Encyclopedia of Life Blog

  By Joshua Drew, EOL/Field Museum PostDoc

Recently I received a message from a collaborator, Dr. Gerry Allen of the Western Australian Museum.  Gerry had written me because he thought he had discovered a new species of coral reef fish and wanted me to do a genetic analysis to help determine if this species was really distinct from other fish. If it was, we also wanted to determine how it fit into the larger tree of life.  Part of my research here at EOL and the Field Museum is not only to describe new species, but also to figure out why and how one species becomes multiple species. This fish looked like a great opportunity to do just that. 

 The particular fish that Gerry had sent me was called Chrysiptera rex and came from the Philippines, which is in the mega-diverse region of the world called the Coral Triangle. I was particularly anxious to look at this case because, while we know that the Coral Triangle is the richest area of marine biodiversity, we do not understand why. I hoped this case might shed some light onto the subject.

 In order to do a proper description we needed to compare our new species with the original.  To do this, we obtained additional samples from Japan, where the species was originally described. These original specimens are called the type locality. Additionally, we knew that this species had significant variation in its color patterns, so with the help of another collaborator, Dr. Mark Erdmann of Conservation International, we collected samples of a different color variety, found in Indonesia.

 When the genetic analysis was done we noticed that the samples grouped into three distinct clusters, one from Taiwan, one from the Philippines and one from Indonesia.  This genetic data, combined with the differences in coloration led us to believe that this fish, which was previously thought to be a single widespread species, was actually a complex mosaic of genetically distinct groups, several of which may be new species.

 Now back to the question of why the Coral Triangle is so diverse - to understand why it is important to understand a little of the geology of the area.  During the ice age, the sea level in this part of the world was up to 200 meters lower.  While today the Coral Triangle is an area of scattered islands and numerous coral reefs, during periods of low sea levels much more land was exposed and those islands were actually mountaintops. 

For marine species during this time there was much less habitat. Essentially, what is currently a contiguous seaway was a series of isolated marine lakes and shallow seas 10,000 years ago. What is really interesting about the study we did was that each genetically distinct color morph was found only in one particular area. In fact, each color morph is mainly restricted to the area covered by those shallow seas.

 What we think happened was that approximately 25,000 years ago, a single species of fish was forced to migrate into several shallow seas as the water level dropped.  Once isolated in these shallow seas, the process of evolution sped up; colors changed and different genes became fixed.  By the time waters rose and the fish were able to move around freely, they had been sequestered for so long that they had become different species.  This process, called vicarance, has been hypothesized as one of the major reasons the Coral Triangle is so diverse. While this is certainly not the only method by which species are created, our example is a clear demonstration of how Earth history and biological history intertwine to create new biodiversity.

 Despite the fact that this project was initially focused on describing new species, throughout our research we were able to take a look into some of the processes that have helped make the Earth such a rich and vibrant place to explore.

Last year, the Australian Biological Resources Study published a study by Arthur Chapman as to the ‘Number of living species in Australia and the world’ (http://www.environment.gov.au/biodiversity/abrs/publications/other/species-numbers/index.html). The revised estimate is 1,900,000. That we are still dealing with estimates reveals that the community of taxonomists has yet to compile a single list of all species. On January 7^th this year, the EOL logs revealed that the number of pages that we deliver passed the 1,900,000 mark. Is this an ‘ Oops’ moment, is the estimate of the numbers of species is wrong, or is EOL getting its numbers wrong?

Olenellus getzi, a cambrian trilobite. Image by Bruce Liebermann, CC-BY license, from trilobites.lifedesks.org

There are a number of reasons why we have more than 1,900,000 pages. For a starter, EOL prepares pages not only for living species, but also for extinct species. For example, there is a page for the thylacine, the wolf-like marsupial carnivore that went extinct in the 20th century (http://www.eol.org/pages/126716). EOL has recently added information from the ‘Trilobites Online Database’ (http:// trilobites.lifedesks.org). All trilobites are extinct, but we still gather information about those organisms. Pages are therefore waiting and become visible in a search or can be discovered when browsing if you use a classification that refers to trilobites – as a search on Olenellus will reveal. Estimates vary as to how many extinct species there are, but probably about 250,000 extinct species have been reported to date. Similarly, EOL has pages not only about species, but also about genera, families, orders and so on – which means that when complete, EOL should have about 2,500,000 pages.

