Friday, September 14, 2012

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.

Collecting Fishes in Vietnam

by Prosanta Chakrabarty and Matt Davis

May 2010

In late January to early February of this year, my postdoc Matt Davis and I traveled to Vietnam to collect some marine fishes from markets. Every year I try to make a trip to Asia to collect rare fishes for the LSU fish collection and for phylogenetic study. The large open markets of Asia allow us to collect a diverse number of species in a relatively short amount of time. Instead of hiring a trawler (upwards of $10K a day) it’s easier to hang out on the docks to grab some freebies off the boats. Typically we collect early in the morning and spend the rest of the day processing the fish (voucher, label, tissue sample, preserve, etc.). Because of the great quantity of fish that we were dealing with it really did take nearly the entire day to process the specimens from each morning’s haul. On this trip we collected roughly 400 different marine species and more than 2,000 specimens in two weeks. We also had a couple of days to do some fresh/ brackish water collecting on the Mekong Delta. The Mekong is one of the world’s oldest and oddest rivers and is home to car-sized catfish, giant stingrays, and other behemoths of the fish world.
         Vietnam is a long narrow country that spans several biotic regions including the Mekong Delta, South China Sea, and Gulf of Thailand. We saw long stretches of amazing beaches, and miles of huge inland sand dunes directly abutting verdant green rainforest. It is also culturally diverse. We saw signs of socialist pride (the old Soviet hammer and sickle was ubiquitous) and French imperialism (baguettes and wrought iron abound), mixed with an Indo-Thai- Chinese culture found nowhere else. The people were extremely courteous and amiable, sometimes too much so, making for a fun cultural experience. Matt in particular was gawked at constantly for being a giant white man with funny colored straight hair.
         Matt and I traveled with four Taiwanese colleagues that had previous experience collecting in Vietnam. It was my first time traveling in Asia without locals to help translate (as the Taiwanese spoke no Vietnamese). This made for some funny and frustrating situations.
         During our trip we traveled to Ho Chi Minh City (Saigon), and the beautiful beach towns of Mui Ne and Nha Trang. The first two things that stood out about Ho Chi Minh City included the amazing diversity of food and the incredible numbers of scooters – the many, many scooters. These scooters zoomed past and parted around you like a school of fish. For the most part there were no traffic signals or even traffic patterns, just a free for all of scooters, taxis, and buses. Many large cities in Asia have similar numbers of scooters on the streets, but they all had some semblance of organization. Our Taiwanese colleagues, who ride scooters in Taiwan quite often, would not rent scooters in Ho Chi Minh, and often remarked how “they drive crazy here.” To cross a street in Vietnam you have to walk deliberately into the non-stop flow of traffic keeping a steady pace so that the traffic will move around you. Amazingly it works, although I thought each time that I would be maimed. When we left Ho Chi Minh we ended up on scooters ourselves to travel between fishing ports. Even in these less populated areas weaving in-and-out of traffic and speeding on the “wrong side” was still a common occurrence.
After a while you get used to it, and even I went out on my own a few times with my little rented ”motobike” to relax and blow the smell of fish out of my clothes.
         The markets we visited (more than 20 in all) were mostly small artisanal fisheries from local fisherman collecting on the South China Sea. The fishes that we were collecting were not always being sold at the market but were often part of the rubbage pile of bycatch. As in most cases the bycatch piles are chock full of strange fishes that no one would purchase for their dinner. It was in these piles that we collected odd silvery eels, fatheaded jawfishes, fleshy dark deepsea fishes, and numerous other oddities that we ichthyologists crave. The markets themselves were also remarkably diverse matching the diets of the locals. You know if the Vietnamese weren’t eating them that the fish must look very strange.
         Matt, who the Taiwanese referred to as “Max” the entire trip, was after some of the fish he studied during his dissertation, in particular the lizardfishes. Lizardfishes include cigar-shaped predatory fishes that dwell along the bottom of the continental slope to depths of around 200 meters. Of particular note were specimens collected of the only mesopelagic lizardfish genus Harpadon, commonly known as the “Bombay Duck” and found only in the Indo-Pacific. (The nickname comes from Indian restaurateurs trying to make the fish sound more appetizing to British diners.) Dried Harpadon is considered a delicacy in parts of Asia, and indeed we often spotted hundreds of dried out specimens lying on the street, a sight that would make Matt cringe each time. In the end we managed to procure quite a few fresh specimens, including a potentially new species that exhibits sexual dimorphism.
Near the end of the trip we went out collecting on the Mekong Delta. It took some work getting to the Mekong and hiring a boat but once aboard we would ask our driver (ask as in point to a boat and to a picture of a fish) to take us toward the small fishing boats trawling the Mekong. It was by trading with boatman that we collected some of the most interesting freshwater and brackish water specimens. Nearly every specimen collected is new to the LSU collection, and some are certainly new to science. The products of the trip will be additional materials for our on going projects on the family level phylogenies of some notable deepsea, bioluminescent, and otherwise poorly studied Western Indo

