Encyclopedia of Life Blog

One of the benefits of the EOL’s many content-sharing agreements is that it stays current by association.  Take the case of scleractinian corals, which were the subject of an EOL synthesis meeting from June 15-19 at the Smithsonian Natural History Museum in Washington D.C.  The order Scleractinia, or ‘stony corals,’ includes reef-building corals, which in the words of the meeting’s proposal, undergirds “the most diverse of all marine ecosystems, tropical shallow-water reefs (Paulay 1997), with estimates of associated species numbers ranging from 1-9 million (Reaka-Kudla 1997).”  And yet, the evolution and systematics of this ecologically crucial group are still fundamentally misunderstood: traditional phylogenies of scleractinian corals based on macromorphological characters have yet to be reconciled with those produced by more current molecular data.  In sponsoring a meeting designed to work towards solving this discrepancy, the EOL’s Biodiversity Synthesis Group effectively ensured that the EOL would eventually inherit a reworked, up-to-date phylogeny of scleractinian corals.

Featuring an international presence—17 participants representing six different countries (the U.S., U.K., Spain, France, the Netherlands, and Poland)—the meeting marked the collaboration of a team of experts whose collective expertise encompassed the taxonomy of both living and fossil scleractinian corals.  After giving individual talks, the participants divided into more focused break-out groups, each assigned to tackle different sections of the phylogeny of scleractinian corals.

The meeting made significant progress on two interlinked fronts: reworking the phylogeny of scleractinian corals to include all forms, from Triassic to living, and constructing a morphological character matrix to delineate micromorphological traits that better reflect molecular results than traditional macromorphological ones.  The first goal followed directly from the gathering of marine biologists, who do phylogenetics research on living taxa using molecular and/or morphologic data, with paleontologists, who study long-term evolutionary history using fossils.  Such synthesis guaranteed that a unified phylogeny would include fossil taxa.

As the second front—isolating new morphological characters—was begun almost from scratch, it took quite a lot of work for break-out groups to get through even a couple of their assigned families.  Combing through images, the participants tried to pick up on microstructural and micromorphological features that could be said to distinguish different genera.  Often, their attention was drawn to septa—calcified, radially-aligned elements that make up the skeleton of a scleractinian polyp—whose shape they described with such makeshift terms as “fan-shaped” or “paddle-shaped.”  Yet these rough-and-ready descriptions laid the groundwork for a classification scheme, both by training scientists to know what traits to look for in the future, and by establishing morphological character states that will later serve as standards to determine type specimens.  In fact, quantifying subjective characters to come up with a morphological character matrix was set as a topic for an upcoming meeting involving many of the same participants.

Lastly, the meeting cemented a content-sharing agreement between the EOL and Corallosphere, an online database featuring nomenclatural and descriptive information for around 1600 nominal scleractinian genera.  In addition to sharing existing species descriptions and images with Corallosphere, the EOL would ultimately inherit the new classification scheme and pages for corresponding type specimens, directly authored by participants identified at the meeting.  This new phylogeny has the potential to reset conservation efforts that aim to preserve major branches of the scleractinian evolutionary tree.  For example, the finding that the dominant reef-building corals of the Atlantic and Pacific come from different lineages—based on molecular rather than conventional macromorphological data, which held the two groups to be monophyletic—identified evolutionary distinctiveness as a conservation priority to be considered along with “diversity and endemicity at the species level” (For more information, see Fukami, H., A.F. Budd, G. Paulay, A. Solé-Cava, C.A. Chen, K. Iwao, and N. Knowlton. 2004.  Conventional Taxonomy Obscures Deep Divergence between Pacific and Atlantic Corals. Nature 427: 832-835).  In any case, regardless of its future implications for conservation, commitment to a new classification scheme constitutes a significant first step for the coral community as well as the EOL.

