Tag Archives: evolution

The Pelican, the Shark, and the Armadillo: Crocodile Evolution Part 1

Crocodiles are very TV-genic – scores of documentaries have focused on them, and most start off with a variant of the following: “Crocodilians are some of the most successful predators on the planet. They survived the dinosaurs, and have remained unchanged for millions of years.”


An American crocodile (Crocodylus acutus). Photo by Tomas Castelazo, licensed under CC BY-SA 2.5.

Today I wanted to write about why that’s not entirely true, and why crocodilian evolution, far from monotonous, is instead dynamic and, like crocodilians themselves, full of surprises.

There are only 23 species of non-extinct crocodilians, compared to 327 turtles and tortoises and more than 9,000 lizards and snakes. The fossil record, however, is full of crocodile relatives, the crocodylomorphs, dating back to at least 225 million years ago (Bronzati et al. 2012; Russel and Wu 1998).

The first crocodylomorphs looked nothing like the crocodiles alive today. Instead they were small, nimble creatures that ran on four long legs. Their sharp teeth reveal a predatory lifestyle, but instead of waiting in ambush at the water’s edge, they were adapted for wandering about over land in search of prey.

These animals, the sphenosuchians, appeared during the Late Triassic period when dinosaurs were just beginning to evolve. With legs pointed down under the body (rather than splayed to the sides), the sphenosuchians were probably terrific at chasing down prey. One such reptile, Hesperosuchus, was about the size of a domestic dog.


Hesperosuchus. Illustration by Nobu Tamura, licensed under CC BY 2.5.

As the dinosaurs began to diversify, so did the crocodylomorphs. Although many stayed small, some got larger, and began to experiment with different lifestyles. I say “experiment” euphemistically, but evolution is blind — circumstances and natural selection simply allowed crocodylomorphs to fill a wider range of niches. There were large, land-dwelling predators, like Protosuchus:


Protosuchus. Illustration by Nobu Tamura, licensed under CC BY 2.5.

There were also marine crocodylomorphs, the thalattosuchians. These, too, were predatory and looked vaguely like modern crocodilians in that they had long jaws, a muscular tails, and laterally flattened bodies (Young et al. 2014). Here, from Europe, are three species of Machimosaurus:


Machimosaurus species. Illustration by M.T. Young et al. (2014), licensed under CC BY 4.0.

Others looked nothing like any modern animals, and had fin-like feet and tails. Dakosaurus, also from Jurassic Europe (Young et al. 2012), had such an un-crocodile-like skull that their fossils were at first mistakenly attributed to dinosaurs.


Dakosaurus maximus. Illustration by M.T. Young et al. (2012), licensed under CC BY 2.5.

Most of the sea crocodiles lived during the Jurassic Period, when dinosaurs on land were becoming truly massive (e.g., spike-tailed Stegosaurus and long-necked Brontosaurus*). Despite an uncanny resemblance, sea crocodiles did not “evolve into” modern crocodiles. Instead they represent an off-shoot of crocodylomorph evolution, a kind of “dead-end” with no modern descendants.

There’s plenty more to say about fossil crocodylomorphs in the Jurassic, but we’ll skip to the Cretaceous, the last period of non-bird dinosaurs with Tyrannosaurus, Triceratops, and the like. Crocodiles, too, were reaching a magnificent crescendo with on of their most diverse lineages, the Notosuchia.

The Cretaceous saw crocodylomorphs occupying all sorts of unusual ecological roles. There were, of course, the usual land-dwelling predators like Baurusuchus:


Baurusuchus. Illustration by Nobu Tamura, licensed under CC BY 2.5.

Others had turned over a new leaf, so to speak, and adopted a life of plant-eating. Simosuchus, one such herbivore (or omnivore — see Buckley et al. 2000), hardly looked like anything you might call a crocodile:


Simosuchus clarki. Illustration by Smokeybjb, licensed under CC BY-SA 3.0.

There were still weirder crocodylomorphs. Armadillosuchus had armor plates over its back — it looked, and quite possibly behaved, very much like a modern armadillo, only 6 feet long and with sharp, fang-like teeth.


Armadillosuchus arrudai. Illustration by Smokeybjb, licensed under CC BY-SA 3.0.

Meanwhile, some of the predatory crocodylomorphs had returned to the water, where they began to take full advantage of the lifestyle that would someday become the trademark of crocodilians. Many could be easily mistaken for true crocodiles — they had long snouts, flattened bodies, and spent their time ambushing visitors to the water’s edge. Some were colossal, and scientists have found evidence that some of the largest species (Sarcosuchus and Deinosuchus) preyed on dinosaurs (Boyd et al. 2013), just as Nile crocodiles today pick off unwary wildebeest and zebras.

Size comparison of two extinct and three living crocodylomorphs. Figure by Matt Martyniuk, licensed under CC BY-SA 3.0.

Size comparison of two extinct and three living crocodylomorphs. Figure by Matt Martyniuk, licensed under CC BY-SA 3.0.

Modern-day crocodilians belong to the Neosuchia (“new crocodiles”). This group also evolved in the Mesozoic and includes such strange beasts as Stomatosuchus, a 30-foot-long behemoth with a broad, spoon-like snout. Paleontologists aren’t sure exactly what it ate, but some suspect the lower jaw supported a pouch-like membrane for gulping fish, just like a pelican (Nopsca 1926).


Stomatosuchus inermis. Photo by Dmitri Bogdanov, licensed under CC BY 3.0.

Neither Sarcosuchus nor Stomatosuchus were “true” crocodilians, but crocodylians start to appear in the fossil record at around the same time. The oldest crocodilian fossils date back around 80 million years, during the Late Cretaceous (Russel and Wu 1998).

Just 15 million more years — a blink of an eye, really — until Earth’s most recent apocalypse. The same mass extinction that wiped out the dinosaurs (except birds), likely caused by a meteor, also wiped out most of the crocodylomorphs. Perhaps owing to their aquatic habits and (relatively) small size, crocodilians were one of the few survivors. A few other groups, like as the sea-faring dyrosaurids, lingered into the so-called Age of Mammals, but these too gradually fell away until only the true crocodiles, alligators, caimans and the gharial remained.

Guarinisuchus munizi, one of the few marine crocodylomorphs after the K-T extinction event. Illustration by Nobu Tamura, licensed under CC BY 3.0.

Guarinisuchus munizi, one of the few marine crocodylomorphs after the K-T extinction event. Illustration by Nobu Tamura, licensed under CC BY 3.0.

So we arrive at the present day, with 23 living species of crocodilians. Those 23 are the survivors survivors, here today because they are adaptable, tough, and a little bit lucky. They bear witness to an ancient lineage of incredibly diverse, versatile, and often bizarre animals, most of which have died. They are the ones that lived through mass extinctions, competition with dinosaurs, and climate change. They may even survive us.


A Nile crocodile (Crocodylus niloticus). Photo by Gianfranco Gori, licensed under CC BY-SA 4.0.

*Brontosaurus may or may not be the same as Apatosaurus. If they are the same, then Brontosaurus is not a valid name. I’m not a paleontologist, so I have no opinion on the matter — I used the name Brontosaurus here since I think it is more recognizable, although I may be wrong about that, too. To learn more, check out this article by zoologist and writer Darren Naish.