That said, we will not simply converge on the two and a half million target soon, but will first grow to vastly exceed this number. The number of pages will slowly come down again to reach the target. The reason for this lies in how EOL collects information and displays it. EOL uses the names of species to gather information together. As the Global Names Index (at. www.globalnames.org) will attest, there are many more names than there are species (GNI knows of almost 20,000,000 names).One cause for the excess of names is a requirement to change a name when the classification of a species changes. Linnaeus created the foundations of contemporary biological classification in the 18th century. At that time, he and his ‘apostles’ only distinguished about 10,000 species, and placed them in about 1300 genera. The expansion to the current number of 1,900,000 species results mostly from the discovery of new species. Those species are now placed in several hundred thousand genera. The intervening 250 years have seen a massive expansion of our awareness of biological diversity. In this process, scientists have tried to refine and debate what species are as they learn more about the nature and evolution of them. They move species from one genus to another so that closely related species are grouped together. As the names of species contain one word for the species and another for the genus in which the species is placed, these moves create new names for the species. The yellow fever mosquito was described by Linnaeus as Culex aegypti, then became known as Aedes aegypti, and more recently was transferred to Stegomyia, to give it yet another name, Stegomyia aegypti. Although the species is unchanged, we have several names for it. Until we find out that the names refer to one species, EOL may have information for it from sources that still use an old name. Only when we are advised that the two names refer to the same species, do we know to bring content under both names together on the same page. Until then, we will have more pages than there are species.

Linnaeus’ original description (above) is: Culex aegypti with white articulations. The size of the common gnat. Color grey from dusky (tawny shading into grey). Legs grey with white rings, small ones about (around) the articulations and in the joints. White spots on the edge of the back on the body, beneath the wings on each side, several of them, placed longitudinally. One white ring at the base of the thorax between it and the body. A white perpendicular line near the eyes, on each side a single small one. Place: Egypt, rarer than the common gnat.The image of Stegomyia aegypti is by Goeldi, and is out of copyright, image of Linnaeus description is out of copyright.

Another reason for the additional pages is that species are not well-defined objects like ‘a car’ or ‘a computer’. Rather they are like the smoke from a snuffed candle, conversations, or clouds. They differ every time you encounter them. They are living and transforming things, changing as the evolutionary process that produces them wends its way through time and across the globe. Genetic experiments are always being made. The pressures on, and opportunities available to, species change such that what a species looks like varies as do the numbers of individuals we would assign to that species. Scientists define – as best they can –each evolving lineage and refer to the products of the evolutionary process as ‘species’. Because of the indefinite nature of species, different experts come up with different points of view. Some think we should treat Gorilla graueri (the lowland gorilla) as the same species as the eastern gorilla (Gorilla beringei). Others think they are different, and yet others want to represent them as different subspecies of the same species. To be able to accommodate all of these points of view, we need to have at least four pages, one for each possible species or subspecies – even though we might have, in the end, a single species.

Gorilla. Image by Brian Gatwicke, CC-BY license.

This is not an isolated case, and is more the norm than an exception. Should we continue to treat the polar bear (Ursus maritimus) as different to Ursus arctos (the brown or grizzly bear) with which it can interbreed; and are zebras and horses members of the same species or not. Most biologists would theorize they should be treated as the same species because they can form hybrids. In contrast, most non-scientists will continue to think of the polar bear as a separate species because it looks different and has an unusual life-style. The different definitions of species are ‘concepts’. In order to show all information about all life, EOL prepares pages for each of these concepts, and again the number of pages grows to exceed the number of species.

