The EOL Biodiversity Synthesis Group and Learning and Education Group have collaborated to create educational species pages on the mammoth (Mammuthus), mastodon (Mammut americanum), giant short-faced bear (Arctodus simus), and two types of giant ground sloths (Megatherium americanum and Mylodontidae).  These pages were created to coincide with the new traveling Mammoth and Mastodon:Titans of the Ice Age exhibition opening at The Field Museum in Chicago, IL, USA and serves as an example for how museums might use EOL with their exhibits.

The species pages contain information on the biology and ecology of these Pleistocene mammals and unique fossil photos from the collections of The Field Museum.  These pages are the perfect complement to the Mammoth and Mastodon:Titans of the Ice Age exhibition.  This exhibition features a 42,000-year-old intact baby mammoth named Lyuba, and allows you to journey back through the Ice Age to view some of Earth’s largest and most awe-inspiring mammals through monumental video installations, hands-on interactive displays, life-sized models, fossil tusks and skulls, and even touchable teeth.  By looking through and reading the Pleistocene mammal species pages, visitors will be better prepared for the exhibit and are sure to have a richer experience.

These Pleistocene mammals pages are not just for viewing and reading.  They can be used as a dynamic tool for exhibition visitors to share what they learned with the world.  The EOL and Natural History Museums page of the Learning and Education Group site has several ideas for classes and families that use these EOL pages.  These activities can be applied to any visit to a natural history museum with exhibits featuring Pleistocene mammals. Some of the activities include: adding text and information found in the exhibition to the species pages, uploading original artwork, and uploading images from a photo scavenger hunt.  Participants will not only enjoy learning about Mammoths and Mastodons, but also help build the Encyclopedia of Life!

These species pages and accompanying activities are EOL’s first endeavor to link with a traveling natural history museum exhibit.  Natural history museums contain a wealth of information on extant and extinct species that can be contributed to help build EOL species pages. There is also great potential for EOL to bring certain digital media opportunities to museums, such as kiosks, flickr cascades, augmented reality, and mobile devices.  In the future museum visitors could download or upload personalized tours which utilize EOL content, display the species photos they take while at the institution, and complete scavenger hunts that explore biodiversity of the institution.  These are just a few of the ways that EOL can become a vital and dynamic part of natural history museums, as well as zoos and aquariums.

The good

When it comes to being a naturalist, or anything resembling the description, you can come pretty close to having a dream job.

Robin Baird is a marine biologist at the Cascadia Research Collective in Washington. For a study surveying the number of Kogia sightings around Hawaii, he and his colleagues spent three years going out on boats to look for two whale species that are rare, seldom sighted and not well known.

Sounds tough, right? It gets even more complicated if you’re not an expert in marine mammals. The species in question–pygmy sperm whales and their close cousins, dwarf sperm whales–resemble sharks with their pointy heads and slits that look an awful lot like gills.

But they’re false gills. And the pointy head–well, that may just be a fluke in natural selection. They’re not at all related to sharks. Kogia breviceps and Kogia sima are both part of the same family as the sperm whale, but it sounds like Baird and his colleagues had more fun looking for these whales than Captain Ahab ever did hunting down Moby Dick.

The main difference between the two species is their size. Pygmies are just a bit bigger. Adult male pygmies can be up to 10 feet long, about the height of a basketball rim, while the largest dwarf sperm whales measure no longer than 8 feet.

Pygmy sperm whales prefer tropical, subtropical and temperate waters (don’t we all), and they are not known to migrate. Marine biologists know very little about them though, because they tend to avoid vessels and can only be seen at a distance. The only time researchers can really get up close to them is when they get stranded.

Now put these factors together:

1) Location: You’re sailing around the Hawaiian Islands for work. Need I say more?

2) The whales are small, but hard to identify down to the species level. It’s a bit of a challenge to get close to them, since they tend to avoid vessels. So there’s a sense of victory when catching up to them and snapping some photos.

These dwarf sperm whale photos come from some of Baird’s expeditions:

(c) Photo Credit: Annie Douglas, Cascadia Research Institute

(c) Photo Credit: Robin Baird, Cascadia Research Institute

3) Since you can’t get close to them, you rely on photos to identify individual whales. Scientists typically look for markings and distinct shapes in the whales’ dorsal fins. When you come back a year later to look for more, you might recognize whales from the previous year. If you do this kind of field work long enough, it’s like attending an annual family reunion!

The bad

Pygmy sperm whales are not often sighted except when they’re stranded or accidentally caught in fishnets. It’s often mothers and calves that get stranded, so the phenomenon might have something to do with motherhood. Sadly, people haven’t been very successful in trying to rescue the animals and return them to their habitats, or to resuscitate them in aquariums..

But while humans may not be up to the task, Pogo the dolphin had the right idea!

And the funny

This may not be the highlight of a naturalist’s career, but here’s an image that’ll imprint these whales in your minds forever.

Aside from their size, pygmy and dwarf sperm whales can be distinguished from other cetaceans—whales, dolphins and porpoises—by a certain behavioural characteristic.

Squids are known to release clouds of ink to confuse predators. It’s handy when the predators don’t expect it, but pygmy and dwarf sperm whales have been observed doing something very similar.

They release clouds of dark fecal matter—yes, that’s right—when they are startled or excited.

After studying some of the stranded whales, biologists have concluded that pygmy and dwarf sperm whales feed largely on cephalopods, including squids. It’s thought that for dwarf sperm whales at least, these dark clouds can be used to distract their prey.

Now there’s no science to back this particular interaction (yet), but just picture the potential battle between these whales and their prey. One side squirts ink, the other expels…poop. The result: one epic battle.

  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.

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 almost 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.

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 about 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.  Such an environment will benefit all of us, from the search engines to school teachers, who want to 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

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!

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. 

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.