Molecular Ecology最新文献

Comparative Population Genomics Reveal the Determinants of Genome Erosion in Two Sympatric Neotropical Falcons.

IF 4.5 1区生物学

Molecular Ecology Pub Date : 2025-02-03 DOI: 10.1111/mec.17686

Nicolas Dussex

{"title":"Comparative Population Genomics Reveal the Determinants of Genome Erosion in Two Sympatric Neotropical Falcons.","authors":"Nicolas Dussex","doi":"10.1111/mec.17686","DOIUrl":"https://doi.org/10.1111/mec.17686","url":null,"abstract":"Studying genetic diversity in endangered species has become an important component of conservation science over the past decades. Thanks to recent developments in sequencing technologies and bioinformatics, genetic parameters of conservation relevance such as neutral and functional genome-wide variation are now routinely estimated. Since inbreeding and deleterious mutations represent significant threats to small and declining populations, assessing the dynamics of these parameters has received particular attention in many recent conservation genomics studies. In this issue of Molecular Ecology, Martin et al. analyse the genomes of two Neotropical falcon species to assess the impact of their contrasting population histories on genome-wide diversity. They show that the Orange-breasted falcon which has had a low long-term population size and has experienced recent population bottlenecks is more inbred but has relatively fewer deleterious variations compared to its sister taxon, the Bat falcon, which is characterised by a larger long-term population size. This study not only provides insights into the role of past demography on the dynamics of deleterious variation in two species with contrasting population histories but also highlights the increasing importance of comparative approaches in population and conservation genomics.","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17686"},"PeriodicalIF":4.5,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078068","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

Correction to "Resistance, Resilience, and Functional Redundancy of Freshwater Bacterioplankton Communities Facing a Gradient of Agricultural Stressors in a Mesocosm Experiment".

IF 4.5 1区生物学

Molecular Ecology Pub Date : 2025-02-03 DOI: 10.1111/mec.17673

引用次数: 0

Evolution of Hybrid Inviability Associated With Chromosome Fusions.

IF 4.5 1区生物学

Molecular Ecology Pub Date : 2025-02-03 DOI: 10.1111/mec.17672

Jesper Boman, Karin Näsvall, Roger Vila, Christer Wiklund, Niclas Backström

{"title":"Evolution of Hybrid Inviability Associated With Chromosome Fusions.","authors":"Jesper Boman, Karin Näsvall, Roger Vila, Christer Wiklund, Niclas Backström","doi":"10.1111/mec.17672","DOIUrl":"https://doi.org/10.1111/mec.17672","url":null,"abstract":"Chromosomal rearrangements, such as inversions, have received considerable attention in the speciation literature due to their hampering effects on recombination. Less is known about how other rearrangements, such as chromosome fissions and fusions, can affect the evolution of reproductive isolation. Here, we use crosses between populations of the wood white butterfly (Leptidea sinapis) with different karyotypes to identify genomic regions associated with hybrid inviability. We map hybrid inviability candidate loci by contrasting allele frequencies between F2 hybrids that survived until the adult stage with individuals of the same cohort that succumbed to hybrid incompatibilities. Hybrid inviability candidate regions have high genetic differentiation between parental populations, reduced recombination rates, and are enriched near chromosome fusions. By analysing sequencing coverage, we exclude aneuploidies as a direct link between hybrid inviability and chromosome fusions. Instead, our results point to an indirect relationship between hybrid inviability and chromosome fusions, possibly related to reduced recombination in fused chromosomes. Thus, we map postzygotic isolation to chromosomal rearrangements, providing crucial empirical evidence for the idea that chromosome number differences between taxa can contribute to speciation.","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17672"},"PeriodicalIF":4.5,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078074","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

Wind Is a Primary Driver of Fungal Dispersal Across a Mainland-Island System.

