Saturday, December 31, 2016

Fish Genomes of 2016 in Review

Biology has been booming with rapid advances in DNA sequencing, and now scientists are able to rapidly map out genomes for more and more species. Genes are the basis of many traits, and so sequencing and comparing genomes can help us understand how these genes differ between species to drive their differences in traits, just as comparing genomes of people with a genetic disorder can help identify what gene or genes are involved. Genes also allow us to reconstruct relationships between species. Knowing the genome sequences of other species hence provides many scientific opportunities to understand their biology, and our own biology.

Fish genomics has come a long way since the initial sequencing of the first few fish genomes: zebrafish, pufferfish, and Japanese ricefish (medaka), which began over a decade ago. Fishes are vertebrates just like humans, so we share many biological characteristics with fish. This means fish can provide information on the origins of human genes, and the structure and function of the human genome. Fish genomes can also empower breeders in aquaculture who may be interested in selecting for traits such as faster growth. And of course, sequencing fish genomes can allow us to understand the genetic make-up of fishes that give different species their unique traits. In 2016, we've seen a rapid increase in the number of fish genomes that have been made available*, and here is a list of the last year and a few of their highlighted findings.

Sinocyclocheilus spp.
Sinocyclocheilus anshuiensis, a cave-obligate fish, labeled
with numerous genetic changes involved in adapting to caves.
Src: Yang et al. 2016

The Chinese barbs of the genus Sinocyclocheilus include many species endemic to China, some of which have entered caves and adapted to cave life. Genetic differences between surface Sinocyclocheilus and cave-adapted Sinocyclocheilus may be involved in adaptation to cave life. This is only the second cave-adapted species that has had its genome sequenced (the first being the Mexican cave tetra, Astyanax mexicanus, published in 2014). Chinese cave barbs and Mexican cave tetras show many similar genetic changes compared to surface fish, such as many genes involved in vision, which is usually lost in the perpetual darkness of caves.

Source. doi:10.1186/s12915-015-0223-4

Turbot, Scophthalmus maximus

Turbot, by © Hans Hillewaert /, CC BY-SA 3.0, Link.
Prior to 2016, only one flatfish had been previously sequenced, the Chinese tongue sole, Cynoglossus semilaevis, in 2014. As a popular food fish, the turbot genome will be important for breeding programs, and the genome sequence helped to study the genetics of body growth, sex determination, and disease resistance, which are important traits in fish culture. They also found certain genes related to vision and fat that may be evidence of adaptation to dark and cold water that it would live in on the ocean floor.

Source. doi: 10.1093/dnares/dsw007

Miiuy croaker, Miichthys miiuy

The miiuy croaker is a species of croaker found in waters of China, Korea, and Japan. These fish appear to be relatively poorly studied, and there's not even a freely available image of this species to use here. Of course, they are economically important and used in aquaculture, hence the authors here focus on genes related to their immune system, and found reduced numbers of adaptive immunity genes but expanded numbers of innate immunity genes compared to many other fishes, and they argue that the innate immunity is robust and compensates for the reduction in adaptive immunity. They also find loss of vision genes related to muddy habitats. The authors also found expansions in genes to taste umami which may be related to its carnivorous diet, and that this phenomenon was replicated in other carnivorous teleosts compared to omnivorous teleosts. Finally, genes related to the sense of smell are also in higher number than in most other fishes.

Source. doi: 10.1038/srep21902

Spotted gar, Lepisosteus oculatus

Spotted gar by By Tino Strauss, CC BY-SA 3.0, Link.
The spotted gar genome is an important new addition to the growing genome menagerie. The spotted gar is the first fish genome sequence of a ray-finned fish that is not a teleost. Almost all ray-finned fishes are teleosts. Teleost fishes arose after their genomes duplicated, so many species (such as model organisms like zebrafish) have two copies of many gene when compared to humans. This makes comparisons between humans and ray-finned fishes more difficult. Since the spotted gar is not a teleost, its genome does not contain this duplication, and thus the new genome sequence helps to form a bridge between fish and human genomics.

Source. doi: 10.1038/ng.3526

Asian seabass, Lates calcarifer

Asian seabass, CC BY 2.5, Link.
The Asian seabass is a large, predatory fish that is an important food source in Southeast Asia. With a broad geographic range from northwestern India stretching all the way to Australia, genetic comparisons of the Asian seabass showed that there are three major populations across its range. Furthermore, while many genomes are highly fragmented (and thus are incompletely assembled), this project combined numerous data sources (e.g. long read sequencing, optical mapping, transcriptome scaffolding) to make this assembly one of the most complete among all fishes, which will be useful for chromosome-level genome comparisons.