I’ll be writing more about crocodilian evolution tomorrow, this time with an amazing species that is alive today. If you want to read more about extinct crocodylomorphs, read this article, also by Darren Naish. If this kind of stuff interests you, I recommend following his blog Tetrapod Zoology at the same link.

Finally, if you are interested in a more technical review of crocodylomorph evolution, some good papers to read are Bronzati et al. (2012) and Russel and Wu (1998), cited below.


Boyd C.A., S.K. Drumheller, and T.A. Gates. 2013. Crocodyliform feeding traces on juvenile ornithischian dinosaurs from the Upper Cretaceous (Campanian) Kaiparowits Formation, Utah. PLOS ONE 8(2): e57605. doi: 10.1371/journal.pone.0057605

Bronzati M., F.C. Montefeltro, and M.C. Langer. 2012. A species-level supertree of Crocodyliformes. Historical Biology 24(6): 598-606.

Buckley G.A., C.A. Brochu, D.W. Krause, and D. Pol. 2000. A pug-nosed crocodyliform from the Late Cretaceous of Madagascar. Nature 405: 941-944.

Nopcsa F. 1926. Neue Beobachtungen an Stomatosuchus. Centralbl. Min. Geol. Palaontol, B212-215.

Russel A. and X.-C. Wu. 1998. The crocodylomorpha at and between geological boundaries: the Baden-Powell approach to change? Zoology 100(3): 164-182.

Young M.T., S. Hua, L. Steel, D. Foffa, S.L. Brusatte, S. Thüring, O. Mateus, J.I. Ruiz-Omeñaca, P. Havlik, T. Lepage, and M. Brandalise de Andrade. 2014. Revision of the Late Jurassic teleosaurid genus Machimosaurus (Crocodylomorpha, Thalattosuchia). Royal Society Open Science doi: 10.1098/rsos.140222

Young M.T., S.L. Brusatte, Marco Brandalise de Andrade, J.B. Desojo, B.L. Beatty, L. Steel, M.S. Fernández, M. Sakamoto, J.I. Ruiz-Omeñaca, and R.R. Schoch. 2012. The cranial osteology and feeding ecology of the mentriorhynchic crocodylomorph genera Dakosaurus and Plesiosuchus from the Late Jurassic of Europe. PLOS ONE 7(9): e44985. doi: 10.1371/journal.pone.0044985


Malaria, Climate Change, and the Next Top Model

by Joseph DeSisto

Both malaria and climate change are complex global problems that scientists are working hard to understand. Malaria, a mosquito-borne disease, kills roughly 600,000 people every year, mostly in Africa. Attempts to control malaria have been massive and relatively well-funded, but the disease continues to pose a serious threat to human life in the tropics. Climate change has no body count (yet), but will dramatically change our planet, altering weather patterns, sea levels, and human life.

These two problem have another thing in common: scientists use mathematical models to try and predict how they will change in the future. For example, climate scientists use past and current data on temperature, carbon emissions, and many other factors, to predict how the earth’s climate will change. Most models anticipate a global temperature increase of 2̊ to 6̊  by the year 2100 (e.g., Paaijmans et al. 2014). Those predictions may not be perfectly accurate, but that is the nature of predictions, and in the absence of time travel, it’s the best we can do.


Anopheles minimus, a malaria-transmitting mosquito. Photo by James Gathany, in public domain.

Malaria, the microbes that cause it, and the mosquitos that carry it, are all affected by temperature. Scientists have tried developing models to predict how malaria infection rates will change as the world gets hotter. In general those predictions have been bleak: models tend to show an increase in the amount of people affected by malaria (e.g. Pascual et al. 2006, Paaijmans et al. 2014), on the basis that warmer temperatures are most hospitable to malaria-carrying mosquitos. They also show malaria spreading to areas that used to be too cool, like South Africa and the southeastern United States. Yet other models show a decrease in malaria on a global scale (Gething et al. 2010), and some suggest an increase in some areas but a decrease in others (Rogers and Randolph 2000).

Before looking forward, it’s important to look back – how has malaria changed in the last few years? The maps below show malaria infection rates (the percentage of people infected) across Africa, in 2000 (left) and 2010 (right). Darker colors mean more malaria.



Photo by Noor et al. (2014), licensed under CC BY 3.0.

The two maps may not look all that different, but look closely. The red arrow points to West Africa, where the darkest area has grown smaller. Malaria is still common there, but has declined. In Kenya and Tanzania (purple arrow), malaria has declined even more. Even though efforts to completely eradicate malaria have failed, improved mosquito control programs have been successful in reducing the threat of malaria in these regions of Africa.

A model is basically an equation, and in the case of malaria it serves to calculate R0: the basic reproduction number. The basic reproduction number is the answer to the question, for each person already afflicted with malaria, to how many other people will their infection spread? This gives us an idea of how many people are likely to contract malaria in a given year.

For example, if R0 is 15, that means every person with malaria is likely to pass it on to fifteen other people – that’s about the R0 value for measles. If R0 is 0.5, then on average, half of all malaria patients will pass their infection on to another. For all diseases, when R0 is less than 1.0, the disease will decline, and if R0 is greater, the disease will increase in the population. Very high values of R0 can lead to pandemic.

Malaria is a complicated disease, affected by all three players: humans, microbes (more on them later), and mosquitos. In turn, each of these players are affected by temperature, moisture, population density, and other local conditions. As a result, malaria’s basic reproductive number varies depending on where you are. In 2007, a group of scientists attempted to calculate R0 for 121 different human populations in Africa (Smith et al. 2007). The study had two important results.

First, R0 varied wildly across Africa. Although the average value was near 115, many populations had values below 10 and many more had values over 1,000. Second, some R0 were extremely high, approaching 10,000. Remember what this means – on average, each person with malaria has the potential to transmit their malaria to 10,000 other people!

In some cases the R0 value was greater than the human population, suggesting that everyone in the population had malaria when of course this was not the case. Is there a problem with the model? The scientists in question didn’t think so. Instead they pointed out that although malaria’s R0 is much higher than for most other diseases, malaria also takes much more time to spread (on average, 200 days per generation) because of its complex life cycle.

The parasites that cause malaria are single-celled, apparently simple, but with strange and complicated lives. I say parasites, plural, because there are at least five species that cause malaria, but all are protozoans in the genus Plasmodium. The cycle, of course, has no “beginning,” but we will start with the oocyst, a kind of “egg sac” containing multiple Plasmodium cells and surrounded by a protective membrane.


A Plasmodium sporozoite (purple). Image by Ute Frevert; false color by Margaret Shear, licensed under CC BY 2.5.

The oocyst lives in the body of a female Anopheles mosquito, and by the time the mosquito lands for a blood meal, the membrane bursts. Single-celled Plasmodium parasites surge forth, down the mosquito’s mouthparts, and into the blood-stream of an unsuspecting human. The freed cells are called sporozoites; they are worm-like and active, and waste no time snaking their way through the host’s body until they reach the liver.

Here the parasites eat, grow, and change shape. They divide and transform into masses of globular cells, similar to oocysts, once again enveloped in a bag-like protective layer. As time goes on, liver becomes tiresome, and the parasites crave blood. The bag of cells bursts, and the Plasmodium cells return to the blood stream. Now they have a new mission: find a red blood cell.

