Tag Archive for antweb

Antkey release

November 15, 2012 4 comments

Andy Suarez and I are excited to announce the release our Antkey.org project. The project was funded by USDA-APHIS-PPQ-CPHST and the Encyclopedia of Life (EOL) Rubenstein Fellowship program to provide an online identification guide to invasive, introduced and commonly intercepted ants.

Download USDA Antkey Announcement

Frontpage of the Antkey.org site

 

Over 15,000 species of ants have been described, and more than 200 have established populations outside of their native ranges. A small subset of these have become highly destructive invaders including five which are currently listed among the world’s 100 worst invasive species. Unfortunately, detection of non-native ants is hampered by the taxonomic specialization required for accurate species identification.  Antkey seeks to mitigate the spread of established introduced ants and prevent the incursion of new introductions by providing quarantine personnel, inspectors and conservation biologists with a user-friendly identification resource specifically designed for non-specialists.

Antkey focuses on over 115 ant species that are introduced, invasive or commonly intercepted in North America and the Pacific Islands. Features include an interactive Lucid key, dynamically generated species pages, a searchable media collection of over 1150 images, over 70 live video clips of introduced ants, a fully illustrated glossary with over 400 terms, a searchable database of introduced ant literature, over 12,000 specimen records of introduced ants imported from Antweb (www.antweb.org), and community features such as blogs, discussion forums and comment options.

Tabbed species page for Linepithema humile on Antkey.org

The interactive Lucid key allows users to start at multiple entry points, skip ambiguous or difficult characters, and keep track of the choices already made. Novice users can use the ‘best’ feature to determine which available characters will lead to the most parsimonious pathway. More advanced users can skip straight to subfamily or genus. The characters are illustrated with original line drawings and link to glossary definitions and additional specimen photographs.

The Antkey taxonomic classification includes 8 subfamilies, 43 genera and 116 valid species. Taxon pages include tabs for overview, descriptions, media, maps, literature and specimens. In addition to original diagnostic descriptions and overview sections, all the species pages dynamically import relevant articles from the Encyclopedia of Life (www.eol.org) and specimen images from Antweb. The Google maps are dynamically generated from specimen data imported from Antweb and distribution data imported from GBIF.

The media feature contains over 1150 images and uses a faceted search tool that allows users to filter images by media gallery, taxonomic name, keywords, description and creator. Each thumbnail links to a lightbox window that displays the standard scaled image and associated metadata, and also offers a link to download the original, full-sized image. All images tagged with a taxon name automatically appear on that taxon’s species page.

Media feature in Antkey allows users to filter their searches based on morphological terms, taxonomic names, image type, media galleries and keywords.

The site includes approximately 75 video clips of 22 species. There are many important identification characters for ant species that are only possible to detect while the ant is alive. The standardized thirty-second video clips feature ants feeding at and recruiting to baits, foraging in natural environments, and entering and exiting their nests. The videos can be downloaded by users or embedded in other webpages.

A fully illustrated glossary of over 400 terms, including all the character states used in the Lucid key, allows users to quickly learn the important morphology needed to make accurate identifications. The terms are integrated throughout the site so that whenever one appears in the text the user can point to it and the definition will automatically display.

One of the greatest strengths of Antkey is that it was developed using the Scratchpads platform.  Scratchpads (http://scratchpads.eu/) is a social networking platform that allows communities to bring taxonomic information together without the limitations of traditional paper-based publications. Web systems and content can be developed and updated in minutes so websites can reflect the latest knowledge of a particular group. The platform also allows multiple authors to create and edit content without using any html code. The Scratchpads platform relies on the content management system Drupal (http://drupal.org/) for its underlying architecture.

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Introduced Ants and POE Ants now on Antweb

February 7, 2012 No comments

Two new projects recently went live on Antweb that are aimed at helping folks identify the ever-growing cadre of invasive, introduced and intercepted ants.

The Introduced Ants project lists 157 species (136 imaged) that have established populations outside of their native range. The project is being curated by Brian Fisher, Andrew Suarez and myself.