Source. doi: 10.1371/journal.pgen.1005954

Atlantic salmon, Salmo salar

Atlantic salmon, by By Hans-Petter Fjeld, CC BY-SA 2.5, Link.
The Atlantic salmon is one of the most important fishery species in the Atlantic. Salmon are teleosts, but have another genome duplication of their own that happened after the first teleost genome duplication, so they have quadruple the number of genes. The salmon genome can help us understand how a genome evolves after a recent genome duplication. Having two copies of a gene may not be necessary, so new copies can be lost, evolve new functions, or the two copies can divide their labor and split their roles. The authors of the study found that most new genes that were retained evolved new roles rather than splitting their roles. The Atlantic salmon is the second salmonid genome sequenced, after the rainbow trout Oncorhynchus mykiss, 2014.

Source. doi: 10.1038/nature17164

Asian Arowana, Scleropages formosus (Again!)

Golden, red, and green morphs of Asian Arowana.
Src: Bian et al. 2016 Link.
The Asian arowana is one of the most highly prized ornamental fishes, as documented in a new book The Dragon Behind The Glass. Sometimes called dragonfish, they are prized for bringing good luck and fortune, and are the most expensive ornamental fish. Hence, it is not surprising that multiple teams were sequencing the Asian Arowana genome, and the first genome sequence was published last year. The species comes in multiple color morphs, and the new paper presents genome sequences for golden, red, and green varieties. The scientists report that eels and bonytongues (the group that arowana belongs to) are each others' closest relatives, that they have found two genes that may play a role in golden coloration, and they find arowana may have ZZ/ZW sex determination (information which may allow breeders to determine the sex of fishes when they are young).

Source. doi: 10.1038/srep24501

Channel Catfish, Ictalurus punctatus

Channel catfish, By U.S. Fish and Wildlife Service. Link.
The channel catfish is the most popular aquaculture catfish species in North America, and this genome sequence will be useful for selective breeding for certain catfish traits. In addition, like all other catfishes, the channel catfish does not have scales. Comparisons of the channel catfish with armored catfishes, as well as comparisons between scaled and naked carps, were used to identify a number of genes related to developing scales and armor in carps and catfishes.

Source. doi: 10.1038/ncomms11757

Mangrove killifish, Kryptolebias marmoratus

Mangrove Killifish, Public Domain.
Unlike most vertebrates, the mangrove killifish is a hermaphroditic, self-fertilizing species. The authors found no unusual changes to the sequences of its sex-determining genes, suggesting gene expression changes may be more important to how these fish evolved to be hermaphrodites. This fish is also extremely tolerant of stressful conditions, and is able to breathe air and hop short distances on land. Future work studying its tolerance will be helped by the newly available genome.

Source. doi: 10.1093/gbe/evw145

Ocean sunfish, Mola mola

Ocean sunfish, by By Per-Ola Norman, Public Domain. Link.
The ocean sunfish is the largest bony fish, and can weigh over two tons. To reach its large size, it has a fast growth rate and a relatively light skeleton that is mostly made of cartilage. The authors of the study found that genes related to growth and bone development have undergone positive selection or rapid evolution, which provides evidence that changes to these genes may have evolved that contribute to its large size. The ocean sunfish is also interesting because it lacks a true tail. Hox genes are well known for determining regions of the body, but the ocean sunfish has apparently not lost any hox genes that might explain the loss of its tail, suggesting some other mechanism determines the lack of its tail.

Source. doi: 10.1186/s13742-016-0144-3

Blacktail butterflyfish, Chaetodon austriacus

Blacktail butterflyfish, by Bernd, CC BY-SA 2.0, Link.
The blacktail butterflyfish represents the first tropical coral reef fish genome sequence published (well, accepted for publication). This genome sequence will be useful in future studies of coral reef fish adaptation, evolution of fishes in the Red Sea, and may eventually help with marine aquaculture of coral reef fishes.

Source. doi: 10.1111/1755-0998.12588

American eel, Anguila rostrata

American eel, By Clinton & Charles Robertson, CC BY 2.0, Link.
The publication of the American eel genome follows the publication of the European eel Anguilla anguilla and Japanese eel Anguilla japonica. Given the rapid improvements in genome sequencing and assembly, it also is the highest quality genome assembly of all eels and relatives. This genome will also be useful for future studies on freshwater eels, including conservation genetics and functional genomic studies.

Link. doi: 10.1111/1755-0998.12608

Japanese flounder, Paralichthys olivaceus

Japanese flounder, By サフィル, CC BY-SA 4.0, Link.

A third flatfish genome was published near the end of this year. Here, among other things, the authors studied one of the most intriguing aspects of flatfish: their asymmetry. Flatfishes start out life as symmetrical larvae, but one eye migrates to other side during development. Thyroid hormone and retinoic acid were found to be important in signaling this development. Unexpectedly, visual pigments are also expressed in the skin to help orchestrate this asymmetrical body development!