Red blood cells are hollow and doughnut-shaped, like inflatable inner tubes. You use them to transport oxygen and carbon dioxide into and out of your body, with every breath. The blood cell’s membrane is thin, almost fluid, and easy for a Plasmodium cell to invade. Once inside, the parasite has two options. It can grow and divide, forming a new mass of cells (like the oocyst). If it does so, these cells will ultimately break out of their shelter to find new red blood cells of their own. More ambitious parasites, however, refrain from dividing. Instead they metamorphose, transforming into either male or female cells.

For the Plasmodium life cycle to complete, a second mosquito is required. The new mosquito lands on a malarial host, sucking up blood and with it, lots of red blood cells. Some of these are empty, but others, if Plasmodium is lucky, contain either male or female hitchhikers. In the mosquito’s digestive system, red blood cells burst open to release their passengers. The freed Plasmodium cells, male and female, meet and unite. Once they do, they are able to multiply and grow into a multi-celled oocyte, full of wriggling sporozoites ready to enter a new human host at the mosquito’s next meal.


A mosquito in the genus Anopheles, capable of transmitting malaria. Photo by Jim Gathany, in public domain.

For this system to work, mosquitos not only have to be infected with Plasmodium, but sporozoites have to be fully developed and ready to pounce when opportunity (i.e., a bite) comes along. Lots of mosquitos need to be biting people, so that at least some will slurp up the male and female cells when they are ready. Mosquitos need to have reasonable lifespans – those that meet their end in a frog’s belly or a spider’s web are of no use to Plasmodium. The mosquitos, in turn, have requirements of their own: they need optimal growing temperatures, pools of water in which to lay their eggs, and plenty of warm-bodied hosts from which to drink.

All of these factors (and many more) are variables that might appear in an equation to calculate R0. Smith and colleagues (2007) used them to calculate the R0 for all those 121 African populations. More recently, a group of scientists and mathematicians got together to predict how R0 will change with the earth’s climate (Ryan et al. 2015).

In general, both mosquitos and Plasmodium can only develop at temperatures between 63̊ and 93̊ F. That’s good, useful information, but not enough — each of Smith’s variables (mosquito life span, number of bites per person, etc.) is affected by temperature, but each in a slightly different way. Only by combining all of these factors, and considering how each will change under future climate conditions, can we accurately predict how the threat of malaria will change over time. That’s what Ryan and colleagues did, and published this month in Vector-Borne and Zoonotic Diseases.

It turns out that if you combine all those variables, you get a much more complex picture of how climate change and malaria interact. Although some areas will get warmer and more suitable for malaria, others will actually get too hot, so malaria will decline.

This particular study shows a decrease in malaria in West Africa, but an increase in East Africa. In other words, the hot-spot for malaria will shift east over the next six decades.


From Ryan et al. (2015), licensed under CC BY 4.0.

In the maps above, purple indicates the greatest increase in malaria transmission rates, while the palest tone indicates a decline in malaria.

Caution is important. When different models produce vastly different results, it usually means that some of those models are better than others. This model happens to consider more factors than many others, which suggest it may be more accurate, but as I have tried to show, malaria is a complex disease that will be affected by temperature in complex, hard-to-predict ways.

Having an idea of what the future might hold can inform us – where should we concentrate efforts to control malaria? Where will malaria pose the greatest threat to human health? This latest model suggests our focus will have to shift as Plasmodium, mosquitos, and malaria follow their optimal temperatures in an eastward march across Africa.


Gething P.W., D.L. Smith, A.P. Patil, A.J. Tatem, R.W. Snow, and S.I. Hay 2010. Climate change and the global malaria recession. Nature 465(7296): 342–346.

Noor A.M., D.K. Kinyoki, C.W. Mundia, C.W. Kabaria, J.W. Mutua, V.A. Alegana, I.S. Fall, and R.W. Snow. 2014. The changing risk of Plasmodium falciparum malaria infection in Africa: 2000-10: a spatial and temporal analysis of transmission intensity. The Lancet 383(9930): 1739-1747.

Paaijmans K.P., J.I. Blanford, R.G. Crane, M.E. Mann, L. Ning, K.V. Schreiber, and M.B. Thomas. 2014. Downscaling reveals diverse effects of anthropogenic climate warming on the potential for local environments to support malaria transmission. Climate Change 125: 479-488.

Pascual M., J.A. Ahumada, L.F. Chaves, X. Rodó, and M. Bouma. 2006. Malaria resurgence in the East African highlands: temperature trends revisited. Proceedings of the National Academy of Sciences U.S.A. 103(15): 5829–5834.

Rogers D.J. and S.E. Randolph. 2000. The global spread of malaria in a future, warmer world. Science 289: 1763–1766.

Ryan S.J., A. McNally, L.R. Johnson, E.A. Mordecai, T. Ben-Horin, K. Paaijmans, and K.D. Lafferty. 2015. Mapping physiological suitability limits for malaria in Africa under climate change. Vector-Borne and Zoonotic Diseases 15(12): ahead of print.

Smith D.L., F.E. McKenzie, R.W. Snow, and S.I. Hay. 2007. Revisiting the basic reproductive number for malaria and its implications for malaria control. PLOS Biology 5(3): e42. doi: 10.1371/journal.pbio.0050042

Two New Species of Ant-Decapitating Fly

by Joseph DeSisto

An ant-decapitating fly. Photo by Scott Bauer, in public domain.

An ant-decapitating fly. Photo by Scott Bauer, in public domain.

Today saw the description of two new species of South American flies, both fire ant parasites that decapitate their victims. The two new species were discovered in Brazil and Argentina, associated with fire ant mounds in their native territory (Plowes et al. 2015).

Ant-decapitating flies, as might be expected, have unusual and macabre life histories. The adults are tiny, just a few millimeters in length, with the general appearance of fruit flies. Instead of hovering around rotten bananas, however, female ant-decapitating flies hang around ant mounds. When the time is right, a fly soars down to meet her victim, using a hooked, needle-like ovipositor to inject an egg into the ant’s head (Porter 1998).

With egg laid, her work is done. The fly departs, ant still intact and seemingly healthy.

A fly attacking a fire ant, hoping to lay its egg on the ant's head. Photo by Sanford Porter, in public domain.

A fly attacking a fire ant, hoping to lay its egg on the ant’s head. Photo by Sanford Porter, in public domain.

Not all is well, however. From the fly’s egg emerges a maggot that, as it grows, eats away at the inside of the ant’s head. At the same time, the maggot secretes chemicals that cause the ant to go mad, fleeing its colony and finding shelter in moist leaf litter. With its host almost spent, the maggot severs the ant’s head, and forms a cocoon or pupa inside the now-hollow shell. Some weeks later, a new fly emerges and takes off in search of a new ant for her offspring.

This all sounds very sinister, but it also could be very useful to humans. As it happens, many of these flies specialize in decapitating fire ants and, in enough numbers, can seriously impact fire ant colonies. Now that invasive fire ants are well-established in the southern U.S., the Department of Agriculture is looking to ant-decapitating flies to control the ants’ march north.

