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  • 1
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    Online Resource
    ATLANTIC ANTS: a data set of ants in Atlantic Forests of South America
    Wiley ; 2022
    In:  Ecology Vol. 103, No. 2 ( 2022-02)
    Details
    In: Ecology, Wiley, Vol. 103, No. 2 ( 2022-02)
    Abstract: Ants, an ecologically successful and numerically dominant group of animals, play key ecological roles as soil engineers, predators, nutrient recyclers, and regulators of plant growth and reproduction in most terrestrial ecosystems. Further, ants are widely used as bioindicators of the ecological impact of land use. We gathered information of ant species in the Atlantic Forest of South America. The ATLANTIC ANTS data set, which is part of the ATLANTIC SERIES data papers, is a compilation of ant records from collections (18,713 records), unpublished data (29,651 records), and published sources (106,910 records; 1,059 references), including papers, theses, dissertations, and book chapters published from 1886 to 2020. In total, the data set contains 153,818 ant records from 7,636 study locations in the Atlantic Forest, representing 10 subfamilies, 99 genera, 1,114 ant species identified with updated taxonomic certainty, and 2,235 morphospecies codes. Our data set reflects the heterogeneity in ant records, which include ants sampled at the beginning of the taxonomic history of myrmecology (the 19th and 20th centuries) and more recent ant surveys designed to address specific questions in ecology and biology. The data set can be used by researchers to develop strategies to deal with different macroecological and region‐wide questions, focusing on assemblages, species occurrences, and distribution patterns. Furthermore, the data can be used to assess the consequences of changes in land use in the Atlantic Forest on different ecological processes. No copyright restrictions apply to the use of this data set, but we request that authors cite this data paper when using these data in publications or teaching events.
    Type of Medium: Online Resource
    ISSN: 0012-9658 , 1939-9170
    URL: Issue
    URL: Article
    DOI: 10.1002/ecy.v103.2
    DOI: 10.1002/ecy.3580
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2022
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    SSG: 12
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  • 2
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    The beetle tree of life reveals that C oleoptera survived end‐ P ermian mass extinction to diversify during the C retaceous terrestrial revolution
    Wiley ; 2015
    In:  Systematic Entomology Vol. 40, No. 4 ( 2015-10), p. 835-880
    Details
    In: Systematic Entomology, Wiley, Vol. 40, No. 4 ( 2015-10), p. 835-880
    Abstract: Here we present a phylogeny of beetles ( I nsecta: C oleoptera) based on DNA sequence data from eight nuclear genes, including six single‐copy nuclear protein‐coding genes, for 367 species representing 172 of 183 extant families. Our results refine existing knowledge of relationships among major groups of beetles. Strepsiptera was confirmed as sister to C oleoptera and each of the suborders of C oleoptera was recovered as monophyletic. Interrelationships among the suborders, namely P olyphaga ( A dephaga ( A rchostemata, M yxophaga)), in our study differ from previous studies. Adephaga comprised two clades corresponding to H ydradephaga and G eadephaga. The series and superfamilies of P olyphaga were mostly monophyletic. The traditional C ucujoidea were recovered in three distantly related clades. Lymexyloidea was recovered within T enebrionoidea. Several of the series and superfamilies of P olyphaga received moderate to maximal clade support in most analyses, for example B uprestoidea, C hrysomeloidea, C occinelloidea, C ucujiformia, C urculionoidea, D ascilloidea, E lateroidea, H isteroidea and H ydrophiloidea. However, many of the relationships within P olyphaga lacked compatible resolution under maximum‐likelihood and B ayesian inference, and/or lacked consistently strong nodal support. Overall, we recovered slightly younger estimated divergence times than previous studies for most groups of beetles. The ordinal split between C oleoptera and S trepsiptera was estimated to have occurred in the E arly P ermian. Crown C oleoptera appeared in the Late P ermian, and only one or two lineages survived the end‐ P ermian mass extinction, with stem group representatives of all four suborders appearing by the end of the T riassic. The basal split in P olyphaga was estimated to have occurred in the T riassic, with the stem groups of most series and superfamilies originating during the T riassic or J urassic. Most extant families of beetles were estimated to have C retaceous origins. Overall, C oleoptera experienced an increase in diversification rate compared to the rest of N europteroidea. Furthermore, 10 family‐level clades, all in suborder P olyphaga, were identified as having experienced significant increases in diversification rate. These include most beetle species with phytophagous habits, but also several groups not typically or primarily associated with plants. Most of these groups originated in the C retaceous, which is also when a majority of the most species‐rich beetle families first appeared. An additional 12 clades showed evidence for significant decreases in diversification rate. These clades are species‐poor in the M odern fauna, but collectively exhibit diverse trophic habits. The apparent success of beetles, as measured by species numbers, may result from their associations with widespread and diverse substrates – especially plants, but also including fungi, wood and leaf litter – but what facilitated these associations in the first place or has allowed these associations to flourish likely varies within and between lineages. Our results provide a uniquely well‐resolved temporal and phylogenetic framework for studying patterns of innovation and diversification in C oleoptera, and a foundation for further sampling and resolution of the beetle tree of life.