Source. doi: 10.1038/ng.3732

Tiger tail seahorse, Hippocampus comes

Hippocampus erectus,
By Will Thomas, CC BY 2.0
Link 1. Link 2.
The seahorse is so unusual it is unclear to many that they are even fish. The authors of this study were interested in genes that underlie some of its unique traits. They found the seahorse genome has the highest evolutionary rate of any of the fish genomes they compared it with. Numerous duplicates of a particular gene (patristacin) were found that was expressed in the male brood pouch, which may be necessary for male pregnancy. A similar gene is also expanded in the live-bearing platyfish that shows female pregnancy, showing that, in this case, different genes in two different fish can play a similar role in pregnancy. In addition, tbx4 is absent from the seahorse genome. This gene is involved in regulating the development of hind limbs, which in fish are the pelvic fins. The absence of this gene is consistent with the absence of pelvic fins in seahorses. The authors of the study then knocked out this gene in zebrafish, and the zebrafish developed without pelvic fins, providing more evidence of its role in pelvic fin development. Finally, lack of certain genes involved with enamel development are missing from the seahorse genome, consistent with the lack of teeth in seahorses. 

Source. doi: 10.1038/nature20595

Gulf pipefish, Syngnathus scovelli

Syngnathus acus, By © Hans Hillewaert, CC BY-SA 4.0, Link.
The gulf pipefish and the seahorse are closely related, and coincidentally their genome sequences were published within a few days of each other. Like seahorses, gulf pipefish lack pelvic fins, teeth, and the males have a brood pouch. These shared adaptations arise from shared genomic characteristics. As with the seahorse genome, these authors found duplicates of the gene patristacin and confirmed they were expressed in the male pipefish brood pouch, and they also found the loss of tbx4 that could be implicated in hind limb loss. 

Source. doi: 10.1186/s13059-016-1126-6

Trinidadian guppy, Poecilia reticulata

Guppy, By Wibowo Djatmiko (Wie146) CC BY-SA 3.0, Link.
The guppy is an important species in studying evolution as an example of rapid adaptation and sexual selection. The genome sequence of the guppy will be informative for understanding the genetics of how this rapid adaptation occurs. By sequencing both male and female guppies, the authors of the study were able to identify genes that were specific to the Y chromosome involved in sex determination, as well as the difference in size and coloration of males compared to females.

Link. doi: 10.1371/journal.pone.0169087

66 other teleost genomes!

Atlantic cod, By Peter from Edinburgh, Scotland,
Uploaded by Amada44, CC BY 2.0. Link.
In the largest study of its kind, 66 partial teleost genomes were simultaneously published in a study looking at the evolution of cod-like fishes (order Gadiformes). The sequencing of the Atlantic cod genome (Gadus morhua) showed that cod lack some of their immune genes (MHC II genes). To compensate, cod have numerous copies of another class of immune genes (MHC I genes). By sequencing the genomes of many species across Gadiformes, the group to which cod belongs to, it turns out that the loss of MHC II is shared by all members of this order, and hence they inherited this loss from their common ancestor. The authors also found evidence that an increase in copies of MHC I genes is correlated with increased rates of speciation in these fishes, which is one of the first studies to my knowledge that finds support for a specific pattern of gene evolution as a cause for generating biodiversity in fishes. Although these genomes are not as high quality and are therefore not as complete as the other genomes that have been published this year, these sequences still provide more opportunity for genome comparisons between fish species, and provide the foundation for future, more-complete genome projects on these species.

Source. doi: 10.1038/ng.3645

With the increased ease of sequencing and assembling genomes, it has also become clear that genome sequences are not the end-all-be-all of biological understanding. By combining new genomes with comparisons of other genome sequences, studies of gene expression through development and in different regions of the body, and testing the function of genes by performing developmental biology experiments in other species, more insights can be gained into the origins of fish biodiversity. More fish genomes will continue to be sequenced, assembled, and mapped in 2017, providing even more opportunities to learn about fish for years to come!

* For people interested in minutiae, I am including species in this list that have been accepted for publication and made available online within 2016, rather than species with an official publication date within 2016. This means that Pimephales promelas and Seriola quinqueradiata, which had their genomes made available in 2015, but not officially published until 2016, were too early to make the cut. 

Tuesday, February 17, 2015

New paper on 3 new species of Peckoltia!

Three new species of armored suckermouth catfish (family Loricariidae), also known as plecos, have been recently described by my advisor Jon Armbruster, David Werneke, and myself! We also reclassified many of the related species, which is based on findings from a recent study of the evolutionary relationships of loricariid catfish that Jon worked on with a number of colleagues. As the paper is open access, I invite you to check it out at ZooKeys.

Peckoltia greedoi (Photo credit Jon Armbruster)
The three new species are of the genus Peckoltia. They are fairly similar, but come from different parts of South America. The number of rivers in the South American rainforest has helped promote isolation and diversification for many groups, including these catfish. In fact, many loricariids are popular in the pet trade. While many people are familiar with common plecos, often used to clean up algae, there are many more species. Aquarists are so into plecos that they import many species before they've even been described, and undescribed species are given an L-number designation by aquarists as a placeholder name until it gets described.

