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      Earth BioGenome Project: Sequencing life for the future of life

      research-article
      Author(s): a , b , c , d , 1 , e , f , g , f , h , i , j , k , l , g , m , n , o , p , q , r , s , t , u , v , w , x , y , z , aa , bb , cc , dd , ee , dd , ff , gg
      Publication date (Electronic):
      Journal: Proceedings of the National Academy of Sciences of the United States of America
      Publisher: National Academy of Sciences
      Keywords: biodiversity, genome sequencing, access and benefit sharing, genomics, data science

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          Abstract

          Increasing our understanding of Earth’s biodiversity and responsibly stewarding its resources are among the most crucial scientific and social challenges of the new millennium. These challenges require fundamental new knowledge of the organization, evolution, functions, and interactions among millions of the planet’s organisms. Herein, we present a perspective on the Earth BioGenome Project (EBP), a moonshot for biology that aims to sequence, catalog, and characterize the genomes of all of Earth’s eukaryotic biodiversity over a period of 10 years. The outcomes of the EBP will inform a broad range of major issues facing humanity, such as the impact of climate change on biodiversity, the conservation of endangered species and ecosystems, and the preservation and enhancement of ecosystem services. We describe hurdles that the project faces, including data-sharing policies that ensure a permanent, freely available resource for future scientific discovery while respecting access and benefit sharing guidelines of the Nagoya Protocol. We also describe scientific and organizational challenges in executing such an ambitious project, and the structure proposed to achieve the project’s goals. The far-reaching potential benefits of creating an open digital repository of genomic information for life on Earth can be realized only by a coordinated international effort.

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          Tree of Life Reveals Clock-Like Speciation and Diversification

          S Blair Hedges, Julie Marin, Michael Suleski … (2015)
          Genomic data are rapidly resolving the tree of living species calibrated to time, the timetree of life, which will provide a framework for research in diverse fields of science. Previous analyses of taxonomically restricted timetrees have found a decline in the rate of diversification in many groups of organisms, often attributed to ecological interactions among species. Here, we have synthesized a global timetree of life from 2,274 studies representing 50,632 species and examined the pattern and rate of diversification as well as the timing of speciation. We found that species diversity has been mostly expanding overall and in many smaller groups of species, and that the rate of diversification in eukaryotes has been mostly constant. We also identified, and avoided, potential biases that may have influenced previous analyses of diversification including low levels of taxon sampling, small clade size, and the inclusion of stem branches in clade analyses. We found consistency in time-to-speciation among plants and animals, ∼2 My, as measured by intervals of crown and stem species times. Together, this clock-like change at different levels suggests that speciation and diversification are processes dominated by random events and that adaptive change is largely a separate process.
          Article 0 comments Cited 462 times – based on 0 reviews     Review now
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            Land-use and climate change risks in the Amazon and the need of a novel sustainable development paradigm.

            Carlos A. Nobre, Gilvan Sampaio, Laura S Borma … (2016)
            For half a century, the process of economic integration of the Amazon has been based on intensive use of renewable and nonrenewable natural resources, which has brought significant basin-wide environmental alterations. The rural development in the Amazonia pushed the agricultural frontier swiftly, resulting in widespread land-cover change, but agriculture in the Amazon has been of low productivity and unsustainable. The loss of biodiversity and continued deforestation will lead to high risks of irreversible change of its tropical forests. It has been established by modeling studies that the Amazon may have two "tipping points," namely, temperature increase of 4 °C or deforestation exceeding 40% of the forest area. If transgressed, large-scale "savannization" of mostly southern and eastern Amazon may take place. The region has warmed about 1 °C over the last 60 y, and total deforestation is reaching 20% of the forested area. The recent significant reductions in deforestation-80% reduction in the Brazilian Amazon in the last decade-opens up opportunities for a novel sustainable development paradigm for the future of the Amazon. We argue for a new development paradigm-away from only attempting to reconcile maximizing conservation versus intensification of traditional agriculture and expansion of hydropower capacity-in which we research, develop, and scale a high-tech innovation approach that sees the Amazon as a global public good of biological assets that can enable the creation of innovative high-value products, services, and platforms through combining advanced digital, biological, and material technologies of the Fourth Industrial Revolution in progress.
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              Contentious relationships in phylogenomic studies can be driven by a handful of genes

