TimeTree: A Resource for Timelines, Timetrees, and Divergence Times.
TL;DR: A major expansion of the TimeTree resource is reported, which more than triples the number of species and more thanTriple thenumber of studies assembled, which will lead to broader and better understanding of the interplay of the change in the biosphere with the diversity of species on Earth.
Abstract: Evolutionary information on species divergence times is fundamental to studies of biodiversity, development, and disease. Molecular dating has enhanced our understanding of the temporal patterns of species divergences over the last five decades, and the number of studies is increasing quickly due to an exponential growth in the available collection of molecular sequences from diverse species and large number of genes. Our TimeTree resource is a public knowledge-base with the primary focus to make available all species divergence times derived using molecular sequence data to scientists, educators, and the general public in a consistent and accessible format. Here, we report a major expansion of the TimeTree resource, which more than triples the number of species (>97,000) and more than triples the number of studies assembled (>3,000). Furthermore, scientists can access not only the divergence time between two species or higher taxa, but also a timetree of a group of species and a timeline that traces a species' evolution through time. The new timetree and timeline visualizations are integrated with display of events on earth and environmental history over geological time, which will lead to broader and better understanding of the interplay of the change in the biosphere with the diversity of species on Earth. The next generation TimeTree resource is publicly available online at http://www.timetree.org.
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TL;DR: This work used a concatenated protein phylogeny as the basis for a bacterial taxonomy that conservatively removes polyphyletic groups and normalizes taxonomic ranks on the basis of relative evolutionary divergence.
Abstract: Taxonomy is an organizing principle of biology and is ideally based on evolutionary relationships among organisms. Development of a robust bacterial taxonomy has been hindered by an inability to obtain most bacteria in pure culture and, to a lesser extent, by the historical use of phenotypes to guide classification. Culture-independent sequencing technologies have matured sufficiently that a comprehensive genome-based taxonomy is now possible. We used a concatenated protein phylogeny as the basis for a bacterial taxonomy that conservatively removes polyphyletic groups and normalizes taxonomic ranks on the basis of relative evolutionary divergence. Under this approach, 58% of the 94,759 genomes comprising the Genome Taxonomy Database had changes to their existing taxonomy. This result includes the description of 99 phyla, including six major monophyletic units from the subdivision of the Proteobacteria, and amalgamation of the Candidate Phyla Radiation into a single phylum. Our taxonomy should enable improved classification of uncultured bacteria and provide a sound basis for ecological and evolutionary studies.
2,098 citations
TL;DR: It is found that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns.
Abstract: Green plants (Viridiplantae) include around 450,000–500,000 species1,2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.
907 citations
National Institutes of Health1, Wellcome Trust Sanger Institute2, University of Cambridge3, Rockefeller University4, University of California, Davis5, Leibniz Association6, Seoul National University7, University of Southern California8, European Bioinformatics Institute9, Dresden University of Technology10, Max Planck Society11, University of St Andrews12, Radboud University Nijmegen13, University of Massachusetts Amherst14, University of Adelaide15, University of Missouri16, East Carolina University17, University of Queensland18, Clemson University19, University of Otago20, University of Arizona21, Natural History Museum22, Bangor University23, University of Konstanz24, Harvard University25, Northeastern University26, University of Antwerp27, National Museum of Natural History28, University of Graz29, University of Florida30, University of Basel31, University of California, Santa Cruz32, Zoological Society of San Diego33, Pacific Biosciences34, Pompeu Fabra University35, University of Maryland, College Park36, Harbin Institute of Technology37, University of Chicago38, Oregon Health & Science University39, Qatar Airways40, Monash University Malaysia Campus41, University of Milan42, Goethe University Frankfurt43, Pennsylvania State University44, University of Los Andes45, Norwegian University of Science and Technology46, University of Copenhagen47, Agency for Science, Technology and Research48, Royal Ontario Museum49, Smithsonian Institution50, Howard Hughes Medical Institute51, Walter Reed Army Institute of Research52, University of East Anglia53, University College Dublin54, University of Illinois at Urbana–Champaign55, La Trobe University56, University of California, San Diego57, Nova Southeastern University58
TL;DR: The Vertebrate Genomes Project (VGP) as mentioned in this paper is an international effort to generate high quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.
Abstract: High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1-4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.
