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Tree of Life Web Project

The Tree of Life Web Project (ToL) is a collaborative online initiative that compiles and presents information on the biodiversity, evolutionary relationships, and phylogenetic history of organisms on Earth, aiming to document all species and major clades through a hierarchical tree structure.^[1]^[2] Initiated around 1988 by biologists David R. Maddison and Katja-Sabine Schulz, with contributions from Wayne P. Maddison, the project transitioned to a web-based format in 1994 and was formally launched in 1996 as one of the earliest efforts to create a comprehensive digital phylogeny of life.^[1] By 2007, it featured over 5,000 branch pages describing clades, nearly 3,000 leaf pages on specific taxa, more than 20,000 images, and contributions from over 540 scientists across 35 countries, with a focus on animals (96% of content) such as insects and cephalopods.^[1] The site's structure includes dynamically generated pages from a MySQL database, educational "treehouses" for thematic explorations, and multimedia elements like movies and sounds to illustrate natural history and evolution.^[1] Over its nearly three decades, the ToL grew to encompass more than 10,000 web pages created by hundreds of expert and amateur contributors worldwide, serving as a key resource for bioscience education, research, and public understanding of evolutionary biology.^[3]^[1] It collaborated with initiatives like the Encyclopedia of Life and provided data for phylogenetic databases, emphasizing open access under Creative Commons licenses.^[1] In November 2025, project director David R. Maddison announced the retirement of the ToL due to sustained funding challenges and resource limitations, noting that the website would transition to offline status while efforts are made to preserve its content as static archives, potentially accessible via tools like the Internet Archive.^[4]

Overview

Purpose and Goals

The Tree of Life Web Project (ToL) serves as a collaborative, web-based resource designed to document and visualize the evolutionary history of life on Earth through a comprehensive phylogenetic framework. Its primary goal is to compile and present detailed information—such as descriptions, images, videos, and sounds—about every species and significant clade, encompassing organisms across the three domains of life, from prokaryotes to eukaryotes, both living and extinct, with content authored by domain experts.^[1] This initiative emphasizes the integration of multimedia elements to illustrate biodiversity and organismal characteristics within an evolutionary context.^[5] Specific objectives of the ToL include fostering greater public appreciation and understanding of biodiversity, evolution, and phylogeny across all educational levels. As a free, non-profit endeavor supported by academic institutions and grants, it functions as an accessible educational tool for scientists, students, teachers, and the broader public, prioritizing peer-reviewed scientific accuracy and freedom from commercial bias.^[1] The project promotes the sharing of phylogenetic data with other databases and the development of analytical tools to support research and learning.^[1] At its core, the ToL employs the "Tree of Life" metaphor, inspired by Darwin's vision of life's evolutionary affinities as an ever-branching diagram, where hypothetical relationships are shown through interconnected branches, each representing a taxonomic group or clade.^[1] This structure allows users to explore the hierarchical organization of life, highlighting common descent and diversification.^[6] The founding vision of the ToL arose from the recognition of significant gaps in accessible phylogenetic information, aiming to create a dynamic digital repository that surpasses static encyclopedias by enabling continuous, expert-led updates through global collaboration.^[1] This approach ensures the resource evolves with scientific advancements, providing a living synthesis of life's evolutionary tree.^[5]

Founding and Administration

The Tree of Life Web Project was conceived in the late 1980s by biologist David R. Maddison, who initially envisioned it as a hypertext-linked phylogenetic resource tied to his software development for MacClade. His brother Wayne P. Maddison joined the effort in 1994, with whom he collaborated on further development.^[1] Development accelerated in 1994 when Wayne P. Maddison joined the effort, leading to the creation of a custom version of MacClade to generate the site's content.^[1] The first prototype was launched online on November 16, 1994, consisting of static web pages hosted on servers in the Maddisons' laboratories at the University of Arizona.^[1] The project received its formal announcement on January 5, 1996, at that time featuring 948 pages distributed across seven computers and marking the beginning of broader community involvement.^[1] Early growth included the first external contribution in June 1995 from crayfish expert Keith Crandall, establishing the volunteer-driven model.^[1] Initial funding came from personal and academic resources at the University of Arizona, with the site gradually integrating into the university's infrastructure for stability and scalability.^[6] As a non-profit academic initiative, the project was overseen by a small editorial team led by David R. Maddison as editor and coordinator, Wayne P. Maddison as a key collaborator, and Katja-Sabine Schulz as managing editor, who joined as a volunteer in the mid-1990s.^[1] It relied heavily on volunteer experts serving as coordinators for phylogenetic branches, without a formal governing board, though an advisory board was planned to enhance oversight.^[1] National Science Foundation grants provided crucial support starting in the early 2000s, including DBI-0078294 in July 2000 for database architecture redesign, enabling a technology overhaul from 2000 to 2004 that paused content additions but modernized the platform.^[1]^[6] Further NSF funding, such as DUE-0333715 and EF-0531754, fueled software development and expansion efforts, culminating in peak activity from 2006 to 2011 with renewed content growth and full-time staff support.^[1]^[6]

