How to improve Lucid3 thumbnails

One of the greatest assets of the Lucid3 software is its capacity to integrate thumbnails of images inserted for character states, features and taxa. Once you insert a full-size image as media, Lucid3 automatically generates a thumbnail. The default thumbnail size is 125×125 pixels, but the user can customize it in Lucid Builder. The resulting thumbnails, however, are rather low quality, and can be significantly improved by using a third party application. I use Picasa to generate my thumbnails, but I am sure there are many other programs that will do just as fine a job. So, here’s how I do it.

1. Locate your thumbnail folder in Key folder > Media > Thumbs. Remember not to change the names or structure of the files within the key folder, because this will have nasty consequences. Notice how all of the thumbnails have the “_TN.jpg” suffix appended to the filename.

2. Copy the ‘Thumbs’ folder to some safe holding space like the desktop to serve as a backup in case things go wrong.

3. Delete all of the images within the ‘Thumbs’ folder.

4. Open the application you plan to use for generating the new and improved thumbnails. In my case, I use Picasa.

5. Open the ‘Images’ folder (Key folder > Media > Images), select all the files, then export them to a new folder (e.g. ‘New Thumbnails’) as 125×125 pixel jpeg’s (or whatever size you’ve customized your key to use).

6.  Now we need to append the ‘_TN’ suffix to the new thumbnails. I use a program called ‘Bulk Rename Utility‘. Open the ‘New Thumbnails’ folder in Bulk Rename Utility. Select all the files. Type ‘_TN’ into the Suffix form of the Add box. Make sure all the files have “_TN.jpg” at the end of them in the ‘New Name’ column. Press ‘Rename’.

Bulk Rename Utility is used to append the '_TN' suffix to the new thumbnails.

 

7. Copy all the updated thumbnail files from the ‘New Thumbnails’ folder into the ‘Thumbs’ folder (Key folder > Media > Thumbs).

 

Original thumbnails generated by Lucid3

New thumbnails generated by Picasa

8. Reload your key in Builder and check for any missing thumbnails. If you find a missing thumbnail, check the file path in the media tab, and then search your ‘Thumbs’ folder for the same filename. Often I find that I need to insert a ‘_1′ before the ‘_TN’ because I’ve accidentally imported multiple copies of the same full size image into Builder, which then automatically appends the ‘_1′ to full size image in the ‘Images’ folder.

Well, the jpeg’s published here do not quite do justice to the difference in quality, but rest assured that replacing the original thumbnails with your own will dramatically improve the aesthetic and quality of your key’s media.

Trampy Linepithema

As I am developing the new update to my Lucid key to invasive ants, I realized it might be a good idea to post some of the illustrations I’m working on as little vignettes of the larger project. When I’m not quite sure about an ant ID, I find myself using the ‘comparison chart’ tab on PIAkey more often than the actual Lucid key. It’s like a quick-access cheat sheet for when you already know the genus and just need a little refresher for distinguishing among a few species.

This chart shows how to tell the very commonly encountered Argentine ant (Linepithema humile) from its less well known, but occasionally intercepted congener L. iniquum. The characters are adapted from Alex Wild’s treatise of the genus (Wild, 2007).

L. humileL. iniquum
Profile
Erect hairs on cephalic dorsum (above eye level) + gastral tergites 1 & 2

No


Yes

Dense pubescence covering mesopleura

Yes


No

number of convexities on profile of mesosomal dorsum

Two


Yes

propodeal shape

Angular


Globular

propodeal spiracle bordering posterior margin of propodeal profile

Yes


No

 

Introduced Ants and POE Ants now on Antweb

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

 

Making regional checklists for ants

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!

Vollenhovia emeryi in Washington DC

Vollenhovia emeryi nesting in dead log. Notice how these cylindrical short-limbed ants are so adept at weaving among their shallow nest tunnels. This colony had hundreds of workers and many queens. Units in mm. Collection data: USA Washington DC, C&O Canal, 16.vi.2011, 38.902739°, 77.057704°, 3m, E.M. Sarnat.

Vollenhovia emeryi is one of the more recent ants to have established in North America. The first record of this Japanese transplant came from Stefan Cover of Harvard’s Museum of Comparative Zoology. Cover discovered the species in 1986 while sampling for ants in Washington, DC. Vollenhovia species tend to be generalists and the native range of the genus is restricted to Asia, northeastern Australia, and the Pacific Islands, and are not generally thought of as successful tramp ants.