Wednesday, September 12, 2012

Measuring the Environmental Impact of the Gulf Oil Spill

November 2010
The oil spill in the Gulf of Mexico was the largest accidental release of oil in history with over 4.9 million barrels (=206 million gallons) released; however, accessing the actual environmental impacts will be very difficult. The largest environmental impact is likely to take place in the part of the world that is most unfamiliar to us and the least studied - the deep sea.
         The well associated with the Deepwater Horizon rig was nearly a mile (1.6 km) below the surface; everything below 1 km from the ocean’s surface is considered the deep sea. This environment is the largest most stable habitat on Earth; it is perpetually in darkness (no sunlight penetrates this region) and is always cold (only 1 to 2°C above freezing). The animals that live there are subject to enormous pressure (hundreds of pounds per inch) and also have to deal with vast amounts of empty space (prey items and mates are difficult to find). These difficult conditions have led to the evolution of some strange-looking organisms. Adaptations for this environment include flashing lures, fleshy black bodies, giant teeth and eyes, and generally odd body shapes and behaviors (see photos on page 4). The majority of animals that live here use bioluminescence (light generated from bacterial symbionts or by the animal itself) to communicate and to attract prey. The common perception that the deep sea is depauperate in terms of species richness and diversity is wrong. The most abundant vertebrate species in the world live in this habitat (lanternfishes, Neoscopelus spp.; bristlemouths, Cyclothone spp.) as do some of the rarest and most bizarre forms known. There are more than 2,000 fish species known from the deep sea (more than all the birds, amphibians and reptiles of North America). One hypothesis of the origin of deep-sea fishes is that the deep ocean is a refuge for the living remnants of primitive lineages that were outcompeted by more advanced forms in ecologically rich habitats like coral reefs. Giving credence to this idea is the fact that advanced spiny-rayed fishes (Acanthomorphs), which make up the majority of extant fishes, are generally absent from the deep sea despite their complete dominance of every other aquatic habitat. Therefore, despite the perception of the deep sea being an ecological desert, it is in fact very rich.
         When the decision was made to allow the release of chemical dispersants below the surface at the source of the oil spill a trade off was being made between two environmental disasters. Allowing all of the oil to come directly to the surface (by not using dispersants) would have meant potentially having the Louisiana shoreline and its fragile marsh and estuarine habitats threatened. Allowing dispersants to be sprayed a mile below the surface meant endangering the deep-sea habitat where the damage would go largely unseen. In the end, we have oil in both habitats. Dispersants had never before been used below the surface and little data exists about how these chemicals breakdown and how they interact with the deep-sea environment. The dispersants that were used, Corexit 9500 and 9527, degrade quickly in warm waters when exposed to sunlight: it is not known how these chemicals break down in the dark and cold deep ocean. There is also no way of dealing with subsurface oil: oil at the surface can be skimmed and burned, treated and broken down. Even if we could treat subsurface oil, it would be difficult to find. We have inadequate tools for discovering oil floating in the water column as either tiny suspended microdroplets or as dense deep-sea plumes. We frankly do not know how long oil combined with dispersants will remain in the environment. We do know that the combination of high atmospheric pressure and darkness certainly allows the oil to be maintained in the deep sea much longer than it can in warm surface waters.
         To study the impact of the oil spill on the Gulf environment, my lab and collaborators at Ohio State University (PI - Daniel Janies) have created a program called SpeciesMap. This program maps the known pre-spill distributions of fishes in the northern Gulf of Mexico (where there are about 600 species known) based on historical records from museum collections (including LSU’s) and the collections of state and federal agencies. These georeferenced data can be incorporated into a NOAA map of the oil spill, and it can be used to compare post-spill and pre-spill distributions (see map above). SpeciesMap provides the user a way to visualize where fishes were collected before the spill and compare collections post-spill to see if any species have been extirpated from certain locations or if they are less abundant than in the past. We can incorporate data about life history to see if spawning grounds have been affected or if migratory routes have changed. SpeciesMap is freely available on-line ( and we have reached our goal of mapping all northern Gulf fishes (see map above for an example). For many species of northern Gulf fish we know little else besides their distributions. This program will help determine if the oil spill permanently changed this environment or if it will quickly rebound.
         My post-doctoral fellow, Matthew Davis, and I have also submitted an NSF proposal to study the deep-sea environment and how it was established. We are targeting three taxonomic groups: batfishes (Ogcocephalidae), cods (Gadiformes), and lizardfishes (Aulopiformes). These groups are notable because they are some of the few lineages that have representatives in the deep sea and in shallow waters. Because of that diversity we can study how the deep sea was invaded and what adaptations need to take place in order to accommodate that transition. The batfishes are a family of anglerfishes that have an unusual flattened body shape that make them look more like moldy crackers with eyes than they do fish (see image on top). This is a group I’ve been interested in ever since moving to Louisiana. Two colleagues, Hsuan-ching Hans” Ho (Academica Sinica, Taiwan) and John Sparks (American Museum of Natural History) and I recently described two new species of pancake batfish from the Gulf of Mexico. These are the two newest species described from the region and one of them is only found off the coast of Louisiana and northern Texas. Amazingly, of the more than 1500 or so fish species found in the Gulf only 73 are endemics (found no where else). This new endemic species, that we call the Louisiana Pancake Batfish (Halieutichthys intermedius), has received a lot of press coverage because of its incredible beauty and because it was discovered in the region of the oil spill.
         The deep sea is home to an amazing diversity of rare and odd forms with many yet to be discovered and many other secrets to be revealed. As we learn more about the effects of the largest environmental disaster in U.S. history we should keep in mind how difficult measuring that impact will really be. The only thing we know with certainty is the fact that we still know very little.

