In the South Pacific for some Ichthyology

In late September my PhD student Bill Ludt and I traveled to the beautiful island of Tahiti to attend the 10^th Indo Pacific Fish Conference. This meeting takes place every four years and I have been anticipating this trip since Bill and I went to the last meeting in Okinawa in 2013. I also knew that I couldn’t go all this way not to collect fishes. As with other conferences in remote locales, and most field trips, it took a while to get permits; we were lucky to get them a day before our planned travel began (even though Bill had been working on them for more than a year).

Also joining us for part of the trip was LSU Biology professor Brant Faircloth. Brant and I submitted a proposal to run a symposium on fish systematics focusing on ultraconserved elements. Our session ultimately became part of a half day symposium called ‘Genes to Genomes: Forging ahead in the study of marine evolution” which we were happy to help organize. (Special thanks to Dr. Michelle Gaither who was the lead organizer and did all the heavy lifting.)

Soon after arriving we knew we were in paradise - an expensive French paradise. My French is passable, but most of the locals we met also spoke English as well their local Polynesian dialects. I always wanted to come to Tahiti, not so much for its fishes or the beautiful teal-colored water, but because I loved the history of Captains Cook and Bligh in this region; and because of films like Marlon Brando’s Mutiny on the Bounty.

We went to the central fish market in Papeete around 5am the first few mornings to see what we could get. We made nice collections of local wrasses, goatfish, and unicornfish among other colorful, if odd-looking, species. At the local grocery store we did come across a large specimen of an Opah, or “Moonfish” which gained some notoriety recently as being “warm blooded” – although some ichthyologists remain unconvinced. Sadly the specimen was too big to collect, and already had it’s gills removed.

Opah at market (left), butterflyfish (top), and unicornfish.

We also traveled to the island of Moorea, which is about a 45min ferry ride from Tahiti. This island is home to, among other things, the Gump Research Station run by UC Berkeley. The Gump helped us get our permits but we were unfortunately unable to collect on Moorea. We had to settle for a lovely day snorkeling in crystal clear water surrounded by lush green mountains.

The conference started a few days after our arrival, and it had about 500 attendees from around the world. Bill, Brant and I all spoke in the first session of the first day after the plenaries. The Indo Pacific Fish Conference is one of my favorites because I get to see many of the European, Asian and African colleagues I often don’t see at conferences in North or South America. Bill and I started several important collaborations that hopefully will make for some fruitful publications over the next few months and years.

Bill, Brant and I in Cook Bay, Moorea; Bill on stage presenting his talk.

Although we didn’t hit the markets again during the meeting, I did get to collect some introduced guppies. The extent of my freshwater fieldwork was putting a bag down into a sewer off the main road in Tahiti and letting it fill with water then pulling the bag out of the water to find that 50 individual guppies had swam into the bag. Many of these specimens were mailed off to a colleague studying the introduction of guppies around the world. He was very happy to get individuals from this distant and isolated population.

            I’ll spare you more details about the fish conference and swimming with humpbacks (as I did) and tiger sharks (as Bill did) and such, but rest assured this was no vacation (although it obviously wasn’t all work either). The conference was a great opportunity to talk about our work, including one collaboration that recently yielded the cover of Systematic Biology (Chakrabarty & Faircloth et al. 2017; left). That publication created some great opportunities to work with other scientists interested in using genomic fragments like ultraconserved elements in their phylogenetic studies of fishes.

Samaki! Samaki! Collecting Fishes in the Mangroves of Tanzania

I traveled to Tanzania this August to collect fishes for the 
Museum of Natural Science, and to help

A beautiful seine pull in low tide.

out folks from the LSU Department of Oceanography and Coastal Sciences (Drs. Mike Polito, Steve Midway and Victor Rivera-Monroy). Having spent the last year as a bureaucrat for the federal government (working as a Program Director for the National Science Foundation) I was eager for some adventure. A little over a year ago Dr. Michael Polito, Assistant Professor in Oceanography, mentioned he would be going to Tanzania and I asked, casually - but sincerely, if I could join him. It really wasn’t much more than that spontaneous self-invite, and the promise to help with vouchering and identifying fishes, that brought me to Tanzania.
       I must admit to being a bit nervous before the trip, there were a lot more unknowns than I am used to. It has been a long time since I went on a collecting trip where I wasn’t the lead, and where I was without other members of my own lab. I wanted to be sure not to get in the way of the research being conducting by Mike and his colleagues. I had also never collected in mainland Africa before; the closest I had ever been was Madagascar (which although close is very different). Perhaps the strangest thing about me going to this trip was the location within Tanzania. Most people interested in the fishes of the region would be headed straight to the famous East African Great Lakes – 85% of the fish landings from Tanzania are still from Lake Victoria. Ichthyologists interested in the marine fauna are more likely to go to Zanzibar (an island off the coast) – but since the Oceanography team was interested in studying mangroves, I would be studying the fishes of the mangroves. Knowing how few ichthyologists had ever collected in the area gave me high hopes that we might have the opportunity to discover new records and perhaps even new species.

The striking difference between low tide and high.

Team Samaki!

Beautiful shrimpfish collected by Mike Polito.

Although I am now a reasonably seasoned ichthyologist, I still don’t know all 40,000 species of fishes; and I knew next to nothing about the ichthyofauna of the region before the trip. Luckily, unlike me, the Oceanography folks like to be prepared. One of Mike’s students, Mario Hernandez, went to Tanzania last year and created a little summary slideshow of the fishes they encountered. Unfortunately for me, few of the fishes were vouchered from the previous expedition, which is one of the reasons I was going this year. Mario’s pictures had me salivating about what we might bring back to the LSUMNS Fish Collection. Unfortunately, the entire trip was nearly upended before we even got started.
 The original plan was to collect in a region called Rufiji – an area with high tides in a very remote area where we would be camping with little access to infrastructure. Unfortunately, some politically motivated problems arose: people were protesting police corruption resulting in some folks being killed. Even if we would likely be safe as foreigners, it would be impossible to get the boats and local help that we needed. The Oceanography team decided instead that they would return to an area they sampled previously: Pangani.
Pangani (specifically Kjongo Bay near the town of Kipumbwe) is a region across from the island of Zanzibar, and about seven hours north by car from the capital Dar es Salaam. Despite being remote as well, this area has quite a bit more infrastructure and creature comforts than Rufiji. In the end we were safe and had very agreeable accommodations, included three square meals a day. More importantly our hosts allowed us to spread dead fish specimens all over the place while we all took samples of otoliths, isotopes, DNA samples, and cores of mangrove mud.
We were traveling to Tanzania to allow the Oceanography team to better understand how the mangroves functioned in the larger ecosystem. Besides Mike and Mario there was Steve Midway and his student Matt Roberts filling out Team Samaki (‘samaki’ is Swahili for fish). There was also Team Mangrove led by Victor Rivera-Monroy and his lab who were taking core samples and other data to better understand the role of mangroves in general. Team Mangrove spent many hours a day out deep in the mangrove forest being tortured by insects and being cut by razor clams and other protruding organic weaponry. When they returned they spent many hours that could have been used for drinking cocktails to clean their equipment and organize their samples.
          The mangroves in Kjongo Bay have a tide that rises and sinks about three meters twice a day. Our boats could only go out while the tides were high enough to allow the boats in and out of the mangroves. Unfortunately, the best collecting time was near the lowest points of the tide when the boats would be stranded. There was always a race against the clock, and we were nearly always stuck somehow – either stuck waiting for the tide (to go up or down), or literally stuck in the mud. Our boats were often stranded when the tide went out. Sometimes we would chant, ‘samaki, samaki’ while rocking our vessel from side to side, trying to steer it into deeper waters.
At one site we suddenly hit a sand bank and the boat was stranded in a few inches of water, while we figured out what to do next I got stung in the temple by a bee, and then stung again on the face, as I swatting furiously Mario yelled out “bees!” and then another person yelled out while pushing us,  “jump into the water!”  We all dove into the shallow water but the bees kept stinging the back of our heads and necks – we swam to the other side of the riverbank to escape. When we looked back at the boat we could see hundreds of bees swarming it. We were each stung about a half dozen times. As we licked our wounds we decided to walk downriver to join another team while we waited for the tide to rise, and to free our boat to drift down river away from the bees.
      As luck would have it that other ‘bee-free site’ was remarkably diverse. We were seining different spots getting lots of different species. These included young grouper, snappers, but also species of a group I know well – the Leiognathidae (or ponyfishes). I had noticed that Mario had seen some of these ponyfishes in markets the previous year but I was still surprised to see ponyfishes in nearly every seine haul we made. I was surprised because adult ponyfishes can be collected nearly anywhere throughout the enormous Indian and Pacific oceans – but adults are bioluminescent and typically found at depths several hundred meters deep – what on Earth are juveniles doing in mangroves alongside mosquitofish and gobies? Part of what I hypothesize is happening is that ponyfishes spawn in shallow waters near the mangroves. Coastal Tanzania is known for its bioluminescencent bays; the light is caused by high concentrations of small glowing organisms. Perhaps ponyfishes ‘gets their glow’ from a bacterium that may be in high concentrations here? Only time, and a $500,000 grant from the National Science Foundation, will tell.
       Some of my days were spent sorting the fishes others were collecting. My job those days were to help with IDs for the project goals of the Oceanography team. It was sometimes hard not to think of the fish collections I curate whenever we got something new. It caused me physical pain and mental anguish to see some rare specimens being torn up for isotope analysis rather than being preserved as pristine specimen for our museum. I had to remember that these specimens may help the Oceanography team better understand how to save these mangroves – and who would want to get in the way of that? In the end I still brought back nearly 500 samples from about 50 species, most new to the collection, and perhaps new to any collections – stay tuned for more on that.

              It was certainly an interesting time to be in Tanzania – a new leader is pushing out 

foreign  interests, trying to cut down on corruption (which also is cutting into the shadow 

economy that benefits many impoverished people). Tourism to Tanzania has also gone down 

dramatically because of increased violence. Despite our efforts to stay safe by choosing Pangani 

over Rafiji we sometimes found ourselves just at the periphery of deadly violence. We began and 

ended our trip in the capital city of Dar es Salaam. And although Dar has traditionally been rather 

safe we heard of several reports of gun violence. Near the end of our trip, a noted elephant 

conservation biologist Wayne Lotter was murdered just a few blocks from a place we were 

visiting. We learned of how he was killed (followed in his taxi from the airport, shot while he sat 

beside his wife) from reading the cover of the New York Times the next day, and not from the local

 news. The news shocked our colleague Lindsey West who runs a local NGO called Seasense. 

Lindsey, who is British, has lived in Tanzania for many years and has been dealing with the 

increase in violence daily. She is extremely efficient and she masterfully arranged for local help 

for us from her many Tanzanian contacts and colleagues. Less shocking to Lindsey was our

report that a corpse had washed up on the beach in Kijongo with its hands and feet cut off 

and a plastic bag around the head. ‘Oh that’s just witchcraft stuff’ nothing we needed to worry 

about. We learned to listen carefully to Lindsey, if she said not to worry, we did not. 

She was ‘dada mkubwa’ big sister, after all.

Perplexing ponies.

               Over the 10 days in Tanzania I was able to see a great many things and learn a few choice Swahili words from the locals that were helping us out. The locals endowed us with some great nicknames too like, “Mzungu mfupi” (‘short white guy’) for Mike, and “Sharobaro” (‘pretty boy’) for Steve. Since Mario, was already ‘the Indian’ (‘Mhindi’), I didn’t really get a name that stuck. I wish I had learned more Swahili but I am thankful to our museum Business Manager, Tammie Jackson, who taught me a few key phrases before I left. If I had learned more from her I might have avoided some mix-ups while trying to purchase everything from full strength formalin (you want 37% of 37%?), to rum and coke (‘coke and lime?’) to ice coffee with milk (for which we were served ice and milk and no coffee). Despite the language barriers it was an amazing time. I thank my Oceanography colleagues Mike, Steve, Victor, (and their students) for letting me tag along on their trip – Asante sana. 