Content and Organization

Hierarchical Structure

The Tree of Life Web Project organizes its content in a tree-like hierarchy that mirrors the phylogenetic structure of life on Earth, beginning with a root node representing all organisms on Earth, including both living and extinct taxa, and branching into major domains—Bacteria, Archaea, and Eukarya—followed by subsequent levels such as phyla, classes, orders, families, genera, and species.^[6] This architecture is stored in a MySQL database where interconnected nodes form the backbone, with each node corresponding to a clade or taxon and attaching multimedia objects like text descriptions and images.^[1] The hierarchy emphasizes evolutionary descent, allowing the entire database to generate dynamic web pages that reflect the branching patterns of biodiversity without a fixed, linear format.^[6] Navigation through this structure is facilitated by hyperlinked branches, enabling users to traverse from broad clades at higher levels to specific taxa at lower ones, with each node serving as a summary page that provides evolutionary context, bibliographic references, and direct links to child or parent pages.^[6] Users can enter the tree via entry points like domain-level pages or use supplementary tools such as search functions, lists of popular or recent taxa, or random page selectors to initiate exploration, after which the phylogenetic pathways guide intuitive progression along evolutionary lines.^[6] This design reinforces "tree-thinking" by visually and structurally connecting organisms through shared ancestry, distinguishing it from flat or categorical databases.^[1] Phylogenies in the project are represented as hypothetical trees based on the scientific consensus prevailing at the time of each entry's creation, incorporating cladograms that illustrate branching relationships alongside textual explanations of monophyly, synapomorphies, and uncertainties.^[6] These representations are not static diagrams but integrated into the page structure, where basal branching points link to the broader Tree of Life, and terminal nodes detail species-level traits or serve as placeholders for undeveloped branches.^[1] The focus remains on clade-based organization rather than strict Linnaean ranks, prioritizing evolutionary relationships over traditional taxonomy.^[6] A distinctive feature of the project's hierarchy is its accommodation of multiple phylogenetic perspectives, avoiding a singular authoritative tree by integrating alternative branching schemes for contentious clades—such as differing views on kingdom-level divisions—with explicit explanations of the rationale behind each.^[6] Updates to pages incorporate new research findings incrementally, preserving historical versions where possible to maintain transparency, while expert coordinators ensure that revisions align with emerging consensus without retroactively altering the foundational structure.^[1] This approach allows the hierarchy to evolve collaboratively, reflecting the dynamic nature of phylogenetic knowledge.^[6]