If the ultimate aim of the Encyclopedia of Life (EOL) is to provide an online home for all species knowledge, the goal of the International Union for the Conservation of Nature and Natural Resources (IUCN) Red List should be understood as broadly similar: its intent is also aggregation, but with a narrower organizing principle—evaluating species’ conservation status.  So it is fitting that the EOL’s Biodiversity Synthesis Group (BioSynC) hosted a synthesis meeting from June 8-12, designed to produce conservation assessments of North American crayfish species that will eventually find their way onto the IUCN Red List and EOL species pages.

Crayfish, along with other freshwater species, are one of the groups subject to a dearth of conservation information on the IUCN Red List.  As such, their assessment is central to the Red List’s efforts to expand its taxonomic coverage in preparation for the IUCN’s 2010 goal of reducing global biodiversity loss.  Because a full assessment of all underrepresented species is simply not feasible, the meeting used the Sample Red List Index (SLRI) approach, which in the words of the IUCN website, aims to improve the Red List’s biodiversity coverage by sampling “species from selected taxonomic groups to provide trends in extinction risk that are more representative of global biodiversity.

The meeting featured twelve scientists from the U.S., Mexico, and the U.K.—all experts on North American crayfish—gathered in the Field Museum’s Biodiversity Synthesis Center for introductory talks and smaller working groups split up according to regional expertise or crayfish taxonomy.  According to Nadia Dewhurst (meeting facilitator and research scientist at the Institute of Zoology, Zoological Society of London) assembling a team of experts is the “most effective way to get large numbers of assessments done” quickly, “producing data you would not see otherwise” because it is more interactive than doing assessments as an individual or remotely via the internet.

Ben Collen (Institute of Zoology, Zoological Society of London and meeting facilitator) explained that, while part of the point of the meeting was to pull together species data or literature that was not previously in the public domain, far more important was the experts’ interpretation of that data.  Being extremely familiar with a certain region or ecosystem, they could assess the scale at which a certain environmental threat operates much more accurately than a scientist foreign to that region.  In the case of crayfish, providing even a statewide context is a large-scale effort that requires coordination of a lot of data on extremely localized populations.

The fruits of their labor are concrete: 398 conservation assessments that didn’t exist previously, as well as all the aggregated content that contributed to making the assessments.  They are hopeful the crayfish assessments will broaden the rather restricted set of species data that currently informs global conservation strategies, especially considering that the threats they have evaluated for North American crayfish may apply broadly across freshwater ecosystems.  At the least, they will have created an up-to-date report on North American crayfish conservation status, a snapshot, which, when held up against a later report, can be used to infer trends in biodiversity change over time.  Furthermore, once these assessments go on the Red List, data-deficient species will be highlighted in the public domain and research reprioritized accordingly.

Though partnership agreements between the IUCN Red List and the EOL are still in tentative stages, Collen admits that it “would be interesting to find EOL information that can inform IUCN species assessments.”  Indeed, glancing at the species pages of either site reveals several information fields common to both.   The intersection of two complementary, scientifically-vetted, customizable repositories of biodiversity content is nothing if not an exciting prospect.

This post was guest written by Matt Von Konrat, organizer of the meeting and collections manager in the Botany Department at the Field Museum.  

Between May 26 and May 29 The Field Museum’s EOL Biodiversity Synthesis Center became the world’s liverwort and hornwort capital as 31 botanists from 13 countries held an historic summit meeting to sort out questions concerning a little-known but widespread group of plants that were the first to colonize land in the Earth’s formative years. The meeting, dedicated to liverworts and hornworts, was part of a biodiversity synthesis meeting with the kind support of the Encyclopedia of Life as well as the National Science Foundation, the Global Biological Information Facility (GBIF), and the Norwegian University of Science and Technology, Trondheim, Norway.

The overall goal of the meeting was to build and further develop an international effort spearheaded by the Early Land Plants Today project (see http://www.early-land-plants-today.org). This includes working towards a synthesis of core data on nomenclature, taxonomy, and geography on a global scale for liverworts and hornworts. The meeting was the first of its kind and was very timely as it provided a unique opportunity to enhance capacity building and increase synergistic activities between several current NSF and GBIF funded projects as well as various international collaborative research and databasing efforts. The meeting cemented existing collaborative efforts as well as providing a forum to develop and forge an untold number new partnerships.