Ichthyological Adventures in Central America Part 1: Collecting Fishes in Costa Rica

May 2011

From February 15 to the 24th the freshwater people in my lab (Caleb McMahan, Dr.Wilfredo Matamoros) and I went on a trip to collect fishes in Costa Rica. Marine postdoctoral fellow, Dr.Matt Davis, was left back in Baton Rouge to hold down the fort. (Don’t worry he will go to Panama with the rest of the lab in March and April, while I stay behind with my very pregnant wife.) Caleb, Will and I were after cichlids, poeciliids (livebearers) and other freshwater species that are related to my NSF funded project in Central America.
         This was my first freshwater collecting trip to Central America in six years and I learned quickly that my team was much better at this than I was and even better than I thought I was. Caleb has been collecting heavily from freshwaters in Mexico, the U.S. and Jamaica for his masters and undergraduate projects and Wilfredo (without exaggeration) is one of the most well respected collectors of Central American fishes alive today. Wilfredo has many years of experience collecting in remote parts of Central America, which is why I brought him aboard as a postdoctoral fellow this past fall. Also with us were two superior Costa Rican collectors, Arturo Anguilo Sibaja and Carlos Garita Alvarado. These two master’s students from the Universidad de Costa Rica were tremendous collectors and they knew many remote sites where we could collect. They were also very intelligent young gentleman who we made fun of constantly (they did the same to us with less success). In the eight days that we were sampling fishes we put nearly 1000 miles on our rented vehicle in a country that has a coastline of 1100 miles. We collected in every major drainage, in 26 localities, and in six out of the seven provinces as we circumnavigated the entire country.
         We collected about 90% of our targeted species. Our final tally was nearly 4000 specimens from over 150 species. It was one of the most successful collecting trips I’ve ever been on, which was a surprise given how we started. After a couple of days of getting settled in San Jose getting our rental car and gear together, we started our drive to the southern Pacific slope in the province of Puntarenas. We arrived just as the sun was setting and found ourselves a nice little beach hotel (one of many Hotel Iguanas that we encountered) with Golfo Dulce and the Pacific just to our west and with Panama to the east. We decided we would sample that night right in the back of the hotel, which was conveniently located on the beach. Although we were primarily after freshwater fishes, marine fish were also on our mind particularly mullets (Mugilidae) a taxon Caleb has an unusual, and perverse, fondness for. After about an hour at the beach we had collected a marine catfish, a spadefish (Ephippidae) a rare threadfin (Polynemidae) and several other species. It was already 9pm and I was toast, but the site of fish made the blood lust come out of Caleb and Will and they decided that we needed to hit a freshwater site, the Rio Coto, that night. The entire time the strange hotel manager was following us around and he even helped (sort of) pull seines on the beach. As we headed off to the Rio Coto he grabbed a couple of beers and hopped into the back of our SUV.
         As I started recording GPS coordinates and writing field notes the UCR students started pulling a seine in the shallows near shore, almost immediately Arturo cried out in pain. He climbed out of the water with a nasty gash across his foot, he said he was pinched by a crab but it looked much worse than anything a crab could impart. He went to lie down and to elevate his foot while we stoically carried on with the fishing, we ended up getting an additional 10 species at that site after about half-an-hour. We called it quits around 10pm with the intention of returning the next morning. Back at the hotel the arduous work of sorting, photographing, IDing, tissue-ing, and labeling began. One of the unfortunate things about collecting is the necessity of processing these materials while fresh. The hotel manager, now completely drunk, did not make things go faster with his bad jokes and shenanigans but any hotel owner who didn’t mind us laying out 100 or so muddy fish across his bathroom floor surrounded by razor blades and alcohol vials is an okay guy in my book. Not to mention the olfactory nightmare that the mix of formalin, ETOH, fish, sweat, beer, and Arturo’s bleeding foot produced. I’m not sure when we got done that night, but as it was with the rest of the trip, we were off early the next morning before we could get too relaxed.
         We didn’t actually catch a cichlid until our eighth field site on the third day of collecting, a fact that had me very worried since we were there primarily to collect members of this family. Cichlids are very species rich in Central America, with over 100 species, and this family has been there for a long time (more than 50 million years in some parts if you believe my publications). Because they are obligate freshwater fish, cichlids can tell us about the history of the geological blocks that make up Central America. Central America is a landbridge that connects North and South America that has only been in its present arrangement of four interconnected geological blocks for the past three million years. The geological blocks are older but their arrangement and the movement of those blocks over the course of the last 60 million years is hotly debated among geologists. The history and phylogenetic relationships of cichlids and other freshwater fishes on these landmasses can tell us a great deal about which geological hypotheses make the most sense. The biological data provide an independent line of evidence for supporting or rejecting the geological theories. Our plan was to collect as many cichlids and other freshwater species as possible. Although we didn’t collect any cichlids at first they started coming in bunches after day three. We ended up with 20 of the 22 species of cichlids we were targeting. It was amazing to see how each river drainage had its own assemblage of endemics. Cichlids are gorgeous fish, almost all have brightly colored bodies and fins and many have blue or lightly colored eyes. (This coloration is why they are among the most popular aquarium fish.) Even though we were not traveling tremendous distances between sites we could see huge differences between upland and lowland sites and between Pacific and Caribbean coasts. Costa Rica is one of the most developed countries in Central America so it was great to see that the diversity of forms were still there. In fact, we know of at least two new species that we are planning on describing. In July Arturo and Carlos will be coming to LSU to help us describe those species and to determine if we have even more new taxa.
Besides the upcoming Panama trip my lab will also be traveling to Nicaragua, Guatemala, El Salvador, Mexico and Honduras over the next few months. Stay tuned....