To the left is a museum specimen of a polar bear / grizzly hybrid. Examples of hybrids are known from museum specimens, zoos, and in the wild. Image by Sarah Hartwell, CC BY license; from WikiMedia

By far the biggest source of the extra pages comes from the different ways that people refer to species. We use names to distinguish each type of organism. Some names are scientific, are in Latin, and follow conventions that can be found in the codes of nomenclature. Others are common names. Even though scientific names are regulated by the codes of nomenclature, they can appear in many different forms. ‘Grevillea glauca’, ‘G. glauca’, ‘Grevillea glauca Banks & Sol. ex Knight’, Grevillea glauca Banks and Solander 1809 are all legitimate ways of writing out the scientific name for the Australian shrub that is used for boomerangs or to assist in hanging out the washing. Although biologists know that these names refer to the same species, a computer registers that the names are different and makes the assumption that they refer to different species. Until the computers are told differently, we will have pages for the information that is attached to each of the names. We expect there to be at least 100,000,000 different names and forms of names that have been used for the 2,000,000 species. As this is the biggest source of the extra pages, EOL works hard to build new software and asks for help from the expert community to ‘reconcile’ these alternative names. A measure of our progress is how well we bring the number down to match the 2 million or so species that we believe exists today.

Grevillea glauca, from Joseph Banks’ ‘journal’ of his 1768-1771 trip on HMS Endeavour that, under the command of James Cook, visited Australia. The fruits give the plant its common name “Bushmans clothes-peg”. Image out of copyright.

A (modified) species page from EOL that contains information about an organism that has not been given a name (an “unidentified bacterium”, itself included within a ‘class’ called “environmental samples”.Recently EOL added information from GenBank – a place where people deposit molecular information. It is now possible to use molecular tools to explore nature. These new approaches are revealing species that seem to be new to science but cannot be identified. In the absence of formal names, those ‘species’ are listed under terms like “Uncultured bacterium HZ_056“ bioreactor sludge metagenome“ or even organisms that are just referred to as “unidentified”. We refer to those terms as ‘surrogates for names’ in the expectation that they will be given formal scientific names in due course. As molecular techniques become cheaper and more powerful, we expect to be deluged with information labeled with surrogate names. At this time, perhaps as much as 20% of the diversity known to EOL is in this form, and these also add significantly to the tally of pages in the site.

A (modified) species page from EOL that contains information about an organism that has not been given a name (an “unidentified bacterium”, itself included within a ‘class’ called “environmental samples”. Original.

Fortunately, many of these problems are hidden behind the scenes. When someone arrives at EOL, they can navigate among species using a classification scheme. They will see only the pages that match up with names in the classification. Obsolete names, or names of species not recognized by the classification are hidden from view. But, if you want to see everything that is in there, the hidden pages can be found through searches after setting the preferences to eliminate filtering.The Encyclopedia of all Life has picked up the challenge of bringing together and organizing information about all life. We do this in order to realize the vision of Ed Wilson (and others) to have a page for every species on Earth. We have invented new ways of managing information about organisms – that is, we are ‘biodiversity informaticians’. We work with other biodiversity informaticians around the world. We call on the tools emerging from computer sciences and invent new tools to organize information so that it can be used better to inform and guide the decisions that we need to make about the future of our world. Most of the current tools are first generation, and they will improve as the discipline of biodiversity informatics grows and matures, and as the need for information becomes more urgent.

Professor E. O. Wilson, Harvard University. Image by Kevin Kelly, available under creative commons license (http://kk.org/ct2/new-media/).

We at EOL rely on innovative computer programs as one of four ways to improve the management of information about biology. The programs and algorithms give us ‘scalability’. That is, they provide the means of working through billions of pieces of information located at thousands of sites and assigning them to the correct species. Our second area addresses the ‘many names for one species’ problem. We are hard at work developing new ways of grouping together alternative names for the same species. The goal of assigning the expected 100,000,000 names to 2 million groups – one for each species –increasingly needs to be done through an open on-line environment that will allow initiatives and experts world-wide to co-operate in improving names management. As an open environment, all of us, from the search engines to school teachers, will benefit as names management will ensure that we find more and miss less information about each species. Thirdly, we will provide web tools with which experts can improve the quality of classifications that are used to organize information and to navigate around sites like EOL. Experts can work together to make sure that nothing is missing, that classifications reflect current thinking, that obsolete names and ideas are properly labeled and hidden from view, and that the groups that include alternative names for the same species are correct. Finally, EOL is building a community of curators who can correct any errors that persist. Anyone with a sharp eye and a commitment to quality is welcome. Balanced progress on these four fronts positions EOL to produce a robust high quality web environment about all life on Earth within the 10-year schedule that we set ourselves.