Liverworts and hornworts are generally very small moss-like plants that grow in most parts of the world. Liverworts (Marchantiophyta) and hornworts (Anthocerophyta) are pivotal in our understanding of early land plant evolution. Although this obscure and elusive group of green plants are generally small in size, they form a conspicuous and important component in many terrestrial ecosystems throughout the world. Estimates of liverwort species numbers range from 4000 to 10,000, they exhibit a remarkable diversity in structure, and include extremely ancient lineages as well as more recent radiations of species-rich crown group assemblages. Hornworts on the other hand have an estimated number of 200 to 300 species. The broad estimate for liverwort species numbers, which is a fundamental research question, illustrates the hot debate contesting such estimates. Recently, liverworts, in concert with mosses and hornworts, have also been considered to play a significant role in the global carbon budget and are potential indicators of global warming as well as exhibiting significant biological activity, e.g., against certain cancer cell lines and microbes. Thus a global data set combining information on liverwort nomenclature, taxonomy, and geography has vast potential, for both the systematic and taxonomic community, as well as the broader biological community.

The 31 participants represented a broad spectrum in age and experience ranging from senior scientists, to postdocs and researchers. Several students from the US and internationally also attended as one goal of the meeting was to raise general awareness and foster further studies. The Field Museum was a natural site for this first gathering of experts because its collection contains over 250,000 bryophyte specimens, one of the world’s largest and most significant.

The combination of full participation combined with break-away groups of taxonomic specialists for selected diverse groups was very successful. It does not happen often in taxonomy! But all participants reached a consensus on the development of working taxon lists for each of the selected taxonomic groups, and produce strategies and targets to achieve a complete lists, including auxiliary data; develop a list of project and individual research databases, discuss how we can more effectively harness this data, garner existing data structures, and discuss how the community can effectively participate in the EOL program. Two very significant outcomes of the meeting were the full discussion in developing a worldwide checklist for liverworts and hornworts, which will be the first ever of its kind. And the unveiling of Lars Söderström’s database that is the fruits of over two decades work, which includes taxonomy, nomenclature and distribution ranges.

All participants, especially organizers Matt von Konrat, Lars Söderström and Anders Hagborg give a huge thanks for Darolyn who helped make the meeting a great success. Thank you Darolyn!

If one of the ideas behind the Indiana Dunes BioBlitz was to give kids a taste of ‘real’ science, the continual downpours on Friday, May 16 seemed intent on driving that point home.  Just as staff from National Geographic, the National Park Service, and the EOL scrambled to move electronic equipment away from encroaching puddles of rain in the inventory tent, the kids too were forced to improvise.  A group of fifth graders from Frank H. Hammond elementary in Munster, Indiana carried a slew of makeshift tools, including binoculars made out of cardboard cylinders, and film canister microscopes.  (Confused as I was by the latter, the girls were happy to explain that you simply unscrew the top, and deposit and observe insects inside the canister, the bottom of which functions as a magnifying glass).

Students seemed to really respond to the theme of the natural world as an outdoor classroom.  General science teacher John Harsh led a group of seventh and eighth graders into the Dunes, where they used FieldScope, National Geographic’s web-based mapping tool, to conduct an informal species survey and collect quantitative information such as species richness and abundance.  Harsh was determined to give his students an authentic first experience in the field by avoiding a “canned” approach that represents data collection as an orderly process occurring in a gleaming laboratory.  Instead, he emphasized the “messiness” of science, and the rain was happy to indulge him.

Marie Studer, head of EOL Education and Outreach, pointed out that this very “messiness” made science more interesting for kids by placing them on a “level playing field” with the scientists and teachers they are learning from.  Take the example of the fifth graders from Hammond elementary, who told me they planned to collect “roly-polies” and to classify plants in their notepads according to “color, shape, and texture.”  Once in the field, these simple tasks no doubt became a little more daunting—collecting slippery specimens in the rain, writing in a soggy notebook, etc.—but students saw that they shared these difficulties with their teachers and group leaders.