“Of the nearly 14,000 described species of ants, over 200 have established populations outside of their native range. Some of these have become highly destructive invaders. In addition to being economically costly in both urban and agricultural areas, invasive ants can modify ecosystems by reducing native ant diversity, negatively affect vertebrate populations, and disrupt ant-plant mutualisms. However, for most introduced ants we know little about their impacts and less about their biology; we often don’t even know where they are from. The goals of the introduced ant page on antweb.org is to collate information on where introduced ants are found, and help provide taxonomic resources for introduced ants. Ultimately, we hope this site will provide information on 1) biogeographic patterns of invasion including the identification of regions that may either produce many invaders or be particularly prone to invasion, and 2) taxonomic perspectives on invasion success. Here we provide a list of introduced ants, that is those ants known to have established populations outside their native range. A far greater number of species have been intercepted at ports of entry but have not become established (see Port of Entry ants).” – Antweb

The Port of Entry Ants project is being curated by Andy Suarez and myself, and is composed of 210 species (192 imaged) that have been intercepted at United States ports of entry. The baseline of this project are the USNM specimens Suarez and Ward (2005) identified to examine the role of opportunity in the unintentional introduction of nonnative ants. Andrea Walked (Suarez Lab, UIUC) has done an excellent job with the imaging, and Michele Esposito (CAS) has helped with the data handling. Hopefully this project will expand to include ants intercepted on an international scale.

Biological invasions are a leading threat to biodiversity, agriculture and the economy. Ants are among the most damaging introduced species, yet we know very little about why some ant species become successful invaders. A major challenge of invasion biology lies in the development of a predictive understanding of invasion processes. However, this is inherently difficult because different characteristics may be important for different species or during different stages of invasion. Subsequently, research on invasive ants needs to examine taxonomic patterns across each of the three distinct stages of invasion: opportunity, establishment and spread.

“To examine the role of opportunity in invasion, we are developing a database of ants intercepted in quarantine worldwide. These data will be used to examine why some species succeed as invaders while others do not. Surprisingly, there is a remarkable diversity of ant species moving around the world as a result of human commerce. However, relatively few species become established suggesting that opportunity alone is insufficient for introduced species to establish and spread.” – Antweb

 

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Making regional checklists for ants

February 7, 2012 One comment

I’m working with Evan Economo and one of his students on putting together a checklist for the ants of the Solomon Islands. I thought it would be a good opportunity to record my workflow in case I do one of these again, and in case someone else is looking to do a similar project.

The proximate goal of this exercise it to produce a species list for Antweb. Down the line though, we also want to publish the checklist to make it easier for future researchers to do a thorough survey of the Solomons, and also to help broaden the global knowledge of ant species distributions.

A checklist is all about the names. The names are coming from three primary pools: (1) specimens we collected in the field, (2) specimens we’ve examined in museum collections, and (3) species occurrences published in the literature.

To begin with, I download the example species list (Excel) that is available on Antweb. (It is also worth reading the accompanying documentation.)

It’s really only necessary to fill out the following columns: Subfamily, Genus, SpeciesName, Species Author Date. For a really solid checklist, though, it’s also nice to have the page number of the original description. For example “Emery, 1897: 581”. And remember, if the species was originally described under a genus different from the current one, the author and date go in parentheses “(Emery 1897): 581”.

Next, I insert a bunch of columns after ‘Species Author Date’ and label them, Source1, Source2, Source3, etc. These columns will serve to record what sources each species occurrence is drawn from.

I also add a new worksheet that I name ‘Sources’ which I use to compile the full citations for all the literature records, websites, etc. from which I will be pulling species occurrence records.

Antbase Distribution Database

A good way to generate a base list of species for a given country is the Antbase Distribution Database. This will generate a list of all species with type specimens from the country, in addition to an assortment of names retrieved from other online databases. Unfortunately, there is no way I know of to easily determine where these latter records come from. In order to verify them (and find records that HOL might have missed), we must use other online resources.