In describing the new species, our colleague, arachnologist Chris Hamilton, remarked that one of the fish looked like Greedo, the bounty hunter from Star Wars: A New Hope. We knew immediately we would have to name the new species Peckoltia greedoi. Peckoltia greedoi comes from the Gurupi River drainage in Brazil. We've gotten some attention for this, and we have been featured as a Name of the Week on EtyFish (a website that maintains a list of fish name etymologies). We also got an article in Auburn's The War Eagle Reader. Plus, we had great response from sci-fi fans, with articles written about our paper on Nerdist, which then spread to a bunch of other sci-fi websites. Peckoltia greedoi also inspired a listing of Star Wars-inspired species! Particularly relevant to our new species, there is a trilobite called Han solo. I suppose it's a good thing species have never crossed paths. Scientists are a nerdy bunch, and it's clear scientists aren't above having fun with naming things.

UPDATE 3/19/2015: It turns out the Greedo catfish had some life in it yet for getting people's attention. About a month and a half after the paper first hit, Auburn University wrote a story on our new species and included a video! This subsequently spread to many news sources including CNN, BBC, The Telegraph, IFLScience, Washington Post, and even IGN! Really exciting to have so much attention, just in time for Taxonomist Appreciation Day!

Peckoltia lujani (Photo credit: Jon Armbruster)
As far as I know, only one of the three species we have described has shown up in the pet trade and gotten an L-number. Peckoltia lujani is, to the best of my knowledge, the species known as L127 in the pet trade. My advisor has described quite a few species from the Orinoco River, and this one adds another species to the count. Peckoltia lujani was named for one of Jon's previous graduate students, Nathan Lujan, who has become a loricariid expert in his own right. Although P. lujani is overlooked by many aquarists since it has a relatively drab color pattern, it is still kept by quite a number of aquarists. Devoted hobbyist aquarists interested in loricariid catfishes watch the scientific literature closely (I myself got into science because of this), and they were excited to have a name to another species that they keep.

We also named a third new species, Peckoltia ephippiata. The name refers to the dark "saddle" color pattern formed by blotches on its back. Peckoltia ephippiata occurs in the Madeira River.

Loricariid specialists and pleco aficionados alike may also be interested in some of the reclassifications that were made. Unfortunately, Peckoltia is a poorly understood genus, as is a closely-related genus Hemiancistrus. These two genera have been thought to be very similar, but Hemiancistrus species could be distinguished from Peckoltia by the angle at which their lower jaws come together, which either form a wide angle in Hemiancistrus or an acute angle in Peckoltia. In an earlier study, using analyses of DNA sequences from hundreds of species, Jon Armbruster and colleagues helped to clear up the relationships. It turns out that jaw angle didn't work very well for determining evolutionary relationships, and so Peckoltia and Hemiancistrus as previously defined were not evolutionarily meaningful (which is a goal of classification). The three new species group with Peckoltia in the molecular phylogeny, but have jaw angles about 90º, so they don't qualify under the traditional definition of Peckoltia; however, since they do group together evolutionarily, we decided to classify them under the genus Peckoltia. The DNA study also found Hemiancistrus included species that are different genera; we resurrected a previously named genus, Ancistomus, to include some of these species, but some of the rest will remain until new genera are named. Peckoltichthys was resurrected for the unusual P. bachi, which was grouped in Peckoltia for a while. Also, the unusual Hemiancistrus pankimpuju was moved to Peckoltia based on its evolutionary relationships.

There's still a lot to find out about these catfish. Unfortunately, right now we don't know what Peckoltia specifically is. Although the species in Peckoltia conforms to our knowledge of the evolutionary relationships of these fish, we don't yet know if there's a specific morphological character that unites the genus as we've currently grouped it. It's a small distinction that is dissatisfying for taxonomy, as being able to identify genera by morphological characters is important when you don't have genetic techniques at hand. However, for now, we leave the taxonomy in an interim state that represents our knowledge of the evolutionary relationships of these fish from genetic sequence data. Hopefully in the future these relationships can be clarified, and we can solidly diagnose these genera.

Monday, February 2, 2015

New Species off the Shelf

When someone discovers a species new to science, the species gets to be named! Exciting, right? Species get named through a formal process called species description. In a species description, the scientist has to describe how the new species looks and how it differs from all previously described species.

Luiz Rocha at the California Academy of Sciences started a fun discussion recently on the FaceBook group of the American Society of Ichthyologists and Herpetologists (ASIH). Prompted by a reporter, he was curious if any of the taxonomist's of the group had experienced discovering a new species, not from going into the field, but by finding it in a natural history collection.

Certainly, many species are found by going to unexplored places. But it turns out you can go to a place and grab a new species off the shelf. These places are natural history museums, such as the American Museum of Natural History in New York, the Field Museum of Natural History in Chicago, or the Smithsonian Natural History Museum, which have huge collections of specimens that are preserved for present and future scientists to study. The vast majority of what a museum holds is never put on exhibit. Museums are extremely important to preserve our biodiversity knowledge from around the world, and because a specimen exists, someone can always go back and check a scientific claim someone makes about a specimen (as long as the museum sticks around and maintains its collections and specimens). When someone describes a new species, they usually store their specimens in a museum so that they can be preserved in perpetuity.

