Taking morphometric measurements using specimen photographs

Taking morphometric measurements using specimen photographs from Eli Sarnat on Vimeo.

In this tutorial I use Adobe Photoshop cs6 Extended Version and a specimen photograph of an ant head to take morphometric measurements. I set a custom measurement scale in Photoshop calibrated to the scale bar embedded in the photograph, then record the measurement taken by using the Ruler Tool. Remember, the measurement will only be as accurate as the scale bar embedded in the photograph. So if the scale bar was not calibrated correctly at the time the photograph was taken, any derivative measurements will also be inaccurate.

Scratchpads tutorial: dealing with nomenclatural changes (new combinations)

Scratchpads tutorial: dealing with nomenclatural changes (new combinations) from Eli Sarnat on Vimeo.

In this tutorial I show one way for updating terms in the biological classification to reflect nomenclatural changes. The situation I deal with here is for a species included in the Antkey.org site which has recently been transferred to a different genus. This nomenclatural act is known in taxonomic jargon as a ‘new combination’.

In this case, the species Monomorium destructor has been transferred to the genus Trichomyrmex. I change the Unit 1 name (genus) of the term Monomorium destructor to Trichomyrmex. Then I add a new taxon term ‘Monomorium destructor‘ as a child to Trichomyrmex destructor and classify it an invalid name associated with Monomorium destructor. This way all the content previously associated with Monomorium destructor will now be associated with Trichomyrmex destructor, and anytime someone searches for the now invalid name Monomorium destructor the user will be directed to the valid combination Trichomyrmex destructor.

Pheidole flavens-complex introduced to the southwestern Pacific

Here’s the story behind the new Bioinvasions Records article on that just came out. Christian Rabeling and Ed Wilson went to Vanuatu a few years back in 2011 because it was one of the few Melanesian islands that Wilson had never collected from. They collected all the ants they could find in a general survey and kindly sent their Pheidole to the Economo lab at OIST so that I could match them against our other Pacific Pheidole collections and Evan could include them in our phylogenetic analysis. Christian and Ev caught some great Pheidole from the island, including this beautifully spinescent endemic from the sexspinosa complex shown below (CASENT0282641).

An elegant Vanuatu endemic ant species (Pheidole epem198, CASENT0282641) from the Pheidole sexspinosa complex

But one species came out in an unexpected branch on the phylogeny. Instead of coming out with the Old World clade with all the other native Melanesian ants, this one species was reliably nested within the New World clade. It’s closest relatives on the tree were two species that had been included in Corrie Moreau’s 2008 Pheidole phylogeny and id’d as P. moerens and P. flavens–both of which are considered to be invasive.

Major worker of a species from the Pheidole flavens-complex from Espiritu Santo, Vanuatu; collection code CR111110-15, specimen code CASENT0248836. (1) Lateral view, (2) fullface view, (3) dorsal view, (4) hypostomal bridge.

Major worker of a species from the Pheidole flavens-complex from Espiritu Santo, Vanuatu; collection code CR111110-15, specimen code CASENT0248836. (1) Lateral view, (2) fullface view, (3) dorsal view, (4) hypostomal bridge.


Minor worker of a species from the Pheidole flavens-complex from Espiritu Santo, Vanuatu; collection code CR111110-15, specimen code CASENT0248835. (5) Lateral view, (6) fullface view, (7) dorsal view

We wanted to let other researchers know about the spread of this trampy species into the Pacific, so we wrote up a rapid communication article for Bioinvasions Records. The idea was to get the basic information about the new discovery out as quickly as possible, so others in the region could be on the lookout for additional incursions.

The most frustrating part of this study was trying to get a name on the species. Unfortunately, the taxonomy of P. flavens and its close relatives like P. moerens and P. exigua is a super sticky mess, rife with infra-specific names, lost holotypes, and inaccurate determinations. It seems like these taxonomic morasses plague trampy species (like P. flavens and friends) much more often than your average ant species.