The remains of a fly's victim. Photo by Sanford Porter, in public domain.

The remains of a fly’s victim. Photo by Sanford Porter, in public domain.

Whether the two new species of ant-decapitating fly will be useful in controlling fire ants remains to be seen. Multiple fly species have already been introduced in states like Texas (Gilbert and Patrock 2002) and Alabama (Porter et al. 2011), where fire ants are a serious problem for agriculture and human health. In these states the flies have become established and already have a tangible impact on fire ant populations.

However, not all species fare equally well. In order to be useful in controlling fire ants, the flies must be able to adapt to the southern U.S. climate, as well as all the new predators they may not have faced in South America.

Plowes and colleagues (2015) suggest that many more unknown species of ant-decapitators live in remote regions of South America. Discovering new species may help scientists figure out which flies will be most successful at colonizing the U.S., and which species will have the biggest impact on fire ant populations.


Gilbert L.E. and R.J.W. Patrock. 2002. Phorid flies for the biological suppression of imported fire ant in Texas: region specific challenges, recent advances and future prospects. Southwestern Entomologist Supplement 25: 7-17.

Plowes R.M., P.J. Folgarait, and L.E. Gilbert. 2015. Pseudacteon notocaudatus and Pseudacteon obtusitus (Diptera: Phoridae), two new species of fire ant parasitoids from South America. Zootaxa 4032(2): 215-220.

Porter S.D., L.F. Graham, S.J. Johnson, L.G. Thead, and J.A. Briano. 2011. The large decapitating fly Pseudacteon litoralis (Diptera: Phoridae): successfully established on fire ant populations in Alabama. Florida Entomologist 94(2): 208-213.

Porter S. D. 1998. Biology and behavior of Pseudacteon decapitating flies (Diptera: Phoridae) that parasitize Solenopsis fire ants (Hymenoptera: Formicidae). Florida Entomologist 81(3): 292-309.

Why Scorpion Venom is So Complex

by Joseph DeSisto

Scorpion venom, like many animal venoms, is incredible complex. It is made up of hundreds of different toxins and other proteins, each with a specific function, all mixed together in a lethal cocktail. Why do scorpions need so many different toxins? Last week, scientists at the Chinese Academy of Sciences published the results of their attempt to answer this question (Zhang et al. 2015).

They began by studying a particular class of proteins found in scorpion venom, which work by attacking the sodium ion-channel proteins in their victims.

The stripe-tailed scorpion, Vaejovis spinigerus, ready for action.. Photo by Joseph DeSisto.

The stripe-tailed scorpion, Vaejovis spinigerus, ready for action. Photo by Joseph DeSisto.

Sodium ion-channels help regulate the amount of sodium inside animal cells, which is vital for cells to function properly. In nerve cells, they are even more important: the change in sodium concentration inside and outside the cell is what transmits electric signals.

Toxins that inhibit sodium channels prevent the nervous system from working, which leads to death if the victim is small (like an insect). Scorpions have toxins called sodium-channel toxins to do exactly that. The puzzle is, scorpions have many different genes that produce sodium-channel toxins, each of which has a slightly different structure.

All proteins are essentially strings that are wound, twisted, and tied into a specific structure. The structure of a protein is critical to its function, since proteins need to have certain shapes in order to interact with each other like a lock and key. All sodium-channel toxins have a portion designated as the “interactive region” — the key — which attaches to a series of loops on the prey’s sodium ion-channel (the lock). If the key fits and the connection is successful, the prey’s ion-channel can no longer function.

A mother stripe-tailed scorpion, carrying young. Photo by Joseph DeSisto.

A mother stripe-tailed scorpion, carrying young. Photo by Joseph DeSisto.

Zhang and his colleagues studied the genome of their scorpion, a desert-dwelling East Asian species known as the Chinese golden scorpion (Mesobuthus martensii). They found no less than 29 different genes coding for sodium channel toxins.

There was a time, perhaps hundreds of millions of years ago, when scorpions only had one gene for sodium-channel toxins. Eventually that gene was duplicated, and thereafter the scorpion genome had multiple copies of the same toxin-producing gene. Since then, each copy of the gene has continued to mutate and evolve in its own direction. Now each toxin, despite having the same basic structure, is just a little bit different from the rest.

As it happens, the genes for sodium ion-channels in a scorpion’s prey also exist in multiple copies, each with minor variations. Zhang and colleagues hypothesized that scorpions need so many varieties of toxins because each toxin can only interact with a specific variety of ion-channel. In other words, scorpion venom needs lots of different keys because the prey have so many different locks.

To test this, the scientists examined the different toxin-gene copies to better understand how they had evolved. Sure enough, the “interactive region,” the key, of each toxin had mutated and evolved much more quickly than the “body” of the toxin. This provided strong evidence that natural selection has caused scorpion venom to evolve different types of toxins to keep up with the ever-evolving ion-channels in their prey.

Scorpions are incredible animals for so many reasons. They have been around for more than 400 million years — as long as there have been insects to hunt on land, scorpions have been there to hunt them. They are amazing and diverse in form, lifestyle, and hunting strategy. How fitting that they should be just as amazing on the molecular level.


Zhang S., B. Gao, and S. Zhu. Target-driven evolution of scorpion toxins. Nature Scientific Reports 5:14973 doi: 10.1038/srep14973

The Bucktoothed Slopefish

by Joseph DeSisto

We all love tales of rare sharks and squid, hauled up from the depths in nets and traps. Just a few days ago, an extremely rare deep-sea shark (the false catshark) was found off the coast of Scotland. Yet it is important to remember that the ocean is a big place and, in a paradoxical sort of way, it’s quite common for fish to be rare.

Enter the slopefishes, a handsome if under-appreciated family of marine fishes. All of the family’s 12 species live in rocky reefs at moderate depths. Most are rare, some extremely so. One species is known only from two specimens which were removed from the stomach of a coelacanth (a much larger fish) near the Comoros Islands. The slopefish were partially digested, so even though they represent new species, scientists have been unable to formally describe and name them (Anderson and Springer 2005). After 36 years, those two fish remain the only known representatives of their kind.

The bucktoothed slopefish. Photo by M.V. Chesalin, licensed under CC BY 3.0.

The bucktoothed slopefish. Photo by M.V. Chesalin, licensed under CC BY 3.0.

The bucktoothed slopefish’s tale might have ended similarly. Scientists named the species in 1974 based on only one specimen, found near the Gulf of Aden between Yemen and Somalia. Later efforts to capture more were fruitless. Finally, earlier this year, a bucktoothed slopefish made its way into a deep-sea fish trap off the coast of Oman (Anderson et al. 2015).

Now that a new specimen is available, we can appreciate the species for what it is: a thing of beauty, scarlet red and stream-lined, with rigid spines along the back. This discovery serves to remind us that the best finds in nature come not merely from knowledge, or even luck, but from days, weeks, or even decades of patience, persistence, and hard work.


Anderson Jr. W.D. and V.G. Springer. 2005. Review of the perciform fish genus Symphysanodon Bleeker (Symphysanodontidae), with descriptions of three new species, S. mona, S. parini, and S. rhax. Zootaxa 996: 1-44.