1924! Just seeing specimens this old is truly valuable,
but identifying a species new to science is cooler!
Of course, I chimed in to the discussion. I got into the fish business to do taxonomy, but alas I don't have funds to go to far-off locales to find new species. Luckily, at the Auburn University Museum of Natural History, there's plenty to do, as my advisor and prior students have led multiple trips to South America to amass one of the largest collections for South American fishes in North America. I have also borrowed a number of specimens from other museums which also represent new species. I have not collected a single one of the species I'm describing, and I hope to describe several before my PhD is done. In fact, I recently submitted a manuscript for two new species of fish, one of which was first collected in 1924, and to my knowledge has not been collected since. Truly a forgotten new species.

And I wasn't alone. Numerous people responded who had described new species. Although many of these were people that specialized in South American fishes, there were other examples as well, from Africa, from Asia, as well as marine fishes, including deep sea fishes. There are so many species left to describe the specialists don't have enough time to describe them. As one member pointed out, there was a recent study where the "shelf life" of new species was calculated, or how long that species had been in a collection before it was formally described. On average, it was calculated a species goes about 21 years before being described. The authors of the study also point out that the vast majority of species are not even recognized as new in the field, and thus collections are important holding tanks for potential new species. Another member pointed out that one of the mother of all shelf lives was publicized last year with the discovery of a new species of beetle collected by Darwin himself, boasting a 180-year gap between collection and description.

A new species I am describing I found on the shelf, labeled as
unidentified with the telltale "sp." for its species.
For some of these specimens that remain to be described in collections, we already know they're there. Any specimens that are unidentified in a collection typically is a big clue. If a specialist wasn't able to identify some specimens to species, it could mean that they don't have expertise with that particular group... But it could also mean that the specimen can't be identified to a currently described species because it is new to science! On the other hand, we might not know that the specimens are a new species until further study. In some cases, new species have been hiding under our noses, under the guise of other already named species they are similar to. This is an increasingly common phenomenon, and species that have been hiding from us have been called "cryptic species." By keeping these specimens around, we can always go back and check if something was hiding from us all along.

It's clear, though, that discovery and description are too different things. Although I'm describing several new species of fish, can I really claim discovery? These fish were found by someone else first, so perhaps I can't claim that? It's because of this disconnect between discovery and description that leads me to avoid using the word "discovery" for the fish I'm describing. All of the fish I'm describing were already clearly different to whoever first tried to identify them and label their jar, but they simply never went ahead and formally described the species. Perhaps one day I'll truly discover a new species. But until then, hopefully I can at least continue describing them!

Thanks to everyone who contributed to the discussion: Rachel Arnold, Ricardo Benine, Andy Bentley, Mike Burns, Barbara Cálegari, Fabio Di Dario, David Ebert, Ben Frable, Les Kaufman, Flávio Lima, Hernan Lopez-Fernandez, Nathan Lujan, Daniel Lumbantobing, Marcelo Melo, Michael Mincarone, Javier Alejandro Maldonado Ocampo, Michael Oliver, Frank Pezold, C. Keith Ray, Luiz Rocha, Norma Salcedo, Scott Van Sant, Vivianne Sant'Anna, David Shiffman, Brian Sidlauskas, Randal Singer, Luke Tornabene, and Richard Vari.

Thursday, January 30, 2014

Thoughts on Smuggled Piranhas

Red-belly piranhas at the Muséum Liège (Belgium)
(photo by Luc Viatour)

Piranhas were smuggled into New York City by an importer called Transship Aquatics. The owner of the company Joel Rakower smuggled almost 40,000 piranhas in 2011 and 2012 from a Hong Kong distributor by having them labeled as silver tetras. That's a pretty fun story in and of itself, but I had various other thoughts on the matter.

How can piranhas be confused with silver tetras?
Piranhas do indeed have sharp teeth,
but they are best exposed by pulling back the lips.
Definitely not something to try at home!
Some people pointed out that piranhas and silver tetras aren't all that similar, and questioned how this confusion could've happened. Part of that confusion probably stems from what most people think of as piranhas, these big, tough-looking fish. But I've actually seen piranhas sold (legally) at pretty small sizes, including similar sizes to the tetras you commonly see around. Given the fact that he sold almost 40,000 piranhas over two years, I'd be pretty confident that most of them were less than 3", no bigger than a silver tetra. Piranha teeth aren't necessarily obvious, either; only when the mouth is protruded and the lips pull back do they really become all that obvious, and on small fish such teeth may be missed. To add to the matter, piranhas and tetras are in fact closely related! So you can imagine piranhas as being quite a lot like tetras, but bigger.