Journey to the End of Central America – An Ichthyological Exploration of the Darién Gap

Or like stout Cortez when with eagle eyes

He star'd at the Pacific—and all his men

Look'd at each other with a wild surmise—

Silent, upon a peak in Darién. 

- from “On First Looking into Chapman's Homer” by John Keats

At the entrance of the Darién National Park

            From May 12-24^th postdoctoral fellow Dr. Fernando Alda, graduate student A.J. Turner and I journeyed south to Panama to collect fishes. Specifically, we were targeting the fishes from the Darién Gap – a region I have hoped to visit since I was a graduate student over 10 years ago doing my PhD on the biogeography of Central American fishes.

            The Darién is one of the most forested areas in Central America, with the majority of forested area in the Darién National Park in the so-called “Darién Gap” – named so because it is the gap in the Pan-American Highway between the North and South American continents. The Darién Gap encompasses the borders between Colombia and Panama and is frequented by drug smugglers and illegal migrants – for that reason it is heavily protected by the armed military and it is difficult to get permits or even help to collect in the area. Fortunately Fernando is patient, hardworking and resourceful. With some difficulty he organized an entire trip for us working with the local Emberá people who are endemic to the region and who have been on this land for hundreds, if not thousands, of years. Fernando also handled all the permits with STRI (the Smithsonian Tropical Research Institute) and the Panamanian government. He did an amazing job arranging this trip. My lab has previously attempted to get into the Darién Gap and failed.

            Before we got into the Darién, we set up at STRI headquarters located in Panama City where we got our official Smithsonian badges and credentials. Our STRI-IDs (or “STRIdees” as we took to calling them) worked wonders around Panama. We were able to get big discounts on museums and entrance into the Panama Canal because of those IDs. We had some time to kill before we got out into the field as we waited for all our permits, so we did some educational sight-seeing. The Miraflores Locks of the Panama Canal, and the newly opened Biomuseo were highlights. I read a book about the making of the canal, “I Took Panama: The Story of Philippe Bunau-Varilla” while we were in Panama and I recommend others to learn about the insane political events surrounding the creation of this engineering marvel – which also led to the creation of the country itself. A new set of expanded locks, which will make the canal almost twice its current size, was also visible in the distance.

            In those first few days we also visited the local fish market in Panama City – the Mercado de Marisco. We were able to get nearly 40 species of marine fishes from this market; these included several species of snook, parrotfishes and croakers. Unfortunately, we saw hundreds of shark bodies with their heads and fins cut off. They were all juveniles and according to A.J. he thought they were all taken from some nursery grounds – it was a sad sight. By sheer coincidence we met up with researchers from Conservation International working on the fisheries of this region while at a restaurant; they said they are working on this shark issue: I hope they get to it quickly.

We ran into lots of non-Panamanians in Panama City, which is unlike any other Central American city; it has a skyline that makes it look more like Dubai, and with a port and mangroves near it, it reminded me of it too. Many people spoke English, and we noted the strong American and European presence almost everywhere.

Although the city was interesting we wanted to get in the water. As we drove the five hours East to the Darién (there isn’t much of a North and South in Panama) we noted how different the rest of Panama is from Panama City. There are many rural communities strung together and lots of farmland. However, over 25% of Panama is protected forest. There are also many areas belonging to autonomous indigenous communities living independent of most Panamanian authority.

Fernando talking to the Embera about our fish.

We entered the town of Yaviza in the Darién province on the 17^th of May and spent the day heading up and sampling along the Río Chico in our long wooden boat (called a “piragua”). At our first field site we unrolled our brand new cast nets and I hurriedly made my first toss – I wanted to catch the first fish – and I got a nice little cichlid. Cichlids are my favorite group of fishes and the focus of much of my research. There have been some trips to Central American where we don’t get cichlids for a few days, and here was one – right off the bat. After that I took to doing my regular job, taking notes, GPS coordinates etc. We collected plenty at this first site on the Chico and it was a good omen for the rest of the trip. We learned pretty quickly, that as usual, despite being professional ichthyologists, the locals are always the best fishermen. Throughout the trip we really enjoyed working with and interacting with the local people. I always love reading about historical explorers interacting with locals and how they treated each other, there were the kind ones like James Cook (kind to most native people, killed by natives on Hawaii), and awful ones like Hernán Cortés (killed lots of native people, died peacefully back in Spain of old age). Side note – “Cortez” as mentioned by John Keats in the poem above, should actually be “Balboa.” Vasco Núñez de Balboa was the one to establish the Darién, and the first European to see the Pacific from the Americas.

We spent the next few days penetrating the Darién National Park. This required us (and sometimes a small horse) to carry our gear and food through the forest trails. This was fun, but exhausting given the heat and mosquitoes. We hiked to most of our sites when we couldn’t boat. The canopy was thick making the forest shaded all manner of green from top to bottom except for the forest floor, which was matted down with damp brown leaves. It was very beautiful. We walked with our guides like leaf-cutter ants in formation, one behind the other, carrying our packs like so many bits of foliage. Living in Baton Rouge you tend to forget about topology. The ups and downs of the hike are something we aren’t accustomed to in this flat town of ours; the humidity and following someone carrying a machete might be a bit more familiar.

This was A.J. Turner’s first field trip, and I had to remind myself of that sometimes. It couldn’t have been easy for him to start his career as a tropical biologists hiking through the Darién Gap, but he did well, and I have no concerns that he will do many of these trips well into the future.

There were some scary moments in the field. At one site near a banana plantation I kept hearing the sounds of tree branches falling. We were sampling in very muddy water so I was barefoot in the mud when one of our guides whistled to me to stop, I saw two men come out of the jungle holding machetes. One walked towards me without looking up and then, thankfully, walked past to cut down some plantains. When they talked to our guides – in the Emberá language, not Spanish – they seemed to be giving a warning. Our guides shuffled us out pretty quickly, which was fine with us. The Emberá are friendly but there is still a lingering wariness of outsiders.

We stayed part of our time in the village of Pijibasal and we sampled with the locals in the Río Perresénico and even had an amazingly fun soccer match with dozens of local kids. They also loved seeing our fish specimens. One of our guides even taught us how to fish for some of the armored catfishes with our hands. By feeling around the rocks you could grab them as they were chewing off the algae. I was unable to do this successfully but the rest of the team all caught fish bare handed.

One of my favorite spots was on the Río Pirre. For some reason the rocks were all tinted a deep green, and others were so brittle they broke apart under your feet despite looking otherwise like ordinary stones. At this site Fernando caught one of the most beautiful fish I’ve ever seen, a big bull earth-eater cichlid, Geophagus crassilabris. This fish had giant fleshy red lips and had lost some of his scales – probably old war wounds from fights with other males for territory. He was a beauty.

I was still thinking about the green rocks when we headed to the Cascades near another one of our campsites – Rancho Frío, home of the giant Harpy Eagle. The river was cool, which was a much-wanted relief given how hot and humid it was. We went up to the base of the falls and although the fish weren’t as interesting as down river it was still an adventure. The guides and Fernando, the most dexterous of us, climbed along a steep (and very wet) rock cliff and got on a shelf above the lowest set of falls. They sampled in the pools above – but I wondered how they would get down. I found out when they slid down through the falls! It looked like fun and it was probably one of those things I would have done before I had kids.

On one night our guide Hayro Cunampio went out with my snorkel, diving flashlight and a spear. We watched while he shot spikey armored catfishes (Ancistrus) and big characins that we hadn’t seen earlier in the day. When we turned off our headlamps and watched him floating in the stream with his bright torch against the darkness it looked like he was floating in space. When he came up he mentioned seeing a striped “macana” – which is the local name for electricfishes. We hadn’t seen any of these yet so I asked Fernando which one he means – “Gymnotus” he said. “We better go get it” I replied. My colleague at University of Louisiana Lafayette mentioned that he hoped we get a Gymnotus – something I thought was a weird request because I didn’t think these were in Panama. It turns out that Fernando was the one that discovered they were there with the first record of its discovery in 2012 [http://www.biotaxa.org/cl/article/view/9.3.655/0]. Fernando rushed out and A.J. and I followed to help. Using a cheap portable amplifier with cut wires we were able to translate these electric fish signals into sound. We stuck the cables under root mats and listened for their calls – Fernando understood their language – and could recognize their species by listening to the pattern – by the volume he could even determine their size. I was with him when he heard what he thought was a big Gymnotus deep in the roots, we missed a couple times with the dipnet, and then on one attempt we saw the characteristic striped patterns of Gymnotus. I’ve never seen anyone so happy to get a fish. Fernando leapt and danced across the stream as if Real Madrid had just one the Superbowl – or whatever Fernando’s favorite soccer club wins championships in. I was glad to see such passion for natural history. The fish was gorgeous too, a long dark-green headed relative of the electric eel; it was a fantastic fish and only the second record of the genus in Panama.

After a few more collecting days, we were back in Panama City – we were a disgusting mosquito bitten, unshaved, smelly lot – but happy. The edge of Central America was everything I had hoped for and more. Plus, I got to see my two newest lab members in the field and I couldn’t be happier to have Fernando and A.J. out there with me and back here at LSU.

On the Amazon and Tapajós rivers

Me and James with our former advisor's favorite fish.

In June of this year graduate student Bill Ludt and I went down to Brazil to attend the Evolution meetings and to do a little fieldwork. The Evolution meetings were in Guarajá but we decided to fly up to Santarém (about 6 hours north of Guarajá) to join the lab of Dr. James Albert from the University of Louisiana Lafayette. James and I both were PhD students in the lab of noted ichthyologist Dr. Bill Fink at the University of Michigan Museum of Zoology (UMMZ) but we didn’t overlap as students (he was there a little over 10 years before me). We actually met for the first time in Brazil in 2004 when I was a graduate student attending the Joint Meeting of Ichthyologists and Herpetologists in Manaus. He was one of the first people I contacted when I found out I would be coming down to work at LSU. We are good friends and he is one of my favorite colleagues. We recently obtained a grant of nearly $800,000 from the National Science Foundation to work on the systematics of fishes from the Neotropics. We were in Santarém to collect fishes from two beautiful rivers that come together there: the clear waters of the Tapajós, and the brown silt and nutrient filled waters of the Amazon. This is a strange mixing of rivers and the fauna is odd here too, you can find sponges, sea gulls, terns, shrimp, and other organisms you would normally associate with being marine. However, the fish fauna is pure Amazonian and completely dominated by a group called the Ostariophysans. These are your catfishes, characins (things like tetras and piranhas) and electric knifefishes (Gymnotiformes), the latter being the group in which Dr. Albert is the world’s foremost expert; he recently had a paper in Science about the genome of the electric eel (which is not an eel at all, but a gymnotiform). There are also many cichlids down here – together there are more than 5000 species of freshwater fishes in the Amazon – about 1/3 of the world’s total! The catfishes alone are quite amazing – the old saying goes “any old fool knows a catfish” but you’ve never seen them like this before. There are nearly 1000 species down here and they include things like the candirú – the notorious parasite of other catfishes that on occasion has been known to swim up the urethra (yep) or anus of unsuspecting bathers. (We have some on display in the LSU MNS Fish exhibit.) There are actually many species of candirú including some freeliving forms and others that are scavengers. One of the species we collected is best known for being discovered inside human cadavers from some unfortunate souls who lost their lives in the Amazon River.

A species of candirú

            When Bill and I arrived in Santarém, Dr. Albert’s lab was just getting into the hotel from a three-day long boat trip. They looked disgusting and I was really jealous: they were muddy, smelly, and all had big smiles on their faces. The Albert lab had struck out the first two days but hit the jackpot on the last day (the day I saw them). They cleaned up and we headed out to get some caipirinhas to celebrate. Santarém is a sleepy river city that besides being the meeting point of the Tapajós and Amazon rivers is also notable for being next to Henry Ford’s abandoned utopian suburbia, Fordlandia. He created an American style village there for rubber plantation fieldworkers under his imagined idyllic conditions – good English schooling, no drinking, and no women – obviously it didn’t last.