IF 4.5 1区生物学

Molecular Ecology Pub Date : 2025-02-03 DOI: 10.1111/mec.17675

D Naranjo-Orrico, O Ovaskainen, B Furneaux, J Purhonen, P A Arancibia, S Burg, N Moser, J Niku, G Tikhonov, E Zakharov, N Monkhouse, N Abrego

{"title":"Wind Is a Primary Driver of Fungal Dispersal Across a Mainland-Island System.","authors":"D Naranjo-Orrico, O Ovaskainen, B Furneaux, J Purhonen, P A Arancibia, S Burg, N Moser, J Niku, G Tikhonov, E Zakharov, N Monkhouse, N Abrego","doi":"10.1111/mec.17675","DOIUrl":"https://doi.org/10.1111/mec.17675","url":null,"abstract":"Dispersal is one of the main processes shaping ecological communities. Yet, for species-rich communities in natural systems, the role of dispersal in community assembly remains relatively less studied compared to other processes. This is the case for fungal communities, for which predictable knowledge about where and how the dispersal propagules move across space is largely lacking. We sampled fungal communities at their dispersal stage in a lake mainland-island system in Finland, using a regular grid of 18 × 18 km, including sites on the mainland, islands and over the water. Fungal communities were screened by applying DNA barcoding to air samples. To assess the factors determining fungal dispersal, we modelled aerial fungal communities with a joint species distribution model, including spore traits, weather-related predictors, and spatial predictors. We found that the probability of occurrence of most species (and consequently species richness measured as the number of OTUs per sample) was lower in low-connectivity sites (water and isolated islands) compared to high-connectivity sites (mainland). There was a strong phylogenetic signal in how the fungal species responded to connectivity, indicating that some taxonomic groups are more dispersal limited than others, although such responses were not structured by their trophic guilds. Furthermore, wind speed influenced how species with different spore sizes responded to connectivity: in low-connectivity sites, species with large sexual spores were detected especially when wind was high, whereas, in high-connectivity sites, they were detected especially when wind was low. This study demonstrates that air fungal dispersal might be more predictable than previously considered and contributes to the mechanistic understanding of fungal air dispersal.","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17675"},"PeriodicalIF":4.5,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078077","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

Comparative Genomics Uncovers Molecular Adaptations for Cetacean Deep-Sea Diving.

IF 4.5 1区生物学

Molecular Ecology Pub Date : 2025-02-03 DOI: 10.1111/mec.17678

Fan Zhang, Tong Zhang, Hao Dong, Jie Jiang, Guang Yang, Inge Seim, Ran Tian

{"title":"Comparative Genomics Uncovers Molecular Adaptations for Cetacean Deep-Sea Diving.","authors":"Fan Zhang, Tong Zhang, Hao Dong, Jie Jiang, Guang Yang, Inge Seim, Ran Tian","doi":"10.1111/mec.17678","DOIUrl":"https://doi.org/10.1111/mec.17678","url":null,"abstract":"Cetaceans show remarkable diversity in diving capability, implying a range of adaptive strategies to hazards such as hydrostatic pressure and oxidative stress, but few studies have considered the evolution of extreme diving. Here, we first examined the relationship between morphological and physiological factors and diving capability and then considered the molecular evolution of candidate deep-sea diving traits in a genomic dataset of cetaceans. Our dataset included six super-divers, sperm whales (families Physeteridae and Kogiidae) and beaked whales (Ziphiidae), species that can dive deeper than 1000 m for about an hour or longer. We found a positive association between diving capability and oxygen-linked globins, and super-diver myoglobin (MB) is under positive selection and harbours a reported functional amino acid change. Blubber thickness was positively associated, likely to provide thermal insulation and hydrostatic pressure resistance. Super-divers have gene changes that may contribute to differences in the composition of outer blubber neutral lipids (triacylglycerols and wax esters), fatty acids and cholesterol. Total lung capacity relative to body mass showed a negative association, ostensibly to limit gas bubbles that can cause decompression sickness. A functional assay suggests that an ATP8B1 amino acid substitution may reduce lung injury in super-divers. Super-diver XDH has two unique amino acids and a decreased ability to produce uric acid under hypoxia when its ROS-generating XO isoform is prevalent, suggesting that it reduces cell damage from oxidative stress and uric acid accumulation in species with prolonged dives. Our study deepens the understanding of how deep-sea diving emerged in the cetacean lineage.","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17678"},"PeriodicalIF":4.5,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078066","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