D Patterson

Senior Taxonomist

Jan 21 2010

Got five minutes? Dive into marine biology and biodiversity through the Podcast of Life and witness science in action through lively, you-are-there stories from the front lines of ocean science. This series of 13 podcasts, hosted by Ari Daniel Shapiro, is brought to you by the Encyclopedia of Life, Smithsonian’s National Museum of Natural History, Atlantic Public Media and a consortium of marine education network partners.

Listen
The first podcast in the series features the North Atlantic Right Whale (Eubalaena glacialis):

Hear how research unfolds at sea in a tiny Zodiac surrounded by creatures half the length of a football field. Playing female whale calls into the water, researcher Susan Parks suddenly finds herself the center of attention of a group of male North Atlantic Right Whales. Will she be able to gather crucial data before a breaching whale crashes down on her boat?

To find out, go to eol.org/podcast. You will be able to listen to the podcast on our website or download it on iTunes. We will add a new podcast every two weeks!

Learn                                                                                                                                                                                                                                                                                             Developed for students of all ages, and especially for those 9-13 years old, these podcasts celebrate marine species with high student appeal and rich and relevant classroom resources available through our education partners.You’ll also find extra audio clips that didn’t fit into a five-minute podcast.

Participate
Each podcast episode offers ways for listeners to call in or record online to add their voices and ideas to the Podcast of Life. Check back often as we will post a new podcast every two weeks and showcase student contributions to the podcasts on our website.

Visit the EOL Learning and Education site to download the podcasts and learn more about opportunities to participate.

Please listen and let us know what you think!

October 22-24, the Biodiversity Synthesis Center hosted an EOL workshop in conjunction with EOL partner Animal Diversity Web. The workshop goals were to broaden the reach and increase the effectiveness of university students authoring species accounts. A diverse group of 22 participants from four countries assembled to present different programs that involve student authorship and gathering of species data. The workshop was an effective mix of presentations, group discussions, and breakout groups. In the presentations, we heard about the successful methods of the ADW program and template, diverse ways that faculty implement the ADW template into their courses, methods and strategy of the complementary AmphibiaWeb authoring process, and other projects around the world that involve students of all ages in the collection of species data (including iSpot, High Tech High’s bay surveys, INBio, marine surveys in the Cape Verde islands, and others). The workshop will yield many important products, including instructor workflow models for integrating student authorship of species accounts into different types of courses, a best practices document for instructors and students, a 2010 RCN proposal to NSF, new content and curators for EOL, and increased use of the ADW species account template in the US and abroad.

The workshop was a first for EOL, co-sponsored by the Synthesis, Learning and Education, and Species Pages Groups, and can only be viewed as a great success.  Thanks to all who participated in 3 days of lively and highly productive discussion. Special thanks to meeting organizers Tricia Jones and Tanya Dewey!

Longevity and the process of aging are topics of perennial human interest as expressed by explorers like Alexander the Great and Juan Ponce de Leon searching for a river or spring to heal or reverse the process of aging or by modern scientists studying biology of aging.  Just a short walk across the MBL campus from EOL’s Biodiversity Informatics group resides the team charged with creating the Biology of Aging portal.

The Biology of Aging (BoA) project, funded by the Ellison Medical Foundation and hosted at the MBL/WHOI Library has two goals. The first is to gather, organize, and share information related to the biology of aging and lifespan development processes across the entire spectra of life and provide that information to EOL and biologists studying the basic processes of aging. A second goal is to develop informatics tools to aid in the discovery of information, trends and hypotheses related to aging.

LigerCat - Explore Biomedical literature

One tool that the BoA team has developed is LigerCat. LigerCat is a tool that helps people search the biomedical literature at PubMed/Medline (National Library of Medicine’s database of articles) and see the results as a tag cloud of biomedically relevant terms. We have used LigerCat to find and display terms for species in EOL. For instance here is the tag cloud for articles related to polar bears (Ursus maritimus ):

Every species with a LigerCat cloud will have “Biomedical Terms” in the Table of Contents section of the page.

Finding Aging Information

In order to gather information about lifespan and other related data we are creating computer applications that can ‘read’ text and extract the relevant information. We use Natural Language Processing (NLP) techniques for extracting information from text. The NLP tool is trained to recognize lifespan related words and phrases. Using tools like this we hope to find more aging information in scanned literature like the Biodiversity Heritage Library. This information will enable scientists to make comparisons over groups of organisms that may lead to the development of a new understanding of the processes of aging and the development of aging related diseases.