What resulted was a first brush with scientific field work flavored by a mutual bonding experience.  Wet socks are a lot more personal than lines in a textbook, and kids that participated in BioBlitz will now have their own experience to draw on rather than rote memory when they think of science.  Moreover, the EOL ensures that the kids’ experience will be preserved permanently in the form of photos they took and uploaded to EOL’s Flickr Group, and FieldScope data they collected.  Hopefully, the body of knowledge the students collected will conjure up fond enough memories to motivate them to add to it.

As e-Biosphere winds down, I wanted to report back on what happened, what I thought was interesting, and what my take-aways were.  The meeting had 483 participants from all over the world (42 countries!).

The set up and program were excellent, with a good diversity of speakers and perspectives.  Among my favorites were Jorge Soberon’s presentation on the need for integration across subdisciplines and fields and at varying scales. Nancy Knowlton’s presentation questioning whether we need to name biodiversity in order to study it and learn from it was probably the most controversial and thought-provoking. And Sandra Knapp’s presentation documenting the motivations and paths that the Solenum project used was informative and a great case study for how to effectively stimulate participation from a broad and diverse group of specialists.

The afternoon breakout session topics were broad and yet, interestingly, produced many common themes.  Group topics included ecology, cybertaxonomy, standards, developing countries, education, and conservation.  Common themes included a need for better standards, better metadata, simplification of contributions and involvement, and better templates. Also discussed were the importance of team building and collaboration, the key role of ecosystem services, and maintaining open access to information.

The main things that I will take away from the meeting are that there have been great advances in biodiversity informatics in the last 20 years, but there is still a long way to go. The field needs to articulate its goals better and communicate these goals with the public and policy makers in a more effective manner. Data sharing and collaboration are critically important to everyone, and major projects like EOL and GBIF need to take the lead in urging standards, creating templates and tools, and outreach.  We have a long way to go, but a great role to play.

Special thanks to the staff at the QE2 conference centre.  The facility is beautiful; bright and airy with stunning views of Westminster Abbey. Also special thanks to the organizing committee for bringing together a great group of speakers and participants.  I hope this becomes an annual thing!  A final thanks to NHM for hosting a lovely evening event (pictured above). Without them, I would not have been able to take the great photo of Jim Hanken and Sir Richard Owen below…

Hello from London! 

The e-Biosphere 2009 meeting has just begun.  Norm MacLeod gave the introductory remarks to open the meeting. MacLeod characterized the meeting’s purpose as addressing two major questions that humanity wrestles with; how do we understand the millions of species with whom we share the planet?  and how can we, as a species, deal effectively and intelligently with these species? Christian Samper, of the Smithsonian and EOL, gave the keynote speech.  As Samper put it, the bioinformatics community needs to forge connections among three different spheres: different types of information, different sources of information, and different users of information.  e-Biosphere’s goal is to facilitate and foster these connections.

EOL is a major sponsor for the meeting (along with CBOL and NHM) and the many EOL staff present are looking forward to a great meeting, with plenty of time for interaction and discussion.  We will be reporting from the meeting periodically over the next three days.

One of the grand challenges in biology is the discovery of the detailed pattern of relatedness among all life forms, reflecting the process of lineage diversification which formed the magnificent evolutionary tree of life. Phylogenetic trees have become central to a range of key questions in biology, from searching for evolutionary patterns and analyzing natural selection, to examining genetic change and evolutionary rules that apply across divergent forms of life.  However, when they get really big—more than a few hundred species—evolutionary trees are difficult to see and explore, a problem Carl Zimmer addressed in a recent New York Times article—“Crunching the Data for the Tree of Life.”  One of the chief difficulties seemed to be compromise: how to focus in on an area while still retaining the broader context of one’s location.  For example, how can a user zoom in on the hummingbirds, while simultaneously retaining a more panoramic view—e.g. their position in relation to other birds, as well as dinosaurs, crocodiles and other animal groups not far away? In addition, how can we visualize large evolutionary trees in a platform rich with data and content, so that while zooming in, out and around the tree of life we have access to massive sources such as the Encyclopedia of Life and the Tree of Life  (TOLweb) content set?

