfred Hubbard, Faith I. Ebhodaghe, Tatiana Vorontsova, Daibin Zhong, Guofa Zhou, Eugenia Lo, Harrysone Atieli, Andrew Githeko, James W. Kazura, Guiyun Yan
{"title":"Assessing Microsatellite Variations in Plasmodium falciparum Following a Decade-Long Antimalaria Campaign in Kenya","authors":"Elizabeth Hemming-Schroeder,&nbsp;Alfred Hubbard,&nbsp;Faith I. Ebhodaghe,&nbsp;Tatiana Vorontsova,&nbsp;Daibin Zhong,&nbsp;Guofa Zhou,&nbsp;Eugenia Lo,&nbsp;Harrysone Atieli,&nbsp;Andrew Githeko,&nbsp;James W. Kazura,&nbsp;Guiyun Yan","doi":"10.1111/mec.17713","DOIUrl":"10.1111/mec.17713","url":null,"abstract":"<div>\u0000 \u0000 <p>Anti-malaria interventions typically reduce the intensity of <i>Plasmodium</i> transmission, but the effects of reduced transmission on <i>P. falciparum</i> population biology remain unclear. Highly polymorphic microsatellite markers in <i>P. falciparum</i> were used to investigate genetic diversity, polyclonality and genetic structure among populations in areas of varying malaria transmission intensity across Kenya. We also assessed relationships between metrics derived from genetic data, transmission intensity estimates and bioclimatic variables. Despite an overall reduction in transmission intensity across Kenya from 2005 to 2014, we found that parasite populations maintained high genetic diversity and that genetic diversity correlated more closely with past transmission intensity estimates in the year 2000 as compared to contemporary estimates in 2014. In contrast, we found genetic structuring to be significant, consistent with our observation of shifting parasite migration patterns in western Kenya. Both genetic diversity and polyclonality increased with higher precipitation in the dry season, revealing the potential impacts of changing climate patterns on parasite population dynamics. Whereas fragmentation of <i>P. falciparum</i> populations increases opportunities for spatially targeted interventions in Kenya, the high genetic diversity of isolates in our study signals enhanced adaptability of parasites.</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 7","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143633285","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}
引用次数: 0
The Transcriptional Landscape of Adaptive Thermal Plasticity Within and Across Generations: The Role of Gene Expression and Alternative Splicing 代内和代间适应性热可塑性的转录景观:基因表达和选择性剪接的作用。
IF 4.5 1区 生物学
Molecular Ecology Pub Date : 2025-03-11 DOI: 10.1111/mec.17715
Fernando Diaz, Luciano M. Matzkin
{"title":"The Transcriptional Landscape of Adaptive Thermal Plasticity Within and Across Generations: The Role of Gene Expression and Alternative Splicing","authors":"Fernando Diaz,&nbsp;Luciano M. Matzkin","doi":"10.1111/mec.17715","DOIUrl":"10.1111/mec.17715","url":null,"abstract":"<div>\u0000 \u0000 <p>There is increasing evidence for the co-occurrence of adaptive within-generation (WGP) and transgenerational (TGP) plasticity and the ecological scenarios driving both types of plasticity. However, some aspects of their transcriptional mechanisms, such as the role of alternative splicing and the consequences of parental acclimation across life stages, have remained elusive. We explore these fundamental questions by considering the desert endemic <i>Drosophila mojavensis</i> for which prior evidence indicates adaptive thermal acclimation within and across generations. We implement a full factorial design to estimate genome-wide patterns of differential gene expression (DE) and alternative splicing (AS) in response to acclimation treatments performed in the parental and offspring generations, as well as considering larval and adult stages. Our results demonstrate that mechanisms of alternative splicing represent a substantial difference between WGP and TGP. These mechanisms contribute substantially to transcriptional plasticity within generations but not across generations. We found a great number of genes associated with transcriptional TGP, which is exclusive to larval stages and not adult samples. Finally, we provide evidence demonstrating opposing transcriptional trajectories in differential gene expression between WGP and TGP. Thus, parental acclimation appears to up-regulate genes that are down-regulated during offspring acclimation. This pattern suggests a possible hypothesis for the mechanisms explaining the compensatory effect of parental acclimation in the offspring generation.</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 7","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143603276","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}