BoA Team

Currently three developers work full time creating the Biology of Aging portal. Ryan Schenk is the Web Application Architect, Lakshmi Manohar Akella is the Natural Language Processing Analyst, and Anthony Goddard is a Developer and Systems Administrator. Dr. Holly Miller is the Project Leader. Cathy Norton is the Director of the MBLWHOI Library. Watch the EOL blog and the Biology of Aging blog for future developments.

BoA Team, left to right (Favorite EOL species): Lakshmi Manohar Akella (lion) Holly Miller (black-capped chickadee ), Cathy Norton (tuatara), Ryan Schenk (hedgehog gourd), Anthony Goddard (polar bear).

From October 5-8^th, BioSynC hosted a working group meeting whose ultimate goal was to develop objective criteria to assess species’ relative vulnerability to global climate change.  The meeting featured 11 participants from the U.S. and Germany and drew together experts from fields that, according to meeting facilitator Dr. Joseph Bernardo, are normally “off in different departments”: ecophysiology, population genetics, quantitative genetics, and phylogenetics. 

            Traditionally, species’ endangerment has been assessed with reference to ecological factors—large-scale criteria such as population size or geographical range size.  But considering that climate change has surpassed habitat loss as the leading threat to global biodiversity, the premise of the ecological model—that populations will recover if their habitat is protected—can no longer be taken for granted.  In his proposal, Bernardo noted that species persistence in the face of climate change will follow from three aspects of biology: “tolerance of changing conditions…; migratory capacity to track optimal habitat patches as climate change ensues; and the evolvability of these two factors in response to changing conditions.”  To measure these three aspects, Bernardo’s working group is choosing empirical physiological and genetic traits that can be applied to all species, mirroring the way IUCN ecological categories objectively determine species conservation status. 

            Take the example which Bernardo gave me: the common cuttlefish (Sepia officinalis).  This species, according to ecological criteria such as population trends and range size, is not threatened.  But according to its physiology, the cuttlefish does not have a very high tolerance for thermal extremes.  And though the cuttlefish has high genetic diversity across its entire range, much of the diversity is restricted to local populations, which implies a low migratory capacity.  All in all, these new data suggest higher susceptibility to the stress of climate change than do ecological criteria. 

            In this second in a series of three meetings, traits hashed out in the first meeting.  were revisited and made operational by application to case studies.  In order to make the new framework analyzable statistically, previously subjective categories such as ‘low, medium, or high’ dispersal potential were defined rigorously, quantified, and given scores.  When asked about the importance of the working group setting, Bernardo was unequivocal: the work is greatly accelerated by this kind of synergy and focused effort, and by the opportunity for synthesis of different fields provided by BioSynC.  The group hopes that the criteria they have developed would ultimately be used by conservation entities such as IUCN and Conservation International.  In addition, their proposed contribution to the EOL covers a variety of content: detailed methods for how to convert empirical data into a parameter estimate, as well as worked case studies linked to their corresponding species pages. 

            What, then, are the implications of this new framework for conservation?  To answer this, Bernardo made an intriguing analogy with genetic counseling.  If I am told I have a high genetic propensity for diabetes, I will do all I can to minimize my environmental susceptibility—i.e. exercise frequently, adjust my diet, etc.  Similarly, the finding that a species is genetically or physiologically vulnerable to climate change might inform strategies to manage it ecologically.  The analogy makes it clear that these physiological and genetic criteria are not meant to replace traditional ecological ones; rather, they would complement each other to create a broader, more complete description of species vulnerability than currently exists. 