Types of Entries

The Tree of Life Web Project features a variety of entry types designed to document biodiversity and evolutionary relationships, primarily through taxon-specific pages that integrate scientific detail with visual aids. Core entries consist of branch pages and leaf pages, which form the backbone of the project's content. Branch pages provide synopses of higher taxonomic groups, such as phyla or families, including introductions to the group's characteristics, discussions of morphological traits, life histories, ecological roles, and evolutionary significance, along with lists of descendant subgroups for navigation.^[1] Leaf pages, in contrast, focus on individual species or terminal taxa without further subdivisions, offering similar detailed overviews tailored to single organisms, such as descriptions of anatomy, behavior, habitat preferences, and phylogenetic context.^[1] These taxon pages collectively exceed 10,000 in number, spanning major biological groups from microorganisms like bacteria to complex animals such as mammals.^[7] Multimedia elements enhance the depth of these entries, incorporating high-resolution images and diagrams—such as anatomical illustrations of skeletal structures or cellular features—to visually support textual descriptions. Videos depicting behaviors, like mating rituals in insects or foraging patterns in birds, and audio recordings of species calls, such as amphibian vocalizations, are also integrated where available, drawn from public domain sources or permissions granted by contributors.^[8] These resources emphasize observable traits and interactions, aiding in the comprehension of ecological and evolutionary dynamics without overwhelming the primary scientific narrative. Supplementary materials accompany the core and multimedia content, including bibliographies of peer-reviewed literature that underpin each entry's claims, often citing foundational studies on phylogeny or taxonomy. Glossaries define technical terms encountered in descriptions, such as "clade" or "symbiosis," while sections on phylogenetic controversies address unresolved debates, for example, in avian evolution regarding the placement of certain bird orders relative to reptiles.^[1] Additional articles and notes, numbering around 550 as of earlier assessments, provide specialized expansions linked to main pages, covering topics like organ systems or fossil transitions.^[1] The project's scope is limited to living organisms and extinct groups with substantial fossil records, ensuring a focus on phylogenetic relevance across the tree of life; human-centric topics are omitted unless they intersect with broader evolutionary contexts, such as comparative primate anatomy.^[6] All entries are organized hierarchically within the overall phylogenetic tree, allowing users to trace lineages from broad domains to specific taxa.^[1]

Contributors and Collaboration

Key Figures and Teams

The Tree of Life Web Project was founded by brothers David R. Maddison and Wayne P. Maddison, both entomologists affiliated with the University of Arizona.^[1]^[9] David R. Maddison served as the lead developer and conceptual designer, drawing from his expertise in phylogenetics to coordinate the project's structure and content oversight, while also authoring foundational pages on beetles and arthropod diversity.^[10]^[4] Wayne P. Maddison contributed as an early content creator and software architect, integrating phylogenetic tools inspired by his work on programs like MacClade, and co-authoring key entries on arthropods that established the project's hierarchical approach to evolutionary relationships.^[1]^[4] Their academic careers at the University of Arizona intertwined closely with the project's early maintenance, hosting its infrastructure and fostering its initial growth through institutional support.^[1] The editorial team consisted of a core group of 5-10 biologists providing oversight and quality control for scientific content.^[1] David R. Maddison acted as the primary editor and coordinator, with Katja-Sabine Schulz serving as managing editor to handle administrative and collaborative aspects.^[1] Specialists like Karl M. Kjer contributed expertise to insect-related pages, particularly on Trichoptera (caddisflies), ensuring taxonomic accuracy in arthropod clades.^[11] Beyond the core team, the project engaged over 540 scientists from more than 35 countries as scientific contributors, who authored detailed phylogenetic entries on specific taxa.^[1] Notable teams came from institutions such as the Smithsonian Institution, where researchers like Stephen Cairns developed pages on scleractinian corals, and the Natural History Museum in London, which provided media and taxonomic input for various invertebrate groups.^[12]^[13] While amateur involvement was limited primarily to media contributions like images and videos, exceeding 200 such inputs, the project's collaborative ethos emphasized expert-driven content to advance phylogenetic understanding. Active contributions to the project largely ceased around 2011 due to resource and software maintenance challenges, though the site remained accessible until its retirement in 2025.^[1]^[4]