Anderson Jr. W.D., M.V. Chesalin, L.A. Jawad, and S.R. Al Shajibi. 2015. Redescription of the percoid fish Symphysanodon andersoni Kotthaus (Symphysanodontidae) from the northwestern Indian Ocean, based on the holotype and the second known specimen. Zootaxa 4021(3): 475-481.

Shrimp-like Amphipods found in Sea Anemones

by Joseph DeSisto

Amphipods are crustaceans, similar to tiny shrimp. There are around 10,000 known species, with more being discovered each year. Most amphipods are marine and live as scavengers or predators, swimming or scuttling after tiny particles of food or plankton. A few are predatory, and use mantis-like front legs to snap up smaller creatures.

Stenothoe marina, related to the newly described amphipods. Photo by Hans Hillewaert, licensed under CC BY-SA 4.0.

Stenothoe marina, related to the newly described amphipods. Photo by Hans Hillewaert, licensed under CC BY-SA 4.0.

Last week’s new species are even more bizarre: they are “associates” living on the bodies of larger animals, ranging from sea anemones to mussels to hermit crabs (Krapp-Schickel and Vader 2015). So what exactly are they doing there?

Anemone-dwelling amphipods spend their time clambering over the tentacles of their host. Sea anemone tentacles are covered in microscopic stingers, to which the amphipods (like clown fish) are immune. Being surrounded by venomous tentacles might protect the amphipods from larger predators.

In turn, amphipods probably scavenge bits of detritus, such as uneaten prey, off the body of the anemone. One amphipod, however, does things a little differently. Instead of scavenging, it lives as a parasite, feeding on the flesh of its sea anemone host (Moore et al. 1994). Regardless, all of these amphipods have grasping, hook-like front legs called gnathopods (silent G), which they use to climb over and within the bodies of other animals.

Sea anemones. Photo by Francois Guillon, licensed under CC BY-SA 4.0.

Sea anemones. Photo by Francois Guillon, licensed under CC BY-SA 4.0.

Mussel-associated amphipods are more peaceful, but not entirely welcome, guests. Mussels are filter-feeders that extract plankton from the water, so instead of eating the mussel, amphipods steal some of the daily plankton catch (Tandberg et al. 2010). They are kleptoparasites, animals that steal their food.

Mussel-dwellers belong to the genus Metopa, and have surprisingly sophisticated lives (Tandberg et al. 2010). Each mussel is home to a single mating pair of adult amphipods, who defend their home against intruders. Most species spend their entire adult lives within the shell of a single mussel. In this time they work hard to raise multiple generations, which grow together until they are ready to head out to sea and find molluscan homes of their own.

A common hermit crab, host to a unique amphipod. Photo © Biopix: N Sloth, licensed under CC BY-NC 3.0.

A common hermit crab, host to a unique amphipod. Photo © Biopix: N Sloth, licensed under CC BY-NC 3.0.

Still other amphipods are described as hermit crab associates, some living on the crab’s acquired snail shell (Krapp-Schickel and Vader 2015). At least one species eats invertebrates that land and begin to grow on the shell. Others, however, live on the bodies of the crabs themselves.

This seems like a risky move. Hermit crabs are rigorous self-cleaners, constantly scrubbing the insides of their shells with specialized, brush-like hind legs. Perhaps the amphipods, by scavenging bits of uneaten food from the crab’s body, are helpful maids to their type-A hosts. If this is the case, hermit crabs may spare their amphipod companions on purpose. We still don’t know if the crab-dwelling amphipods are helpful cleaners or true parasites — if the latter is true, they must be well-adapted to avoid detection by their hosts.


Krapp-Schickel T. and W.J.M. Vader. 2015. Stenothoids living with or on other animals (Crustacea, Amphipoda). Zoosystematics and Evolution 91(2): 215-246.

Moore P.G., P.S. Rainbow, and W. Vader. 1994. On the feeding and comparative biology of iron in coelenterate-associated gammaridean Amphipoda (Crustacea) from N. Norway. Journal of Experimental Marine Biology and Ecology 178: 205-231.

Tandberg A.H.S., C. Schandler, and F. Pleijel. 2010. First record of the association between the amphipod Metopa alderi and the bivalve Musculus. Marine Biodiversity Records 3, e. 5, 2 pp.

Sea Spiders and the Rise of the Chelicerates

by Joseph DeSisto

Sea spiders are small, eight-legged marine arthropods with a vaguely spider-like appearance: members of the obscure class Pycnogonida. Most of the 1300 or so species are predatory, feeding on jellyfish, sponges, and other soft-bodied marine invertebrates. After eight-leggedness and predatory habits, the similarities with spiders end.

A yellow-kneed sea spider. Photo by Sylke Rohrlach, licensed under CC BY-SA 2.0.

A yellow-kneed sea spider. Photo by Sylke Rohrlach, licensed under CC BY-SA 2.0.

So what exactly are sea spiders? For a long time they were considered to be the most ancient members of an already-ancient group of animals: the Chelicerata, which includes the arachnids and the horseshoe crabs (Dunlop and Arango 2005). These animals are united by their possession of chelicerae, a kind of mouthpart.

Chelicerae are extremely versatile, and in the 450-odd million years they’ve been around, natural selection has resulted in a huge diversity of forms. A spider’s chelicerae, for example, are hollow and capable of injecting venom into prey. Scorpion chelicerae, on the other hand, are smaller and used for chewing up food. Some harvestmen (daddy-long-legs) have long chelicerae with pincers at the end, useful for grabbing prey.

Sea spiders have chelicerae too — sort of. Their mouthparts at least are similar to chelicerae, but because they’ve been subject to hundreds of millions of years of evolution, it isn’t easy to discern their “true” identity. Modern sea spiders have hollow, tube-like chelicerae, which they use to suck out the insides of their prey.

 licensed under CC BY-SA 4.0.

A sea spider using its chelicerae to prey on a hydroid. Photo by Bernard Picton, licensed under CC BY-SA 4.0.

Classification can get complicated. To understand where sea spiders fit into the tree of life, we must ask the question: are sea spider chelicerae “real” chelicerae? That might sound like a silly question — after all, “chelicerae” is just a term we made up. But what we really mean is, are sea spider chelicerae homologous with the chelicerae of arachnids and horseshoe crabs? If they are, then sea spiders and the other chelicerates inherited their mouthparts from the same common ancestor. If not, chelicerae evolved twice: once in sea spiders, and separately in the “true” Chelicerata.

In 2005, Amy Maxmen and colleagues carefully studied the chelicerae of sea spiders and found that they emerged from a different part of the body than in other arthropods. It seemed that in sea spiders, chelicerae emerged from the same segment that contained the eyes (but not mouthparts) in other chelicerates. This suggested that sea spiders were not true chelicerates, but instead formed their own group, which Maxmen et al. (2005) hypothesized to be the oldest living arthropod lineage.

A sea spider -- the red hanging structure contains the mouthparts. Photo by Scott C. France, licensed under CC BY-SA 2.0.

A sea spider — the red hanging structure contains the mouthparts. Photo by Scott C. France, licensed under CC BY-SA 2.0.

In arthropods and other segmented animals, Hox genes are responsible for making sure that all the right body parts develop on all the right segments. It was surprising, then, when a 2006 study found that the Hox genes place chelicerae on the same segments in sea spiders and in arachnids (Jager et al. 2006). Apparently, this segment was shifted backwards in sea spiders, creating confusion.