647 citations
National Institutes of Health1, Wellcome Trust Sanger Institute2, Rockefeller University3, University of California, Davis4, European Bioinformatics Institute5, Seoul National University6, Max Planck Society7, Durham University8, University of Massachusetts Amherst9, University of Adelaide10, University of Missouri11, East Carolina University12, University of Queensland13, Queen Mary University of London14, Wellington Management Company15, University of Arizona16, Natural History Museum17, Bangor University18, University of Konstanz19, Northeastern University20, Naturalis21, University of Graz22, Florida Museum of Natural History23, University of California, Santa Cruz24, Pacific Biosciences25, University of Maryland, College Park26, Harbin Institute of Technology27, University of Chicago28, Oregon Health & Science University29, Monash University Malaysia Campus30, University of Milan31, University of Copenhagen32, Pennsylvania State University33, University of Los Andes34, Agency for Science, Technology and Research35, Royal Ontario Museum36, Smithsonian Conservation Biology Institute37, University of East Anglia38, Pompeu Fabra University39, University College Dublin40, University of Illinois at Urbana–Champaign41, La Trobe University42, University of California, San Diego43, UPRRP College of Natural Sciences44, Dresden University of Technology45
TL;DR: The Vertebrate Genomes Project is embarked on, an effort to generate high-quality, complete reference genomes for all ~70,000 extant vertebrate species and help enable a new era of discovery across the life sciences.
Abstract: High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are only available for a few non-microbial species. To address this issue, the international Genome 10K (G10K) consortium has worked over a five-year period to evaluate and develop cost-effective methods for assembling the most accurate and complete reference genomes to date. Here we summarize these developments, introduce a set of quality standards, and present lessons learned from sequencing and assembling 16 species representing major vertebrate lineages (mammals, birds, reptiles, amphibians, teleost fishes and cartilaginous fishes). We confirm that long-read sequencing technologies are essential for maximizing genome quality and that unresolved complex repeats and haplotype heterozygosity are major sources of error in assemblies. Our new assemblies identify and correct substantial errors in some of the best historical reference genomes. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an effort to generate high-quality, complete reference genomes for all ~70,000 extant vertebrate species and help enable a new era of discovery across the life sciences.
567 citations
VU University Amsterdam1, Leibniz Institute for Neurobiology2, Broad Institute3, Tufts University4, University of Southern California5, Cornell University6, Johns Hopkins University School of Medicine7, Johns Hopkins University8, Max Planck Society9, Harvard University10, KAIST11, Utrecht University12, University of Lausanne13, University of Rome Tor Vergata14, European Bioinformatics Institute15, University of Milan16, Autonomous University of Barcelona17, Yale University18, Swiss Institute of Bioinformatics19, Stanford University20, University of California, San Francisco21, Genentech22, Howard Hughes Medical Institute23, National University of Singapore24, Montreal Neurological Institute and Hospital25, University of Southampton26
TL;DR: It is shown that synaptic genes are exceptionally well conserved and less tolerant to mutations than other genes, and among de novo variants associated with neurodevelopmental disorders, including schizophrenia.
425 citations
Cites background from "TimeTree: A Resource for Timelines,..."
...The first wave of emergence of SynGO genes was prior to the last eukaryotic common ancestor (LECA), approximately 1,800 million years ago (mya) (Kumar et al., 2017)....
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References
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01 Jan 2013
TL;DR: The recent completion of drilling at Vostok station in East Antarctica has allowed the extension of the ice record of atmospheric composition and climate to the past four glacial-interglacial cycles.
Abstract: The recent completion of drilling at Vostok station in East Antarctica has allowed the extension of the ice record of atmospheric composition and climate to the past four glacial–interglacial cycles. The succession of changes through each climate cycle and termination was similar, and atmospheric and climate properties oscillated between stable bounds. Interglacial periods differed in temporal evolution and duration. Atmospheric concentrations of carbon dioxide and methane correlate well with Antarctic air-temperature throughout the record. Present-day atmospheric burdens of these two important greenhouse gases seem to have been unprecedented during the past 420,000 years.
5,469 citations
TL;DR: The recent completion of drilling at Vostok station in East Antarctica has allowed the extension of the ice record of atmospheric composition and climate to the past four glacial-interglacial cycles as discussed by the authors.