Why is it that trampy species so often belong to species-complexes? What are species-complexes, anyways? I suppose I’d define them as geographically distinct populations that are somewhere on the continuum of streching from a recently coalesced species radiation on one end to a network of geographically isolated groups with some low amount of gene flow still persisting. For the taxonomist or even the molecular systematist there is no clear way to know whether to call these things five geographically isolated species or one widespread species.

Whatever the population on Vanuatu turns out to be, it doesn’t match the neotype of P. flavens or the syntypes of P. moerens, so for now we have to settle for calling it a member of the flavens-complex and hope that someone tries to untangle this taxonomic knot in the near future.

EM Sarnat, C Rabeling, EP Economo & EO Wilson (2014) First record of a species from the New World Pheidole flavens-complex (Hymenoptera: Formicidae) introduced to the southwestern Pacific. Bioinvasions Records 3: 301-307. | PDF


How to identify Solenopsis invicta using Antkey

In this tutorial I demonstrate a few different approaches to identifying Solenopsis invicta, also known as the Red Imported Fire Ant (RIFA), using Antkey. The key can be accessed at antkey.org/content/key.

How to identify Solenopsis invicta using Antkey from Eli Sarnat on Vimeo.

How to use Antkey’s Lucid3 interactive key

In this tutorial I demonstrate how to make the most effective use of Antkey’s interactive Lucid3 key for identifying invasive and introduced ants. There are tips on how to use features like the ‘best’ and ‘next best’ buttons, what the different panels mean, how to make effective use of thumbnail and pop-up images and how to adjust the text size.

How to use Lucid Key for identifying ants from Eli Sarnat on Vimeo.


2014 July 21-31 Borneo: Maliau Basin
Organized by the California Academy of Sciences
Application link
Pay Course fees before July 1 (Pay online)

Ant Course 2014 - Borneo


July 20 participants arrive in Kota Kinabalu
July 21 Depart Kota Kinabalu : 6-8  hour bus ride to Maliau Basin
July 31 Depart Maliau Basin to Kota Kinabalu

COURSE OBJECTIVES. – ANT COURSE is designed for systematists, ecologists, behaviorists, conservation biologists, and other biologists whose research requires a greater understanding of ant taxonomy and field techniques.  In 2014, emphasis is on the identification of the ant genera and species occurring in the Asian tropics.  Lectures will include background information on the ecology, life histories and evolution of ants.  Field trips emphasize collecting and sampling techniques, and associated lab work focuses specimen preparation, sorting and labeling.  Information on equipment, literature, and myrmecological contacts are also presented.

COURSE SIGNIFICANCE. – Ant Course is a unique opportunity to acquire training that is unavailable elsewhere.  This course will provide students with 1) the confidence and skills to identify Southeast Asian tropical ant genera; 2) an understanding of modern specimen processing and curation techniques; 3) an appreciation for the biological diversity of ants; and 4) experience keying to the species level.

SPONSORED BY. – California Academy of Sciences and The Arthur Lawrence Green Memorial Fund, Museum of Comparative Zoology, Harvard University

LOCATION. – ANT COURSE will be based at the Maliau Basin Studies Centre in in Sabah, Malaysia.  The Centre is part of the Maliau Basin Conservation Area that includes 12 forest types, comprising mainly lower montane forest dominated by Agathis trees, montane heath forest and lowland, and hill diperocarp forest.

PARTICIPANT ACCEPTANCE CRITERIA. – ANT COURSE is open to all interested individuals, including students, professors and motivated amateurs (citizen scientists). Priority will be given to those students for whom the course will have a significant impact on their research with ants. We aim to include students with a diverse interest in biology, including ant systematics, ecology, behavioral biology, genetics, and conservation.  An entomological background is not required.  The high instructor to student ratio will allow students to receive individual attention. ANT COURSE is presented in English and limited to 30 participants

COSTS. – Course fees for the 10-day COURSE are $975 for current students (undergraduate and graduate) and $1275 for non-students (postdocs and professionals).  Transportation costs between home and Koto Kinabalu, and hotel fees in Kota Kinabalu are to be borne by all participants. Pay course fees by July 1 at: https://www.calacademy.org/tickets/ant_course/.

