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  • 1
    Online Resource
    Online Resource
    Whole-genome sequencing reveals host factors underlying critical COVID-19
    Springer Science and Business Media LLC ; 2022
    In:  Nature Vol. 607, No. 7917 ( 2022-07-07), p. 97-103
    Details
    In: Nature, Springer Science and Business Media LLC, Vol. 607, No. 7917 ( 2022-07-07), p. 97-103
    Abstract: Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care 1 or hospitalization 2–4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling ( IL10RB and PLSCR1 ), leucocyte differentiation ( BCL11A ) and blood-type antigen secretor status ( FUT2 ). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase ( ATP11A ), and increased expression of a mucin ( MUC1 )—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules ( SELE , ICAM5 and CD209 ) and the coagulation factor F8 , all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease.
    Type of Medium: Online Resource
    ISSN: 0028-0836 , 1476-4687
    URL: Article
    DOI: 10.1038/s41586-022-04576-6
    RVK:
    TA 1000
    RVK:
    UA 1000
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    WA 15000
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 120714-3
    detail.hit.zdb_id: 1413423-8
    SSG: 11
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  • 2
    Online Resource
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    Mapping the human genetic architecture of COVID-19
    Springer Science and Business Media LLC ; 2021
    In:  Nature Vol. 600, No. 7889 ( 2021-12-16), p. 472-477
    Details
    In: Nature, Springer Science and Business Media LLC, Vol. 600, No. 7889 ( 2021-12-16), p. 472-477
    Abstract: The genetic make-up of an individual contributes to the susceptibility and response to viral infection. Although environmental, clinical and social factors have a role in the chance of exposure to SARS-CoV-2 and the severity of COVID-19 1,2 , host genetics may also be important. Identifying host-specific genetic factors may reveal biological mechanisms of therapeutic relevance and clarify causal relationships of modifiable environmental risk factors for SARS-CoV-2 infection and outcomes. We formed a global network of researchers to investigate the role of human genetics in SARS-CoV-2 infection and COVID-19 severity. Here we describe the results of three genome-wide association meta-analyses that consist of up to 49,562 patients with COVID-19 from 46 studies across 19 countries. We report 13 genome-wide significant loci that are associated with SARS-CoV-2 infection or severe manifestations of COVID-19. Several of these loci correspond to previously documented associations to lung or autoimmune and inflammatory diseases 3–7 . They also represent potentially actionable mechanisms in response to infection. Mendelian randomization analyses support a causal role for smoking and body-mass index for severe COVID-19 although not for type II diabetes. The identification of novel host genetic factors associated with COVID-19 was made possible by the community of human genetics researchers coming together to prioritize the sharing of data, results, resources and analytical frameworks. This working model of international collaboration underscores what is possible for future genetic discoveries in emerging pandemics, or indeed for any complex human disease.
    Type of Medium: Online Resource
    ISSN: 0028-0836 , 1476-4687
    URL: Article
    DOI: 10.1038/s41586-021-03767-x
    RVK:
    TA 1000
    RVK:
    UA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 120714-3
    detail.hit.zdb_id: 1413423-8
    SSG: 11
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  • 3
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    Coding for Life: Designing a Platform for Projecting and Protecting Global Biodiversity
    Oxford University Press (OUP) ; 2022
    In:  BioScience Vol. 72, No. 1 ( 2022-01-06), p. 91-104
    Details
    In: BioScience, Oxford University Press (OUP), Vol. 72, No. 1 ( 2022-01-06), p. 91-104
    Abstract: Time is running out to limit further devastating losses of biodiversity and nature's contributions to humans. Addressing this crisis requires accurate predictions about which species and ecosystems are most at risk to ensure efficient use of limited conservation and management resources. We review existing biodiversity projection models and discover problematic gaps. Current models usually cannot easily be reconfigured for other species or systems, omit key biological processes, and cannot accommodate feedbacks with Earth system dynamics. To fill these gaps, we envision an adaptable, accessible, and universal biodiversity modeling platform that can project essential biodiversity variables, explore the implications of divergent socioeconomic scenarios, and compare conservation and management strategies. We design a roadmap for implementing this vision and demonstrate that building this biodiversity forecasting platform is possible and practical.