Over the years, scientists have tried comparing the DNA of many arthropods to try and understand how they are related to one another. One of the most comprehensive studies (Regier et al. 2010) placed sea spiders comfortably within the Chelicerata, as the group’s oldest (i.e., basal-most) lineage. Since then there has been little debate: sea spiders may be some of the oldest arthropods on earth, but they really are chelicerates, after all (Giribet and Edgecombe 2012). That is, until new evidence comes along to shake things up again.


Dunlop J.A. and C.P. Arango. 2005. Pyncogonid affinities: a review. Journal of Zoological Systematics and Evolutionary Research 43(1): 8-21.

Giribet G. and G.D. Edgecombe. 2012. Reevaluating the arthropod tree of life. Annual Review of Entomology 57: 167-186.

Jager M., J. Murienne, C. Clabaut, J. Deutsch, H. Le Guyader, and M. Manuel. 2006. Homology of arthropod anterior appendages revealed by Hox gene expression in a sea spider. Nature 441: 506-508.

Maxmen A., W.E. Browne, M.Q. Martindale, and G. Giribet. Neuroanatomy of sea spiders implies an appendicular origin of the protocerebral segment. Nature 437: 1144-1148.

Regier J.C., J.W. Schultz, A. Zwick, A. Hussey, B. Ball, R. Wetzer, J.W. Martin, and C.W. Cunningham. 2010. Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature 463: 1079-1083.

Poisonous Frogs, Beetles, and Birds

by Joseph DeSisto

Meet the golden poison frog of Colombia’s coastal rain forests. This frog, one of nearly 200 species of poison frogs, is by far the most toxic. A single frog packs enough poison to kill 10,000 mice, or 10 or more humans (Myers et al. 1978).

The golden poison frog (Phyllobates terribilis). Photo by Brian Gratwicke, licensed under CC BY 2.0.

The golden poison frog (Phyllobates terribilis). Photo by Brian Gratwicke, licensed under CC BY 2.0.

For the golden poison frog and its close relatives in the genus Phyllobates, batrachotoxin is the weapon of choice. Batrachotoxin acts on the nervous system, opening up the membranes of nerve cells so they can no longer carry signals to and from the brain. Death comes from paralysis, which leads to heart failure.

The golden poison frog was only discovered in 1971 when scientists found them around an indigenous Colombian (Emberá Chocó) village (Myers et al. 1978). The Emberá use the frogs to lace poison darts, with which they hunt game in the surrounding forest. The frog-handlers were careful to cover their hands with leaves, with good reason. Scientists who touched the frog felt a strong burning sensation, and they stressed in their initial description that:

The new species is potentially dangerous to handle: One freshly caught frog may contain up to 1900 micrograms (µg) of toxins, only a fraction of which would be lethal to man if enough skin secretion came into contact with an open wound.”(Myers et al. 1978, pp. 311)

The black-legged poison frog (Phyllobates bicolor), closely related to terribilis but not quite as toxic. Photo by Drriss and Marrionn, licensed under CC BY-NC-SA 2.0.

The black-legged poison frog (Phyllobates bicolor), closely related to terribilis but not quite as toxic. Photo by Drriss and Marrionn, licensed under CC BY-NC-SA 2.0.

It is important, as the frog’s discoverers remind us, “to be cautionary, not alarmist” (Myers et al. 1978, pp. 340). Even though in theory these frogs are dangerous, there is no record of a person ever being killed by one. Although the poison can go through a person’s skin, it seldom does so in enough quantity to injure. The frogs do not bite. So if you see golden poison frogs while exploring in Colombia, do not panic, but be wary. However delicious and lemon-drop-colored they may seem, definitely don’t try eat them.

Golden poison frogs are sometimes sold in the pet trade, since they lose their poison after being taken out of the wild. This is probably because frogs get batrachotoxin from their food: soft-winged beetles that make the toxin themselves (Dumbacher et al. 2004). In captivity, frog-keepers give their pets a blander diet of crickets and fruit flies, which don’t contain batrachotoxin.

An example of a soft-winged beetle, in the same family as those eaten by poison frogs. Photo by Udo Schmidt, licensed under CC BY-SA 2.0.

An example of a soft-winged beetle, not the same species, but in the same family as those eaten by poison frogs. Photo by Udo Schmidt, licensed under CC BY-SA 2.0.

Soft-winged beetles are found all over the world, especially in the tropics, but so far only a few other animals are known to eat them and use their batrachotoxins. Three of these are poison frogs, all found in a small rain forest region of Colombia. The others are birds. Yes, there are poisonous birds, and even though this blog is explicitly not about birds or mammals, I’m going to break that rule today.

The hooded pitohui (Pitohui dichrous) -- both males and females are brightly colored. Photo by Katerina Tvardikova, licensed under CC BY-NC-SA 3.0.

The hooded pitohui (Pitohui dichrous) — both males and females are brightly colored. Photo by Katerina Tvardikova, licensed under CC BY-NC-SA 3.0.

The toxic birds are all found in New Guinean rain forests, and most belong to a group of insect-eaters called pitohius (pronounced PI-to-hooies). Pitohui birds are related to the orioles and blackbirds found in more temperate climes. Shown above is the hooded pitohui, first found to be poisonous when a bird researcher handled one and left with a tingling, burning sensation in his hand.

Later study showed that the hooded pitohui, along with two other related species, has feathers laced with batrachotoxins (Dumbacher et al. 1992). More than a decade later, the same scientists demonstrated that toxin-wielding pitohui birds eat soft-winged beetles, and that these same beetles are loaded with batrachotoxin (Dumbacher et al. 2004). Despite being toxic, the birds are not nearly as dangerous as golden poison frogs, and there is little risk to a careful handler.

The variable pitohui (Pitohui kirhocephalus), not as showy as its cousin, but toxic all the same. Photo by Katerina Tvardikova, licensed under CC BY-NC-SA 3.0.

The variable pitohui (Pitohui kirhocephalus), not as showy as its hooded cousin, but toxic all the same. Photo by Katerina Tvardikova, licensed under CC BY-NC-SA 3.0.

Several more birds are now known to use batrachotoxins, and all are found in New Guinea (Weldon 2000). Many of them have similar red-and-black color patterns. By having similar colors, multiple bird species can work together to “educate” predators who might not be aware of the poisonous feathers (Dumbacher and Fleischer 2001). To make matters even more interesting, the toxins in bird feathers apparently serve as a repellent to parasitic lice (Dumbacher 1999).

We may continue to learn more about these amazing birds and their lives, or we may not. Most of these birds are becoming rarer and rarer as New Guinean rain forest is slashed and burnt, tilled and grazed into nothing.

I’ve written several articles about poisons and venoms: click here to learn about brown recluse venom and here to learn about tetrodotoxin, a poison used by many fish as well as newts, snails, and blue-ringed octopuses.

Darren Naish, writer of the superb science blog Tetrapod Zoology, writes often about birds. Click here for one of his articles on a poisonous New Guinean species. Note that the article is not on his most recent blog site, which is updated regularly at the first link to Scientific American.