Monday, September 10, 2012

A Year of Ichthyology Expeditions in Central America.

by Caleb D. McMahan (Feb 2011)

2011 was quite a busy year for fieldwork in the Fish Section here at the LSU Museum of Natural Science. In 2011, LSUMNS ichthyologists have done extensive fieldwork in Costa Rica, Panama, El Salvador, Nicaragua, and Honduras. All were highly successful and productive expeditions. While primarily interested in certain target species (e.g. cichlids), we made collections of numerous other groups of fishes that will play a huge role in helping to untangle the biogeographic history of the region.

Post-doctoral researchers Wilfredo Matamoros, Matthew Davis, and I spent March 30th to April 14th of 2011 collecting fishes throughout Panama. We first flew into the capital, Panama City, rented a vehicle and drove east to the Darien Province. As you travel towards the Darien in Panama reaching the Río Bayano and Río Tuíra drainages, you begin to see a fairly drastic transition in the diversity of fishes, with higher diversity of primarily South American groups (e.g. armored catfishes, tetras). We then traveled to western Panama, as well as Bocas del Toro. From May 29th – June 13th (2011), Wilfredo and I traveled to El Salvador. The primary purpose of this trip was to fill in some taxonomic gaps for cichlids that are part of ongoing morphological and molecular systematic studies in the Chakrabarty lab. The trip was a huge success and we were able to collect specimens of nearly every species of freshwater fish in the country.
    In addition to fieldwork, Wilfredo led a small class on statistics for students at the University of El Salvador. I was asked to lead a workshop with ichthyology students at the university on proper museum techniques for preservation and storage of specimens of fishes. Parker House (an undergraduate researcher in our lab finishing up his senior year) joined Wilfredo and me from the 31st of July to August 17th for fieldwork in Nicaragua. After flying into the capital of Managua, we boarded very small planes and flew to the jungles of La Moskitia. In Puerto Cabezas we hired a couple of guides and left the coast by boat. We went down the coast until reaching the mouth of the Río Prinzapolka. We spent many days traveling throughout the lower reaches of this river, as well as adjacent drainage, the Río Wawa. Many of the specimens we collected comprise
Paraneetroplus maculicauda
the vast majority of available material for fishes from this region. One of the target species for myself was Paraneetroplus maculicauda, a widespread species of cichlid I am currently studying. The trip was very productive and I was able to collect enough material for my anatomical and genetic studies. After leaving La Moskitia we collected around Managua and throughout the Nicaraguan Lakes, home to some endemic species of cichlids. Parker had to return to LSU for the start of classes; however, Wilfredo and I flew from Nicaragua to Honduras and spent August 17th to September 29th
collecting throughout the country. After first arriving to Honduras, Wilfredo and I were invited to attend a meeting and workshop of environmental officials for Honduras. Wilfredo was asked to discuss some of his ecological work and to lead a statistical workshop using R. I was asked to give a seminar on my research on the Mountain Mullet (Agnostomus monticola) – a freshwater species common throughout Honduras. After the meeting our first trip was to Copán and the Río Motagua drainage. This area is geologically very important for understanding historical biogeography of biota in this region. We were primarily after Theraps microphthalmus, a riverine cichlid species part of a group I have been working on. From Copán we traveled back to Tegucigalpa to collect different species of fishes. After collecting in several localities throughout the Pacific drainages of Honduras, we traveled to La Ceiba on the Caribbean coast. We spent quite a bit of time in the Río Cangrejal collecting specimens of Theraps wesseli, a species Wilfredo is actively studying. We also visited the town of Trujilo. While Wilfredo went off looking for freshwater species (cichlids, guppies), I spent two days working with local fishermen in Laguna Guaimoreto. We collected numerous species (e.g. snook, catfishes, anchovies, silversides, cichlids, guppies, stingrays).
      This was just a very brief summary of a busy – but highly successful – year of fieldwork for LSUMNS ichthyologists! In total, we added roughly 100,000
new specimens to the LSUMNS Fish Collection, and over 2,000 tissue samples to the Fish Tissue Collection. 2012 is off to a great start with Wilfredo taking another LSU undergraduate, Justin Kutz, to Honduras for additional fieldwork for most of January. There is little doubt the Fish Collection at the LSUMNS now has one of the better holdings of specimens and associated tissues of neotropical fishes.

Wednesday, September 5, 2012


Welcome to the LSU Ichthyology blog. Here the students, postdocs, and curator of fishes muse about recent travels and papers. Learn more about us at or follow us on Twitter at @LSU_Fish

The Death Goby and Her Kin

The day Hurricane Isaac rolled through Baton Rouge (Aug 28th) saw the publication of what I consider the best project that I’ve ever been a part of: a paper showing the sister relationship between Milyeringa, a genus of cavefishes from Australia and Typhleotris, a genus of cavefishes from Madagascar. [Get the original open access paper by clicking here: Chakrabarty et al. 2012] I’d like to tell the tale of the Malagasy trip that was the inception of the project and to tell a bit about the story behind the paper before diving into the science.

When I was a young boy dreaming of being a zoologist, I dreamt of going to far off countries and discovering wildly amazing new creatures in places no one has ever been. In my childhood nightmares I feared the dark and being trapped in small spaces. My trips to Madagascar and Australia fulfilled both the dreams and nightmares of my youth.