NESCent, the National Evolutionary Synthesis Center, hosted representatives from EOL and the major national biology centers Oct 6-7.  The meeting focused on how EOL and the national centers can communicate effectively about science and can improve science education training and programs.  Although the centers have different foci (evolution = NESCent, ecological observations = NEON, plants = iPlant, mathematical biology = NIMBioS, biodiversity = EOL BioSynC, ecology = NCEAS), they have a common mission to advance scientific knowledge, to improve understanding about science, and to help train future scientists.  All of the centers host postdoctoral scientists, interns, and synthesis meetings, but their methods for training and communication vary widely. Centers use combinations of press releases, blogs, twitter, facebook, local NPR stations, local reporters, and news services to get their message out.  The centers range in age from 15 years (NCEAS) to 0 years (NEON) and we spent a lot of time discussing best practices and learning from the more senior centers.  EOL was represented by Audrey Aronowsky (Synthesis Group) and Tracy Barbaro (L&E Group).  The meeting was an excellent opportunity for EOL to collaborate with the national bio centers for potential EOL content, but more importantly for increasing the public’s awareness of and interest in science.

We released version 2.15 of our code to all 115+ LifeDesks sites today. This was a particularly important release because we rewrote a lot of code, dug deep into solving some performance issues, and reconstructed the databases for all LifeDesks to accommodate these changes. The aim of this release was to have a better storage and presentation mechanism for applying tags with specific biological meaning to names. We used this mechanism for ranks, common name language codes, and taxonomic relationships (e.g. the term “synonym”) between names because it allows users to add/remove terms. We thought this was pretty cool, so we opened the gates to allow LifeDesk owners to create their own biological flag ontology and populate it with terms. For example, you may create an ontology called “Biogeographic Region” and populate it with terms “Nearctic”, “Palearctic”, “Holarctic” and the like. Similarly, you could make a flag type called “Habitat” and populate it with terms “Marine”, “Terrestrial” or “Freshwater”.

The classification editor is currently the place where these flags get applied to names, but we’re thinking of other ways to make this much easier and faster. A spreadsheet editor would certainly help in this situation.

We concentrated most on the storage mechanism for these biological flags, but made a first pass at presenting these on taxon pages, which are visible in a special panel called “Biological Flags” on the right side of the page. Eventually, we’ll think of ways to make these

flags clickable and ultimately, ways to share these flags to EOL. We’re also thinking about mechanisms for flags to be shared across LifeDesks so we have our eye on GBIF Vocabularies.

On the eve of another BioSynC synthesis meeting–a meeting on global climate change starts this Monday–we have a moment to step back and reflect on this distinctive way of doing science.  What are synthesis meetings, exactly?  And why do we host them again?  The following is a transcript of an interview I conducted with Dr. Mark Westneat, director of BioSynC.

What do you see as the main benefit of a biodiversity synthesis center (BioSynC) that hosts interdisciplinary meetings in biodiversity science?

Mark: I think hosting meetings is actually a means to an end, with the goal being new ideas, new approaches to tackling thorny problems that are difficult to address using current data sets and current technology.  We want to use synthesis meetings to push EOL toward solutions for some of the long-standing problems in biology: phylogenetic visualization, biogeography, using informatics for conservation biology…We also anticipate and have experienced that new questions pop up all the time at meetings, which is a really exciting part of having them.

What do you think it is about biodiversity science that so demands synthesis?

Mark: NESCent and NCEAS (National Center for Ecological Analysis and Synthesis) have hit on two of the really integrative, multi-faceted disciplines of biology that need synthesis: evolution and ecology.  Multi-species interactions, historical factors—very complex scientific questions.  Synthesis benefits that greatly.  I think biodiversity science is at an interface between evolution and ecology, but just the knowledge of how many species there are on Earth and what their names are—really basic knowledge—is woefully unknown.  Until we know it, and can develop good online resources for it, that hinders what NESCent and some of these other synthesis centers are trying to do.  It also hinders conservation biology.  That lack of biodiversity information is a sort of ball-and-chain that slows science down.  So I think one of the big benefits of the EOL and the synthesis we do with it and for it is to speed science up by collecting that basic information and making it available for research, to answer that perplexing question we have now and move on to the next one. 

How are BioSynC meetings distinct from the NESCent models they are based on?

Mark: Well, all our meetings have the common theme of using or contributing to the EOL to accelerate the pace of scientific discovery, which is unique.  They may be focused on building a completely different database.  The first meeting we had here, on Bryozoans, was run by Scott Lidgard.  He was basically building BryoZone, this other database, but we knew it was going to be a partner with EOL, that it would directly feed into EOL and enable research.

At what stage are you at in a scientific problem when most meetings are convened?