Contribution Guidelines

The Tree of Life Web Project operated on a volunteer-driven model where contributions were coordinated hierarchically to maintain scientific rigor, with experts proposing and authoring content for specific branches or taxa rather than allowing open editing like a wiki.^[1] Submissions typically began with experts contacting branch coordinators via email or web forms to propose pages, after which approved contributors used specialized tools like TreeGrow—a database interface—for drafting scientific text directly into the system.^[1] Editors reviewed submissions for accuracy and consistency before publication, with revisions tracked through version history and unique, date-stamped URLs for each iteration, enabling precise citation and accountability.^[1] Content standards emphasized peer-reviewed equivalence, requiring all entries to synthesize and cite primary literature without introducing original research or unpublished data.^[1] Phylogenetic representations derived from established published hypotheses, integrated into the site's navigational tree structure to reflect current understanding of evolutionary relationships.^[1] Review levels varied—ranging from basic editor checks by project administrators to coordinator oversight by domain systematists and full peer review by external experts—with status indicators displayed on each page to inform users of the validation depth.^[1] Distinct roles facilitated collaboration: scientific authors, often drawn from over 500 experts worldwide, focused on writing descriptive text and phylogenetic summaries; media contributors supplied images, videos, and audio files accompanied by detailed metadata such as collection details and permissions; and "treehouse" volunteers developed supplementary educational materials like lesson plans attached to core pages.^[1] This division ensured specialized input while integrating contributions hierarchically into the broader tree.^[1] Guidelines evolved to address challenges in a decentralized, expert-led effort, particularly in resolving disputes over controversial phylogenetic branches through coordinator-mediated consensus rather than majority vote.^[1] To promote accessibility, all content was released under open licenses, with contributors encouraged to adopt Creative Commons terms allowing reuse and adaptation while requiring attribution.^[1] This framework balanced volunteer participation with quality control, though it limited rapid updates compared to more fluid platforms.^[1]

Features and Resources

Interactive Elements

The Tree of Life Web Project incorporated several interactive elements designed to facilitate user engagement with its phylogenetic content, primarily through search, navigation, and basic visualization tools integrated into its web-based interface. Users could perform advanced text searches by entering taxon names, keywords, or phrases directly into the site's search function, which retrieved relevant pages from the database of over 10,000 entries on biodiversity and evolutionary relationships. For instance, enclosing phrases in quotation marks, such as "intestinal parasite," enabled precise querying to locate specific discussions or organism descriptions across the site's content.^[14] This search capability supported exploration by contributor or thematic focus, though it relied on keyword matching rather than semantic analysis.^[1] Navigation within the project followed a dynamic, hierarchical structure modeled on the phylogenetic tree of life, allowing users to traverse from broad branches (higher taxa) to leaf pages (specific species or clades) via linked menus and evolutionary pathways. This tree-based browsing reinforced conceptual understanding of descent with modification, with dynamic page generation ensuring that content loaded contextually based on the user's path through the phylogeny. The system supported basic interactivity, such as toggling glossaries or customizing views of page elements, to enhance readability and focus on key phylogenetic details.^[1] As of its development phase, plans were outlined for more advanced web-based tree viewers, though implementation remained limited to static diagrams integrated into navigable pages.^[1] Visualization tools centered on cladograms and phylogenetic diagrams embedded in individual pages, which illustrated branching patterns and evolutionary relationships for taxa. These diagrams, often hand-drawn or generated from phylogenetic analyses, allowed users to expand or collapse sections indirectly through navigation links rather than direct manipulation, providing a conceptual layer of interactivity tied to the site's tree logic. Export options for these visuals were not natively supported in advanced formats like SVG or PDF, but users could capture diagrams via standard browser printing or saving functions. The project's technical backbone, established in the late 1990s and refined through the 2000s, utilized a MySQL database to store the core tree structure of interconnected nodes, with pages dynamically assembled using custom software like the TreeGrow system introduced in 2002.^[1] This database-driven approach enabled real-time querying and linkage, though mobile responsiveness was constrained due to the legacy architecture, limiting seamless access on smaller devices.^[1] User-oriented features included integration with external phylogenetic tools and databases via web services, such as links to Mesquite software for advanced analysis and connections to resources like the Encyclopedia of Life for supplementary data. While personalized watchlists for tracking taxa were not implemented, feedback mechanisms allowed users to report errors or suggest updates through contact forms tied to the administration, fostering collaborative refinement of content. These elements extended basic exploration, with brief ties to educational modules for structured learning, though the core interactivity prioritized phylogenetic navigation over multimedia playback or advanced simulations.^[1] Following the project's retirement announcement in November 2025, these interactive features are no longer accessible online, but efforts are being made to preserve the content as static archives, potentially via the Internet Archive.^[4]