Since the inability of current software tools to perform these important visualization tasks represents a major challenge in computational biology, it is natural that the problem of tree visualization belongs to computer scientists and graphic designers, as well as evolutionary biologists.  To address this challenge, a group of tree-thinking representatives from evolutionary biology, academic computing, and the software and graphics industry participated in a meeting from May 1-3, designed to synthesize various approaches to tree visualization.  Sponsored by the EOL Biodiversity Synthesis Group, it featured 32 participants from the U.S. and Canada and consisted of a series of talks and group discussion, followed by more focused break-out sessions.

The meeting made progress on several initiatives that will benefit biodiversity research and education.  First, it committed a group of people to the goal of developing evolutionary visualization tools, and came up with proposal themes for several funding efforts.  Second, new software tools were conceived and the design process begun:  our software company participants were particularly interested in audience selection and software design.  One of the most exciting aspects for a general audience was the synergy achieved between existing projects like TOLWeb and Harvard’s INVOLV touch –table project, with industry representatives that can provide experienced guidance for reaching a public audience.  Third, interoperability was a common theme at the meeting, with representatives from EOL, TOL, Mesquite  and TreeBASE committed to the development of APIs (application program interface’s) and standards that will allow intercommunication.

Lastly, the meeting was a fun and highly active brainstorming session, an important facet of good synthesis meetings.  A cursory glance at the meeting room—its walls covered with post-it notes and scrawled-on dry erase boards—might have been enough to convince an onlooker that the brainstorming process had swallowed up the goal of organized synthesis.  However, Dr. Karen Cranston, postdoctoral research scientist at the Biodiversity Synthesis Center, called the meeting “amazingly productive,” especially considering the fact that people from such diverse backgrounds were thrown together for only two and a half days.  The general feeling was that the synthesis meeting is a fitting format to attack interdisciplinary problems in science, and to meet the goal of developing an NSF grant.  By inviting diverse input from the very beginning, the meeting identified a broader range of basic questions and generated greater enthusiasm, than a smaller scale approach that would have tried to enlist outside interest for a project with a pre-defined scope.

Many of the presentations introduced concepts or programs in keeping with a Google Earth model for tree visualization.  Tamara Munzner, of the University of British Columbia, presented a program called Tree Juxtaposer that can keep a desired clade or tip of the tree visible by treating it like a landmark.  While anchoring themselves to one spot with this ‘guaranteed visibility,’ users can explore the rest of the two dimensional tree space with fish-eye lenses and other zooming devices.  Greg Jordan of the European Bioinformatics Institute described a similar program called Phylowidget, which allows users to customize their viewing by hiding or showing different regions of tree data.  However, both these programs have to meet the challenge of working at a scale larger than a few thousand species.

One of the larger themes of the meeting was that a successful tree visualization tool will mean more than a neat gadget with a fancy user interface.  Dr. Cranston characterized “visual exploration” as a key step in the scientific process following data collection.  Organizing morphological or molecular information into a tree structure allows scientists to immediately see patterns they might otherwise miss if they compared traits as numbers—that is, if the visual element were removed.  Moreover, plotting data in trees imposes an evolutionary focus on the problem of species comparison from the very beginning.  Instead of arbitrarily comparing numbers, scientists compare them according to evolutionary categories, such as homologous traits.  Rather than hiding evolutionary relationships and questions, the data showcases these things because it has already been parsed according to an evolutionary framework.  But scientists cannot stop at visualizing one tree; they must compare a large collection of ‘best’ possible trees generated by phylogenetic analysis.  David Hillis (University of Texas at Austin) and Katherine St. John (Lehmann College, City University of New York) addressed this topic of tree set visualization—how to compare and summarize large collections of trees by structure and branching pattern.