Silver tetra (Ctenobrycon spilurus)
Photo from FishBase
One thing that's interesting is, as an aquarist of about 15 years, I can tell you that silver tetras are not very common in the pet trade. You can find some information on the internet on them easily enough, but searching silver tetra usually pulls up the very different silver tip tetra, which is a mainstay in the aquarium industry. So silver tetras aren't exactly a fish that people have a lot of direct experience with, so it might be hard to tell a small piranha from a tetra.

Juvenile Catoprion mento wimple piranha
Full disclosure: This is not the common
red-belly piranha species that was likely involved.
(Photo by Charles & Clint)

Though perhaps piranhas take it even further than rough similarity. Juvenile piranhas and tetras live in the same rivers, and some piranha species have been seen to school with other tetras, feeding off of the unsuspecting school members (Nico & Taphorn 1988). It's been suggested that juvenile piranhas actually mimic the tetras to get away with this! As far as I know, direct mimicry of piranhas with silver tetras has not been reported, but it's not that hard to imagine that juvenile piranhas and tetras might be confused with each other.

That's a long way to go for piranhas!
Piranhas are from tropical rivers in South America, so it's interesting that the fish are from Hong Kong. Hong Kong of course is on the other side of the planet from both South America and New York, so if you wanted a direct source of piranhas you'd think it'd be easier to get them from South America itself. That's not necessarily the cheapest way, though. There are ornamental fish farms in a number of tropical Asian countries. I'd be willing to wager that these piranhas were captive bred on such a farm, shipped to Hong Kong, and then to New York. Crazy how trade of a South American fish doesn't need South America's involvement at all!

There are ornamental fish farms in Florida, but piranhas are illegal to own in Florida too, so they couldn't come from there.

This whole point about piranha legality actually raises another question. Piranhas are illegal in many states, including New York, California, Georgia, Texas, Washington, and Florida (although some of these states allow permits and licenses). These states contain some of the biggest international airports, and thus shouldn't even be able to import piranhas. It's surprising piranhas come in that much at all given that the main pathways in are theoretically limited or cut off, but I have seen them quite often in states where they are legal.

What did he do with them after smuggling them in?
From their website, Transship Aquatics says they supply fishes to wholesalers. But how are the wholesalers supposed to know what they're ordering? I'm going to admit that I have no idea what happened here. Piranhas are illegal in New York so Transship Aquatics probably couldn't put piranhas on their lists, and labeling them as silver tetra on the list would probably lead to some real confusion. Maybe they did it all under the table. Alternatively, since piranha prohibitions are spotty across the states, it might be possible for some sellers in other states ordering piranhas to simply not know they are banned in New York.

At what cost?
This guy smuggled "39,548 piranhas, worth $37,376." I assume these are the cost to Transship Aquatics, since they're really low for anyone that only sees retail prices on fish. Almost no fish in the pet trade is sold under a buck a piece on retail. I'm not sure what these were being sold at, but I'd wager the typical prices could range anywhere between $4-10 if these fish are as small as I think and prices are how I remember them (piranhas are illegal in my current state). So it's potentially big money for anyone involved, although the money has to be divided amongst the various links from exporter, to importer, to wholesaler, and to retailer. Generally, though, the major hike in prices happens at the retail level; many of the more common fish are staggeringly cheaper earlier in the distribution chain. For fish that are wild-caught, fishermen often get paid very little relative to the prices that the fish command in the pet trade.

It's a good thing piranhas are banned in New York, right?
I'd also like to mention that piranhas are typically not all that aggressive, despite the mythology that surrounds them. It's been written on quite a bit but I'll just point you to Prosanta Chakrabarty's commentary on a recent incident where people in Argentina were bitten by a school of piranhas. Piranhas are dangerous, for sure, especially when cornered or captured. They have strong bites and sharp enough teeth that piranha jaws can be used to give haircuts. So like other wild animals, you do have to be careful around piranhas, but they're not man-eating killers.

Even though there are 40,000 extra piranhas in New York (or elsewhere?), there's nothing to worry about. There's little chance piranhas can survive the frozen winter in New York. However, the aquarium trade is definitely a main pathway for invasive species to reach the United States. All aquarists should be urged not to release their fishes into the wild, which is extremely irresponsible. I can see that these bans in some of the more southerly states as more valid. In any case, I hope that the piranhas have found good, legal homes.

Red-belly piranha at the Newport, Kentucky aquarium
(Photo by Greg Hume)
Piranhas are pretty cool fish, though. They are often found at public aquaria, too, so if you ever get the chance, you'll see they can actually be pretty mellow.

Tuesday, October 15, 2013

The PhD-Faculty Gap

Source: Nature Biotechnology. The figure caption said the following:
"Since 1982, almost 800,000 PhDs were awarded in science and engineering (S&E) fields, whereas only about 100,000 academic faculty positions were created in those fields within the same time frame. The number of S&E PhDs awarded annually has also increased over this time frame, from ~19,000 in 1982 to ~36,000 in 2011. The number of faculty positions created each year, however, has not changed, with roughly 3,000 new positions created annually."
The above figure has been making the rounds on the internet. It's from a recent essay in Nature Biotechnology. This isn't even the main focus of the essay, as it's only used to introduce the topic, but it's been getting a lot more attention than the essay's actual content.