    Type of Medium: Online Resource
    ISSN: 0006-3568 , 1525-3244
    URL: Article
    DOI: 10.1093/biosci/biab099
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    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2066019-4
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  • 4
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    Corrigendum: Coding for Life: Designing a Platform for Projecting and Protecting Global Biodiversity
    Oxford University Press (OUP) ; 2022
    In:  BioScience Vol. 72, No. 1 ( 2022-01-06), p. 106-106
    Details
    In: BioScience, Oxford University Press (OUP), Vol. 72, No. 1 ( 2022-01-06), p. 106-106
    Type of Medium: Online Resource
    ISSN: 0006-3568 , 1525-3244
    URL: Article
    DOI: 10.1093/biosci/biab127
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    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2066019-4
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  • 5
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    The Complexity of Urban Eco-evolutionary Dynamics
    Oxford University Press (OUP) ; 2020
    In:  BioScience Vol. 70, No. 9 ( 2020-09-18), p. 772-793
    Details
    In: BioScience, Oxford University Press (OUP), Vol. 70, No. 9 ( 2020-09-18), p. 772-793
    Abstract: Urbanization is changing Earth's ecosystems by altering the interactions and feedbacks between the fundamental ecological and evolutionary processes that maintain life. Humans in cities alter the eco-evolutionary play by simultaneously changing both the actors and the stage on which the eco-evolutionary play takes place. Urbanization modifies land surfaces, microclimates, habitat connectivity, ecological networks, food webs, species diversity, and species composition. These environmental changes can lead to changes in phenotypic, genetic, and cultural makeup of wild populations that have important consequences for ecosystem function and the essential services that nature provides to human society, such as nutrient cycling, pollination, seed dispersal, food production, and water and air purification. Understanding and monitoring urbanization-induced evolutionary changes is important to inform strategies to achieve sustainability. In the present article, we propose that understanding these dynamics requires rigorous characterization of urbanizing regions as rapidly evolving, tightly coupled human–natural systems. We explore how the emergent properties of urbanization affect eco-evolutionary dynamics across space and time. We identify five key urban drivers of change—habitat modification, connectivity, heterogeneity, novel disturbances, and biotic interactions—and highlight the direct consequences of urbanization-driven eco-evolutionary change for nature's contributions to people. Then, we explore five emerging complexities—landscape complexity, urban discontinuities, socio-ecological heterogeneity, cross-scale interactions, legacies and time lags—that need to be tackled in future research. We propose that the evolving metacommunity concept provides a powerful framework to study urban eco-evolutionary dynamics.