Sinkhole fever and the Death Goby.
Fig1. The dreaded sinkhole.
I went to Madagascar shortly before my postdoc ended at the AMNH (American Museum of Natural History) and after I had been hired at LSU (Louisiana State University) in the summer of 2008. It was a weird period in my career when I was probably focusing more on the future than the present. My wife and I were in the process of buying our first house; in fact I was signing documents (including my LSU contract) up to the moment I was getting into the cab headed to the airport. The trip to Madagascar came at the perfect time for me; I was done with the stresses of having to find a job, and was ready for something to highlight the end of my old position. As luck would have it the Constantine S. Niarchos Expedition Fund provided my postdoctoral mentor, John Sparks (Curator, AMNH), with a grant to travel to Madagascar and collect blind gobies. I actually didn’t pay much attention to why we were going to Madagascar, I just knew I wanted to go: I’ve always wanted to go. My first work in science, as an undergrad with Melanie Stiassny, was on Malagasy cichlids (Stiassny et al. 2001) and I always saw Madagascar as one of the last remaining wild places on Earth. I was so busy buying a house in Baton Rouge, negotiating my start-up, and packing for the trip that I really didn’t know much about the actual taxa we were after in Madagascar. I had been working on bioluminescent fishes my entire postdoc and never worked with gobies or caves before. I figured I would catch-up on these subjects during the plane ride over to Antananarivo (Tana). As it happened I did more catching up with Scott “Scuppy” Holtz (now a grad student at Cal State Fullerton) and Phil Willink (then at the Field Museum) who were joining John and I in the field. By the time we got around to our first field site (after much stamping of documents, preparation of materials, shaking of hands, and days of impossibly slow and shaky driving across terrible Malagasy “roads”) I sort of had an idea that we would be collecting some rarely seen and poorly understood freshwater cavefishes, namely two species of Typhleotris. Most of what we knew about these species was from their original descriptions (in the 1930s and 50s) and that others had noted that they share a striking resemblance to the cavefishes of Western Australia. John had done a ton of research on the caves of the region, and with the help of the wonderful Steve Goodman, discovered a large sinkhole that was mentioned in a French geologist’s dissertation that possibly contained blind cavefishes. Sinkholes are not caves, they are exposed to the open air and sunlight; what is visable is just part of a larger subterranean habitat (i.e., a karst window). I was horrified and impressed when I was first confronted by this football-field sized sunken lake (Fig 1). The vintany, as the locals called it, made my heart sink into my stomach. ‘What could possibly live down there?,’ I thought to myself. I was trying not to let my nervousness show when Scuppy secured a flimsy chain ladder to a dangling tree at the edge of the sinkhole. As luck would have it I went into the water first while the others secured more equipment. The first part of the climb down over the lip of the sinkhole was particularly nerve-racking because you couldn’t see over the edge to your next foothold. The local guides sat a safe distance away with no interest in getting closer to the insides of this strange pit.
As I snorkeled I started thinking of what I would do if I encountered one of the huge Nile crocodiles this region is famous for. I felt a bit like a miner’s canary, but I didn’t see anything: no fish, no crocs, no beluga whales. All I encountered were some spiders and insects and a beautiful view of the deep dark waters below. As I climbed back up the ladder I saw John and Phil were getting ready to head down. They swam for a long while and after some 25 minutes John yelled out, “I got one.”