Abstract: The recent completion of drilling at Vostok station in East Antarctica has allowed the extension of the ice record of atmospheric composition and climate to the past four glacial–interglacial cycles. The succession of changes through each climate cycle and termination was similar, and atmospheric and climate properties oscillated between stable bounds. Interglacial periods differed in temporal evolution and duration. Atmospheric concentrations of carbon dioxide and methane correlate well with Antarctic air-temperature throughout the record. Present-day atmospheric burdens of these two important greenhouse gases seem to have been unprecedented during the past 420,000 years.
5,109 citations
"TimeTree: A Resource for Timelines,..." refers methods in this paper
...The new TimeTree resource now adds data from asteroid impacts (Earth Impact Database), solar luminosity (Gough 1981), and atmosphere composition, including oxygen (Holland 2006) and carbon dioxide (Berner 1990; Petit et al. 1999; Hessler et al. 2004; Beerling and Royer 2011)....
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TL;DR: The last 3.85 Gyr of Earth history have been divided into five stages, and atmospheric oxygen levels probably rose to a maximum value of ca 0.3 atm during the Carboniferous before returning to its present value.
Abstract: The last 3.85Gyr of Earth history have been divided into five stages. During stage 1 (3.852.45Gyr ago (Ga)) the atmosphere was largely or entirely anoxic, as were the oceans, with the possible exce...
1,238 citations
TL;DR: TimeTree brings time estimates from molecular data together in a consistent format and uses a hierarchical structure, corresponding to the tree of life, to maximize their utility.
Abstract: Summary: Biologists and other scientists routinely need to know times of divergence between species and to construct phylogenies calibrated to time (timetrees). Published studies reporting time estimates from molecular data have been increasing rapidly, but the data have been largely inaccessible to the greater community of scientists because of their complexity. TimeTree brings these data together in a consistent format and uses a hierarchical structure, corresponding to the tree of life, to maximize their utility. Results are presented and summarized, allowing users to quickly determine the range and robustness of time estimates and the degree of consensus from the published literature.
Availability: TimeTree is available at http://www.timetree.net
Contact: [email protected]
1,137 citations
"TimeTree: A Resource for Timelines,..." refers background or methods in this paper
...using all the source (study) timetrees as input to the Hierarchical Average Linkage methods presented in Hedges et al. (2015). TimeTree Resource ....
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...Thus, the TimeTree project has been advancing the process of knowledge discovery by enabling data-driven retrieval of peer-reviewed publications and estimates of time of divergence between species that are relevant to the user’s query (Hedges et al. 2006; Kumar and Hedges 2011)....
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...To make these results easily accessible to evolutionary and non-evolutionary biologists, we are collecting and synthesizing divergence time estimates from all published studies in the TimeTree resource (Hedges et al. 2006; Kumar and Hedges 2011)....
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...This new approach is very quick for mining all relevant studies, because the previous method to scan each study individually (Hedges et al. 2006) becomes time consuming due to a large number of taxa in timetrees of each study and the number of studies in the database....
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...Solid circles mark nodes that map directly to the NCBI Taxonomy and the open circles indicate nodes that were created during the polytomy resolution process described in Hedges et al. (2015). A geologic timescale (showing eons, eras, periods, epochs, and ages) is rendered directly below the timetree (fig....
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TL;DR: A global timetree of life synthesized from 2,274 studies representing 50,632 species and examined the pattern and rate of diversification as well as the timing of speciation suggests that speciation and diversification are processes dominated by random events and that adaptive change is largely a separate process.
Abstract: 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.
809 citations
"TimeTree: A Resource for Timelines,..." refers background or methods in this paper
...…acquisition of timetree data, their standardization, and the assembly of a global timetree (Timetree of Life, TTOL) based on individual timetrees are available in Hedges et al. (2015), where evolutionary and biodiversity analyses of these data were presented for 50,632 species from 2,274 studies....
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...Hedges et al. (2015) method also evaluates support for each resulting resolution by examining the number of timetree topologies in the database that are concordant with that resolution....
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...We added an additional 1,000 studies and utilized Hedges et al. (2015) method to assemble a timetree of 97,000 species....
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...1 in Hedges et al. 2015)....
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...Solid circles mark nodes that map directly to the NCBI Taxonomy and the open circles indicate nodes that were created during the polytomy resolution process described in Hedges et al. (2015)....
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