The next morning we first headed out to the local fish market. This was a rather large market with four rows of stalls with fish ranging from small anchovies to giant pirarucu (the bonytongue, arapaima). This was in a large outdoor stall and one of the vendors was even able to call in the famous pink river dolphins with a few fish treats. (There is an old Brazilian myth about how these dolphins don hats at night and hit on the women.) We purchased some of the more notable species and headed out to the water. We walked on to a little chartered boat, “The Calypso,” so named because the captain of the boat was obsessed with this kind of music and about a tenth of the boat was filled by a giant set of speakers and a strobe-light disco ball. James got a great deal on the boat and it fit their trawling net they brought from Lafayette. The captain was also quite knowledgeable about fishing in the area. Besides Bill and I, there was James and four of his students, plus the captain and two helpful staff. It may sound like a lot for a 30ft boat but it was rather comfy. We set up a large trawl net at the back end of the boat and sometimes we would take a smaller boat to set out a long (almost 100ft gill net). The captain always picked me to go out and pull in these gill nets. I felt like the kid in the classroom that the teacher always pushed to test their limits. But I soon realized he picked me because I was the only one who could cast net so he wanted me to cast while we waited for the fish to hit the gillnet. We had a successful first day and Bill and I had a fun time interacting with the Albert lab and the staff on the boat. We headed back to the hotel that night and James and one of his students left the next day for some pre-meeting organizing in São Paulo. (James ran a Parametric Biogeography session for the Evolution Meetings.) It was just me and the students on the boat for the next few days and it was a great time. We teased each other giving each other nicknames – Jack from Los Angeles who showered twice a day was “Hollywood,” Max was YCE because he was a “young Clint Eastwood” – and the rest of the pseudonyms I’ll keep a secret between the fishing crew of the Calypso. Besides the teasing we had a lot of amazing samples come in: piranhas, arowanas, cichlids and of course lots of catfish, knifefish, and tetras.

            The first night we strung up our hammocks and were rudely awakened to a violent storm surge. The winds knocked our hammocks together and the Captain and crew were calm but clearly concerned, they had to “batten down the hatches” on our little 30ft’er and sailed us into safer waters. Around 5am he started getting phone calls on a regular basis as we learned a larger boat owned by the captain’s friend had sank. A similar swell happened the next day, with lightening and thunder forcing us to take cover again. It was a bit disconcerting knowing that you are a bit of a sitting duck in the middle of the remote Amazon far from any other people. We were surprised by the strength of the storms, luckily neither lasted long and we were able to get along with our business.

     I loved fishing for little small things on our little side boat we were pulling along the Calypso. We collected many of the cichlids and bony tongues this way and some other rare things. One of my favorites times was going out at night with just a dinky flashlight to small patches of reeds, we were often remarkable successful with just a dipnet and a castnet. Often while I was out on the little boat the rest of the group used hook-and-line to pull in a catch. The crew of the boat, particularly “Donnie” our cook, was quite adept at catching large piranha. One of these, the black piranha (Serrasalmus rhombeus) was such a nice specimen with beautiful interlocking teeth that without thinking I tagged it and sank it into formalin; I realized later that Donnie had intended to cook that fish that night. I felt awful but hopefully made up for it by bringing in other fishes for dinner.

    On our last night out we were pleasantly surprised by the captain finally putting on his speakers and setting the volume to 11. Luckily we were in such a remote place that there was no one that could complain about the noise. He even put on his strobe-light disco ball. We brought some caipirinhas and beers to the roof of the boat and watched the stars and the dense forest around us.

After a few days of not showering and getting muddy and smelly we were glad to be brought back on shore in Santarém. I was ecstatic for our adventures and still feel so lucky to get to do this for a living as part of my job at the LSU MNS.

On Being A Natural History Curator

I’ve wanted to be a curator ever since I learned that it was a real job. What I’ve learned since is that “curator” can mean many things depending on where it is being applied. At the Natural History Museum in London for instance the people called “curators” are what most people at a U.S. museum would call “collection’s managers” while they call “researchers” those who we would call “curators.” (Don’t worry it will get more confusing.) Most people in the academic museum community (I include in “museum” things like herbariums, etc.) view curatorial positions as generally doing some or all of the following: (1) managing (overseeing) a collection, (2) doing collections-based research (3) building a collection via fieldwork, (4) managing loans and gifts from these collections, (5) maintaining these collections (everything from replacing old jars and labels to upgrading the data-basing software). Most curators do some but not all these things because some of these duties fall on the collection’s staff including collection’s managers and graduate curatorial assistants (if they have the luxury of having such help). Most curators are doing collections-based research, which can include everything from range expansion documentation, to taxonomy (descriptions of new species, revisionary systematics), to cutting-edge evolutionary or ecological studies.

            Curatorial positions are often highly sought after because, as oppose to many other academic positions, they can require little or no teaching, can include time for fieldwork, and are often viewed as more fun than your typical arm-chair or strictly lab-based science. It should be noted that many people do fieldwork that aren’t curators, and some curators do little fieldwork (shame on them). Also some curatorial positions have the same teaching load as “regular” professors, but most have a reduced load. We curators sometimes joke that our duties include 50% research, 50% teaching and 50% curation. It is true that we receive little credit for good curation, but the same may be said about teaching well. It is really nearly 100% research that is being evaluated for someone on the tenure-track; however, rather than being a burden, a collection for a curator is a major research tool. A curator can use the products of fieldwork and past collections to investigate deep Earth history or broad biological questions. When stable isotope researchers investigating pollution in the Great Lakes need samples of whitefish from the past 150 years, they can do so knowing that the University of Michigan Museum of Zoology has many such specimens. When someone thinks they may have a new species of woodpecker they can visit the many museums that have closely related species to their putative new taxon for comparison. The geographic variation, color morphs, sexual dimorphism, ontogenetic variation, etc., present in many of the species on Earth are housed in collections somewhere. Not to mention that much of the DNA and RNA based work being done on animal, plant, fungal and microbial life is based on collections. Because curators are the experts on a particular taxon, they are often insuring that the correct scientific identification is connected to the specimen. Without collections and curators a lab tech that doesn’t know a coelacanth from a goldfish might report scientific findings from the wrong species. (This happens more often that you think as tissue samples from specimens that are not vouchered in a collection get used more and more often – see more on that HERE]

            Some curators at university-based museums (like LSU, Michigan, Berkeley, Yale, Harvard to name a few) are professors in academic departments at those universities. These can be 100% academic appointments where the curator is seen as a full time member of both the museum and the department, or part time appointments (e.g., 50%). These appointments typically mean part or all of the pay, teaching and service obligations rest within the larger academic department. Some university-based museums are completely autonomous and are their own separate unit (usually with some adjunct status with another academic department). Some museums are completely public without any official connection to a university (e.g., Smithsonian, American Museum of Natural History). The role curators are playing at each of these institutions can be highly variable but generally include the five duties described above.

            I’m still not exactly sure how I lucked out at getting a curatorial position. I suppose if I were to give advice to someone wanting to become a curator that I would say a few things I did might have put me on the right track. Training at a museum as an undergrad, grad student or postdoc will put you in touch with the relatively small museum community. There aren’t that many jobs in museums, but there are fewer people qualified and competing for a position like “curator of amphibians and reptiles” than say “ecologist.” The latter may get hundreds of applications at a typical university, curatorial positions typically have less than 50 applicants, and of those maybe 10 have the collections-based research experience to be considered. Doing fieldwork, publishing work based on collections, and being a curatorial assistant as a grad student can help you get that collections-based experience. As with applying for any job publishing lots of good papers, speaking at conferences and getting grants will certainly get you on the fast track to a job. However, papers alone won’t get you a curatorial position unless you also have a collections-based research program to promote.

I was lucky enough to give a TEDx talk about natural history collections recently, view it here https://www.youtube.com/watch?v=IL-9bplZa0E). Also is you want to learn more about curation or collections, please feel free to contact me for advice, I will try my give you a frank answer or point you in the direction of a real expert.

Back to the Middle East for more Fishes

Some fish identified and labelled in English and Arabic by students.

Bill Ludt and I returned to the Middle East this April going back to Kuwait and adding Abu Dhabi to make our regional collections. Again, we had the wonderful LSU alum Dr. Jim Bishop host us.  Jim organized and had specimens waiting for us collected by Kuwaiti research vessels in advance of our arrival. We also were asked to present a five-day short course at the Kuwait Institute of Scientific Research (KISR) titled “Taxonomy and Identification of Fishes from the Arabian Gulf” – teaching this course allowed us to pay for this trip and make our collections which otherwise would have been impossible. Each morning we lectured from 9 to 11:30, and each afternoon we held two-hour labs. It was exhausting but fulfilling work, for both the instructors and students. In the lectures we covered topics ranging from taxonomy, systematics, and museum studies of fishes, to early explorers of the region (Jim’s section) and the geology of the Arabian Gulf (Bill’s section). In the lab we sorted the collections made in the previous weeks by a KISR research vessel, and the students learned to use keys and identification guides to put scientific names on each specimen. They also created their own characters to help with identification. There were 19 students in all, many of them from KISR but some coming from as far away as Oman and the United Arab Emirates. The first language of all the students was Arabic, and although they all spoke English, the language used in field guides can be quite obscure even to a native English speaker. My job was to help them understand the regional guides and to help them personalize their own guide to fishes from the region. I pointed out to them the oddity that an American was teaching them about their fishes, but LSU has one of the best recent collections of Persian Gulf fishes in the world (thanks to our past efforts). I also pressed upon them the need to create a reference collection of vouchered fishes somewhere in Kuwait. No natural history collection exists anywhere in the Arabian Peninsula (the nearest one is in Iran). I pointed out to them that if there is loss of species from an oil spill or climate change, that there is only institutional memory to make note of the shifting or declining diversity. A reference collection could help keep better track of the changing diversity.

Students seining in Kuwait Bay.                                                      Dissection of a butterflyray.

            We went through nearly 100 species from the Gulf during the class. Bill and I brought back hundreds of specimens and tissue samples to LSU, many of which are new to collections (we sampled 100 different species last year). With Kuwait having only about 350 species, we now have many of those at LSU.

Early morning fish market.

The High Line at NYU Abu Dhabi.

            After the course was completed Bill and I flew to the United Arab Emirates to the newly built New York University, Abu Dhabi (NYU) campus. As a New Yorker I spent much of my teenage years loafing around lower Manhattan trying to decide what fun thing to do. The area around NYU was where all the cool college kids hung around and as an awkward high schooler it looked like paradise. Now as a grizzled, rapidly aging professor, NYU Abu Dhabi looked a lot like academic paradise. It was a relatively small campus (<25 buildings) but arranged in a beautiful way with the top floors connected by an overpass walkway that was a replica of the famous High Line in New York. The dorms, labs, and classrooms had an ultramodern design and it appeared that no expense was spared. No expense, it seemed, was ever spared in Abu Dhabi; buildings were being put up as fast as weeds in a Louisiana garden. We saw the sites of new Louvre and Guggenheim museums being built along with dozens of new skyscrapers. It was a sight to behold. We were hosted by the lab of Dr. John Bert an NYU faculty member who works on the local marine fauna (mostly corals). Each day Bill and I ventured out to the local fish market, which was luckily quite expansive, and got a fair sampling of the regional fauna (around 40 species) over the course of several days. One day we ventured out at 5am to see the fish come in and it was quite an amazing sight. There were many hundreds of groupers, butterfish, mackerel, and other important food fishes being auctioned off for sale throughout the region. Unfortunately for us, there was little bycatch (the left over unsold and undesirable fish that typically have a great diversity from which to sample). Many of the fishes being sold were caught by traps and so there is a limit to the range of species being collected. This limit may be good for the environment but not so great for a visiting ichthyologist. Bill and I spent our afternoons sorting, identifying and prepping the specimens, which we did in a beautiful shared molecular lab space. In past trips we are often stuck stinking up a hotel bathroom with formalin and rapidly decomposing fish; in this luxurious lab setting we wore fresh new white lab coats and prepped under a fume hood.

            Teaching the fish course and getting the collections from Abu Dhabi and Kuwait led Bill and I to come up with some pretty good ideas for additional research projects. We are again in discussions to return to the region for sometime next year. Stay tuned for more about our Middle Eastern adventures in the future.

Jim showing some beautiful fish plates from a historical regional book.

