Molecular Ecology最新文献_第2页

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

Temporal Changes in Tasmanian Devil Genetic Diversity at Sites With and Without Supplementation.

IF 4.5 1区生物学

Molecular Ecology Pub Date : 2025-01-31 DOI: 10.1111/mec.17671

Andrea L Schraven, Elspeth A McLennan, Katherine A Farquharson, Andrew V Lee, Katherine Belov, Samantha Fox, Catherine E Grueber, Carolyn J Hogg

{"title":"Temporal Changes in Tasmanian Devil Genetic Diversity at Sites With and Without Supplementation.","authors":"Andrea L Schraven, Elspeth A McLennan, Katherine A Farquharson, Andrew V Lee, Katherine Belov, Samantha Fox, Catherine E Grueber, Carolyn J Hogg","doi":"10.1111/mec.17671","DOIUrl":"https://doi.org/10.1111/mec.17671","url":null,"abstract":"Management interventions for threatened species are well documented with genetic data now playing a pivotal role in informing their outcomes. However, in situ actions like supplementations (releasing individuals into an existing population) are often restricted to a singular site. Considerable research and management effort have been dedicated to conserving the Tasmanian devil (Sarcophilus harrisii), offering a unique opportunity to investigate the temporal genetic consequences of supplementation at multiple sites, in comparison to outcomes observed in the absence of management interventions. Using 1,778 genome-wide SNPs across 1,546 individuals, we compared four wild-supplemented sites to four monitoring-only sites (not supplemented; control sites) over 9 years (2014-2022). At the study completion, genetic differentiation among supplemented sites had significantly decreased compared to among not-supplemented sites. We found statistically significant variation in genetic change over time between sites using linear mixed-effects modelling with random slopes. Investigating this among-site variation showed that three of the supplemented sites conformed to predictions that supplementations would have a positive impact on the genetic diversity of devils at these sites. We predicted no change over time at our fourth site due to the observed relatively high gene flow, however, this site did not align with predictions, instead showing decreased genetic diversity and increased relatedness. Amongst not supplemented sites, there was no consistent pattern of temporal genetic change, suggesting devil sites across Tasmania are highly heterogeneous, likely reflecting variation in site connectivity and genetic drift. Our study demonstrates that long-term concurrent monitoring of multiple sites, including controls, is necessary to contextualise the influence of management interventions on natural species fluctuations.","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17671"},"PeriodicalIF":4.5,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143072966","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

Seascape Genomics of Elacatinus punctiulatus (Ginsburg, 1938): Understanding the Historical and Contemporary Drivers of Population Structure in the Gulf of California.

IF 4.5 1区生物学

Molecular Ecology Pub Date : 2025-01-31 DOI: 10.1111/mec.17668

Vladimir Salvador De Jesús-Bonilla, Alejandra Quintero-Grijalva, Pedro Cruz-Hernández, Raúl Octavio Martínez-Rincón, Norma Y Hernández-Saavedra, Fausto Valenzuela-Quiñonez

{"title":"Seascape Genomics of Elacatinus punctiulatus (Ginsburg, 1938): Understanding the Historical and Contemporary Drivers of Population Structure in the Gulf of California.","authors":"Vladimir Salvador De Jesús-Bonilla, Alejandra Quintero-Grijalva, Pedro Cruz-Hernández, Raúl Octavio Martínez-Rincón, Norma Y Hernández-Saavedra, Fausto Valenzuela-Quiñonez","doi":"10.1111/mec.17668","DOIUrl":"https://doi.org/10.1111/mec.17668","url":null,"abstract":"The genomic diversity and population structure of marine species represents a complex mosaic shaped by historical and contemporary environmental seascape features that maintain or alter it over time. The Gulf of California (GC) is an interior sea with a dynamic history during its formation and a contemporary environmental and oceanographic complexity; hence, it is a suitable system to test the effect of historical and contemporary factors on genomic diversity in marine species. We investigated the genomic seascape of the redhead goby (Elacatinus puncticulatus; Ginsburg, 1938), a cryptobenthic marine fish, to gain insights into the historical and contemporary drivers shaping its population structure in the GC. A total of 4802 SNPs markers were analysed, with 3775 loci classified as neutral markers and 27 as outlier markers potentially under selection. Both markers demonstrated population structure, with the neutral markers showing two main groups corresponding to northern and southern locatities. The outlier markers identified an additional genetic group emerging in the central area of the sampled localities. Genetic differentiation between the North and South regions and historical demographic simulations was consistent with ancient divergence (1.04 Mya) and secondary contact (0.15 Mya). The genomic environmental association analysis revealed a possible adaptive scenario linked to ocean temperature. The study highlights the importance of historical events, contemporary environmental factors, and oceanographic circulation in shaping the genetic structure of E. puncticulatus populations in the GC.","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17668"},"PeriodicalIF":4.5,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143062743","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 "Genome-wide population affinities and signatures of adaptation in hydruntines, sussemiones and Asian wild asses".

IF 4.5 1区生物学

Molecular Ecology Pub Date : 2025-01-29 DOI: 10.1111/mec.17674

引用次数: 0

Genomic Footprints of Hybridisation in North Atlantic Eels (Anguilla anguilla and A. rostrata).

IF 4.5 1区生物学

Molecular Ecology Pub Date : 2025-01-29 DOI: 10.1111/mec.17664

Aja Noersgaard Buur Tengstedt, Shenglin Liu, Magnus W Jacobsen, Gabriela Ulmo-Diaz, Bjarni Jónsson, Jose Martin Pujolar, Michael M Hansen

{"title":"Genomic Footprints of Hybridisation in North Atlantic Eels (Anguilla anguilla and A. rostrata).","authors":"Aja Noersgaard Buur Tengstedt, Shenglin Liu, Magnus W Jacobsen, Gabriela Ulmo-Diaz, Bjarni Jónsson, Jose Martin Pujolar, Michael M Hansen","doi":"10.1111/mec.17664","DOIUrl":"https://doi.org/10.1111/mec.17664","url":null,"abstract":"Understanding interspecific introgressive hybridisation and the biological significance of introgressed variation remains an important goal in population genomics. European (Anguilla anguilla) and American eel (A. rostrata) represent a remarkable case of hybridisation. Both are panmictic and spawn in partial sympatry in the Sargasso Sea, occasionally producing viable, fertile hybrids, primarily found in Iceland. We studied introgressive hybridisation from American into European eel using whole-genome sequences of 78 individuals, including European, American and 21 putative hybrid eels. Previous studies using few genetic markers could not resolve whether hybridisation involved simple unidirectional backcrossing or a more complex hybrid swarm scenario. However, local ancestry inference along individual chromosomes revealed that Icelandic hybrids were primarily F1 or first-generation backcrosses towards European eel, with some showing more complex backcrossing. All European eels outside Iceland contained short chromosomal blocks from American eel, indicating a porous genome. We found no evidence for previously hypothesised geographical gradients of introgression in European eel outside Iceland. Several chromosomal regions showed high interspecific divergence, but haplotype blocks introgressed from American eel were identified both within and outside these regions. There was little correspondence between regions of high relative (FST) and absolute divergence (dXY), with the former reflecting selective sweeps within species or reduced recombination rather than barrier loci. A single genomic region showed evidence of repeated introgression from American into European eel under positive selection in both species. The study illustrates that species can maintain genetic integrity despite porous genomes and that standing variation in one species can potentially be available for future adaptive responses in the other species.","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17664"},"PeriodicalIF":4.5,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143057587","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