The graph does oversimplify things. For example, it includes engineers, who I've heard enjoy more job positions outside of academia than people such as ichthyologists. The graph doesn't show at all if there's an increase in positions outside of academia. Many PhDs are still trained by academics for an academic job, and that this is entrenched in academic culture. Some professors still view academia as the end-all be-all for their students, and if their students want to explore other careers or don't make it into academia, that is the equivalent of failure. Students still unwisely go into academia, not sure what the academic job market is like, myself included. Sure, the academic job is not the only job path, but this is not heavily emphasized, and many PhDs are resigned to trying to go into academia since no other options are made clear to them. This figure shows how the academic job market is getting increasingly competitive.

Of course, this isn't news. Here are three other graphics that people already made to portray the gap between PhDs being awarded and the number that can actually get hired as faculty.

Source: Nature
Nature covered this PhD gap in 2011 in a special on the future of the PhD. In articles like The PhD Factory, Nature showed various graphics that showed that the job market for those targeting an academic life is becoming increasingly competitive. There are lots and lots of PhDs, translating into lots and lots of postdocs, and the faculty job pool isn't increasing enough to keep up with it.

Source: PhD Comics

PhD Comics is well known among academics for its satirical look at life as a graduate student. The above comic really drives it home. Darwin noticed that reproducing organisms would be limited by resources, causing competition. The populations of faculty (and available funding) are also limited, resulting in extreme competition among PhDs to get academic jobs. Quite simply, it's not sustainable for PhD students to expect to be going into academia, as there are only a few jobs out there.

Source: The Royal Society. This figure focuses on the UK. The original caption:
"This diagram illustrates the transition points in typical academic scientific careers following a PhD and shows the flow of scientifically-trained people into other sectors. It is a simplified snapshot based on recent data from HEFCE33, the Research Base Funders Forum and from the Higher Education Statistics Agency’s (HESA) annual Destinations of Leavers from Higher Education’ (DLHE) survey. It also draws on Vitae’s analysis of the DLHE survey. It does not show career breaks or moves back into academic science from other sectors."
This last one shows a particularly bleak picture for those aiming for a faculty position, where less than .5% of PhD students actually become a professor. It's from The Royal Society, but regardless the disparity between PhDs produced and the faculty positions available is not unique to the UK. Needless to say there are many other people that have written about this problem, and other figures out there that neatly display the problem.

If the increasing competition for jobs wasn't enough, there many other reasons not to go to graduate school

The problem has been known for quite a while and people have thought about various ways to fix it, such as slashing the number of students accepted into PhD programs, or by getting schools to better prepare PhD students to do things besides going into academia (which can be hard to expect professors that went into academia to do for their students). You can read many of these suggestions in Nature's special I mentioned earlier. These dismal job prospects prompted the authors, who are graduate students themselves, to take control of their own futures, and most of the article goes into how the authors formed a group (and eventually a company) that provides consulting to start-up companies and their university's Office of Technology Management. It's really interesting and really quite impressive. On the other hand, it's so different from the current system, it's hard to imagine. But that's probably what we need.

I don't know how to fix the PhD. But one day I hope there will be an infographic that shows that the Phd-Faculty gap doesn't matter.

Friday, August 16, 2013

Pufferfish Love Nests

Mysterious undersea circles...
Image by Yoji Okata
Male pufferfish Torquigener sp.
Image by Yoji Okata

Last year, images of these strange, undersea geometric structures first appeared on the internet. These rippling structures were discovered in 1995 by Japanese diver and photographer Yoji Okata. They are about 6 feet (2 m) across and are found off the coast of Japan in about 80 feet of water. Although initially mysterious, in 2011 it was found that these structures were built by little male pufferfish of the genus Torquigener, which themselves are no larger than about 5 inches (12 cm).
Male pufferfish at work building the nest.
The scale of the nest in comparison to the fish can be appreciated.
Image by Yoji Okata

It turns out the male pufferfish build these large nests to attract females to mate. Males going out of there way to do things to attract females is a familiar theme across animal life. Male bowerbirds are well known for building intricate nests to attract females. While nest-building is well-known among many species of fish, building the nest with these radial peaks and valleys, as well as decorating it with shells, has never been seen before.

In July, the scientific paper describing these nests and the pufferfish behavior appeared in the journal Scientific Reports, a relatively new journal published by Nature Publishing Group. But even cooler than that, it came with new pictures and videos! The appearance of the paper caused a small resurgence in social media on the discussion of the pufferfish. No one's really mentioned the videos, though, which is a shame because the paper is actually open access and so the videos are free to watch! If a picture is worth a thousand words than video is even better, right?