    Type of Medium: Online Resource
    ISSN: 0307-6970 , 1365-3113
    URL: Issue
    URL: Article
    DOI: 10.1111/syen.2015.40.issue-4
    DOI: 10.1111/syen.12132
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2015
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  • 3
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    Draft genome of the globally widespread and invasive Argentine ant ( Linepithema humile )
    Proceedings of the National Academy of Sciences ; 2011
    In:  Proceedings of the National Academy of Sciences Vol. 108, No. 14 ( 2011-04-05), p. 5673-5678
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 108, No. 14 ( 2011-04-05), p. 5673-5678
    Abstract: Ants are some of the most abundant and familiar animals on Earth, and they play vital roles in most terrestrial ecosystems. Although all ants are eusocial, and display a variety of complex and fascinating behaviors, few genomic resources exist for them. Here, we report the draft genome sequence of a particularly widespread and well-studied species, the invasive Argentine ant ( Linepithema humile ), which was accomplished using a combination of 454 (Roche) and Illumina sequencing and community-based funding rather than federal grant support. Manual annotation of 〉 1,000 genes from a variety of different gene families and functional classes reveals unique features of the Argentine ant's biology, as well as similarities to Apis mellifera and Nasonia vitripennis . Distinctive features of the Argentine ant genome include remarkable expansions of gustatory (116 genes) and odorant receptors (367 genes), an abundance of cytochrome P450 genes ( 〉 110), lineage-specific expansions of yellow/major royal jelly proteins and desaturases, and complete CpG DNA methylation and RNAi toolkits. The Argentine ant genome contains fewer immune genes than Drosophila and Tribolium , which may reflect the prominent role played by behavioral and chemical suppression of pathogens. Analysis of the ratio of observed to expected CpG nucleotides for genes in the reproductive development and apoptosis pathways suggests higher levels of methylation than in the genome overall. The resources provided by this genome sequence will offer an abundance of tools for researchers seeking to illuminate the fascinating biology of this emerging model organism.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.1008617108
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2011
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
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  • 4
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    Molecular phylogeny of the H ydroscaphidae ( C oleoptera: M yxophaga) with description of a remarkable new lineage from the G uiana S hield
    Wiley ; 2015
    In:  Systematic Entomology Vol. 40, No. 1 ( 2015-01), p. 214-229
    Details
    In: Systematic Entomology, Wiley, Vol. 40, No. 1 ( 2015-01), p. 214-229
    Abstract: The phylogeny of the aquatic beetle family H ydroscaphidae is inferred from one mitochondrial ( COI ) and five nuclear ( 18S , 28S , wingless , arginine kinase and CAD ) genes. Bayesian, maximum likelihood and maximum parsimony analyses were conducted on a combined dataset that included representatives from all three described hydroscaphid genera, three new species of the family of uncertain placement, and representatives from the myxophagan families S phaeriusidae, T orridincolidae and L epiceridae. All analyses strongly supported a set of nearly identical trees in which (i) the monophyly of H ydroscaphidae and all its constituent genera is affirmed, (ii) the nearly cosmopolitan genus Hydroscapha is sister to the remaining and exclusively N eotropical genera, and (iii) the new, morphologically aberrant taxa from the G uiana S hield form a monophylum separate from any described genus. Here, we review each genus of the family including the description of Confossa S hort, J oly, G arcía & M addison gen.n. to accommodate three new species: C. sculptura sp.n. , C. falcata sp.n. and C. minima sp.n. The new genus possesses a remarkable perforated abdominal surface that we hypothesize serves as a respiratory plastron. We also present a key to the genera and a catalogue of species of the family.
    Type of Medium: Online Resource
    ISSN: 0307-6970 , 1365-3113
    URL: Issue
    URL: Article
    DOI: 10.1111/syen.2015.40.issue-1
    DOI: 10.1111/syen.12097
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2015
    detail.hit.zdb_id: 2020957-5
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  • 5
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    Evolution of the Neotropical ant genus Linepithema
    Wiley ; 2009
    In:  Systematic Entomology Vol. 34, No. 1 ( 2009-01), p. 49-62
    Details
    In: Systematic Entomology, Wiley, Vol. 34, No. 1 ( 2009-01), p. 49-62
    Abstract: Abstract A comprehensive species‐level phylogeny of the ant genus Linepithema Mayr, a Neotropical group best known for the invasive Argentine ant L. humile (Mayr), is inferred for the first time using fragments from three nuclear loci [wingless (WG), long‐wavelength rhodopsin (LWR) and internal transcribed spacer (ITS‐2)] and the mitochondrial cytochrome oxidase subunit I (COI) gene. Monophyly of the genus is strongly supported in parsimony, likelihood and Bayesian analyses of the concatenated data, as is the monophyly of four species groups defined previously on the basis of morphology. An Andean species, L. oblongum (Santschi), is the sister taxon of the Argentine ant. Eight of the 11 species whose monophyly was testable in the analysis were inferred to be monophyletic. Several instances of species paraphyly and one case of mitochondrial introgression suggest that complex population genetic processes underpin the patterns of diversity in Linepithema , and that simple genetic approaches to taxonomy such as DNA barcoding should be treated with caution. A maximum likelihood reconstruction of ancestral distributions suggests that Linepithema is of southern South American origin and that populations in the Greater Antilles are the result of four independent colonization events.