Adaptive Divergence and Functional Convergence: The Evolution of Pulmonary Gene Expression in Amphibians of the Qingzang Plateau.

IF 4.5 1区生物学

Molecular Ecology Pub Date : 2025-02-03 DOI: 10.1111/mec.17663

Liming Chang, Wei Zhu, Qiheng Chen, Chunlin Zhao, Lulu Sui, Cheng Shen, Qunde Zhang, Bin Wang, Jianping Jiang

{"title":"Adaptive Divergence and Functional Convergence: The Evolution of Pulmonary Gene Expression in Amphibians of the Qingzang Plateau.","authors":"Liming Chang, Wei Zhu, Qiheng Chen, Chunlin Zhao, Lulu Sui, Cheng Shen, Qunde Zhang, Bin Wang, Jianping Jiang","doi":"10.1111/mec.17663","DOIUrl":"https://doi.org/10.1111/mec.17663","url":null,"abstract":"The Qingzang Plateau, with its harsh environmental conditions-low oxygen, high ultraviolet radiation and significant temperature fluctuations-demands specialised adaptations for survival. While genetic adaptations have been extensively studied, gene expression's role in amphibian adaptation to high elevations remains understudied. This study analysed pulmonary gene expression in 119 amphibians across the plateau to explore how genetic and environmental factors shape expression evolution. Transcriptomic analyses revealed significant interspecies variation, driven by environmental factors like temperature, oxygen levels, UVB radiation and precipitation. Principal Component and Mantel analyses found no significant correlation between gene expression divergence and genetic distance. Instead, species-specific traits and environmental pressures were pivotal in shaping expression patterns. PERMANOVA analysis showed environmental factors had varying impacts on species. For instance, Bufo gargarizans exhibited a strong gene expression response to multiple environmental factors, while Scutiger boulengeri was less influenced, reflecting diverse adaptive strategies. Functional enrichment analysis highlighted convergence in key biological processes, such as energy metabolism, apoptosis and autophagy, despite species-specific gene expression differences. These processes are critical for surviving the plateau's extremes. The findings suggest that gene expression evolution in amphibians on the Qingzang Plateau is shaped by both genetic diversity and environmental pressures. Although gene expression profiles vary, they converge on essential functions, offering insights into adaptation mechanisms in extreme environments.","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17663"},"PeriodicalIF":4.5,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078062","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

DNA Methylation Associates With Sex-Specific Effects of Experimentally Increased Yolk Testosterone in Wild Nestlings. DNA甲基化与野生雏鸟卵黄睾酮实验增加的性别特异性效应相关。

IF 4.5 1区生物学

Molecular Ecology Pub Date : 2025-02-01 Epub Date: 2025-01-06 DOI: 10.1111/mec.17647

Bernice Sepers, Suvi Ruuskanen, Tjomme van Mastrigt, A Christa Mateman, Kees van Oers