引用次数: 0
Robust Sensory Traits Across Light Habitats: Visual Signals but Not Receptors Vary in Centrarchids Inhabiting Distinct Photic Environments 在不同的光环境中,中央树的视觉信号而非受体不同。
IF 4.5 1区 生物学
Molecular Ecology Pub Date : 2025-03-11 DOI: 10.1111/mec.17721
César Bertinetti, Camille Mosley, Stuart Jones, Julián Torres-Dowdall
{"title":"Robust Sensory Traits Across Light Habitats: Visual Signals but Not Receptors Vary in Centrarchids Inhabiting Distinct Photic Environments","authors":"César Bertinetti,&nbsp;Camille Mosley,&nbsp;Stuart Jones,&nbsp;Julián Torres-Dowdall","doi":"10.1111/mec.17721","DOIUrl":"10.1111/mec.17721","url":null,"abstract":"<p>Visual communication in fish is often shaped by their light environment, which influences both sensory (e.g., eye size, opsin gene expression) and signalling traits (e.g., body reflectance). This study explores the phenotypic variation in the visual communication traits of six species of centrarchids (Centrarchidae) inhabiting two contrasting light environments. We measured morphological, molecular and signalling traits to determine their variation across photic conditions. Our findings reveal significant interspecific variation in sensory traits but no consistent phenotypic variation between light environments. Centrarchids showed robust visual systems with green-sensitive <i>rh2</i> and red-sensitive <i>lws</i> opsin genes representing the main chromatic channels, with their expression remaining largely unaffected between distinct light habitats. We also found significant molecular evolution in the visual opsin genes, although these changes were not associated with environmental conditions. However, body reflectance displayed species-specific responses to environmental conditions, suggesting that signalling traits may be more flexible than sensory traits. Overall, our results challenge the generality of the current paradigm in visual ecology, which portrays visual systems in fish as highly tunable owing to photic conditions. Our study highlights the potential evolutionary or developmental constraints on centrarchid visual systems and their implications for adaptability to various habitats and novel environmental threats.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 8","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17721","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143595902","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}
引用次数: 0
Genomic Insights Into the Origin, Decline and Recovery of the Once Critically Endangered Iberian Lynx. 对曾经极度濒危的伊比利亚猞猁的起源、衰落和恢复的基因组研究。
IF 4.5 1区 生物学
Molecular Ecology Pub Date : 2025-03-11 DOI: 10.1111/mec.17719
José A Godoy, Enrico Bazzicalupo, Mireia Casas-Marce, Fernando Cruz, Jesús Fernández, Malin Hasselgren, Daniel Kleinman-Ruiz, Lorena Lorenzo-Fernández, María Lucena-Perez, Elena Marmesat, Begoña Martínez-Cruz, Lucía Mayor-Fidalgo, Laia Pérez-Sorribes, Laura Soriano
{"title":"Genomic Insights Into the Origin, Decline and Recovery of the Once Critically Endangered Iberian Lynx.","authors":"José A Godoy, Enrico Bazzicalupo, Mireia Casas-Marce, Fernando Cruz, Jesús Fernández, Malin Hasselgren, Daniel Kleinman-Ruiz, Lorena Lorenzo-Fernández, María Lucena-Perez, Elena Marmesat, Begoña Martínez-Cruz, Lucía Mayor-Fidalgo, Laia Pérez-Sorribes, Laura Soriano","doi":"10.1111/mec.17719","DOIUrl":"https://doi.org/10.1111/mec.17719","url":null,"abstract":"<p><p>The Iberian lynx was at the brink of extinction by the year 2000 but has since then, and thanks to intensive conservation measures, gone through a remarkable recovery, providing a much-welcomed and encouraging conservation success story. Genetic issues have probably contributed to the decline in the past, and the genetic management of inbreeding and genetic diversity is likely contributing to its recent