    Type of Medium: Online Resource
    ISSN: 0307-6970 , 1365-3113
    URL: Issue
    URL: Article
    DOI: 10.1111/sen.2009.34.issue-1
    DOI: 10.1111/j.1365-3113.2008.00435.x
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2009
    detail.hit.zdb_id: 2020957-5
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  • 6
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    Effects of tree mortality caused by a bark beetle outbreak on the ant community in the S an B ernardino N ational F orest
    Wiley ; 2013
    In:  Ecological Entomology Vol. 38, No. 5 ( 2013-10), p. 439-447
    Details
    In: Ecological Entomology, Wiley, Vol. 38, No. 5 ( 2013-10), p. 439-447
    Abstract: A severe bark beetle outbreak caused very high levels of tree mortality in the S an B ernardino N ational F orest in southern C alifornia in 2003. In 2009, the impact of the outbreak on the ant community was examined by pitfall‐trapping ants in 15 sites that saw high tree mortality (‘red’ sites) and 15 sites that suffered little or no tree mortality (‘green’ sites) during the outbreak. Ant species turnover between green and red sites was low, and no invasive species were observed. However, changes in the abundances of various species resulted in a significant alteration of the ant community. If the ant community is an accurate bioindicator of other taxa in this forest, the effects of the bark beetle outbreak may be described as dramatic but not catastrophic or irreversible. The changes in the ant community are consistent with the hypothesis that this community is structured by nest site limitation rather than inter‐specific competition or thermal limitation.
    Type of Medium: Online Resource
    ISSN: 0307-6946 , 1365-2311
    URL: Issue
    URL: Article
    DOI: 10.1111/een.2013.38.issue-5
    DOI: 10.1111/een.12031
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2013
    detail.hit.zdb_id: 2020189-8
    detail.hit.zdb_id: 196048-9
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  • 7
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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
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  • 8
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    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
    RVK:
    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
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  • 9
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    A second update on mapping the human genetic architecture of COVID-19
    Springer Science and Business Media LLC ; 2023
    In:  Nature Vol. 621, No. 7977 ( 2023-09-07), p. E7-E26
    Details
    In: Nature, Springer Science and Business Media LLC, Vol. 621, No. 7977 ( 2023-09-07), p. E7-E26
    Type of Medium: Online Resource
    ISSN: 0028-0836 , 1476-4687
    URL: Article
    DOI: 10.1038/s41586-023-06355-3
    RVK:
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    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 120714-3
    detail.hit.zdb_id: 1413423-8
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  • 10
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    GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19
    Springer Science and Business Media LLC ; 2023
    In:  Nature Vol. 617, No. 7962 ( 2023-05-25), p. 764-768
    Details
    In: Nature, Springer Science and Business Media LLC, Vol. 617, No. 7962 ( 2023-05-25), p. 764-768
    Abstract: Critical illness in COVID-19 is an extreme and clinically homogeneous disease phenotype that we have previously shown 1 to be highly efficient for discovery of genetic associations 2 . Despite the advanced stage of illness at presentation, we have shown that host genetics in patients who are critically ill with COVID-19 can identify immunomodulatory therapies with strong beneficial effects in this group 3 . Here we analyse 24,202 cases of COVID-19 with critical illness comprising a combination of microarray genotype and whole-genome sequencing data from cases of critical illness in the international GenOMICC (11,440 cases) study, combined with other studies recruiting hospitalized patients with a strong focus on severe and critical disease: ISARIC4C (676 cases) and the SCOURGE consortium (5,934 cases). To put these results in the context of existing work, we conduct a meta-analysis of the new GenOMICC genome-wide association study (GWAS) results with previously published data. We find 49 genome-wide significant associations, of which 16 have not been reported previously. To investigate the therapeutic implications of these findings, we infer the structural consequences of protein-coding variants, and combine our GWAS results with gene expression data using a monocyte transcriptome-wide association study (TWAS) model, as well as gene and protein expression using Mendelian randomization. We identify potentially druggable targets in multiple systems, including inflammatory signalling ( JAK1 ), monocyte–macrophage activation and endothelial permeability ( PDE4A ), immunometabolism ( SLC2A5 and AK5 ), and host factors required for viral entry and replication ( TMPRSS2 and RAB2A ).
    Type of Medium: Online Resource
    ISSN: 0028-0836 , 1476-4687
    URL: Article
    DOI: 10.1038/s41586-023-06034-3
    RVK:
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    RVK:
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    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 120714-3
    detail.hit.zdb_id: 1413423-8
    SSG: 11
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