            None of this again would be possible without the help of Jim Bishop, who not only was extraordinary in his efforts to get us fish and the right connections throughout the region, but with his wife Ginni put us up at their home and fed us like we were part of their family. Thanks Jim and Ginni!

Caving in Northern Alabama

     In May I felt the twinge of wanderlust that sometimes takes over me: I needed to get out into the wilderness, and see things others had not seen. Luckily I received an invite to do just that, even though it was in perhaps the most ordinary place on Earth - Scottsboro, Alabama. It was a place I knew little about, that perhaps few besides its own residents know much about. But this was a wonderful place; home to the southern most stretch of the Appalachians, it looks like something closer to the Smoky Mountains than the bayou. The fog is thick, the mountains tall and verdant, the air a refreshing cool. I was here to go caving and, of course, to look for cavefish.

            Louisiana has caves, but no cavefish - a great disappointment. Alabama has caves, and perhaps an undescribed diversity of cavefishes - a great surprise. I’d fallen in love with caves in Madagascar, where I had first encountered them. I had been wholly unprepared then. Those Malagasy caves, full of strange life – odd birds, angry eels, giant-white-hairy spiders, big snappy crustaceans - was so new and unknown that I thought I was in Conan Doyle’s ‘Lost World.’ Madagascar got me hooked on caves for life. When Dr. Matthew Niemiller, one of the world’s preeminent young cave biologists, invited me to “no-where Alabama,” I happily accepted.

A little blind cave crawfish. I did not eat it, but I thought about it.

            Scottsboro is relatively close to Tuscaloosa; home to our LSU football (if not academic rivals) at the University of Alabama. I stopped over to visit their Museum of Natural History on my drive up from Baton Rouge. I found their museum quite beautiful, and their fish collections (in another building) in a much better housing than my own. I was glad to see our rivals on their own turf; and I was quite envious of their collections space and the wonderful Randy Singer, their collections manager, who was showing me around. After that brief visit I continued my drive to northern Alabama. I knew I was in cave country when the thick fog rolled in, I started to see limestone in the rock formations, and my car was pushing the limits climbing steep mountain passes.

            Our target was Limrock Cave, and Dr. Niemiller and colleagues from Auburn joined me near there in Scottsboro. Auburn recently provided their fish curator, Jon Armbruster, with a new building of which I am also extremely envious. (I hope someone out there is getting the hint.) Jon brought along his students Pam Hart and Charles Stephen. I met up with them that first night and was amazed to learn that Charles had not only also went to McGill University like me for undergrad, but also the same tiny Macdonald College campus. He studies pseudoscorpions, of which I know nothing, to his and my great disappointment. These little critters are very cool, especially, like most other things, the cave adapted forms.

            After gearing up and a short hike we were at our target, Limrock Blowing Cave. It was pretty amazing. Rather than the homogenous setting I expected from a North American cave there was quite a lot of habitat diversity, with deep mud in some spots, long windy paths, cool clear water in streams and pools, boulders in collapsed sections (“breakdowns”), narrow passages we could barely squeeze through and great big stalagmite and stalactite chandeliers in large open spaces - and always that utterly complete darkness and silence. Thank goodness for our headlamps and spare batteries. I would occasionally turn off the light and sit quietly just to take in how very dark, cold and quiet it was. The entire cave was nearly 10,000 feet in length, with lots of odd turns, tight crawls, high waters, and cold temperatures to give you enough of a thrill to make you feel like you are on an adventure. But there were also a great many cave animals, wholly unfamiliar to me. We looked for everything, insects, crawfish, spiders, salamanders and fish. We found a great many of these. What we didn’t find are bats; there was plenty of evidence that they were once there in great numbers but they became extirpated due to the scourge of the deadly white-nose syndrome.

Charles in a tight spot.

            Earlier this year Matthew and I described a new species of cavefish from Indiana, that we named Amblyopisis hoosieri, the Hoosier Cavefish. This odd creature garnered us some press because according to some reporters it looks like the human male’s reproductive organ. It is also the first cavefish described from the U.S. in 40 years and its anus is positioned directly behind its head – an odd place even for a fish (some reporters dubbed this a “neck anus”). North America actually has a great many cavefish species, at least compared to the poorly known stygobitic fauna of the rest of the globe. Matthew, on the strength of DNA evidence noted that the cavefish from north of the Ohio River (in Indiana) were quite distinct from those from south of the river (in Kentucky). This evidence set up an easy species description based on morphology of the new Indiana species to distinguish it from the species in Kentucky. It was also pleasing to name a new fish species after the birthplace of American ichthyology. We named the new species, Amblyopsis hoosieri after the “Hoosiers” of Indiana University because the new species is found very close to IU and because David Starr Jordan had once been university president. Jordan is also the most recent common academic ancestor to most, if not all, practicing North American ichthyologists. (He also was a social Darwinist, and may have killed off the founder of Stanford University shortly after he took over as president of that university.) In addition, the first female ichthyologist, Rosa Smith Eigenmann, wife of another noted Indiana ichthyologist, Carl Eigenmann, were also at IU. We named the new Indiana species to make note of the strong influence of IU on American ichthyology. I wanted to collect some of these North American cavefish for the first time so I travelled to Scottsboro, Alabama.

Target organism captured.

            Again we saw a great many cave adapted species from salamanders, to blind pigment-free crawfish, to Charles’s pseudoscorpions, to machete-wielding-Alabama hill people. I wore a double-layered wet suit with kneepads, helmet and lamp and I was sort of prepared for the cold and darkness of the cave, still I was having too much fun to notice any discomfort. We were after Typhlichthys subterraneus, which oddly for a cavefish is found in a rather wide and disjunct distribution. We found only three specimens all within an hour time span of the five hours we were in the cave. Each capture was thrilling. These blind depigmented thumb-sized fish were not hard to capture once you found them: a quick flick of the dip net was enough to bag one. Being blind and not used to predators chasing them, they were basically sitting ducks. I had the privilege of being there when two of them were caught. (I can claim only a single assist when I whiffed after kicking up one cavefish out of the depths with my boots, and which Jon Armbruster deftly captured– he caught all three.) It was a great deal of cold, wet, fun.

            Scientifically, it is unclear the significance of these specimens as of yet and I should say this is a Master’s students project at Auburn. I can say I am hooked again on cavefish and have some interesting Mexican material I can’t wait to tell you about. I’ll save that for another time…..

Media pumps up a little girl’s science project then viciously takes her down. Leave this kid alone!

A week ago!

 This week!

What happened? Here is a timeline from Christie Wilcox’s (@NerdyChristie)  http://blogs.discovermagazine.com/science-sushi/2014/07/24/proceeding-upriver-timeline-arrington-jud-dispute-estuarine-lionfish/#.U9J996iLn9i

This is my take:

A precocious little kid did a science fair experiment for her school. It received attention because it is on a dangerous invasive and because a child did the work. She likely got the idea for the experimental design from her father, who probably got the idea from colleagues.

            Because people are interested in the topic and it was such a slow news week (besides the three airplane crashes, Israel/Palestine conflict etc.) this thing went viral. Anyway, who wouldn’t cheer for a young girl who discovered something cool, novel, and useful at the tender age of 12. But just as quickly as some were there to praise our new rising star, so too were they there to take her down just as quickly. Unfortunately, in this case the star/victim is a little girl with an interest in science. The media just made her an example of the climate for scientists today and women in science in general. The media’s interpretation of science is at fault here too. The headline that made me flinch the most was “Did [used her name] steal a marine biologist’s study for her 6^th grade science project?” What a despicable thing to use a child’s real name in such a negative heading. Shameful.

            The timeline from Christie Wilcox above is the best thing to read out there from this "story." Shame on the reporters who wrote this girl's name in their stories and made it sound like she “plagiarized” another person’s work. She did not copy someone else’s work, the worst case is if she didn’t mention the work done before her as much as she could/should have.  This is a child people. At least keep her name out of this. Maybe she made a mistake in remembering how she came up with this project certainly it was influenced by the work of one of her father’s colleagues and perhaps in reading all of this wonderful press she started to rethink where these ideas originated. When talking to the press we often build narratives from our scientific work, we all stood on someone else’s shoulders and on the works of those that came before us. What happened here was a little scientific progress by a child that turned into a wider cultural regression.

  I understand the concerns of Zachary Jud, the PhD student who feels his work was slighted. He deserves credit for his work, but here is the thing - people are talking about his original work because of this little girl. The original work is already published and already got a little press, it is great that people are talking about this project again. This little kid has brought a lot of attention to it. Did she intentionally leave the original research out of the story to make her science fair research sound even better? I don’t think so. Even if she did, she’s only 13 now and kids make mistakes sometimes, but especially when talking to the media. If you are a scientist that has ever been asked “How did you come up with this project?” you know that it can be a very tough question to answer succinctly and you sometimes leave out details about all the influences you had in the past that got you to that point. Now imagine answering questions like that when you were 13 with an adult asking you the questions.

If you want to blame someone here blame the adults, blame the media, but don’t blame a little girl who just was trying to do a little science she was interested in.

 

Make the link between specimens and genetic products as transparent as possible. #collectingisessential

I think the biggest issue molecular systematists will face in the future will be the pervasiveness of many genetic sequences from misidentified organisms. Our inability to track down the actual animal, plant, or fungus that many of our published genetic sequences come from is already a huge problem. There are plenty of sequences on GenBank and other sources from which we blindly download sequences trusting that this COI sequence from Coryphaena hippurus is actually from a dolphinfish and not an actual dolphin. Although there are lots of checks and balances to make sure that sequence of COI are actually from COI, and that these sequences lack stop codons, there isn’t much to check the accurate identification of the source specimen (a.k.a the voucher). Very few of the millions of sequences on GenBank can be tracked back to an organism deposited in a collection. If you download that sequence of dolphinfish and put it in your phylogeny and it falls out somewhere really weird then you can do a blast search and it will tell you that it is actually probably from a dolphin (if that is the case). But most of us are working at a much finer phylogenetic scale. We are building phylogenies of genera, families, or orders. At this finer scale it is very easy for someone to misidentify a species. (Google images of species from your favorite genus and see how similar congeners are in appearance.) Sequences generated from a misidentified specimen can easily end up on GenBank and often in the phylogeny of the day, and they do.

A wise mentor of mine used to say that every museum label has a question mark after the identification. I would say the same about the identifications on GenBank sequences except the nice thing about the museum specimens is that an expert on the group can one day come and positively identify the species based on the specimens: Not so with most GenBank data. The sequence is out there and if you have the right genus and not the right species it is highly unlikely that someone will catch that error anytime soon. It is quite likely in fact that many others will continue using those sequences, inadvertently perpetuating the error.

My colleagues and I want to put the power of identification back in the hands of taxonomists. I think it is safe to say that most people uploading sequences to GenBank are not experts in the organisms they are studying. They are trusting someone else to do positive identifications for them or they have collected some tissue samples from something they think they know very well but they may not. I see studies all the time where the samples were collected, tissue samples taken and the animals, and the carcasses of those animals were discarded (rather than kept in a permanent collection). That’s really not good, and a waste. First of all names change all the time. What if the study species is later split into two species; which one was the one you collected? What is needed is an unbroken and transparent link between the voucher and the genetic data.

Based on our observations that few researchers provide a link between their genetic data and collections data, either on GenBank or in their publications, a few of us [Carole Baldwin (Curator at the Smithsonian), Larry Page (Curator at the Florida Museum of Natural History) and my student and I] got together and created a nomenclature that should help remind people of the importance of making the link between specimens and genetic products as transparent as possible. The nomenclature is called GenSeq and it works something like this: The quality (trustworthiness if you prefer) of any given genetic sequence is based on how likely the identification of the voucher specimen is correct.  In our nomenclature the highest ranked, best sequences come from primary type specimens, like a holotype. A holotype cannot be misidentified because it is the main specimen chosen to represent the species when it was first described. Sequences from the primary types are ranked as genseq-1, the highest ranking in our system, because those sequences are from specimens with the highest likelihood of being correct identified. Sequences from secondary types (other specimens used in the original description of the species and designated as paratypes or other secondary types) are ranked second, genseq-2. This is followed by specimens from the type locality (same locality as where those primary type specimens were collected), genseq-3. Specimens that are vouchered but not from the type locality or type series as above are in genseq-4. Most sequences from specimens positively identified and deposited in permanent collections will be in that fourth category. The last category, genseq-5, is for photo vouchers. Although not ideal it is sometimes necessary to release an organism that you have taken a tissue sample from (think of something really big, or very rare). Also photo vouchers are necessary in cases where specimens are so small that the body of the organism is destroyed in the process of sampling its DNA. In these rare cases a photo is the best you can do to keep a record for identifying the species in the future. (Read more about photo vouchers versus actual specimens on Twitter using #collectingisessential or (see our paper here); you almost always need more than a photo to positively identify most creatures.