Educational Tools

The Tree of Life Web Project incorporated Treehouses as dedicated educational modules attached to specific taxon pages, enabling users to create and share customized content such as lesson plans, quizzes, interactive activities, games, stories, investigations, and multimedia resources focused on evolutionary relationships and biodiversity.^[15] These modules allowed teachers and students to develop original materials using the project's web-based data entry tools, incorporating images, audio, movies, and text to explore phylogenetic concepts in an engaging manner.^[16] Examples include student-created Treehouses on topics like clownfish adaptations, dog breeds' evolutionary history, and retroviruses, produced by middle school, high school, undergraduate, and graduate learners under supervision.^[6] Complementing these modules were various learning aids designed to support beginners in understanding phylogeny and organismal diversity, including an integrated glossary that highlighted technical terms across the site with rollover definitions for quick reference.^[15] The project also featured a comprehensive FAQ section addressing foundational questions about evolutionary trees, such as how phylogenies are constructed and interpreted.^[17] Multimedia galleries within taxon entries provided captioned images and videos that explained evolutionary adaptations, such as morphological changes in lineages, to facilitate visual learning.^[1] These resources targeted educational settings, particularly K-12 classrooms and undergraduate courses, with content aligned to curricula like AP Biology to teach evolution, cladistics, and biodiversity through structured activities.^[18] Hands-on projects encouraged participants to construct personal phylogenetic trees or annotate existing ones, fostering active engagement with scientific methods and data visualization.^[6] A distinctive initiative involved supervised student contributions to Treehouses, where learners "adopted" a taxon to research and compile educational content, promoting collaborative learning while adhering to the project's editorial standards.^[16] Following the project's retirement in November 2025, these educational tools are preserved in archival efforts to maintain access to the materials.^[4]

Impact and Legacy

Usage Statistics

The Tree of Life Web Project reached its peak popularity around 2006, attracting over 2.5 million unique visitors annually.^[4] Usage declined steadily in subsequent years, dropping to approximately 125,000 unique visitors per year by 2023, amid broader shifts in online biodiversity resources and reduced updates to the site.^[4] The project's audience was predominantly academic, serving researchers, students, and educators who utilized it for phylogenetic and biodiversity education; reports from teachers in 2023 highlighted its continued value in classrooms despite the site's dormancy.^[4] Access was global, with visitors from 198 countries and territories during peak periods, and significant traffic originating from educational institutions worldwide.^[4] The project's influence extended to scholarly work, where its content and structure have been referenced in academic papers exploring phylogeny and biodiversity.^[19]

Evaluations and Criticisms

The Tree of Life Web Project (ToL) has been lauded for its in-depth coverage of niche taxa, such as arthropods, where expert-contributed pages provide detailed phylogenetic and morphological insights that serve as a model for collaborative systematics in invertebrate taxonomy.^[19] Its high accuracy stems from authorship by specialists, including Ph.D. holders and museum curators, combined with a rigorous peer-review process that surpasses many scientific journals in transparency and scrutiny levels.^[6] Furthermore, ToL innovatively integrates phylogenetic trees with visual elements like diagrams, images, movies, and sounds, enabling users to explore evolutionary relationships in an intuitive, tree-based structure that promotes "tree-thinking."^[20] Expert reviews have underscored ToL's value as an educational and research resource. A 2007 paper in Zootaxa positioned the project as an exemplary framework for assembling and disseminating phylogenetic knowledge through global collaboration among over 540 biologists from 35 countries.^[19] In comparisons to the Encyclopedia of Life (EOL), ToL excels in its phylogenetic emphasis and expert-driven content but offers lesser overall breadth and visual dynamism, focusing more on evolutionary hierarchies than species-level multimedia aggregation.^[6] Criticisms of ToL center on its uneven coverage and limitations in scalability. The project encompasses fewer than 1% of named species, with stronger representation in macroscopic groups like arthropods and vertebrates compared to microbes and other underrepresented lineages, reflecting challenges in collaborative completion across the full tree of life.^[21] Major updates ceased around 2011, resulting in some phylogenies becoming outdated amid rapid advances in molecular systematics, while the interface—prioritizing graphical navigation over computational tools—has been critiqued for limited reusability in automated analyses and research workflows.^[21] Over time, ToL evolved from early static pages lacking multimedia to a database-driven platform by 2002, incorporating over 20,000 images and enhanced accessibility features; however, persistent funding constraints hampered further expansion and maintenance.^[1] In November 2025, the project's retirement was announced due to funding challenges, but efforts are underway to preserve its content as static archives, ensuring continued access via tools like the Internet Archive and maintaining its legacy as a foundational resource in evolutionary biology.^[4]