recovery. The species was an early adopter of genetic and genomic approaches, and the combination of an extreme decline, an intensive monitoring and management programme and extensive genomic resources and data makes the Iberian lynx an excellent model for conservation genomics. Here, we review how genetic and genomic data have contributed to the knowledge of the species evolutionary and demographic history, the evaluation of the genetic status of the species through time, including historical and ancient data, and how this information has prompted and guided conservation actions. In the process, genomics provided valuable insights into the dynamics of functional variation in bottlenecked populations and the consequences of intraspecific and interspecific admixtures. In more applied terms, the species is subjected to an ambitious genetic monitoring and management programme, covering captive, remnant and reintroduced populations, which has succeeded in improving the genetic status of the species and thereby contributed to its recovery. Current genomic work aims at expanding these contributions with novel genomic resources and data while capitalising on extensive demographic and genealogical data provided by the ongoing non-invasive genetic monitoring programme.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17719"},"PeriodicalIF":4.5,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143603275","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}
引用次数: 0
Allopatric Speciation and Interspecific Gene Flow Driven by Niche Conservatism of Diploderma Tree Lizards in Taiwan 台湾树蜥蜴生态位保守性驱动的异域物种形成与种间基因流动。
IF 4.5 1区 生物学
Molecular Ecology Pub Date : 2025-03-07 DOI: 10.1111/mec.17718
Tzong-Han Lin, Zong-Yu Shen, Ming-Hsun Chou, Pei-Wei Sun, Chin-Chia Shen, Jen-Pan Huang, Si-Min Lin
{"title":"Allopatric Speciation and Interspecific Gene Flow Driven by Niche Conservatism of Diploderma Tree Lizards in Taiwan","authors":"Tzong-Han Lin,&nbsp;Zong-Yu Shen,&nbsp;Ming-Hsun Chou,&nbsp;Pei-Wei Sun,&nbsp;Chin-Chia Shen,&nbsp;Jen-Pan Huang,&nbsp;Si-Min Lin","doi":"10.1111/mec.17718","DOIUrl":"10.1111/mec.17718","url":null,"abstract":"<div>\u0000 \u0000 <p>Allopatric speciation is a widely accepted hypothesis for species distributed across geographic barriers. Meanwhile, niche conservatism, the tendency of species to retain their ancestral ecological traits, helps reinforce genetic differentiation by stabilising species distributions over time and reducing the role of competition in shaping range boundaries. In contrast, hybridisation can occur at the edges of distribution after secondary contact following climatic or geological events, leading to a reduction in genetic divergence between divergent lineages. In this study, we investigated the role of geographic barriers, niche conservatism and gene flow in the speciation history of <i>Diploderma</i> species in Taiwan, where geographically distinct taxa share similar environmental preferences. By using ddRAD-seq data, seven distinct genetic clusters were identified with two putatively new cryptic species in \u0000 <i>D. brevipes</i>\u0000 and <i>D. polygonatum</i>. Most sister species pairs share similar climatic niches based on niche equivalency and similarity tests. We further detected significant historical gene flow between lineages of \u0000 <i>D. brevipes</i>\u0000 and <i>D. polygonatum</i>, where secondary contact might have occurred because of palaeoclimate changes and historical demographic expansion. Our results demonstrate that niche conservatism does not always act in concert to strengthen the result of allopatric speciation; instead, it may also lead to gene flow between divergent lineages following secondary contact. On the other hand, postdivergence gene flow may be a creating force generating phenotypic diversity in sexually selected traits in our study system. The underestimated species diversity of <i>Diploderma</i> in Taiwan requires further taxonomic work in the future.</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 8","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143571514","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}
引用次数: 0
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