Dataset Information

Landscape Population Genomics of Forsythia (Forsythia suspensa) Reveal That Ecological Habitats Determine the Adaptive Evolution of Species.

ABSTRACT: Understanding the genetic mechanisms of adaptation to environmental variables is a key concern in molecular ecology and evolutionary biology. Determining the adaptive evolutionary direction and evaluating the adaptation status of species can improve our understanding of these mechanisms. In this study, we sampled 20 populations of Forsythia suspensa to infer the relationship between environmental variables and adaptive genetic variations. Population structure analysis revealed that four genetic groups of F. suspensa exist resulting from divergent selection driven by seven environmental variables. A total of 26 outlier loci were identified by both BayeScan and FDIST2, 23 of which were environment-associated loci (EAL). Environmental association analysis revealed that the environmental variables related to the ecological habitats of F. suspensa are associated with high numbers of EAL. Results of EAL characterization in F. suspensa are consistent with the hypothesis that ecological habitats determine the adaptive evolution of this species. Moreover, a model of species adaptation to environmental variables was proposed in this study. The adaptation model was used to further evaluate the adaptation status of F. suspensa to environmental variables. This study will be useful to help us in understanding the adaptive evolution of species in regions lacking strong selection pressure.

SUBMITTER: Yang J

PROVIDER: S-EPMC5380681 | biostudies-other | 2017

REPOSITORIES: biostudies-other

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Landscape Population Genomics of Forsythia (<i>Forsythia suspensa</i>) Reveal That Ecological Habitats Determine the Adaptive Evolution of Species.

Yang Jie J Miao Cai-Yun CY Mao Run-Li RL Li Yong Y

Frontiers in plant science 20170405

Understanding the genetic mechanisms of adaptation to environmental variables is a key concern in molecular ecology and evolutionary biology. Determining the adaptive evolutionary direction and evaluating the adaptation status of species can improve our understanding of these mechanisms. In this study, we sampled 20 populations of <i>Forsythia suspensa</i> to infer the relationship between environmental variables and adaptive genetic variations. Population structure analysis revealed that four g ...[more]

PMID: 28424728

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Project description:Deciphering the genomic variation that represents microevolutionary processes toward species divergence is key to understanding microbial speciation, which has long been under debate. Streptomycetes are filamentous bacteria that are ubiquitous in nature and the richest source of antibiotics; however, their speciation processes remain unknown. To tackle this issue, we performed a comprehensive population genomics analysis on Streptomyces albidoflavus residing in different habitats and with a worldwide distribution and identified and characterized the foundational changes within the species. We detected three well-defined phylogenomic clades, of which clades I and III mainly contained free-living (soil/marine) and insect-associated strains, respectively, and clade II had a mixed origin. By performing genome-wide association studies (GWAS), we identified a number of genetic variants associated with free-living or entomic (denoting or relating to insects) habitats in both the accessory and core genomes. These variants contributed collectively to the population structure and had annotated or confirmed functions that likely facilitate differential adaptation of the species. In addition, we detected higher levels of homologous recombination within each clade and in the free-living group than within the whole species and in the entomic group. A subset of the insect-associated strains (clade III) showed a relatively independent evolutionary trajectory with more symbiosis-favorable genes but little genetic interchange with the other lineages. Our results demonstrate that ecological adaptation promotes genetic differentiation in S. albidoflavus, suggesting a model of ecological speciation with gene flow in streptomycetes.IMPORTANCE Species are the fundamental units of ecology and evolution, and speciation leads to the astounding diversity of life on Earth. Studying speciation is thus of great significance to understand, protect, and exploit biodiversity, but it is a challenge in the microbial world. In this study, using population genomics, we placed Streptomyces albidoflavus strains in a spectrum of speciation and showed that the genetic differences between phylogenomic clusters evolved mainly by environmental selection and gene-specific sweeps. These findings highlight the role of ecology in structuring recombining bacterial species, making a step toward a deeper understanding of microbial speciation. Our results also raise concerns of an underrated microbial diversity at the intraspecies level, which can be utilized for mining of ecologically relevant natural products.

Project description:BackgroundConnections between habitats are key to a full understanding of anthropic impacts on ecosystems. Freshwater habitats are especially biodiverse, yet depend on exchange with terrestrial habitats. White storks (Ciconia ciconia) are widespread opportunists that often forage in landfills and then visit wetlands, among other habitats. It is well known that white storks ingest contaminants at landfills (such as plastics and antibiotic resistant bacteria), which can be then deposited in other habitats through their faeces and regurgitated pellets.MethodsWe characterized the role of white storks in habitat connectivity by analyzing GPS data from populations breeding in Germany and wintering from Spain to Morocco. We overlaid GPS tracks on a land-use surface to construct a spatially-explicit network in which nodes were sites, and links were direct flights. We then calculated centrality metrics, identified spatial modules, and quantified overall connections between habitat types. For regional networks in southern Spain and northern Morocco, we built Exponential Random Graph Models (ERGMs) to explain network topologies as a response to node habitat.ResultsFor Spain and Morocco combined, we built a directed spatial network with 114 nodes and 370 valued links. Landfills were the habitat type most connected to others, as measured by direct flights. The relevance of landfills was confirmed in both ERGMs, with significant positive effects of this habitat as a source of flights. In the ERGM for southern Spain, we found significant positive effects of rice fields and salines (solar saltworks) as sinks for flights. By contrast, in the ERGM for northern Morocco, we found a significant positive effect of marshes as a sink for flights.ConclusionsThese results illustrate how white storks connect landfills with terrestrial and aquatic habitats, some of which are managed for food production. We identified specific interconnected habitat patches across Spain and Morocco that could be used for further studies on biovectoring of pollutants, pathogens and other propagules.

Dataset Information

Landscape Population Genomics of Forsythia (Forsythia suspensa) Reveal That Ecological Habitats Determine the Adaptive Evolution of Species.

Publications

Landscape Population Genomics of Forsythia (<i>Forsythia suspensa</i>) Reveal That Ecological Habitats Determine the Adaptive Evolution of Species.

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