Mark: Ah, at various stages.  Taxonomic problems—for example taxonomy of flies, or of decapod crustaceans—tend to be more mature; all the people in the room are experts in a group within that clade.  Most of them know each other already and the pathway to resolving taxonomic problems is pretty clear.  These meetings are really important for the EOL because they make possible research on diverse content aggregated in one place.

In some of the other meetings, where the questions are more raw, I think the participants argue a bit more, even about what the important question is.  For example, the tree viz meeting had software developers, corporate representatives, and computational and taxonomic biologists.  I think there was a lot of mind-expansion and enlightenment going on, with the participants really listening to and challenging one another.  So meetings come in different flavors.

Describe the structure of a typical synthesis meeting.

Mark: They vary, but the typical large meeting starts with individual talks to get everyone up to speed on each other’s perspectives.  You don’t want to spend too much time giving these talks, because that’s not really synthesis.  After every one knows each other, then you break out into discussion groups and start to synthesize, to debate, ask what the data sets are, and who’s going to do what.  We ask participants to sign up for tasks that will continue beyond the synthesis meeting itself.  Many meetings have a section where they outline a paper or grapple with the nitty-gritty of outlining a grant proposal on the topic.  This really focuses your thinking: ‘how will we address the key question in a 15 page NSF grant?’  At each stage we encourage people to think about how what they’re doing interfaces with the EOL.

How do you feel about the public perception of scientists as workers in isolation, making discoveries through flashes of insight?  How do synthesis meetings come in here?

Mark: I love being hidden in my lab by myself, because I do so many meetings and interviews like this one [laughs].  Being in the lab is an important part of science.  But synthesis meetings are equally important: that’s where you get new ideas, cross-fertilization of disciplines, and you can then go back to your lab with a new idea you got from meetings.  I think that makes your science better, but you still have to go back the lab and pursue it.   It can be a bit lonely, but I think synthesis meetings—camaraderie, group effort—make up for that.  Some of the best ideas that come out of synthesis meetings come from standing around the coffee pot or at the restaurant with a bottle of wine, or after the meeting, or in between official sessions.  That’s often when the real deals, the real ideas get hashed out.

What do you consider products of a successful meeting?

Mark: Really, the most important product is enthusiasm and the trading of ideas on how to advance biodiversity research using the EOL.  In terms of tangible products: grant proposals, publications that come out of collaborations, species page content that enables current and future research, researchers signing up for curation of species pages or life-desks to funnel content, regional EOLs.  We had a meeting in Fiji where there was a group of people working to contribute to a regional EOL down there; we developed grants and papers on biogeography and conservation, talked about student training and local involvement, and they also translated the EOL video into Fijian.

What are your thoughts on the future of synthesis meetings?

Mark: We are grassroots, so we are driven by what the community wants to do.  We have our favorite themes: phylogeny, biogeography, conservation.  But plans for synthesis meeting on the depictions of biodiversity in art are very exciting to me because I think one of the most promising ways to have intellectual breakthroughs is where we’re blending biodiversity with some other area of human endeavor, like art or music or history or linguistics.  Those kinds of image collections might be really interesting in the context of EOL.  There might be papers written on the history of some particular kind of species art that hadn’t been tracked before just because we haven’t collected all the images in one place.   The EOL’s going to collect a lot of stuff in one place which will be available and searchable.  And then it’ll be sort of like ‘aha, look at that!’  [Laughs]  That’s what we’re after—that ‘aha’ moment.

This post was guest written by Nick Pyenson, the organizer of the meeting. Nick is currently a Natural Sciences and Engineering Research Council of Canada Postdoctoral Fellow in the Department of Zoology, at the University of British Columbia, Vancouver, BC, Canada.

Recently, EOL hosted a synthesis meeting on the evolution of marine tetrapods August 11-13, 2009, at the EOL Biodiversity Synthesis Center in the Field Museum. Among vertebrates, marine tetrapods (four limbed vertebrates) include organisms like whales, sea cows, sea turtles and penguins; although they are distantly related to one another phylogenetically, each lineage of marine tetrapod represents an independent invasion of marine environments from terrestrial ancestry.