FELLOWSHIPS. – Those interested in attending the course should seek all possible avenues to secure funding on their own for the course.  Each year we strive to raise funds to support a few students by offering discounted tuition fees. You should only apply for the Ant Course fellowship if you cannot find other support and it is essential for your participation in the course. Please notify the course if your funding request status changes before the application due date.

COURSE APPLICATION. – Application and course information at http://www.antweb.org.  The first step is to fill out a form at: https://docs.google.com/forms/d/1Z5Fu8DHxqW5EGFkiLbxi4mHWpnc2Tn0vzmN5ctvXj1g/viewform

Note this form requires a short statement of your research interests and future plans and a statement of your reasons for wishing to participate in the course. Also requires is one letter of reference from a professor or colleague familiar with your work to be submitted by the referee at: https://docs.google.com/forms/d/152l4Y8qbyhB-7c4Tq9bw8gr5om3iGGIs335XMKXuI90/viewform

You will be notified of your acceptance to the Course around APRIL 15-20.

ANT COURSE is limited to 30 participants.  Selection of participants will be carried out by committee, based on your reasons for wishing to take the course at this time.  Priority will be given to those students for whom the course will have a significant impact on their research with ants.  Because the Course is offered yearly, and because many well-qualified candidates are not accepted because of limited capacity, we urge applicants not selected for this session to apply again the following year.


Brian Fisher (Coordinator), Leeanne Alsonso, Himender Bharti, Katsuyuki Eguchi , Flavia Esteves, Brian Fisher, Benoit Guénard , Roberto Keller, Laurent Keller, Jack Longino, Corrie Moreau, Chrstian Peeters, Simon Robson, Eli Sarnat, Steve Shattuck, Andy Suarez, Phil Ward

Malaysian Collaborators

Dr. Charles Varaippan, Director & Dr. Bakhtiar Yahya, Institute for Tropical Biology & Conservation, University of Malaysia, Sabah; Dr. Arthur Y. C. Chung, Forest Research Centre, Sabah Forestry Department

New line drawings for undescribed Fijian Pristomyrmex

Here are a few line drawings I am working on for the description of an undescribed species of Fijian Pristomyrmex. In the Ants of Fiji monograph, this species is listed as Pristomyrmex sp. FJ02.

Full face view of Pristomyrmex sp. FJ02. Line drawings can allow for better representation of important taxonomic features compared to specimen photographs. For example, the mandibular tooth structure is essential for Pristomyrmex species identification. The mandibular teeth on the specimen photograph used as a template for this illustration were obscured and difficult to see. The line drawing shows them quite clearly.

Rendering the characteristic foveae (circular depressions) of Pristomyrmex was a bit challenging, and I am sure my method could use some improvement. I began by using the Ellipse Tool to get the basic shapes, and then rotated them according to the template specimen. Next I used the eraser tool to break the foveae that appeared somewhat shallow. I then selected all the ‘broken’ foveae and applied a stroke profile that tapers strongly on both ends. For the ‘unbroken’ foveae I selected each individually and used the Width Tool to constrict the ellipses at a single point.

Profile of Pristomyrmex sp. FJ02. Of the over 50 known species of Pristomyrmex, this is only the second that lacks propodeal spines. The other, P. inermis, occurs in New Guinea.

I also used a new technique for the hairs on this illustration. I decided to use the Outline Stroke function for all of the hairs, and selected a white outline stroke. This allows for a white break where hairs overlap the ant profile and other strokes.

The Ants of Fiji – Print and PDF out now

Figure 1. Photographs of Fijian ants. A) Acropyga sp. FJ02 (endemic) carrying mealybug. B) Hypoponera eutrepta (endemic) carrying larva. C) Tetramorium lanuginosum (introduced). D) Camponotus dentatus (endemic). E) Odontomachus simillimus (Pacific native). F) Camponotus polynesicus (endemic).