{"title":"DNA Methylation Associates With Sex-Specific Effects of Experimentally Increased Yolk Testosterone in Wild Nestlings.","authors":"Bernice Sepers, Suvi Ruuskanen, Tjomme van Mastrigt, A Christa Mateman, Kees van Oers","doi":"10.1111/mec.17647","DOIUrl":"10.1111/mec.17647","url":null,"abstract":"Maternal hormones can profoundly impact offspring physiology and behaviour in sex-dependent ways. Yet little is known about the molecular mechanisms linking these maternal effects to offspring phenotypes. DNA methylation, an epigenetic mechanism, is suggested to facilitate maternal androgens' effects. To assess whether phenotypic changes induced by maternal androgens associate with DNA methylation changes, we experimentally manipulated yolk testosterone levels in wild great tit eggs (Parus major) and quantified phenotypic and DNA methylation changes in the hatched offspring. While we found no effect on the handing stress response, increased yolk testosterone levels decreased the begging probability, emphasised sex differences in fledging mass, and affected methylation at 763 CpG sites, but always in a sex-specific way. These sites are associated with genes involved in growth, oxidative stress, and reproduction, suggesting sex-specific trade-offs to balance the costs and benefits of exposure to high yolk testosterone levels. Future studies should assess if these effects extend beyond the nestling stage and impact fitness.","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17647"},"PeriodicalIF":4.5,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142930078","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

Recent Origin of a Range-Restricted Species With Subsequent Introgression in its Widespread Congener in the Phyteuma spicatum Group (Campanulaceae). 一个分布范围受限的物种的最新起源及其广泛分布的同属植物 Phyteuma spicatum 组（金钟罩科）的后续传入。

IF 4.5 1区生物学

Molecular Ecology Pub Date : 2025-02-01 Epub Date: 2024-12-13 DOI: 10.1111/mec.17624

Dennis Larsson, Petra Šarhanová, Ovidiu Paun, Gerald M Schneeweiss

{"title":"Recent Origin of a Range-Restricted Species With Subsequent Introgression in its Widespread Congener in the Phyteuma spicatum Group (Campanulaceae).","authors":"Dennis Larsson, Petra Šarhanová, Ovidiu Paun, Gerald M Schneeweiss","doi":"10.1111/mec.17624","DOIUrl":"10.1111/mec.17624","url":null,"abstract":"Understanding the causes of restricted geographic distributions is of major interest to evolutionary and conservation biologists. Inferring historical factors has often relied on ad hoc interpretations of genetic data, and hypothesis testing within a statistical framework under different demographic scenarios remains underutilised. Using coalescent modelling on RAD-sequencing data, we (i) test hypotheses about the origin of Phyteuma gallicum (Campanulaceae), a range-restricted endemic of central France sympatric with its widespread congener Ph. spicatum, and (ii) date its origin, irrespective of its mode of origin, to test the hypothesis that the restricted range is due to a recent time of origin. The best supported model of origin is one of a dichotomous split of Ph. gallicum, confirmed as distinct species, and the Central European Ph. nigrum with subsequent gene flow between Ph. gallicum and Ph. spicatum. The split of Ph. gallicum and Ph. nigrum is estimated at 45-55,000 years ago. Coalescent modelling on genomic data not only clarified the mode of origin (dichotomous speciation instead of a previously hypothesised hybridogenic origin) but also identified recency of speciation as a sufficient, although likely not the sole, factor to explain the restricted distribution range. Coalescent modelling strongly improves our understanding of the evolution of range-restricted species that are frequently of conservation concern, as is the case for Ph. gallicum.","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17624"},"PeriodicalIF":4.5,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11754710/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142823659","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

Environmental Stress and Resource Availability Affect the Maintenance of Genetic Variation in a Dominant Marsh Plant (Spartina alterniflora). 环境胁迫和资源可利用性影响沼泽优势植物互花米草遗传变异的维持。

IF 4.5 1区生物学

Molecular Ecology Pub Date : 2025-02-01 Epub Date: 2024-12-17 DOI: 10.1111/mec.17628