Anything without a clear link to a voucher (specimen or photo) doesn’t get one of these GenSeq tags. We recommend that systematist avoid using genetic data from which the source is unknown or unrecorded (and therefore lacks a GenSeq tag). After all, wouldn’t you prefer to know all the sequences you used were from organisms that were correctly identified by an expert? In an age where there is so much data available from so many species it is time to be picky. If you can download a sequence upload by someone who ‘kind of sorta’ thinks it is from a coelacanth, or the one where the voucher was identified by an expert and the specimen deposited in a permanent collection (where you can check it yourself if you need to) - wouldn’t you always choose the latter.

Right now many systematist, whether they admit it or not, will just not use sequences in a phylogeny if they originally end up in a clearly “wrong” place on the phylogenetic tree. That isn’t very scientific. Knowing it is in the “wrong” place in the first place is subjective. Of course most systematists will do a blast search and try to find alternative sequences, but the point is that the most rigorous approach is to make sure the specimen it came from was positively identified in the first place. We hope this GenSeq nomenclature is a short cut to doing just that.

We have published the GenSeq nomenclature here. And below is a poster we are presenting at some meetings that gives an overview of the idea. We hope people use it (by including a table in their paper linking GenBank #s to voucher #s and adding these GenSeq ranks). Too often people write in their publications something like: “Sequences were uploaded to GenBank and correspond to JK123332-JK678738.” That sentence tells us almost nothing. Not only do we not know what specimen might go with which sequences, we don’t even know which species goes with which sequences. If you then go to GenBank and download those sequences you will have the species - but little else (most people do not report the voucher numbers, if there are any). That’s a shame and something we hope to change. So the take home message is: Always link your genetic data to your voucher’s information! 

 P.S. - the 'Journal of Fish Biology' and' ZooKeys' have added the GenSeq nomenclature recommendations to their Instruction to Authors.

Another post for 'Southern Fried Science' - Don’t build a new inter-ocean canal across Nicaragua

Check out my new guest post for 'Southern Fried Science' -

Don’t build a new inter-ocean canal across Nicaragua

Can’t wait to get back to Kuwait: Fishes from the Arabian Gulf

Bill Ludt, Jim Bishop and me in downtown Kuwait City.

From June 13^th to the 22^nd my PhD student, Bill Ludt, and I travelled to Kuwait to collect fishes for the LSU Museum of Natural Science ichthyology collection. (This was the 3^rd trip that Bill and I have now made to Asia in the last two years.) Over my career I’ve made collections from much of the Indo-West Pacific but am lacking some critical Middle East collections. The Middle East is underrepresented in most fish collections worldwide and because many of the species from the region are poorly known there is a potential that some of them are new to science. When Dr. Jim Bishop invited us to go to Kuwait last year I knew it would be an opportunity we shouldn’t pass up.

            Jim Bishop is familiar to many people in the LSU community; he is an alumnus and a great sponsor of art and research at Louisiana State University. Jim has a wonderful enthusiasm about the work being done at the museum, and he has provided many specimens to our collections in the past. He is also one of the most cultured, kind, and energetic individuals I have ever met. Bill and I were lucky enough to stay with Jim and his wonderful wife Virginia at their home in Kuwait City. We frankly could not have figured our way out of the local airport without them, let alone find the fishes we were targeting. Kuwait is an interesting country with a rich and ancient history that was transformed by the unimaginable wealth that came about through the oil industry. All throughout the places we visited you can see this dichotomy between an ancient desert civilization and a transitioning modern society. The temperature was rarely below 100 degrees even at night, and frequently much higher - this was the desert after all, but the roadways were green with introduced shrubbery that was irrigated with desalinated seawater. Locals wore traditional Islamic garbs (abbeys for women, dishdashas for men) but there were also many expats from India, Syria and the West. It wasn’t always clear when we were seeing the real Kuwait or just the veneer around it.

Bill Ludt rocking the guitarfish.

            Our first days were spent going through the many collections Jim had already obtained for us. Through his work at KISR (Kuwait Institute for Scientific Research) he was able to arrange for specimens of notable material to be held for our visit. These specimens were collected by boat trawls in and around the Arabian Gulf (what we call the Persian Gulf) over the past few years. By the end of the first day we had already gone through hundreds of samples that were a very good representation of Kuwait’s ichthyofauna. Jim had meticulous notes for these materials and much of it was preserved in alcohol (rather than fixed in formalin) so we were able to take DNA samples as well. The majority of the materials that we brought back to LSU are these collections from KISR. We also made substantial collections from the local fish markets, which included material from Iran, Saudi Arabia and Iraq. The local fishmongers sold an amazing variety of species on a daily basis. Although the exact localities of this material will remain unknown it was nice to get additional material from around region. We also did some collecting of samples from the oceans ourselves going out at low tide to collect blennies, gobies and toadfishes from the sandy intertidal zone.

Mudskipper: a fish that doesn't mind being out of water.

We were also able to catch a few mudskippers on one of our last collecting days; these fishes are among my favorite animals to catch, and my least favorite fish to anesthetize. These fishes, which spend most of their time out of the water, are incredibly cute, with big bulgy eyes at the top of their heads and an expressive “face” that makes them look like muppets. They live in muddy areas and keep water trapped in their gills while they scurry about the surface building territories and escape routes. The mud they live in is hard to traverse and the larger individuals were in waist deep mud that made it impossible for us to catch them. We stuck mostly to the shoreline trying to catch smaller individuals. Even these small ones are amazingly adept at getting away. We saw hundreds of these mudskippers and ended up catching only about ten. We were covered in mud by the end of the day and the incredible heat made the conditions rather harsh but ‘mudskippering’ is always great fun.

            All in all we brought back close to 80 species from Kuwait and the Arabian Gulf and roughly 300 new tissue samples and close to 500 specimens. We also built an important relationship with the folks at KISR. Jim invited me to give a presentation there and my talk, “What We Learned from the 2010 Gulf of Mexico Oil Spill: and other projects from Louisiana State University” was well received.  We have also started some collaborative projects with researchers at KISR. We are trying to arrange making a short course in ichthyology that Bill and I would teach sometime in the spring at KISR, and hopefully we will try to sample from other parts of the Middle East as well. In fact this article is hopefully just the first of many we will produce from these trips to the birthplace of civilization.

A stonefish, the most venomous of all fishes.

Southern Fried for a Day - Collecting organisms to save their species

Check out my guest post for 'Southern Fried Science' - http://www.southernfriedscience.com/?p=16957 - this was in response to the Minteer et al. paper in Science that says we don't need to collect specimens anymore. Ummm... yes we do -

Collecting organisms to save their species

 

A Proposal for a New #Altmetric, the Influence Score, to Accompany the H-Index and to Help Evaluate a Scientist’s Impact on Society

The H-index is among the most widely used metrics for evaluating the quality and quantity of a scientist’s publications; but what about their influence on society? Here I introduce the Influence Score that can help an outside reviewer better understand a person’s impact not just among other scientists but among the general public and those outside of academia. If the ultimate goal is to evaluate a person’s true overall role as a scientist, I think we should be considering how they communicate with all people not just other scientists (which is the case with the H-index). The new index can be used to accompany the H-index, but also incorporates it. All elements of the Influence Score can be looked up through simple Google and Twitter/Facebook searches.

            The H-index can be easily calculated in Google Scholar, I prefer it to the Web of Science or Scopus because Google Scholar counts books and other

Fig.1. Google Scholar Profile Page Showing H-Index in Red Box.

non-traditional peer-reviewed publications: and it is free! To calculate the H-index you essentially count down the number of publications and their citations until the numbers no longer overlap. A person with an H-index of 5, has at least 5 papers with 5 citations. Read more HERE to learn how to calculate the H-index.) Because a scientist’s main role is still to communicate their science among peers (via peer review), the Influence Score multiples their H-index by 100, and down weights the other elements, which are a little easier to accumulate (e.g., # of twitter followers).  I chose the H-index over say, total number of citations (which might be more similar to # of followers), because it is easier to calculate for a given researcher, especially one without a Google Scholar profile (Fig.1). 

            The other measures of the Influence score includes a measure of their visibility with the press (i.e, the Press Index or P-Index for short). Using Google News, one simple puts the person’s name in the search box and counts the number of articles that are found, which Google also does for you (Fig.2). Because

Fig 2. Red box shows Google News P-index.

Google News is only searching through a relatively recent window of time, few scientists will have much more than a few articles about them. Sometimes it is worth googling the person with “science” following their name, as I did for James Watson (e.g., “James Watson science”), to distinguish him from other news articles about people with the same name. This measure largely is to bump up those scientists truly making a social impact as newsmakers. That is without bumping them up too much, I’m trying to avoid giving too much influence to “celebrity scientists” that don’t do much science of their own. Therefore, I suggest that you divide the total number of search results of the Press Index by 100 so that this score is not completely overweighing the person’s academic accomplishments represented by the (albeit crude) measure of the H-index. Folks like James Cameron that are great promoters of science, but are best known for other things, are intentionally excluded here. If someone could separate press about science related activities from all others, they obviously could still be included. This is also the most dynamic element of the score because it can change so rapidly. Jane Goodall can skyrocket to the top of the list with the publication of a new book.

Fig.3. Twitter and Facebook Fan pages showing # of followers.

            The third part of the Influence Score considers your sway in social media (i.e, the Social Media Index or SM-index for short), specifically Twitter or Facebook. For someone on Twitter you get 1pt for every follower. For someone not on Twitter but that has either a Facebook “Fan” Page or Facebook “followers,” you get 1pt per fan or follower. You don’t get points for regular old Facebook “friends” because that isn’t necessarily measuring your scientific influence. If they have both a Facebook Fan page and a Twitter handle you only get points for whichever is the higher value. To learn more about the role of twitter for outreach read David Shiffman’s @whysharksmatter excellent article HERE).  As with the Press-Index you divide the total number by 100; again this is to allow the more academic H-index to still have some weight. The reason being that someone with 40,000 Twitter followers and an H-index of 0 might not really be more influential than a scientist with an H-index of 40 and only 4000 twitter followers.

            The Influence Score is then the total of your (H-Index X 100) + (Press index/100) + (Social Media-Index/100). I would round this to the nearest integer. All three can be discovered relatively easily through searches (e.g. GoogleScholar, GoogleNews, and a Facebook/Twitter search). Below I’ve compiled a list of some of the most well known scientists and have calculated their Influence Score. I’ve also added folks randomly that I admire that might not be the most famous folks but that I hope will be one day, I think adopting the Influence Score might help them get the recognition they deserve for the impact they have in society. This metric is imperfect: but I hope it is a good start.

I would like to thank Paige Brown @FromTheLabBench and her class #manship4002 for helping me figure out a more user-friendly way to compile this Influence Score. Also would like to thank Joshua Drew (@Drew_Lab) and David Shiffman (@WhySharksMatter) for their comments and advice.