To learn more about the relationship between lice and toxic pitohui birds, click here to read an excellent article by Bianca Boss-Bishop on the aptly-named blog Parasite of the Day.


Dumbacher J.P. 1999. Evolution of toxicity in Pitohuis: I. effects of homobatrachotoxin on chewing lice (order: Phthiraptera). The Auk, 116: 957-963.

Dumbacher J.P., A. Wako, S.R. Derrickson, A. Samuelson, and T.F. Spande. 2004. Melyrid beetles (Choresine): a putative source for the Batrachotoxin alkaloids found in poison-dart frogs and toxic passerine birds. Proceedings of the National Academy of Sciences U.S.A. 101(45): 15857-15860.

Dumbacher J. P., B.M. Beehler, T. F. Spande, H. M. Garra¡o, and J.W. Daly. 1992. Homobatrachotoxin in the genus Pitohui: chemical defense in birds? Science 258: 799-801.

Dumbacher J.P. and R.C. Fleischer. 2001. Phylogenetic evidence for colour pattern convergence in toxic pitohuis: Müllerian mimicry in birds? Proceedings of the Royal Society of London B 268(1480): 1971-1976.

Myers C.W., J.W. Daly, and B. Malkin. 1978. A dangerously toxic new frog (Phyllobates) used by Emberá Indians of western Colombia, with a discussion of blowgun fabrication and dart poisoning. Bulletin of the American Museum of Natural History 161(2): 311-365.

Weldon P.J. 2000. Avian chemical defense: toxic birds not of a feather. Proceedings of the National Academy of Sciences U.S.A. 97(24): 12948-12949.

The Alligator’s Nest

by Joseph DeSisto

If you are careless in wandering along the swamps of the southeastern United States, you may hear this sound emanating from the brush:

[Recording by Adam Britton, used with permission.]

That is the hiss of an angry American alligator — if you hear it on land, you may have stumbled upon an alligator nest. If so, do not delay in your retreat. A mother alligator’s warning is no bluff.

An American alligator (Alligator mississippiensis) from South Carolina. Photo by Gareth Rasberry, licensed under CC BY-SA 3.0.

An American alligator (Alligator mississippiensis) from South Carolina. Photo by Gareth Rasberry, licensed under CC BY-SA 3.0.

If you could stay, however, you might be surprised at the tenderness with which alligators treat their offspring. When a female is ready to lay, she hauls herself on shore and finds a shaded, protected area not too far from the water. She lays her eggs in a pile of mud and leaf litter, then heaps more litter on top of them, so that the end result is a leaf-and-mud pile 2-3 feet tall and 5-7 feet wide (McIlhenny 1935).

A thick layer of insulating leaves also keeps the eggs at a more-or-less constant temperature. On a daily basis, even though the environment might go through wild changes in temperature, the inside of the nest stays within 3° F (Chabreck 1973). Alligator eggs usually take around 2 months to develop, and stable temperatures are critical.

Baby American alligators from the Okefenokee Swamp in Georgia. Photo by William Stamps Howard, licensed under CC BY-SA 3.0.

Baby American alligators from the Okefenokee Swamp in Georgia. Photo by William Stamps Howard, licensed under CC BY-SA 3.0.

In human beings, the presence or absence of a Y chromosome decides whether one develops into a male or female. In other words, human sex determination is chromosome-dependent. Alligators instead, like many reptiles, show temperature-dependent sex determination. Between days 20 and 35 of incubation, if eggs are kept between 86° and 93°F, a roughly even mixture of females and males will be the result (Ferguson and Joanen 1983). If, however, the batch stays above 93°, only males will emerge, and if below 86°, only females.

Alligator babies aren’t the only things that grow in alligator nests. The heap of dead leaves, twigs, and mud provides a haven for bacteria and other microorganisms. As bacteria digest the rotting vegetation, they produce heat — enough to keep the eggs 3-4° warmer than the habitat outside the nest (Chabreck 1973). In fact, bacteria keep alligator nests so consistently warm that the nests are also home to unique, heat-loving fungi (Tansey 1973).

More baby alligators! Photo by Ianaré Sévi, licensed under CC BY-SA 3.0.

More baby alligators! Photo by Ianaré Sévi, licensed under CC BY-SA 3.0.

Eggs, alligator or otherwise, look simple but are surprisingly complex. The “solid” shell is mostly made of calcium, but it’s far from a perfect seal — the whole surface is peppered with thousands of tiny holes, allowing the egg to take in oxygen and water, while “exhaling” carbon dioxide (Kern and Ferguson 1997). The thickness of the shell must be precise — too thin and the egg is easily crushed or infected by disease, but too thick and breathing, drinking, and hatching become difficult.

On alligator farms, where alligators are bred and raised for their skins, roughly 30-60% of eggs hatch successfully. Meanwhile more than 90% of alligator eggs hatch successfully in the wild (Kern and Ferguson 1997), as long as the nest isn’t flooded or raided by predators first. Experiments have shown that captive alligator eggs are less porous than their wild counterparts, and of the captive eggs, the least porous are doomed to die before hatching (Wink et al. 1990). Captive alligator eggs also have much thicker shells than wild eggs. So where is the difference coming from?

A baby American alligator. Photo by Ianaré Sévi, licensed under CC BY-SA 3.0.

A baby American alligator. Photo by Ianaré Sévi, licensed under CC BY-SA 3.0.

The bacteria in wild alligator nests, aside from producing heat, also produce acids. These acids aren’t strong or abundant enough to harm the developing reptiles, but over the 2 months it takes for them to develop, acids gradually erode the hard, calcium shell around each egg (Ferguson 1981). By the time the alligator is ready to hatch, its shell is significantly thinner than when the egg was first laid — just thin enough for the hatchling to easily break through.

[Recording by Adam Britton, used with permission.]

As they leave their eggs, baby alligators sound an alarm to their mother, who industriously digs them out of the nest where they spent the first two months of their lives. Although these months might seem uneventful, they are in fact full of challenges, which alligator eggs, however simple and unassuming, have ways to overcome.  Those hatchlings that survive face yet another gauntlet of obstacles, including predators and ruthless competition from their siblings. It’s tough being a baby alligator, and maybe even tougher being an egg, but the toughest few have a chance to become some of the most awe-inspiring top predators in North America.

Dr. Adam Britton, a crocodile researcher at the Charles Darwin University in Northern Territory, Australia, has graciously allowed me to use the audio files in this article. More files, along with a wealth of information about crocodilian biology and conservation, can be found at his website, crocodilian.com.


Chabreck R.H. 1973. Temperature variation in nests of the American alligator. Herpetologica 29(1): 48-51.

Ferguson M.W.J. 1981. Increased porosity of the incubating alligator eggshell caused by extrinsic microbial degradation. Experientia 37(3): 252-255.

Ferguson M.W.J. and T. Joanen. 1983. Temperature-dependent sex determination in Alligator mississippiensis. Journal of Zoology 200(2): 143-177.

Kern M.D. and M.W.J. Ferguson. 1997. Gas permeability of American alligator eggs and its anatomical basis. Physiological Zoology 70(5): 530-546.

McIlhenny E.A. 1935. The Alligator’s Life History. Christopher Publishing House, Boston. 117 pp.