    Type of Medium: Online Resource
    ISSN: 0006-3568 , 1525-3244
    URL: Article
    DOI: 10.1093/biosci/biaa079
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 2066019-4
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  • 6
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    Evolutionary origins for ecological patterns in space
    Proceedings of the National Academy of Sciences ; 2020
    In:  Proceedings of the National Academy of Sciences Vol. 117, No. 30 ( 2020-07-28), p. 17482-17490
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 117, No. 30 ( 2020-07-28), p. 17482-17490
    Abstract: Historically, many biologists assumed that evolution and ecology acted independently because evolution occurred over distances too great to influence most ecological patterns. Today, evidence indicates that evolution can operate over a range of spatial scales, including fine spatial scales. Thus, evolutionary divergence across space might frequently interact with the mechanisms that also determine spatial ecological patterns. Here, we synthesize insights from 500 eco-evolutionary studies and develop a predictive framework that seeks to understand whether and when evolution amplifies, dampens, or creates ecological patterns. We demonstrate that local adaptation can alter everything from spatial variation in population abundances to ecosystem properties. We uncover 14 mechanisms that can mediate the outcome of evolution on spatial ecological patterns. Sometimes, evolution amplifies environmental variation, especially when selection enhances resource uptake or patch selection. The local evolution of foundation or keystone species can create ecological patterns where none existed originally. However, most often, we find that evolution dampens existing environmental gradients, because local adaptation evens out fitness across environments and thus counteracts the variation in associated ecological patterns. Consequently, evolution generally smooths out the underlying heterogeneity in nature, making the world appear less ragged than it would be in the absence of evolution. We end by highlighting the future research needed to inform a fully integrated and predictive biology that accounts for eco-evolutionary interactions in both space and time.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.1918960117
    RVK:
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    RVK:
    WA 15000
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2020
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
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  • 7
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    Using seasonal genomic changes to understand historical adaptation to new environments: Parallel selection on stickleback in highly‐variable estuaries
    Wiley ; 2021
    In:  Molecular Ecology Vol. 30, No. 9 ( 2021-05), p. 2054-2064
    Details
    In: Molecular Ecology, Wiley, Vol. 30, No. 9 ( 2021-05), p. 2054-2064
    Abstract: Parallel evolution is considered strong evidence for natural selection. However, few studies have investigated the process of parallel selection as it plays out in real time. The common approach is to study historical signatures of selection in populations already well adapted to different environments. Here, to document selection under natural conditions, we study six populations of threespine stickleback ( Gasterosteus aculeatus ) inhabiting bar‐built estuaries that undergo seasonal cycles of environmental changes. Estuaries are periodically isolated from the ocean due to sandbar formation during dry summer months, with concurrent environmental shifts that resemble the long‐term changes associated with postglacial colonization of freshwater habitats by marine populations. We used pooled whole‐genome sequencing to track seasonal allele frequency changes in six of these populations and search for signatures of natural selection. We found consistent changes in allele frequency across estuaries, suggesting a potential role for parallel selection. Functional enrichment among candidate genes included transmembrane ion transport and calcium binding, which are important for osmoregulation and ion balance. The genomic changes that occur in threespine stickleback from bar‐built estuaries could provide a glimpse into the early stages of adaptation that have occurred in many historical marine to freshwater transitions.
    Type of Medium: Online Resource
    ISSN: 0962-1083 , 1365-294X
    URL: Issue
    URL: Article
    DOI: 10.1111/mec.v30.9
    DOI: 10.1111/mec.15879
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2021
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    detail.hit.zdb_id: 1126687-9
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  • 8
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    Biological invasions alter the structure of a tropical freshwater food web
    Wiley ; 2023
    In:  Ecology
    Details
    In: Ecology, Wiley
    Abstract: Biological invasions are expected to alter food web structure, but there are limited empirical data directly comparing invaded versus uninvaded food webs, particularly in species‐rich, tropical systems. We characterize for the first time the food web of Lake Gatun – a diverse and highly‐invaded tropical freshwater lake within the Panama Canal. We used stable isotope analysis to reconstruct the trophic structure of the fish community of Lake Gatun, and to compare it to that of a minimally‐invaded reference lake, Lake Bayano. We found significant differences between the trophic structures of these two Neotropical lakes, notably that Lake Gatun's fish community was characterized by a longer food chain, greater isotopic diversity, a broader range of trophic positions and body sizes, and shifts in the isotopic positions of several native taxa relative to Lake Bayano. The degree of isotopic overlap between native and non‐native trophic guilds in Lake Gatun was variable, with herbivores exhibiting the lowest (20 – 29%) overlap, and carnivores the greatest (81 – 100%). Overall, our results provide some of the first empirical evidence for the ways in which multiple introduced and native species may partition isotopic space in a species‐rich tropical freshwater food web.