Fossils of early whales (Basilosaurus and Rodhocetus) from the Eocene, on display at the Field Museum of Natural History (photo: N.D. Pyenson) and

Reconstruction of Waimanu, the oldest known penguin from New Zealand, on a Paleocene beach, about 58-60 million years ago. (illustraton: C. Gaskin, R. E. Fordyce, University of Otago Geology Museum).

Over the past 250 million years, no fewer than five different mammal lineages (e.g, whales, pinnipeds, sea cows) and over a dozen different reptile lineages (e.g., mosasaurs, ichthyosaurs, turtles, snakes) have independently entered marine environments at various times during the Mesozoic and Cenozoic. Attempts to understand the patterns of marine tetrapod evolution, and the processes that shape them, have unfortunately been limited to individual groups. The goal of this synthesis meeting was to fuse Mesozoic and Cenozoic perspectives on the evolution of marine tetrapods, as a way to provide a first approach at understanding broad-scale patterns and potential causes across all relevant time periods.

The meeting was organized and lead by Nick Pyenson (University of British Columbia & Smithsonian Institution), and featured 11 participants from Japan, New Zealand, Canada, the United Kingdom, Germany and the U.S. Participants in the meeting reflected a varied cross-section of vertebrate paleontologists, ranging from senior faculty to graduate students. Together, the group undertook a busy three day schedule of talks, discussion, conference calls with specific EOL staff, and active work using database platforms like the Paleobiology Database (PBDB) and EOL’s LifeDesks.

The first day of the meeting consisted of some brief introductions, and remarks by Audrey Aronowsky about EOL, Biodiverisity Heritage Library (BHL), and a variety of useful platforms and programs through BioSynC. The rest of the day then consisted of 20 minute talks by each participant (sometimes in groups), followed by 10 minutes of open discussion (a rarity in typical meetings). Given the wide range of topics, taxonomic groups, and time periods, participants received a pageantry of different marine tetrapod groups (both living and extinct), with stimulating questions and discussions about the specific issues (e.g., generating comprehensive compilations of diversity for different time periods; biases of the rock record; and correlations with sea-level, tectonic and climatic changes).

The second day of the meeting started with a teleconference with EOL staff Katja Schulz, Peter Mangiafico, Eli Agbayani, and Lisa Walley. Here, participants discussed with EOL staff the process of adding extinct taxa on to EOL webpages, and generating dynamic linkages of content between EOL and the PBDB. Later in the morning, we held a teleconference with Matt Kosnik (Smithsonian Institution), who introduced the group to different aspects of the PBDB. Then, participant Mark Uhen (George Mason University and Board Member of PBDB), the group on a tour of how PBDB works, and how to enter occurence data from published fossil accounts into the PBDB, thereby generating the fundamental data needed to merge marine tetrapods across the Mesozoic and Cenozoic. It is hoped that EOL and PBDB can continue to foster an on-going partnership in the future.

On the third and last day of the meeting, the group focused on two aspects: using EOL LifeDesk as a way to build species pages for marine tetrapods (both living and extinct), as well as outreach through the Understanding Evolution and Understanding Sciences webpages, hosted by the University of California Museum of Paleontology. Lisa Walley and Katja Schulz provided an introduction to LifeDesks, and the group quickly grasped the power of the platform; see this example of Chonecetus goedertorum, an extinct toothed baleen whale, written by meeting participant Felix Marx (University of Otago). The group aims to complete about 100 species pages of marine tetrapods through the LifeDesks platform. For outreach, the group heard from David R. Lindberg (UC Berkeley and Co-PI on the Understanding Evolution and Science webpages), who provided a tour of the aforementioned pages and a preliminary discussion of developing a module on marine tetrapod evolution for the webpages.

Towards the end of the third day, the group re-assessed the entire meeting, generating some summary points about the evolution of marine tetrapods, but, more importantly, a “to do” list for further actions, which includes at least two meeting symposia and future grant applications to extramural funding agencies. Overall, this meeting provided the crucial first steps towards synthesizing our knowledge of marine tetrapod evolution, and, with the tools and approaches discussed at BioSynC, we are well-poised to tackle the rest of our objectives. We wish to thank EOL and BioSynC for funding, the latter and the Field Museum of Natural History for hosting the meeting, and especially thank BioSynC Director Mark Westneat, Audrey Aronowsky, and, of course, Darolyn Striley for helping make the meeting a successful and enjoyable time.