Scientist	H-Index x 100	Press Index /100 (total articles according to GoogleNews)	Social Media Index /100 (Twitter/or Facebook followers)	Influence Score
Stephen Hawking	8400	781	9,591	18,772
Neil deGrasse Tyson	600	14	16,100	16,714
Richard Dawkins	4000	36	8,870	12,906
Bill Nye	100	140	11,500	11,740
Jared Diamond	10800	104	208	11,112
J. Craig Venter	9600	20	186	9,806
E.O. Wilson	8800	64	12	8,876
Steven Chu	8200	17	212	8,429
Buzz Aldrin	0	10	8,150	8,160
Sean B. Carroll	7500	.01	0	7,500
Jane Goodall	4500	21	1,650	6,171
Ed Yong	0	.12	4,660	4,660
Jane Lubchenco	4600	.71	0	4,601
Jack Horner	3600	.16	18	3,618
Carl Zimmer	1700	3.83	1700	3,404
Amanda Vincent	3200	0	3	3,203
Neil Shubin	3100	3.94	9	3,113
David Attenborough	1500	45	1,423	2,968
James Watson	2600	18	0	2,618
Hope Jahren	2200	0.01	24	2,224
Eugenie Clark	2200	0.01	0	2,200
Eugenie Scott	1800	0.06	71	1,871
David Shiffman	200	0.04	1,470	1,670
Sylvia Earle	1400	1	213	1,614

Note: As always I would like feedback on this post and if people have suggestions for changes or additions to the metric. Please e-mail me at prosanta@lsu.edu

Piranha Frenzy or just Media Frenzy?

Piranhas did not "attack" 70+ people in Argentina on Christmas day in a feeding frenzy; the only frenzy here is the news medias desire to report this story (ABC, Fox, Discovery, BBC, etc. have all reported it). From what I can gather, several people, one a young girl, were bitten in the Parana River near Rosario, Argentina. Some people may have lost parts of (and perhaps entire) digits according to some of the reports. The Parana River does have piranhas but none at the scene said it was piranhas, but rather ‘palometas.’ Piranhas in a feeding frenzy can consume animals as large as humans in seconds, but they are very picky about their food source and reports of human attacks are few (see paper here). Most people who lose a finger to a piranha have lost it after mishandling it on a hook or in a net out of the water. Piranhas in a frenzy will take off more than your finger tip. Several news agencies report the fishes are “palometas’ and show images or mention a common species of jack; however, all jacks are marine so they wouldn’t be in the freshwaters of the Parana River. Pygocentrus palometa was described as a Venezuelan piranha species that is likely not a valid species (see Catalog of Fishes), and not known from Argentina. My guess is a few people were bitten by other biting tetras common to the area (Hoplias?); these bites may have scared lots of other people out of the water.

[UPDATE: I do think these were piranha bites now, having talked to some fellow ichthyologists. These were probably defensive bites from one of the local species they call palometas - Serrasalmus maculatus, S. spilopleura, or Pygocentrus nattereri]

Piranha 3D is a great movie, but it is not real.

Given the high temperatures of the day perhaps more people were bathing than usual and if the area is dammed, as much of the Parana is, the fish may have felt trapped, especially if breeding. These fishes were likely biting as a defense from the many people in the crowded water. If piranhas want to eat something, they will do so quite thoroughly, they won't peck. They will bite to protect themselves and that is not what I would call an "attack."

How this became an international media story is another mystery, but the name of the river likely caused some to guess that piranhas were the culprits. That, and some good pics of people with bloody toes.

Unfortunately, it does sound like some people were hurt, I hope they recover quickly. However, the news media should be accountable for the many errors in this sensationalized story.

On Sarcopterygii

Introduction

Sarcopterygii, or the lobe-finned fishes, includes the coelacanths, lungfishes, fishes involved in the transition to land, and all tetrapods (mammals, amphibians, and reptiles [the birds, turtles, crocodiles, and squamates]). The lobe-finned fishes are Devonian in age and the sister group to Actinopterygii, or ray-finned fishes. Actinopterygii and Sarcopterygii are nearly of equal size (c. 30,000 spp. each). Actinopterygii is dominated by the teleost fishes, just as Sarcopterygii is dominated by tetrapods. In this essay, the focus will be the non-tetrapod members of Sarcopterygii, as I study fishes; however, it is worth noting many of the skeletal elements and organ systems of tetrapods originated in our aquatic sarcopterygian ancestors.  Had actinopterygians been the group to take charge as the vertebrate class to dominate land, terrestrial vertebrates would look very different.  It is likely that we would breathe through our mouths alone or through our skin, be much smaller, and be hugging the ground with soft rays holding us up against gravity rather than digits and wrist bones. It was the advent of internal nostrils, or choanae, in aquatic sarcopterygians that permitted us to breathe through our noses;

The rare ray-finned fish that can "walk" on land, the mudskipper. Image from http://www.studentsoftheworld.info/sites/animals/shadows.php

likewise, our forelimb and hindlimb bones all originated with lobe-finned fishes. As it were, the story of the water to land transition is remarkably well known given an excellent series of transitional fossils that fill the steps in the gap between “fishes” and early tetrapods. Some of these intermediate fossils, like the famous Tiktallik rosea, tell us about the evolution of everything from the “neck” to the origin of sturdy ribs and limbs. Luckily for us, there are still extant aquatic lobe-finned fishes. Although they were not directly involved in the terrestrial transition, they can tell us a great deal about how ancient lobed-fins lived. Today only lungfishes and coelacanths survive as the aquatic members of this lineage. These two forms themselves have continued to evolve from our common ancestor, and they each have an amazing array of novelties.

Evolution and Systematics

            Coelacanths belong to Actinistia (or Coelacanthimorpha), which has a long fossil record (Mid-Devonian to Late Cretaceous) and that is species rich relative to the two species extant today (83 valid fossil species in nine worldwide families). Members of Actinistia are easily recognized by their tri-lobed diphycercal tail (the vertebral column enters the middle lobe). Known as fossils from both marine and freshwater deposits, they were thought to have gone extinct over 65 million years ago, until a living species was discovered in 1938 to much fanfare. (The discovery of both living species have spectacular stories behind them. See www.dinofish.com)

          Lungfishes are members of Dipnoi (themselves part of the larger group Porolepimorpha, largely made up of extinct forms). This clade also evolved in Early Devonian freshwaters, and is represented in the fossil record by more than 100 species in more than 50 genera. Their great fossil record of lungfishes was likely aided by their ability to estivate. These fishes can protect themselves from drought by building a mucous-mud cocoon. They enter periods of estivation that in modern forms can last up to four years; many individuals in the past have expired waiting for that next rain. These individuals and their cocoons make for spectacular, if plaintive, fossils. From fossil forms, we see a trend toward the reduction of bone (in the skull, scales, and fins). Unique plate-like grinding toothplates easily help place extinct and extant forms as each other’s closest relatives.

            Tetrapodomorphs are the intermediate forms between the first tetrapods to conquer land and their piscine ancestors. They are all limbed, extinct early Devonian forms, and air-breathers. They include Osteolepimorpha (rhipidistians), Rhizodontiformes, and Elpistostegalians. It is the tetrapodomorphs, in particular the Elpistostegalians (which includes Tiktallik) and not coelacanths or lungfishes, that are the closest relatives to tetrapods.  

A modern day coelacanth, Latimeria chalumnae.

Physical Characteristics

Both lungfishes and coelacanths can reach large sizes, approaching 2 m, although lungfishes are much more slender bodied. Both groups have a number of derived features that make each group unique. Coelacanths have a special rostral electroreceptive organ, a vertebral column that is secondarily reduced, no maxilla, and an intercranial joint found in many extinct fish lineages but no other living species. Coelacanths have only external nostrils (no choanae) and a large fat-filled gas bladder (no lung). These two latter features have been used by some authors as evidence that these fishes are ancestral to lungfishes (which have both lungs and choanae), but these primitive features may have more to do with the current ecology of these animals than their biological history.

            There are three extant families of lungfishes: Ceratodontidae of Australia, Lepidosirenidae of South America, and Protopteridae of Africa.  Lungfishes are easily recognized by their continuous rear fins that connect their dorsal, caudal, and anal fins.  The Australian Lungfish (Neoceratodus forsteri) has a number of pleisiomorphic morphological features that resemble fossil forms more so than the other extant lineages. Instead of the tiny worm-like fins of the other species, the Australian form has broad flat fins, large scales, and unpaired lungs (versus small scales and paired lungs in the other taxa). Lungfishes eat both plant and animal material, including ray-finned fishes and invertebrates.

Reproductive Biology

              Coelacanths are ovoviviparous; they retain eggs in the body cavity. The young hatch and develop internally. African and South American lungfishes make nests where females lay eggs, and males guard the nests. The Australian species lays its eggs on aquatic plants. The African and South American forms have young with large external gills that often cause them to be mistaken for salamanders.

Conservation

               The conservation status of most lungfishes is poorly known, but the Australian lungfish is uncommon, confined to just four rivers in Queensland.

Among coelacanths, Latimeria chalumnae is found off the eastern to southeastern coast of Africa and around the Comoros Islands and Madagascar, and L. menadoensis is only known from Sulawesi, Indonesia. Coelacanths are found at depths beyond the range of most artisanal fishermen (150 to 253m), but accidental capture occurs frequently enough that some estimate that as much as 5% of the adult population is captured annually. Coelacanths aggregate and rest in caves; they may be limited by the number of these sites that are available.  

Significance to Humans

               As Moyle and Cech state, “probably no single event in the history of ichthyology has received more public attention than the discovery of the coelacanth (Latimeria chalumnae) in 1938.” The discovery of this large, deep sea, limbed, fish-link-to-man made for fantastic headlines.  Lungfishes, too, have a spectacular mix of features that make them popular aquarium fishes. Both sarcopterygian fish clades are important to humans for their unique position on the other side of the coin to the vertebrate transition to land.

References

Bemis, W.E, Burggren, W.W., Kemp, N.E. (1987) The biology and evolution of lungfishes. Alan R. Liss, Inc., New York.

Carroll, R.L. 1996. Vertebrate paleontology and evolution. W.H. Freeman. New York.

Helfman, G.S., Collette, B.B, Facey, D.E., Bowen, B.W. 2009. The diversity of fishes, 2^nd ed. Wiley Blackwell, West Sussex, UK.

Moyle, P.B., and Cech Jr., J.J. (2004) Fishes, an introduction to ichthyology, 5^th edition. Prentice Hall, New Jersey.

Musick, J.A., Bruton, M.N., Balon, E.K. (1991) The biology of Latimeria chalumnae and             evolution of coelacanths.  Environmental Biology of Fishes 32, 1-435.

Interview with Edward Drinker Cope and End Cheer at the Joint Meeting of Ichthyologists and Herpetologists 2013 Banquet

The real E.D. Cope

The following is text from the final banquet of the Joint Meeting of Ichthyologists and Herpetologists meeting in July 2013 in Albuquerque, New Mexico. I was MC and brought up a very special guest played by Brian Sidlauskas. (PC: Prosanta Chakrabarty; Cope text in italics)

PC: On this 100th anniversary of our journal Copeia, I'd like to call our namesake, and Bruce Collette’s college roomate, Edward Drinker Cope.

PC: Dr. Cope what an absolute honor it is to have you up here with us. You look remarkably well preserved for someone who has been dead for more than 120yrs and sick for 150.

COPE: Yes, yes, it must be an honor for yall - not everyday that you get to meet the Neotype of your own species.

By the way has someone seen my skull The knucklehead that made me the Neotype borrowed it from the Academy in Philadelphia and never brought it back. I thought Lundberg and Sabaj would have found it by now. Has anyone checked Lundberg’s office?

PC: Well I'd like to ask you what you think about the the journal Copeia.

COPE: Well I am pleased by the honor but I wish our impact factor was a whole number. I mean my personal H-index is higher than all of Copeia! Couldn’t you have named a better journal after me like Science or Nature or maybe Herpetologica?

PC: How about the ASIH society are we living up to your name?

Well I would be remiss not to mention that I have still published more papers than everyone in this room combined.

Tom Near (Yale Professor): Othniel C. Marsh says they are mostly crap descriptions

COPE: Stuff it Yale boy, go cuddle with your grand pappy Marsh!

PC: Fellas, fellas, take it easy, let's get back to the questions here. Dr. Cope what do you think of the next generation of ichthyologists and herpetologists here today, the students. Can you speak directly to them.