Scientists and educators hope to embed tree visualization technology into third-party websites, thereby linking tree images with existing species description or data.  The tree visualization project initiated in the recent meeting will be tightly linked with the Encyclopedia of Life, so that people can browse the catalog of EOL species via phylogenetic trees rather than taxonomic hierarchy.  The educational potential of such a platform is immense: a single node on a tree would simultaneously reveal a species’ evolutionary history and biodiversity information, and direct users interested in either to learn about the other.

A fitting tool for a science bound together by Theodosius Dobzhansky’s famous doctrine, ‘Nothing in biology makes sense except in the light of evolution,’ a science whose most basic subjects—species—are both universes unto themselves and parts of a larger whole.

The TreeViz participants outside the Field Museum in Chicago.

Hello from Fairfax, VA and the campus of George Mason University.  EOL has an exhibit and demonstration booth at the International Marine Conservation Congress, staffed by new EOL-er Jeff Holmes from Education/Learning/Outreach, EOL’s WhyReef specialist Beth Sanzenbacher, and me. We are here to spread the word about EOL; to give demonstrations of the site, Flickr uploading, LifeDesks, WhyReef, and EOL curating, and to talk about the EOL fellows program and proposing EOL synthesis meetings.

The response from the Marine Conservation community has been good so far.  Visitors have been enthusiastic about the Undergraduate Initiative to author species pages, becoming EOL content providers, and proposing synthesis meetings.

There have also been some great presentations on marine species (blue whales! spiny lobsters! oysters!), the design of marine protected areas, and coral reef conservation. The meeting is a great combination of presentations, workshops, discussion groups, and posters, so there is always something going on.  We hope that EOL’s presence at this meeting will stimulate the marine conservation community to become more involved with EOL.  I am sure that we will see lots more content and curators in the future!

Well, things are winding down here at the Indiana Dunes BioBlitz.  The blitz officially ended 2 hours ago, but people are still out finding species, still in the tents identifying species, and still enjoying themselves.  Its been a GREAT day; bright and filled with species.

We continued helping people to upload images to LifeDesk and Flickr and we showed several school and grad student groups EOL.  We also continued to explore the dunes and find biodiversity.  We saw lots of plants and flies.  We also saw frogs, beetles, fungi, and even scat!

The species count continues to grow as more scientists return from the field and enter their data, but the count is currently……….

We’ll report back with more stories from the blitz when we are all back home.  It was an amazing experience and a great way for families and school groups to learn about their local ecosystem.

Hello from the Science Inventory tent at the Indiana Dunes BioBlitz!  We have had a memorable Blitz so far; with so much heavy rain that the National Parks Service was forced to turn off the power to the Inventory tent.  This shut down our operations temporarily, but we survived the flood and came back stronger than before.

Before the rains, we had concentrated on taking groups (mostly students) around the dunes, testing out National Geographic’s FieldScope, helping kids to see and identify birds, flies, plants, turtles, and frogs, and trying to get some good video footage of science in action.  We had a great time, but were so busy seeing things and helping people that we neglected to get content onto EOL.  After the power outage, we split into 2 groups; one group still taking students out and finding species and the other getting species information and content onto EOL by interviewing scientists coming in from the field and by uploading all of the images we had taken earlier in the day.

We have had success demonstrating Lifedesk, helping people to upload their images to EOL using Flickr, and telling people about EOL and our outreach efforts.

Its Day 2 now and the sun has just broken through the clouds (yay!!!!!!!!!).  We are continuing our split efforts; dry and happy.

Thanks to all of the EOL staff who have assisted with the event: forecaster Darolyn, shivering Beth, turtle-trapping Jim, bird-calling Jason,  LifeDesk master Torsten, roving reporter Kannan, field marshall Tracy, super networker Marie, and loiterer Kris.  Also thanks to our devoted extended family: super trooper Sarah and rainsuit Ken.