How then did this demure little species come to arrive in the capital city of the United States? The answer might be linked to a tale often told of that city’s namesake, George Washington. Legend has it that when George Washington was a six-year-old lad he chopped down a cherry tree. When confronted by his father, young George replied, “I cannot tell a lie, father, you know I cannot tell a lie! I did cut it with my little hatchet.”

Cherry trees may, in fact, have been how Vollenhovia emeryi became introduced into the United States. Japan has gifted the cities of Washington DC and Philadelphia thousands of cherry trees during the past century, many of which were planted in localities where V. emeryi is known to occur. Dan Kjar raises the possibility that colonies of these little ants stowed away in the rootballs of the cherry trees, and have slowly been expanding their range along the riparian habitats of the District of Colombia, Virginia, Maryland, and Pennsylvania ever since.

During my recent research trip to the Smithsonian’s entomology collection I took a brief expedition in search of a Vollenhovia emeryi colony to collect and film. Dan Kjar suggested I take a look around the C & O Canal area near Georgetown. By the time I exited the Metro station it was pouring down rain, so I concentrated my search to a relatively dry area under a freeway overpass. Searching for invasive ants often leads one to rather unsavory habitats, such as dumps, ports, and urban filth. After turning over all variety of garbage and refuse in search of a colony, I finally found one nesting under a dry branch.


Eli Sarnat collecting live colony of Vollenhovia emeryi from beneath an overpass in Washington DC. Notice the graffiti and garbage strewn across the site. Invasive ant research is not always the stuff of romance.

I took some video of the ants as they scurried about in their signature slinky style. Then I searched about the garbage some more until I found a suitable empty Gatorade bottle and a mismatched cap into which I collected the live colony. The colony had many queens, so I split it in two. One colony is now residing happily in Ted Schultz’s ant lab at the Smithsonian, and the other is at the Suarez Lab at UIUC. Alex Wild took some excellent photographs of these ants from the Suarez lab colony that are available on his Myrmecos website.

Following the ants

I was born and raised in the San Francisco Bay Area’s coast range where I spent my earliest years on hand and knee amongst oak woodlands, peering under stones and logs for creatures more fantastical than any children’s book could illustrate. When it came time to choose a project for my high school thesis, I argued that the many hallmarks of human civilization – notably the domestication of crops and animals, division of labor, slavery, warfare and altruism – were achieved by ant civilization while our own ancestors were eking out an obscure existence in the African treetops.

This fascination with ants, which remains the focus of current research, was fostered by a predisposition for staring at the ground, a family vacation to the jungles of Central America, and an early reading of E.O. Wilson and Bert Hölldobler’s “The Ants” and “Journey to the Ants.” My interest in these small creatures led to a job at the Essig Museum of Entomology as an undergraduate at University of California Berkeley, and to an impressionable semester abroad in Costa Rica with the Organization for Tropical Studies. After a year working on an organic farm in Mendocino, and a summer stint in the Smithsonian’s insect collection, I joined Phil Ward’s ant systematics lab to pursue a doctoral degree in entomology from UC Davis.

Although my dissertation research would eventually settle on the systematics, biogeography, and conservation of the Fijian ant fauna, my initial plan was to use phylogenetic comparative methods to determine what life-history traits allow an inordinate number of Tetramorium ants to break free of their native ranges and spread across the globe as successful tramp species. My first pursuit of these globe-trotting invasives and their endemic sister-species took me to the Pacific islands of New Caledonia, Fiji, and New Guinea. The challenges of conducting research in New Guinea colluded with the persuasive arguments of Dr. David Olson – a fellow ant enthusiast who was directing a conservation organization in Fiji, to pivot my thesis work towards the more achievable goal of revising the ant fauna of the Fijian archipelago – a feat last attempted nearly a century ago. Invasive ants found a way back into my research program when, during my fieldwork in Fiji, I became involved with an international coalition seeking to protect Pacific Island nations against the environmental, agricultural, and human health impacts being wrought by invasive ant incursions. In this capacity, and with funding assistance from the USDA and Biosecurity New Zealand, I developed the web-based resource PIAkey: an identification guide to invasive ants of the Pacific Islands.

In addition to continuing my work on the systematics, biogeography, and conservation of Pacific ants, I am now working as a postdoc with Dr. Andrew Suarez (University of Illinois at Urbana-Champaign) on expanding the geographic and taxonomic scope of PIAkey to include the introduced ants of North America. Both of these projects will be significantly enhanced by the opportunities afforded by EOL.