Male pufferfish building a nest, using his fins and body to dig valleys.
Photo by K. Ito

The only image of a pufferfish in the entire paper isn't anything new compared to the images that were already out there, but yet again demonstrates a male Torquigener hard at work building a nest. You can see how the male pufferfish uses its fins and body to dig the valleys into the sand. The male pufferfish will take seven to nine days to build the entire nest, but when attracting females is the game males across the animal kingdom do some pretty involved things.

The paper also describes the nest-building behavior more specifically, includes the steps for how the nests change over time and how the pufferfish behaves over time, and some video documentation.
Caption from paper: "Changes in the circular structure constructed by male pufferfish. (a) Early stage; (b) middle stage; (c) final stage; and (d) after spawning of the same circular structure of K1 in Figure 2. Photograph by Y. Okata on 23, 27, 29 June, and 6 July 2012, respectively."

The above image shows off the stages of nest-building. The nests start off roughly circular, and the valleys and hills get more pronounced over time (a-c). Not longer after spawning, however, the structure is left alone (d) and fades away.

Several videos are also available in the supplementary information, where you can the various male pufferfish digging behaviors. You can see how it uses its bodies and then waves its fins around, sometime sinking down into a spot and beating its fins to dig deeper pits. You can also see how the male pufferfish nicely fits in the valleys. The pufferfish keeps the center smooth with fine sand particles, and at the end of construction gives it a pattern (c). There's even a shot where it picks up stuff (which the paper says are shells) with its mouth and puts it down on the outer peaks. The last video is of the male attempting to court a female. Definitely very cool behavior to watch!

Sand particles from the nest the day before spawning and the day before hatching.
If the male is successful at courting the female, they will spawn and the eggs are laid in the central portion. Like in many fishes, the male will be the primary caretaker, and the female goes off on her own while the male hangs around for about 6 more days to care for the eggs, during which he stops maintaining the nest structure (d). Lack of maintenance of the nest also reduces the amount of fine sand particles in the center of the nest. Because of this, it's inferred that the complex nest building seems to be important for attractive females, but not so much for actually raising the young.

While the nest is already just pretty neat to look at and impressive to boot, according to the paper, the radial pattern, the central patch of fine sand, and the decoration of the nest with shells are apparently all characteristics never seen in fish nests before. Also, the peaks and valleys of the nest affect the flow of water, and allow for fine sand particles to flow into the valleys, which are then moved to the inner circle by the male. Interestingly enough, the male pufferfish don't re-use their nests. The authors hypothesize that this could be because the fine sand particles get used up, and so they have to find a new site to rebuild.

All in all, this is pretty cool behavior, but plenty of questions remain. The authors note that the specific reasons the nests are designed are unknown; why does the puffer build the nest symmetrically, or with certain numbers of peaks and valleys, certain peak heights and valley depths? How does it choose how to decorate the nest site with shells? There are further questions as well. What's the function of fine sand particles in attracting females? Do other Torquigener species build nests?

These types of discoveries also stress how little we still know about the deep. It was only two years ago when the puffers were finally observed building nests. We can be sure that other secrets remain to discover under the sea.

Wednesday, August 14, 2013

First Post

Photo by Damian Gadal
So here's my blog! Finally. Here it is, done, I've taken the first step.

This blog will be generally a science blog, but I can't promise that I won't dive down unrelated rabbit holes that catch my fancy. After all, it's my blog, I can pretty much do what I want with it.

I'm a graduate student studying fish biology at Auburn University. There are many great reasons for graduate students to blog. An article from Scientific American came out in April titled "Why grad students should be required to blog"; the author Maria Konnikova says that blogging gives quick and regular exercises to research a topic, synthesize it, and write it all down, skills which are useful to graduate students who will be doing just that. Shortly after, C. Titus Brown followed up with a post echoing this benefit, as well as how blogging gets himself thinking. A post even came out just today by Scott Wagers in Nature's Soapbox Science on the topic of how science blogging can help you learn.

And of course, blogging rolls into scientific communication, and there are tons of people saying that scientists need to communicate better. There's an ever growing number of scientists that are fighting the good fight: Steven Hawking, Neil DeGrasse Tyson, Brian Cox, Richard Dawkins, are some particularly notable contemporary scientists who are doing just that. If you think about it, what do these people have in common? They wrote, and not just for other scientists (as we are required to do under the "publish or perish" paradigm). As such, I will write too.

Photo by Tommy Huynh
These benefits and others have been getting me thinking I need to start a blog for quite a while. Of course, as a graduate student I'm fairly busy, but that's not the only thing that was stopping me. When I pursue things I tend to want to do them well. It's a little bit ambition and it's a little bit perfectionism. There is no shortage of good science writing on the internet nowadays. There will be a little more science writing now, and you can be the judge of how good it is.

Every great journey starts with the first step. So whether or not this blog ever becomes great, it won't become anything without a first post. Let's see where it takes me.