‘Got one, what?’ I thought.
Fig 2. A new species of Typhleotris.
He passed the specimen to Scup who climbed up the chain ladder with an ease I wish I possessed. I looked at this little beast, no longer than my pinky, and as dark as a Hershey’s chocolate. How strange this creature was: it lacked eyes and had a smooth bony head (Fig 2). Why would there be an eyeless fish here? Why is it so darkly colored?  The water is clear and sunlight penetrates as far as you can see; the sinkhole appeared more than 50 meters deep, perhaps more. What lies beneath, the French geologist’s dissertation told us, was a subterranean groundwater connection to caves several kilometers away. After some time John yelled out again: he had gotten another one. Around this time I started to get nauseous, I had ingested some of the water while snorkeling and it wasn’t sitting well. I tried not to think about it while I dutifully took photos, GPS coordinates, and tissue samples. The locals had warned me that this was a revered site and that I should not urinate near the mouth of the sinkhole. I didn’t need to pee but I did need to vomit, although the water was clear it was full of loose vegetation and was effectively a pit trap for anything unlucky enough to fall in.
I walked out of sight of everyone and vomited the sinkhole water I had accidentally ingested. I came back to my notebook, camera and specimen just in time for the second specimen to be brought up to me. John and Phil who had been swimming for more than an hour finally came up. This second specimen was dark and eyeless like the first one, and a similar size. John and Phil told me they had seen others but those individuals slowly sank away into the deep just out of reach. The dark coloration is a great camouflage and the fish are certainly aware of their surroundings, enough so to move away from larger moving objects splashing around. Were this species white, as most subterranean species are, it would have been easy pickings for birds that could strike from above and perhaps even to swimming snakes or other creatures that could handle the initial 30ft descent.
We were feeling pretty good about ourselves having collected something amazing from the very first site. We were in good spirits when we retreated back to our camp. A couple days later when we started collecting at a new location a little further north it became clear that all was not well. In deference to my colleagues I won’t replay how sick the team got, but it was pretty scary stuff - especially given how far we were from civilization. I think I was spared major illness because I expelled most of the water I had ingested while snorkeling. We jokingly named the mysterious illness “sinkhole fever,” but seeing your mentor and friend so ill that you consider using the satellite phone to call in a helicopter is no joke. The next day we sent Scuppy and John back to Tana. Scuppy went to a hotel to rest up while John flew back to New York.
            We did quite a bit more collection after that. Phil and I went to a dozen or so more caves over the next week and had quite the amazing experience in the southeastern part of Madagascar. Scuppy, who had recovered well in Tana, was well enough to join me for a trip to the northern tip of Madagascar (Ankarana) after Phil departed. In the north, Scuppy and I collected both blind and sighted members of Glossogobius, sometimes right next to each other.  Those caves in the north remain the most spectacular places I’ve ever been, but it will always be the vintany, home of the darkly pigmented “Death Goby,” that will be the defining site of the trip. [The description of this darkly pigmented form is in press and should come out later this year.]