              Xing-Xing Shen, Chris Hittinger, Antonis Rokas (2017)
              Phylogenomic studies have resolved countless branches of the tree of life (ToL), but remain strongly contradictory on certain, contentious relationships. Here, we employ a maximum likelihood framework to quantify the distribution of phylogenetic signal among genes and sites for 17 contentious branches and 6 well-established control branches in plant, animal, and fungal phylogenomic data matrices. We find that resolution in some of these 17 branches rests on a single gene or a few sites, and that removal of a single gene in concatenation analyses or a single site from every gene in coalescence-based analyses diminishes support and can alter the inferred topology. These results suggest that tiny subsets of very large data matrices drive the resolution of specific internodes, providing a dissection of the distribution of support and observed incongruence in phylogenomic analyses. We submit that quantifying the distribution of phylogenetic signal in phylogenomic data is essential for evaluating whether branches, especially contentious ones, are truly resolved. Finally, we offer one detailed example of such an evaluation for the controversy regarding the earliest-branching metazoan phylum, where examination of the distributions of gene-wise and site-wise phylogenetic signal across 8 data matrices consistently supports ctenophores as sister group to all other metazoans.
              Article 0 comments Cited 170 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Proc Natl Acad Sci U S A
                Journal ID (iso-abbrev): Proc. Natl. Acad. Sci. U.S.A
                Journal ID (hwp): pnas
                Journal ID (pmc): pnas
                Journal ID (publisher-id): PNAS
                Title: Proceedings of the National Academy of Sciences of the United States of America
                Publisher: National Academy of Sciences
                ISSN (Print): 0027-8424
                ISSN (Electronic): 1091-6490
                Publication date (Print): 24 April 2018
                Publication date (Electronic): 23 April 2018
                Volume: 115
                Issue: 17
                Pages: 4325-4333
                Affiliations
                [1] aDepartment of Evolution and Ecology, University of California , Davis, CA 95616;
                [2] bDepartment of Population Health and Reproduction, School of Veterinary Medicine, University of California , Davis, CA 95616;
                [3] cThe John Muir Institute of the Environment, University of California , Davis, CA 95616;
                [4] dThe University of California, Davis Genome Center, University of California , Davis, CA 95616;
                [5] eCarl R. Woese Institute for Genomic Biology, Department of Entomology, and Neuroscience Program, University of Illinois at Urbana–Champaign , Urbana, IL 61801;
                [6] fNational Museum of Natural History, Smithsonian Institution , Washington, DC 20013;
                [7] g Royal Botanic Gardens , Kew, Richmond, Surrey TW9 3AE, United Kingdom;
                [8] hComputational Biology Institute, Milken Institute School of Public Health, George Washington University , Washington, DC 20052;
                [9] iDepartment of Genetics, University of Cambridge , Cambridge CB10 1SA, United Kingdom;
                [10] j Wellcome Trust Sanger Institute , Cambridge CB10 1SA, United Kingdom;
                [11] kDepartment of Organismic and Evolutionary Biology, Harvard University , Cambridge, MA 02138;
                [12] lMuseum of Comparative Zoology, Harvard University , Cambridge, MA 02138;
                [13] mNatural History Museum of Denmark, University of Copenhagen , 1350 Copenhagen, Denmark;
                [14] nUniversity Museum, Norwegian University of Science and Technology , N-7491 Trondheim, Norway;
                [15] oDepartment of Health Policy and Management, Milken Institute School of Public Health, George Washington University , Washington, DC 20052;
                [16] p US Department of Energy Joint Genome Institute , Walnut Creek, CA 94598;
                [17] qDepartment of Plant and Microbial Biology, University of California, Berkeley , CA 94720;
                [18] rAgricultural Research Center, US Department of Agriculture , Beltsville, MD 20705;
                [19] sUC Santa Cruz Genomics Institute, University of California , Santa Cruz, CA 95064;
                [20] tHoward Hughes Medical Institute, University of California , Santa Cruz, CA 95064;
                [21] uLaboratory of Neurogenetics of Language, The Rockefeller University , New York, NY 10065;
                [22] vConservation Biology Institute, National Zoological Park, Smithsonian Institution , Front Royal, VA 22630;
                [23] wNovim Group, University of California , Santa Barbara, CA 93106;
                [24] xHuman Genome Sequencing Center, Baylor College of Medicine , Houston, TX 77030;
                [25] y World Economic Forum’s Global Future Council on Environment and Natural Resource Security , Cologny/Geneva CH-1223, Switzerland;
                [26] z Space Time Ventures , São Paulo, SP, 05449-050, Brazil;
                [27] aaDepartmento de Botanica, Instituto de Biociencia, Universidade de São Paulo , São Paulo, SP 05508-090, Brazil;
                [28] bbSão Paulo Research Foundation (FAPESP), SP 05468-901, Brazil;
                [29] ccFlorida Museum of Natural History, University of Florida , Gainesville, FL 32611;
                [30] ddChina National Genebank, BGI-Shenzhen , 518083 Shenzhen, Guangdong, China;
                [31] ee BGI-Shenzhen , 518083 Shenzhen, Guangdong, China;
                [32] ffSection for Ecology and Evolution, Department of Biology, University of Copenhagen , DK-2100 Copenhagen, Denmark;
                [33] ggState Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences , 650223 Kunming, China
                Author notes
                1To whom correspondence should be addressed. Email: Lewin@ 123456ucdavis.edu .

                Edited by John C. Avise, University of California, Irvine, CA, and approved March 15, 2018 (received for review January 6, 2018)

                Author contributions: H.A.L., J.C., and K.A.C. analyzed data; and H.A.L., G.E.R., W.J.K., W.J.B., K.A.C., R.D., S.V.E., F.F., M.T.P.G., M.M.G., I.V.G., K.J.H., D.H., E.D.J., W.E.D.J., A.P., S.R., J.C.C.-R., M.-A.v.S., P.S.S., X.X., H.Y., and G.Z. wrote the paper.

                Author information
                http://orcid.org/0000-0002-0836-3389
                http://orcid.org/0000-0003-2535-6217
                Article
                Accession ID: PMC5924910 Pmcid ID: PMC5924910 Pmc-uid ID: 5924910 Publisher ID: 201720115
                DOI: 10.1073/pnas.1720115115
                PMC ID: 5924910
                PubMed ID: 29686065
                SO-VID: b8da0331-c7ee-402f-bc8b-78f60a1770ad
                Copyright statement: Copyright @ 2018
                License:

                Published under the PNAS license.

                History
                Page count
                Pages: 9
                Categories
                Subject: Perspective
                Subject: Biological Sciences
                Subject: Evolution

                Keywords: data science,genomics,access and benefit sharing,genome sequencing,biodiversity
                Data availability:
                Keywords: data science, genomics, access and benefit sharing, genome sequencing, biodiversity

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