Current Status

Updates and Maintenance

The Tree of Life Web Project actively added new pages until 2011, reaching approximately 10,000 pages in total, after which no further content expansions occurred.^[6]^[4] Minor revisions to existing pages continued sporadically in the years following, but these were limited and inconsistent. The last major software update, which involved transitioning to a dynamic database system, took place in February 2002, with the server relocation to Oregon State University occurring in 2009.^[1]^[4] Maintenance of the project relied heavily on volunteer contributions from over 540 scientific experts across 35 countries, supplemented by limited funding from National Science Foundation grants such as DBI-0078294, DUE-0333715, and EF-0531754, which supported operations through the mid-2000s.^[1] These resources proved insufficient to sustain long-term development, particularly as competition from newer initiatives like the Encyclopedia of Life and Wikispecies drew away potential contributors and reduced overall momentum.^[4] Several factors contributed to the project's decline, including shifting priorities among its founders; for instance, co-founder Wayne Maddison relocated from the University of Arizona to the University of British Columbia in 2003, while the project's server moved to Oregon State University in 2009. The aging technology stack, originally built in the 1990s and early 2000s, became increasingly difficult to maintain, posing security risks that ultimately required disconnection from the internet.^[4] With no dedicated funding secured after 2011, volunteer-driven efforts could not overcome these technical and logistical hurdles.^[1] In November 2025, the project was officially retired due to unsustainable resource constraints, confirming that the absence of new content since 2011 marked the end of active development.^[4] This decision was announced by project administrator David R. Maddison on November 2, 2025, highlighting the inability to update the outdated software or foster ongoing contributions.^[4]

Archiving Efforts

Following the project's retirement announcement in November 2025, the website was taken offline due to security concerns, and as of November 20, 2025, tolweb.org remains inaccessible. Efforts are underway to create a static snapshot of the entire site for preservation, with the goal of making the content available in a read-only format in the future.^[4] External archiving efforts include comprehensive captures by the Internet Archive's Wayback Machine, such as the detailed snapshot dated October 3, 2025, which preserves the site's structure and pages for historical reference; additionally, downloadable datasets, including the ToL Tree Structure XML file, enable offline access and analysis.^[22]^[23] The project's data portability is facilitated by its licensing under Creative Commons Attribution-NonCommercial-ShareAlike terms, which allow for republication, adaptation, and reuse by researchers and educators worldwide, provided proper attribution is given.^[23] To ensure long-term future access, the project encourages integrations of its biodiversity information into broader databases and repositories, though no formal active migration initiatives are underway; community discussions have highlighted the need for institutional endorsements, such as from the National Science Foundation, to support sustained preservation and accessibility.^[4]

References

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[PDF] Zootaxa,The Tree of Life Web Project - Magnolia Press
Dec 21, 2007 · The Tree of Life Web Project (ToL) provides information on the evolutionary tree of life and diversity of life on Earth. It aims to document ...
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The Tree of Life Web Project (ToL) is a collaborative effort of biologists and nature enthusiasts from around the world. On more than 10,000 World Wide Web ...
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This project was created for those interested in locating information about a particular group of organisms, identification keys, figures, ...
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ToL podcasts are audio and video materials to guide your exploration of Life on Earth. ... Tree of Life Web Project" funded by the “Anyplace Access for Arizonans ...
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The desire became the Tree of Life Web Project, and Maddison is its director. It's hard to see biodiversity without seeing it through the lens of a ...
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Tree of Life web project, Scleractinia, Octocoral Research Center. Research Interests. Taxonomy, zoogeography, functional morphology, mineralogy, and ...
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Natural History Museum, London cat. no. BMNH 20060134. Type, Paratype. Image Use, creative commons This media file is licensed under the Creative Commons ...
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May 21, 2006 · With your teachers, you can build “treehouses”—special pages on the Tree of Life Project Web site where you can post your own scientific studies ...<|control11|><|separator|>
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How do I cite a Tree of Life page or the Tree of Life Project as a whole? How are Tree of Life authors selected? How can I become a Tree of Life contributor?
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May 13, 2013 · ... Tree of Life Web project [16] with 16000 species, and the APG tree ... branch of the selected tree with provenance metadata and branch length.<|separator|>
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