    Type of Medium: Online Resource
    ISSN: 0012-9658 , 1939-9170
    URL: Article
    DOI: 10.1002/ecy.4173
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2023
    detail.hit.zdb_id: 1797-8
    detail.hit.zdb_id: 2010140-5
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  • 9
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    Compiling forty years of guppy research to investigate the factors contributing to (non)parallel evolution
    Wiley ; 2022
    In:  Journal of Evolutionary Biology Vol. 35, No. 11 ( 2022-11), p. 1414-1431
    Details
    In: Journal of Evolutionary Biology, Wiley, Vol. 35, No. 11 ( 2022-11), p. 1414-1431
    Abstract: Examples of parallel evolution have been crucial for our understanding of adaptation via natural selection. However, strong parallelism is not always observed even in seemingly similar environments where natural selection is expected to favour similar phenotypes. Leveraging this variation in parallelism within well‐researched study systems can provide insight into the factors that contribute to variation in adaptive responses. Here we analyse the results of 36 studies reporting 446 average trait values in Trinidadian guppies, Poecilia reticulata , from different predation regimes. We examine how the extent of predator‐driven phenotypic parallelism is influenced by six factors: sex, trait type, rearing environment, ecological complexity, evolutionary history, and time since colonization. Analyses show that parallel evolution in guppies is highly variable and weak on average, with only 24.7% of the variation among populations being explained by predation regime. Levels of parallelism appeared to be especially weak for colour traits, and parallelism decreased with increasing complexity of evolutionary history (i.e., when estimates of parallelism from populations within a single drainage were compared to estimates of parallelism from populations pooled between two major drainages). Suggestive – but not significant – trends that warrant further research include interactions between the sexes and different trait categories. Quantifying and accounting for these and other sources of variation among evolutionary ‘replicates’ can be leveraged to better understand the extent to which seemingly similar environments drive parallel and nonparallel aspects of phenotypic divergence.
    Type of Medium: Online Resource
    ISSN: 1010-061X , 1420-9101
    URL: Issue
    URL: Article
    DOI: 10.1111/jeb.v35.11
    DOI: 10.1111/jeb.14086
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 92624-3
    detail.hit.zdb_id: 1465318-7
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  • 10
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    Resistance and resilience of genetic and phenotypic diversity to “black swan” flood events: A retrospective analysis with historical samples of guppies
    Wiley ; 2021
    In:  Molecular Ecology Vol. 30, No. 4 ( 2021-02), p. 1017-1028
    Details
    In: Molecular Ecology, Wiley, Vol. 30, No. 4 ( 2021-02), p. 1017-1028
    Abstract: Rare extreme “black swan” disturbances can impact ecosystems in many ways, such as destroying habitats, depleting resources, and causing high mortality. In rivers, for instance, exceptional floods that occur infrequently (e.g., so‐called “50‐year floods”) can strongly impact the abundance of fishes and other aquatic organisms. Beyond such ecological effects, these floods could also impact intraspecific diversity by elevating genetic drift or dispersal and by imposing strong selection, which could then influence the population's ability to recover from disturbance. And yet, natural systems might be resistant (show little change) or resilient (show rapid recovery) even to rare extreme events – perhaps as a result of selection due to past events. We considered these possibilities in two rivers where native guppies experienced two extreme floods – one in 2005 and another in 2016. For each river, we selected four sites and used archived “historical” samples to compare levels of genetic and phenotypic diversity before vs. after floods. Genetic diversity was represented by 33 neutral microsatellite markers, and phenotypic diversity was represented by body length and male melanic (black) colour. We found that genetic diversity and population structure was mostly “resistant” to even these extreme floods; whereas the larger impacts on phenotypic diversity were short‐lived, suggesting additional “resilience”. We discuss the determinants of these two outcomes for guppies facing floods, and then consider the general implications for the resistance and resilience of intraspecific variation to black swan disturbances.
    Type of Medium: Online Resource
    ISSN: 0962-1083 , 1365-294X
    URL: Issue
    URL: Article
    DOI: 10.1111/mec.v30.4
    DOI: 10.1111/mec.15782
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2021
    detail.hit.zdb_id: 2020749-9
    detail.hit.zdb_id: 1126687-9
    SSG: 12
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