Robyn A Zerebecki, A Randall Hughes

{"title":"Environmental Stress and Resource Availability Affect the Maintenance of Genetic Variation in a Dominant Marsh Plant (Spartina alterniflora).","authors":"Robyn A Zerebecki, A Randall Hughes","doi":"10.1111/mec.17628","DOIUrl":"10.1111/mec.17628","url":null,"abstract":"Changes in genetic variation, and particularly documented declines in genetic diversity, influence not only evolutionary potential but also current ecological function. Given this context, it is essential to understand what abiotic and biotic factors promote or disrupt the maintenance of genetic variation in natural populations. To address this knowledge gap in the context of salt marsh plants, we established a three-year field experiment, testing the independent and interactive effects of nutrient availability and physical stress on the maintenance of plant (Spartina alterniflora) genotypic diversity. We found that in environments with high physical stress (i.e., low marsh elevations), diversity declined over time. However, the addition of nutrients promoted the maintenance of Spartina genotypic diversity across the physical stress gradient. We also observed changes in genotypic composition and genetic divergence across environmental stress treatments, indicating variation among Spartina genotypes in their response to these factors. Our results suggest that tidal inundation acts a selective gradient within coastal marshes, altering genotypic diversity and composition across the landscape. Moreover, our work highlights that the effects of increasing inundation due to continued sea-level rise on the maintenance of diversity may be modulated by concomitant changes in nutrient inputs, with cascading effects on marsh structure and function.","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17628"},"PeriodicalIF":4.5,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142833341","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

Recent Range Expansion and Genomic Admixture in a Kleptoparasitic Spider, Argyrodes lanyuensis: A Case of Adaptive Introgression on Small, Isolated Islands of the Taiwan-Philippine Transition Zone? 克隆寄生蛛（Argyrodes lanyuensis）最近的分布区扩展和基因组融合：台湾-菲律宾过渡带孤立小岛上的适应性引入案例？

IF 4.5 1区生物学

Molecular Ecology Pub Date : 2025-02-01 Epub Date: 2024-12-17 DOI: 10.1111/mec.17630

Mae A Responte, Cheng-Yu Wu, Noraya U Elias, Rafe M Brown, Chia-Yen Dai, Yong-Chao Su

{"title":"Recent Range Expansion and Genomic Admixture in a Kleptoparasitic Spider, Argyrodes lanyuensis: A Case of Adaptive Introgression on Small, Isolated Islands of the Taiwan-Philippine Transition Zone?","authors":"Mae A Responte, Cheng-Yu Wu, Noraya U Elias, Rafe M Brown, Chia-Yen Dai, Yong-Chao Su","doi":"10.1111/mec.17630","DOIUrl":"10.1111/mec.17630","url":null,"abstract":"Adaptive introgression involves the acquisition of advantageous genetic variants through hybridisation, which are subsequently favoured by natural selection due to their association with beneficial traits. Here, we analysed speciation patterns of the kleptoparasitic spider, Argyrodes lanyuensis, through genomic analyses and tested for possible genetic evidence of adaptive introgression at the Taiwan-Philippines transition zone. Our study used highly polymorphic SNPs to demonstrate that speciation occurred when the Hualien (on Taiwan Island + Green Island) and Orchid Island + Philippine lineages separated during the early to mid-Pleistocene. The best colonisation model suggested by approximate Bayesian computation and random forests and biogeographical analyses supported an inference of a bottleneck during speciation, an interpretation reinforced by observation of lower FST values and reduced genetic diversity of the Orchid Island + Philippines lineage. We also found the highest support for the occurrence of introgression on the youngest island (Green Island) of the Taiwan-Philippines transition zone based on the ABBA-BABA test. Our study highlights the inference of two noteworthy species (Hualien + Green Island and Orchid Island + Philippines) based on our species delimitation tests, with gene flow between Green Island and Orchid Island that indicates introgression. The potential adaptive alleles in Green Island population, which are under balancing selection, provide initial evidence of possible rare case of adaptive introgression. This could represent an evolutionary response to a newly formed niche (or novel geographical context) lying between the tropical climate of the Philippines and the subtropical climate of Hualien, Taiwan.","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17630"},"PeriodicalIF":4.5,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142833385","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