COPE: Well I think they are bunch of sissies – that’s what I think if you really want to know. All I hear is "I'll never get a job, there are no curator positions, nah, nah, nah”

You think I had a job? I turned down jobs so I could do field work. I had to buy the house next to me to even have a place to store my specimens. Besides even Chakrabarty got a friggin job – obviously they’ll hire anyone these days.

 

The ghost of E.D. Cope as played by Brian Sidlauskas

PC: Uh thanks, I guess. They are supposedly making a movie called Bone Wars about your career and rivalry with Marsh. Marsh was set to be played by James Gandofini until his recent passing. What do you think of being played by Steve Carrel?

COPE: Just dandy I suppose. Marsh was going to be played by Tony Soprano and I get the 4^th male lead in Anchorman 2. Maybe that Gandolfini is dead they can replace Marsh with an actor with a closer resemblance. Maybe Snooki from Jersey Shore or the chubby kid from Jerry McGuire.

I just hope they don’t say anything about all my STD’s like they did in the book.

PC: Well I gotta ask would you like to clear up the rumor that you regularly dipped your, uhh…member…in formaldehyde to ease the symptoms of syphilis.

COPE: That is an utter falsehood [slams fist on table!]

I only dipped half my penis in formaldehyde.....

Although it was the back half.

Okay then Dr. Cope thank for clearing that up I guess. Thank you again for being such an inspiration to the society.

COPE: By the way I have not seen a penny of the dues as royalties for that matter. You know the Academy didn’t want to pay me either and I’ve been cursing them since. If you ever want your impact factor to be above one I suggest you pay up. I accept payment in drinks remember my middle name is Drinker!

-      Now I’m afraid that this has gone on long enough. I actually submitted a 1/2 page species description to Copeia and I just got 18 pages of reviewer comments back, including accusations of character assassination, specimen theft, collecting without an approved IACUC protocol and destruction of field sites with dynamite. Lies, all of it!  I have a rebuttal to write.

-       I also have to go check my H-index. Anyway - adios for Albuquerque, and don’t forget those drinks later for Edward Drinker. 

Prosanta and E.D. Cope toasting and roasting.

LATER ON THAT EVENING....Cope's parts in italics

It has been a great meeting. At this time I want to bring up Dr. Cope once again….to help me with a toast, so please raise a glass and drink!

Here’s to 100yrs of Copeia

A hundred years of cheers, a hundred years of beers

A hundred years of graduate student tears

Here’s to Copeia..

Here’s to 15page reviews for 5 page species descriptions

Here’s to cold blooded lower vertebrates and mass extinctions

Here’s to Copeia, the finest fish and herp journal in the land

Here’s to Copeia the ONLY fish and herp journal in the land

Here’s to 100 more years of our beautiful journal being fresh and new

The first edition was stapled together, the last one will be too

TOGETHER: Well 3 cheers for Copeia. May you last forever and never die!

Nah, nah, nah, hey, hey, hey, goodbye!!!

Goodbye Albuquerque! 

 

Ichthyology trip to Japan: Conference Piggybacking

At the end of June, my PhD student Bill Ludt and I went to Okinawa for the 9^th Indo-Pacific Fish Conference (IPFC), and then traveled to Tokyo to do a market survey and collection at the famous Tsukiji Market. The IPFC is held every 4 years and it is a mix of an ichthyology and evolution conferences that is important for everyone working on fishes in the region. This year’s conference was particularly important for me because it included a Percomorph Symposium that dealt with higher-level fish systematics and included a series of well-known and well-respected speakers (obviously I wasn’t invited to speak), and it was one of the most important single days in systematic ichthyology signaling in a paradigm shift in our discipline.

Bill Ludt:Tuna Hunter

        The meeting is typically held in an interesting and beautiful location that is usually a great spot for collecting fishes too. The last IPFC in 2009 was in Perth, Australia; at that meeting I was able to get away to collect cavefish from Exmouth in the northern part of the country. This year’s conference was relatively small, with only 500 people, but it is a great conference for networking with other like-minded scientists. Both Bill and I left with several new collaborations that we are truly excited about.

Okinawa is at the southern reaches of Japan, closer to Taipei, Taiwan than to Tokyo and with a rich history of its own. (It may be fighting for its independence as a sovereign nation in the near future.) The conference center was a few steps from a beach and a crystal clear blue ocean, but there was little time to enjoy it. The talks were fantastic and groundbreaking with lots of new systematic efforts highlighting new molecular techniques. The next generation of sequencing is here and I was very excited to talk about ultraconserved elements and our project on using massively parallel sequencing to resolve the basal relationships of Ostariophysi (a group of 10,000 species that includes catfishes, electric knifefishes, tetras, piranhas, goldfish, and over 70% of freshwater fishes; this lineage alone represents 1 in every 6 species of vertebrate). After a few years of giving talks about projects I had just recently published I loved talking about something so fresh that I didn’t have results to talk about until a week before we were set to leave. Bill on the other hand was much better prepared and he gave an excellent talk on Prionurus, a group of surgeonfishes (so named because of razor sharp barbs near their tail). This genus of seven species are distributed in cold waters in disjunct areas that are essentially anti-tropical. Bill presented a dated phylogeny that helped explain their evolutionary history and unusual distribution. Directly following his talk several very well known scientists approached him and I was proud of him as he began making a name for himself in the fish world.

Tsukiji Market.

Bluefin tuna auction.

After the conference Bill and I flew up to Tokyo, which was another world all together. As a New York City kid that thinks he is well traveled (Japan was my 24^th country visited) I was surprised by how mesmerized I was by this ultramodern city that still had plenty of old world charm. The largest city in the world humbled me in its size, diversity and culture. Along with exploring a new city, our main goal was to collect as many species as we could at the world’s largest fish market, Tsukiji. This is home of the world famous bluefin tuna auction where last year a single individual sold for 1.7 million dollars. The bluefin is highly endangered and could go extinct by the next decade or so. Sought after for its crimson meat that is a result of a countercurrent circulation that endows this great species with the ability to travel at amazing speeds also has made it one of the most sought after national resources in the world. Bluefin are flown in from around the world and I’ve actually seen individuals collected in Sri Lanka that would quickly make their way to Tokyo via private jet. Bill and I couldn’t resist heading to the market at 3am to observe the proceedings. The auction doesn’t take place until 5am but in order to get in to see the trading of bluefin you need to be ahead of the pack. The auction itself is rather quaint despite the high stakes: gentlemen (I saw no female participants) with flashlights and dower faces looked closely at the exposed red meat of the tunas like a mechanic evaluating the engine of a Lamborghini. The huge fish sold quickly and we were ushered away just as fast. Tsukiji itself was a bit of a disappointment to me. As the world’s largest fish market I was expecting to find a large assortment of species that boatmen were delivering directly to the wholesalers. In large markets in Thailand and Taiwan I saw enormous ships bring in thousands (if not millions) of fish to the banks and saw sellers buying up what they could: what they didn’t want was discarded in large piles. These large piles hide an exceptionally diverse assortment of rare species and often included deep-sea creatures that would be very difficult to get otherwise. Deep-sea research vessels can charge upwards of $30K a day, but at the bycatch trash piles the fish are free and the hard work is done for you. Unfortunately, Tsukiji is a different monster all together. The market is only open to the public from 9-10am. The rest of the time from 5am, the wholesalers are packing up specimens that are being brought in from all over the world and setting them up to be shipped out to other locations around the world. It is more of a post office sorting center than the all-purpose warehouse I expected. So that meant I found no bycatch pile and only fish that are being eating and sold for a profit. Many of the vendors’ booths, and there were over 100 of them, would not sell to us because they only sold 10kg at a time or some other fixed weight. We had a bit more luck when we explained we were scientists but because we came when the annoying tourists were also there we got many strange looks and curt replies when we inquired about purchasing the different species. In the end we only ended up with about 30 species and perhaps 50 individuals. However, since most of them are new to our collection it was certainly worth it. It just wasn’t what we expected from what we had heard about the market in the past.

Processing fish in the middle of a crowded Tokyo street.

Overall it was a memorable and productive trip both in terms of collaborations made and fishes collected. I most certainly want to return to Japan to do some proper collecting in the future.

Ichthyological Adventures in Central America Part 2: Collecting Fishes in Guatemala

Caleb at some Mayan ruins in Yaxhá.

           From February 28^th to March 12^th my 3^rd yr PhD student Caleb McMahan and I traveled to Guatemala to collect and study fishes for the museum. This trip was particularly exciting because we had worked on obtaining permits from Guatemala for over three years. It was only through the networking of Caleb and my former postdoc Dr. Wilfredo Matamoros at the Congreso Nacional de Ictiología conference in Chiapas, Mexico (2012) that we were able to finally get some contacts that could help us. The trip was also very exciting for me because with these collections it meant that my lab had been to every Central American country. We’ve sampled Costa Rica (2011), El Salvador (2011), Panama (2011), Nicaragua (2011) and Honduras (4 times since 2010). I traveled to Belize as part of my dissertation work in 2004. Guatemala would be a real prize because no outside ichthyologists have intensively sampled the native freshwater fishes since Donn Rosen and Reeve Bailey in 1974. Both of those gentlemen are my heroes. Rosen was a former curator at the American Museum of Natural History and was instrumental in founding the field of historical biogeography. Bailey was a curator of fishes at the University of Michigan Museum of Zoology and was collecting into his mid 90s while I was a there as a grad student (he passed away at age 100 a few years ago).

The Guatemala Fishing Team, from left to right, Diego Elias, Yasmin Quintana, Prosanta Chakrabarty, Caleb McMahan and Christian Barrientos.

            In Guatemala, we were aided by Christian Barrientos who is currently a PhD student at the University of Florida and a Guatemalan native. A-soon-to-be finished undergraduate, Diego Elias, and a Guatemalan environmental agent, Yasmin Quintana, also joined us to complete the collecting team.

Thorichthys pasionis

            Guatemala has a notable geological history as well as a biological one. The northern portion of the country is part of the Yucatan Peninsula (the Maya Block that is the southern portion of geologic North America) that is primarily in southern Mexico and parts of Belize. The more southern portion of the country is part of the Chortis Block that includes El Salvador, Honduras and parts of Nicaragua; this block is geologically on the Caribbean tectonic plate. The North American and Caribbean plates are separated by the Motagua fault that runs through Guatemala. You can see the difference as you drive along the central highway passing from the mountainous, limestone-rich Yucatan to the flatter more earthy Chortis Block.  We spent most of our time sampling within the Yucatan portion (Peten) where cenotes, caves and other primary limestone habitats were abundant. The karstic landscape gives a notable blue green tint to much of the freshwaters in the Yucatan region so that you could get fooled into thinking you are collecting in the tropical ocean if were not for the fact that you were surrounded by lush green inland forests.

Early morning casting in Lago de Peten.

            We began our trip, as we often do, landing in the capital city airport, Guatemala City in this case – and, as is typically the case – site seeing was restricted to what could be viewed from the car window on the way out to the countryside.  Luckily, the rich Mayan history of Guatemala has left much behind and we even sampled in the shadows of some giant ruins in Yaxhá (where the reality show Survivor was filmed in 2005). The perpetual frightening growl of the otherwise adorable Howler monkey also seemed to add to the sense that we were in a mythical, prehistoric land. Among our primary targets were the cichlid fishes of the region - about 23 species. Many of these are very important to our continued studies of Central American fishes and their biogeographic history. We sampled first along the Caribbean Slope in Lago Izabal, waking each morning before dawn and sampling until dusk. It was exhausting but well worth it. We typically collected from a boat that took us along to various sites that were otherwise inaccessible by foot. Using castnets and seines we collected the black-belt cichlid, Vieja maculicauda and several other beautiful species of cichlids I had only seen as colorless specimens in jars or from aquarist photos. One of the species we were collecting was Paraneetroplus melanurus that Caleb had studied and synonymized with another popular species (i.e., he found that the two species were in fact just one - much to the chagrin of the cichlid aquarists).