Back Home.
            On returning from Madagascar I effectively was done at AMNH and was now a new faculty member at LSU. All the sequencing and analysis was done at LSU for the project that would eventually become our PLoS paper. The addition of Matt Davis as my postdoc, the first person to join my lab in 2010, really transformed how we viewed our data. I am not a goby biologist, and although we had some gobies collected we didn’t have enough for a wide-scale global phylogeny. Luckily there was already a well-sampled phylogeny completed using mitochondrial genes (Thacker 2009). It was our intention from the start to stick our newly collected samples in with the previous data available on GenBank. The other piece of the puzzle was the Milyeringa from Australia. Several of the genes for this species had been sampled already for a few specimens loaned to Chris Thacker, but not a large sampling. In my 2009 trip to Australia I collected some additional specimens, including what turned out to be a new species of Milyeringa (described in Chakrabarty, 2010). With both pieces of the puzzle sequenced we discovered what we and others had suspected, these two cave lineages, now separated by more than 6,000km of Indian Ocean, are sister taxa.

The Paper.
Fig 3: Summary of the relationships of Gobiiformes. See original PLoS paper for details.
            The cavefish paper describing the relationship between Milyeringa and Typhleotris published in PLoS One includes John Sparks and Matt Davis (now at the Field Museum in Chicago) as co-authors (Chakrabarty et al. 2012); everyone contributed equally. The dated phylogeny we present for Gobiiformes is the only time-calibrated phylogeny of this extremely diverse group and uses mostly taxa that had been sampled by others for molecular data (again mostly from Thacker, 2009). Our main concern for this paper was the relationships among blind and cave dwelling forms. For further discussion of goby relationships see the recently published Biology of Gobies (Patzner et al., 2011; or papers like Hoese and Gill, 1993; Larson, 2009; or Thacker, 2009). Besides the five species of Milyeringa and Typhleotris we also included blind members of Glossogobius (also collected in the 2008 trip) and Typhlogobius in our phylogeny. Less than 1% of described fish species are blind, and a stygobitic (aquatic cave dwelling) lifestyle has only evolved in 20 families of the 500 or so families of bony fishes. Stygobitic forms are especially poorly known among gobies. Besides those mentioned above there is Caecogobius (from Philippine caves), Oxyeleotris (from Papua, and the only blind eleotrid we don’t have samples for) and a few species of Luciogobius and Typhlogobius, found in seaside caves in marine or brackish water). Given the limited number of blind gobies species known it probably isn’t a surprise that our optimization recovered the common ancestor of Milyeringa and Typhleotris also as a blind taxon, with independent origins of blindness recovered for both Glossogobius and Typhlogobius (Fig 3). When collecting Glossogobius in Madagascar, I couldn’t help but notice how different they were from the Typhleotris we collected in the first part of the trip. We could easily scoop up most individuals of Typhleotris with a simple swipe of a dipnet (or even our hands) while individuals of Glossogobius ankaranensis were much more skittish and swam away at almost the same speed as the sighted G. callidus that we collected in the same caves. Individuals of G. ankaranensis that we collected were depigmented and blind but you could still see the remnants of a dark bead-sized lens right where the full eyes would be, implying a more recent loss of sight. The Typhleotris species had bone covering the region of the orbit and no eye to speak of. The specimens of Milyeringa I sampled in Australia look very much like their cousins in Madagascar. I couldn’t help but note the red dirt and baobab trees that are also common to the regions where these fishes are found; I like to image that this must have been what parts of Gondwana looked like.
            Using what limited data there is on goby fossils, and using a number of outgroups that did have a good fossil record, we were able to date the divergences across the tree and as it is related to our node of interest. Incorporating the error bars around the divergence estimates, we recovered ages that were congruent with the break up of eastern Gondwana. A couple of caveats come with this: (1) our phylogeny uses four mitochondrial genes, so it is essentially dated on a single locus, and, (2) Australia and Madagascar were never directly abutting in any current Gondwanan model, India and Antarctica were always in between.