The print and full color, open-access pdf versions of the Ants of Fiji (Sarnat & Economo, 2012) are now available. The 400-page monograph reviews the entire known Fijian ant fauna, and includes the results of a recently completed archipelago-wide biodiversity inventory. A total of 187 ant species representing 43 genera are recognized here with an illustrated key to genera, synopses of each species, keys to species of all genera, and a species list. The work is heavily illustrated with specimen images, distribution maps, and habitat elevation charts.


Sarnat, E.M. & Economo, E.P. (2012) Ants of Fiji. University of California Publications in Entomology, 132, 1-398. [pdf]


Expert from the introduction section

Biologists have long sought to document and understand the unique evolution and ecology of island biotas. Oceanic archipelagos are often adorned with spectacular evolutionary radiations and unique ecosystems. These distinctive faunas, however, are highly vulnerable to human activities, climate change, and introduction of exotic species. Among island ant faunas, perhaps nowhere are these themes so prominently on display as in the Fijian archipelago.

The Fijian terrestrial biota was assembled during approximately 20 million years of over-water colonization, in situ evolution and speciation, and more recently through the arrival of species as stowaways on canoes, galleys and battleships (Figure 1). Today’s Fijian ant fauna is characterized by extreme geographic isolation from source areas, differentiation and pattern formation among islands, and contemporary invasions. The list of species occurring in Fiji, which continues to grow, includes both widespread dominant species and rare taxonomic oddities.

The motivation of this study is to provide an update to W. M. Mann’s (1921) monograph The Ants of the Fiji Islands, published 89 years ago. At the time, Mann lamented that the insect fauna of Fiji had been almost entirely neglected, and the limited knowledge accrued in the years since his publication is even more lamentable. With the recent collection of a large number of ant specimens in recent years, and a surge of interest in biodiversity research and conservation in Fiji, the opportunity has arrived to synthesize the taxonomy of the Fijian ant fauna for new generations of biologists. Our goal is to provide a resource that will allow a scientist to collect an ant specimen anywhere in Fiji and connect it to information on its taxonomy, geographic distribution, habitat distribution and natural history. With 187 species distributed over seven islands of moderate size, and hundreds of smaller islands, the system represents a diverse yet tractable fauna that can be useful for testing hypotheses in evolutionary biology, island biogeography, community ecology, invasion biology and other disciplines.

It would be remiss to conclude this introduction without a note of recognition and thanks to the people of Fiji. Mann (1921) wrote in the introduction of his own treatise on Fijian ants, “I shall remember the native Fijians…as the kindliest, most hospitable folk I have known.” Eighty-nine years later, we both share those sentiments and add our admiration for the Fijians’ thoughtful stewardship of their native lands. We hope this small study will be useful for scientific discovery and conservation of Fiji’s fascinating natural heritage in the generations to come.

Antkey release

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.

Revisiting the ants of Melanesia and the taxon cycle: historical and human-mediated invasions of a tropical archipelago

Evan Economo and I have a new paper out on the Taxon Cycle. The taxon cycle is a hypothesis advanced by E.O. Wilson that predicts a process in which successive waves of widespread disturbance-tolerant species from continental systems colonize marginal habitat on islands, expand into less disturbed forest interiors, radiate into isolated high-elevation endemics, and then either colonize a new island island or go extinct. Evan Economo and I found strong support for the hypothesis by analyzing the distributions of 183 Fijian ant species belonging to four endemism classes across disturbance and elevation gradients. Evan, Lacey Knowles and I recently received an NSF grant to build upon this work and the Pheidole research I published with Corrie Moreau.

Economo & Sarnat, 2012

Economo, E.P. & Sarnat, E.M. (2012) Revisiting the ants of Melanesia and the taxon cycle: historical and human-mediated invasions of a tropical archipelago. American Naturalist, 180, E1-E16. [pdf]