A nice "blanco"

            One of my favorite sites was Lago de Peten. Ever since I started working with cichlids as a graduate student I always wanted to catch “blancos,” Petenia splendida from Lake Peten. Not only did we collect them, we had enough to eat (it’s always good when your study animal is as delicious as it is phylogenetically important). Our local hosts are doing several ecological studies on the fishes in these lakes and they were surprised to see us catch several species they had not seen before in that area. I told them that it was all based on Caleb’s fishing skills. Caleb has quickly become one of the best-known ichthyologists studying Central America. He worked there for his Master’s degree at Southeastern Louisiana University but his reputation has grown greatly in the past few years, and deservedly so. I would put his knowledge of the fishes of these regions up against anyone alive today. He was recently rewarded for his efforts in studying the region with a National Science Foundation Doctoral Dissertation Grant. Caleb also won the prestigious Stoye Award at the Annual Meeting of Ichthyologists and Herpetologists, this award is the highest prize a fish student can get as a graduate student.

Mouth of the Coban, flowing out of a cave.

            One of our last field sites was in Coban, an area we were eager to sample because it is a very different system than the Río Usumacinta system we had sampled most of the trip. Unfortunately, our first Coban site smelled like a sewer. After retrieving my first castnet throw all I managed to pull out of the water was some weird white filmy material. As a faux-Cajan I cast by putting one end of the net in my teeth: this technique has its drawbacks. Just as I put the cast in my teeth for the next throw I was informed that the white filmy material was toilet paper: a clear sign that this water was full of untreated sewage. After washing my mouth out thoroughly we decided to move on. Luckily we were able to get much better sites downstream where gringo tourists were happily inner tubing. Some of our best collections were actually from local kids that were snorkeling and spearing the fish with makeshift spear guns. I envied their skill and was glad they happily exchanged their haul for a few quetzales (the local currency, named after the national bird - a type of trogon).

Caleb and Prosanta and their makeshift back-of-the-truck fish laboratory.

            Overall the trip was a success. We collected over 59 species, nearly 600 tissue samples and about 2000 specimens. There is much of Guatemala left unexplored because permission has to be granted by local native communities who can be weary of outsiders (which include local non-native peoples). Despite my desire to go to those areas I’m glad they are protected by people who care about their land and freshwaters. Yasmin and Diego are set to work up our collection at LSU in May and we look forward to figuring out if we have any new species. We most certainly made collections that other Neotropical ichthyologists will be quite envious of.  

Collecting Fishes for a Biodiversity Workshop in Singapore

PC and Bill Ludt in Singapore

From October 15^th to November 2^nd last year my PhD student Bill Ludt and I traveled to be part of the Singapore Jahore Strait Marine Biodiversity Workshop. I had traveled to Singapore in 2007 to collect but mainly spent all my time at markets where I purchased fish that were being sold. (Market collecting can barely be considered fieldwork, the fish are brought to you after all; however, it is an excellent way to get a lot of diversity quickly and cheaply.) In my previous trip to Singapore I had assumed that this tiny island nation was essentially a giant city with little wildlife or remaining forest. That is why I was pleasantly surprised when I discovered that the workshop would take place on Pulau Ubin, a small island off the northern coast of “mainland” Singapore. Pulau Ubin is almost completely forested except for a few residents, bike paths for ecotourists, and an OBS (Outward Bound School) camp where we stayed most of the time.  The island is only 10sq km (about an 1/6 the size of Manhattan) but it is so densely forested that it sustains a large wild boar population that we saw frequently.

Fig 1: Anchovy, Coilia

This small island is also the location of the last reported tiger sighting (in the 1980s) on Singapore. (A tiger was famously shot under the Long Bar at the Raffles Hotel in 1902, that bar is also the birthplace of the notorious cocktail, the Singapore Sling.) We also saw wild otters a myriad of colorful birds (including an elusive Great Billed Heron), and of course, lots of cool fish. However, unlike my last Singapore trip we collected most of these fish ourselves and ended up collecting nearly 2,000 specimens from 250 species. We collected mostly using 15’ beach seines, but also using dipnets in mangroves, gillnets, and via trawls on a small ocean research vessel.

Fig 2. Stonefish

            This was a different experience than my previous collecting trips. I was invited to collect as the “fish expert” along with international experts in other groups including, bryozoans, anemones, isopods, copepods, etc. In all there were about 20 invited zoologists and dozens of local scientists and volunteers from the Raffles Museum and other local institutions. Each day we would sign up for one of three or four field trips to various parts of the island or mainland. Then we would go on a well-organized trip to that locality and collect alongside other experts for several hours before being returned to the lab at the OBS camp to sort, ID, photograph, tag and tissue the specimens. Bill and I would not only deal with the samples that we collected but also fishes that others collected for us. In the end we ended up having specimens from over 60 field sites in the nearly three weeks we were there.

            The OBS camp was an interesting place. Breakfast, lunch and dinner were served there in a regular schedule and in a regular pattern that we quickly grew tired of. The food wasn’t awful but we knew that just over the Serangoon Harbor there was the most delicious food in the world. Mainland Singapore has its own unique cuisine but also serves food from all over Asia. Bill and I savored each Roti Chennai, Chai Tea, and Chili Crab that we could get our hands on.

Fig 3

            In the end the trip was a wonderful success. We collected many species that were new to our LSU collections and that are rare in collections outside of Asia. Among the highlights is a specimen of Coilia, a bioluminescent anchovy (Fig1), a highly venomous and dangerous stonefish (Fig2) and several species of archerfishes (Fig3). The archerfish samples were particularly important. These fish hang out near the surface of the water and spit out a small squirt of water at leaves above them to make insects attached to those leaves fall into the water below. The fish then eat those insects. This unique behavior would make you think they are closely tied to the land but they have a rather wide distribution across several continents. My former labmate at the University of Michigan, Heok Hee Ng, who now works in Singapore and I will be working up the phylogeny of this group in the future.

            Besides establishing this collaboration and meeting many international experts this was also Bill’s first international field trip. He did an excellent job and he and I will be collecting again in Japan this summer. We can only hope that these future trips will be equally successful.

Going Down Under: Caving for Fish in Australia

November 2009

         In May and part of June, I traveled to Western Australia for a three-week trip that was equal parts collecting, museum work, and fish conference. For this trip I had to go down under, literally. The first part of the trip involved entering some tight subterranean habitats in search of blind cave fish. The second part of the trip was working up some bioluminescent fishes collected for me at the Western Australia Museum in Perth and the third leg was the Indo-Pacific Fish Conference in Freemantle. It was a very interesting and worthwhile adventure all around. This trip was also notable at a personal level because I was able to have my wife, Annemarie Noël, join me. I’ll spare you the details about the conference (I won an award!) and museum work (I found a new species!) so that I can focus on the collecting.

         The collecting trip was nearly derailed before it got started. Despite more than six months of planning and negotiation, my permits were nullified at the last minute. The permits were voided because of a miscommunication between the Western Australia Museum (WAM) and the Australian government. The timing could not have been worse; I got the news via e-mail the Friday before I was to leave. Because our Friday morning is already Saturday in Australia, I was unable to remedy the situation before my flights. I spent the entire time traveling to Australia worried sick that I wouldn’t be able to collect. After flying for what seemed like three days (actually only two days) and finally arriving in Perth I immediately called the collection manager of the WAM. She explained that there was a terrible misunderstanding and that she would talk to the government to reinstate my permit. Unfortunately the new permits were much more limiting than the originals, but certainly better than nothing.

         The next morning Annemarie and I boarded a flight to Exmouth, which is about 1300km north of Perth. The town of Exmouth is in the Northwest Cape, a small peninsula that is nearly the most western tip of Australia. Around that peninsula, also called Ningaloo, is the only part of Australia with cave fish. Their habitat is distributed around the few hundred kilometers of the peninsula. Only one species is known, Milyeringa veritas, commonly known as the blind gudgeon. Based on some preliminary work I suspect that there is more than one species. These fish are poorly known and the populations are likely much bigger than the few specimens we find in caves. Their real homes are the inaccessible underground water chambers that span many kilometers.

I became interested in blind subterranean fishes after collecting them in parts of Madagascar last year. The first thing I noticed about the Northwest Cape of Australia is how much it resembles Southeastern Madagascar. Both locations are dry landscapes with a bright maroon colored soil, baobab trees and short stubby brush. The other thing they have in common is the presence of blind, pigment-less, subterranean fishes. From my previous work I learned that the closest relative of the blind fishes in Madagascar are the blind fish in Australia. These helpless blind aquatic animals can’t travel 10 feet out of the caves let alone across the Indian Ocean. Their long history of living underground and being isolated from predators made pigment and vision unnecessary. The only explanation for the disjunct distribution of this Malagasy/Australian lineage is that these fishes were once part of a continuous landmass that subsequently broke apart. That former continuous landmass is known as Gondwana, and it included both Australia and Madagascar and possibly the common ancestor of these fishes. These fishes are part of a lineage that has survived the 130 million years since the break up of Gondwana. They’ve managed to survive in isolation oblivious to the changes above ground. The extinction of non- avian dinosaurs, bolide strikes, climate change, and the rise of humanity has not caused them to blink an eye (if they had eyes to blink).

On our first collecting day, we went to six locations where Milyeringa had been collected previously. At our first site, Woburi Rockhole, we drove a little bit off the road in Exmouth to a small hole in the ground that led to a larger underground chamber. We had to shimmie down a metal pole that was rigged up for cave divers to enter from above into the water below.

         As we entered you could see fossil marine shells in the limestone deposits lining the walls of the entrance. Inside the cave, which was tiny compared to what I experienced in Madagascar, we saw eight specimens of Milyeringa veritas. I was glad to have Annemarie with me as this was her first experience with caves. Inside the cave we found the skeleton of a large kangaroo that must have fallen into the cave about a month earlier. We were lucky we didn’t discover it a week earlier because it was surrounded by thousands of fresh fly egg casings. It will make for a fine fossil one day. We spent about a half an hour in the cave before moving on. The next sites were mostly wells that were built next to small enclosed caves. Aboriginals had used the caves to get ground water for hundreds of years and you could still see the shards on the ground from the shells they once used to bring up water. Later settlers built wells for easier access to the water. I shimmied down some of the wells by pressing my back and hands against the wall while my feet were pressed against the other side. In other wells our guide, the wonderful spelunker Darren Brooks, used repelling equipment to drop sometimes more than 30 feet to get to the water and fish below.

         The most interesting cave was a site we entered on the second day. At first glance I thought it would be impossible to enter. The entrance was just two small holes, one that looked to be about 45 inches around and the other perhaps 15 inches around. Neither looked particularly inviting. The larger opening and the tunnel below were so tight that I needed to take my helmet off in order to fit. The cave itself was shaped like an Erlenmeyer flask with a tight elbow shaped entrance. After dropping a small chain ladder down the hole (making the entrance even tighter) we slowly slipped down about 15 feet into a small pocket that led to a short horizontal shelf that led to another drop of 15 feet into the main chamber. This chamber was filled with water and luckily a couple of blind gudgeon. We needed the ladder for the last drop because there was nothing to grab onto for the last ten feet. The bowl shaped chamber was dark and damp and the high CO2 levels meant that we couldn’t stay there very long. We collected a single specimen from that cave and headed back out. The climb back out of that cave was one of the scariest most physically challenging things I’ve ever done. After climbing out of the first chamber relatively easy I made a stupid mistake and tried to exit by climbing out facing a different direction than I had gone in. I found myself stuck like a fly in a pitcher plant.

I could feel the cool air above me but I couldn’t move my arms above my head nor could I move my knees to leverage myself upward. It was extremely claustrophobic and terribly frustrating. After doing the equivalent of a hundred push ups and making no progress in getting out I headed back down to turn around. Finally, after 15 minutes of scraping myself against limestone and brushing biting ants from my face, I got out. All for a little blind fish – but in the end it was worth it. (My wife took excruciating video of my progress out of the cave that nobody reading this will ever see.)

The collecting part of the trip was much shorter than I had hoped but I gained enough materials to do what I had intended. Before heading to Perth Annemarie and I decided to do something completely different from hunting little three-inch fish in holes. We went swimming with the largest fish, the whale sharks. After dealing with dark and tight spaces it was great to actually get into the great Indian Ocean and follow some 20 foot sharks around for a day. The remainder of the trip was also fruitful and enlightening but nothing will be as memorable as our time in the Northwest Cape.