Hymenoptera Online (HOL)

The next names I add are from previous literature records. The most significant publication was Mann’s 1919 Ants of the Solomon Islands. In order to generate a species list from Mann (1919), I search for the author in Antbase.org, and then click the citation link. This takes me to the Hymenoptera Online (HOL) page for Mann (1919). The ‘Taxon citations’ window lists all the names reported in that publication, with links to the online citations for the original descriptions.

I then copy the list and paste it into a new worksheet labelled ‘Mann, 1919’. Since this is my first source, I add ‘Mann, 1919’ and the full citation to the ‘Sources’ worksheet.

Now it’s time to cross-check the master species list I’ve generated with the Mann (1919) list. If the name is already on my master list, I add ‘Mann, 1919’ next to it in the ‘Source1’ column. If the name is not on the master list, I add it in and mark the source.

CAUTION: it looks like the names in the HOL ‘Mann, 1919’ list include species Mann includes in some of his keys that do not occur in the Solomons. The only way to catch these discrepancies is to look at the publication, itself. So once again, there is no substitute for human eyeballs and original publications.

AntCat

Many of the names that appear in Mann (1919) have either been transferred to a different genus or have been synonymized with an older species name. This requires me to cross-reference each of Mann’s species names with the current nomenclature using AntCat (which is more up-to-date than HOL). I type the old name into the search box and see whether it is valid, has been transferred to another genus, or is a junior synonym or homonym of an older name. If these names correspond to valid names that are not already on my list, I add them in making sure to copy the species author (author of the original description) and date into the ‘Species Author Date’ field. As I mentioned before, I’m also including the page number of the species description.

FORMIS

Now for the obscure literature records. To find these I use FORMIS. As an Endnote user, I make sure I have the most recent edition of FORMIS and open the library. I’ll make a new ‘group’ on the lefthand sidebar called ‘Solomon Island records’. Then I’ll type ‘Solomon Is’ into the search box to hopefully get a list of all (or nearly all!) published ant literature that mentions the Solomon Islands in the title, abstract or keywords. If it is relevant, I’ll add it to the new ‘Solomon Island records’ group I made. For each relevant citation, I’ll make a new worksheet tab in my Excel workbook and rename it with the author-date.

References with species lists for the region

The easiest papers to mine are restricted to the Solomon Islands, and have a list of species separated by semicolons in the abstract or keywords. If this is the case, I copy the names to the appropriate Excel worksheet tab. I’ll use the ‘convert text to columns’ feature to make each name populate a different column in ‘Row 1’. Then I’ll select all the names and copy them to the clipboard. Next I click on Cell 2A and then use the ‘paste special’ feature and select ‘transpose’. Now all the names are on different rows. Delete Row 1.

Once again, these names need to be vetted with AntCat to make sure they are valid. If not, I change them to the valid name. If the name is new to my master list, I add it, making sure to fill in all the appropriate fields, including the ‘Source’ field.

Other references

Other references will require more thorough searching. Global or larger-scale geographic revisions are an example of this type. For these, I will try and get a pdf of the article. If it is an older one, I’ll use the ‘OCR text recognition’ feature available in Adobe Acrobat to convert the pdf images into readable text. Then I search the text for ‘Solomon’, to see which species were collected from the Solomon Islands. These, too, I will add as new names to the master list if they were not there already, or add the citation to a ‘Source’ column.

Bolton’s Catalog

Another resource for mining locality info is the PDF version of Bolton’s Catalog that is (as of this post) being periodically updated on the Global Ant Project site. By searching for ‘Solomon’ we can retrieve all species for which the Solomon Islands serves as the type locality.

Specimens we collected

The next names and records I incorporate into checklist are from specimens that we collected ourselves in 2008. We identified and compared these with type material and determined specimens at the USNM. Next to these names, I add ‘EMS/EPE, 2008’ in the appropriate ‘source’ column.

This project is on hiatus for awhile, but I hope to return to it in the near future, and will update this posting when I do!

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