Tansey M.R. 1973. Isolation of thermophilic fungi from alligator nesting material. Mycologia 65(3): 594-601.

Wink C.S., R.M. Elsey, and M. Bouvier. 1990. Porosity of eggshells from wild and captive, pen-reared alligators (Alligator mississippiensis). Journal of Morphology 203(1): 35-39.

Life in Blackwater

by Joseph DeSisto

Just a few years before Darwin published his work on evolution by natural selection, his contemporary, Alfred Russel Wallace, finished a four-year-long tour of the Amazon Basin. During these travels he explored the Amazon River and its tributaries, met with indigenous tribes, and collected a shipload of biological specimens, which he planned to return to England to sell. Sadly the ship and all its contents, save a few notes and sketches, were lost in a fire at sea. From those notes was forged a book documenting Wallace’s travels and his observations on natural history in the Amazon (Wallace 1853).

When Wallace began to explore the Rio Negro or “Black River,” the Amazon’s largest tributary, he noticed that the water seemed darkly stained, like tea or coffee. Similar, smaller rivers could be found across the Amazon — such rivers were usually deep, slow-moving, and wound through forests or swamps. “Blackwater” (aside from being an episode of Game of Thrones) is the name Wallace (1853) used to describe these stained waterways. Where the blackwater of the Rio Negro meets the silt-laden, “whitewater” of the Amazon, the transition is sharp and visible from space.

The junction of the whitewater Amazon (left) and the blackwater Rio Negro (right) near Manaus, Brazil. Photo by Lecomte, licensed under CC BY-SA 3.0.

The junction of the whitewater Amazon (left) and the blackwater Rio Negro (right) near Manaus, Brazil. Photo by Lecomte, licensed under CC BY-SA 3.0.

Not only do blackwater rivers look like tea, they effectively are tea — the color comes from tannins, organic molecules that seep into the water as certain types of tannin-bearing plants die and decompose (Janzen 1974). Whether a river has blackwater or not depends entirely on the plant life growing at its banks. In life, certain plants use tannins as a protection against insects. In death, the tannins play a new role, altering the aquatic environment and the life therein.

Blackwater rivers have a very different chemistry than other water bodies. They are more acidic but lower in oxygen, nutrients, and the dissolved elements many animals need (Ribeiro and Darwich 1993). There are, therefore, fewer animals in blackwater than in clearwater or whitewater. Snails and some other invertebrates, for example, need calcium to build their shells, and these do not fare well in low-calcium blackwater rivers. With fewer invertebrates to eat, fish and other predators are relatively scarce. Yet there is life in blackwater, and although it is a bit harder to find, it is unique and, in its own way, amazing.

A bdelloid rotifer. Photo by Donald Hobern, licensed under CC BY 2.0.

A bdelloid rotifer, found in a wet clump of moss. Photo by Donald Hobern, licensed under CC BY 2.0.

The deformed-zucchini-shaped thing above is in fact an animal, smaller than a grain of sand, called a rotifer. Rotifers can be found almost anywhere with moisture, though you’d need a microscope to spot them. They feed on tiny particles of all kinds, from bits of detritus and algae to bacteria and other single-celled organisms. Despite being tiny, rotifers are relatively complex creatures with minute brains, feelers, and a large mouth surrounded by hair-like appendages called cilia. Some species even have simple eyes.

When a rotifer wishes to swim, it simply vibrates the cilia to pull its body forward. The cilia are also important in feeding — if the rotifer is anchored by its “tail” end, the vibrating cilia create a water current that draw particles towards the mouth. Rotifers eat pretty much the same way street-sweepers sweep. Below is a video of what this looks like:

[Video credit is to “NotFromUtrecht,” licensed under CC BY-SA 3.0.]

In the Amazon Basin, blackwater is dominated by rotifers which, unlike many planktonic invertebrates, do not need calcium or other dissolved minerals to construct cells. At the junction of the Rio Negro and the Amazon River, rotifer populations can be up to ten times higher in the blackwater than in whitewater (Ribeiro and Darwich 1993), even though the two extremes are separated by only a few feet of transition. The same pattern exists in Argentina, where a different “Rio Negro” (also blackwater) meets the whitewater Rio Salado (Frutas 1998).

As long as there are rotifers and other blackwater-tolerant plankton around, fish can also live in blackwater, but low nutrient and oxygen levels make it difficult for them to do so. Still, some very special fish have evolved to tolerate blackwater, and perhaps the most recognizable of these is the neon tetra, a fish made famous by its popularity in home aquariums.

The neon tetra (Paracheirodon innesi), a popular aquarium fish. Photo by Holger Krisp, licensed under CC BY 3.0.

The neon tetra (Paracheirodon innesi), a popular aquarium fish. Photo by Holger Krisp, licensed under CC BY 3.0.

In Rio Negro (Brazil, not Argentina), fish are not especially abundant, but many of the species that live there are endemic. Of the 700 or so fish known from the river, around 100 are found nowhere else on earth. Among these fish is the cardinal tetra, a close relative of the neon tetra with similarly vivid red and blue streaks. Another is the cururu, a freshwater stingray.

Freshwater stingrays are common in the Amazon Basin, where they are considered to be more dangerous even than piranhas. The greatest abundance and diversity of stingrays is found in the whitewater, but surveys have revealed there are several species that prefer blackwater, and at least two in the genus Pomatotrygon are found exclusively in the blackwater of the Rio Negro (Duncan and Fernandes 2010). One of these is the cururu ray, a unique species that has only been discovered in the last decade.

One of the cururu ray's closest relatives, the porcupine river stingray (Potamotrygon histrix). Photo by Jim Capaldi, licensed under CC BY 2.0.

One of the cururu ray’s closest relatives, the porcupine river stingray (Potamotrygon histrix). Photo by Jim Capaldi, licensed under CC BY 2.0.

Studying the cururu ray has helped us understand what is required for a fish to thrive in blackwater. First, the extremely low levels of sodium, chlorine, and other salts in blackwater presents a problem, since fish and all other animals require salts to keep their bodies running. The cururu, like many fish in Rio Negro, can survive with far less sodium and chlorine than most other fish, but it is also more efficient at extracting salts from the water, however scarce they may be (Wood et al. 2002).These rays also have gills with finger-like projections, adapted to be as efficient as possible in gathering both salts and oxygen from blackwater (Duncan et al. 2010).

Although scientists have known for some time that the cururu ray represents an undescribed species, it has yet to be given a Latin name. Many more new species may yet be discovered in the tannin-soaked waters of Rio Negro and other blackwater rivers. Unique places yield unique creatures, often with amazing stories.


Duncan W.P. and M.N. Fernandes. 2010. Physicochemical characterization of the white, black, and clearwater rivers of the Amazon Basin and its implications on the distribution of freshwater stingrays (Chondrichthyes, Potamotrygonidae). Pan-American Journal of Aquatic Sciences 5(3): 454-464.

Duncan W. P., O.T.F. Costa, M.M. Sakuragui, and M.N. Fernandes. 2010. Functional morphology of the gill in Amazonian freshwater stingrays (Chondrichthyes: Potamotrygonidae): implications for adaptation to freshwater. Physiological and Biochemical Zoology 83: 19-32.

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