            Part of the early criticism we have received for our paper is that we don’t discuss the basal relationships of the other gobies in our dated phylogeny (see FB thread below). We didn’t discuss the other non-blind taxa much because we are fully cognizant of the fact that outside of the subterranean taxa of interest we did not collect most of the other gobies in our tree. Although certainly our dated phylogeny is unique, we do think a discussion of gobiiform relationships is better suited for a paper by those with vested interests in those relationships. Our interests centered around the relationships among the blind members. Our tree was the first to incorporate several of these lineages but we didn’t add many new taxa and no new genes from previous work on Gobiiformes. Our approach of using Bayesian inference to estimate the phylogeny and divergence times simultaneously while using a more expansive outgroup sampling may be novel, but the real work on gobies will have to come from the addition of morphological and nuclear characters by folks who know these taxa better than us (I’m looking at you Chris Thacker, Luke Tornabene and others). My co-authors and I were trying to get a better understanding of the relationships of the subterranean lineages, so forgive us if we did not mention the rest of the tree much, or cite particular papers discussing those relationships.
As for caveat #2: are we suggesting that there are likely cavefishes in India that may be related to Milyeringa and Typhleotris? Or that they were on Antarctica? Possibly, one can only speculate about “missing” lineages. We continue to discover that our knowledge of major geological events are not quite as stable as we once thought. (Remember when the Closure of the Isthmus of Panama was only 3.5mya?) I think assuming that the current timing and scenario of the break-up of Gondwana is the last word on the subject would be a mistake. One intriguing possibility is of a possible direct connection between Madagascar and Australia in a land connection called Pandora (Parenti and Ebach, 2010). The cavefishes in their current incarnation as Milyeringa and Typhletoris are probably not capable of dispersing much beyond their isolated aquatic cave systems but that doesn’t mean that the cave systems themselves haven’t moved around and evolved. More than likely they did, just look at the karst window that gave rise to the Death Goby. The scenario I picture in my head is of a widespread lineage probably composed of both cave dwelling and non-subterranean species on eastern Gondwana; the drifting continents then separated this lineage. Most of the members of this lineage slowly went extinct with time (while adding a few new ones now and again) and all that remains today are a handful of species in isolated caves in Madagascar and Australia. What better way to escape extinction that to hide out in a cave? (Just ask Al Qaeda.) Of course there are other potential scenarios, as we discuss in our paper, this one is just the most palatable for me. However, without evidence of sighted members of the Milyeringa + Typhleotris clade, the simplest conclusion is that the ancestor was a blind cavefish too (as we report in the paper).
Any way you slice it, the best explanation we currently have for this lineage of cave dwellers remains that they are a Gondwanan relict. Given their very limited dispersal ability (blind, restricted to their cave habitats) and the ancient age we recover for them, it would seem that this group might be one of the best cases for a group that shows a vicariant Gondwanan pattern.

Chakrabarty, P., (2010) Status and phylogeny of Milyeringidae, with the description of a new blind cave fish from Australia, Milyeringa brooksi, n. sp. Zootaxa 2557:19-28.

Chakrabarty, P., Davis, M.P., Sparks, J.S. (2012) First reported case of a trans-oceanic sister-group relationship between vertebrate troglobites. PLoS One 7:e44083 (pg.1-8).

Hoese, D.F. and Gill, A.C. (1993) Phylogenetic relationships of eleotridae fishes (Perciformes: Gobioidei) Bulletin of Marine Science 52: 415-440.

Larson, H.K. (2009) Review of the gobiid fish genera, Eugnathogobius and Pseudogobiopsis (Gobioidei: Gobiidae: Gobionellinae), with descriptions of three new species. The Raffles Bulletin of Zoology 57: 127-181.

Parenti, L.R. and Ebach, M.C. (2010) Wallacea deconstructed. In: Beyond Cladistics: The Branching of a Paradigm (D.M. Williams and S. Knapp, eds.) University of California, pp. 303-318.

Stiassny, M.L.J., Chakrabarty, P. , Loiselle, P. (2001) Relationships of the Madagascan cichlid genus Paretroplus, with a description of a new species from the Betsiboka River drainage of northwestern Madagascar. Ichthyological Explorations of Freshwaters 12: 29 – 40.

Thacker C.E. (2009) Phylogeny of Gobioidei and placement within Acanthomorpha, with a new classification and investigation of diversification and character evolution. Copeia 2009: 93­–104.