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