Shedding some light on lanternfish

Diaphus parri, a lanternfish from the Coral Sea. Img: Adrian Flynn

Adrian Flynn’s PhD is about myctophids, or lanternfishes.  These are not well known to most people, but they’re probably among the most abundant animals on the planet, because they live in the largest habitat there is: the deep mid-waters of all the oceans of the world, neither near the surface nor on the bottom, what scientists call the mesopelagic zone (meso = middle, pelagic = in the water column).  Lanternfish, as the name implies, produce their own light from organs arrayed on the skin of the head and body.  These organs, which generate light through the action of the enzyme luciferase, allow the fish to signal each other, to find food and to disguise their own outline against the gloom from above, when seen from below.  Its a neat trick, but not nearly unique in the deep pelagic zone.  Indeed, it seems that just about everything down there makes light in some form or another (if you want some google fodder for that, check out Edith Widder’s work, she’s got a great talk on Ted.com too).  Lanternfishes can be hard to study because they’re hard to collect in tact; they’re sort of flabby and the skin comes off very easily. But not to be deterred, Adrian is undertaking an ambitious study of how different species of lanternfishes are distributed from the tropic of Capricorn to the waters of the Antarctic - their biogeography - and also how the numbers of any given species are affected by oceanographic factors like major currents and places where deep nutrient-rich water comes up to the surface (upwelling). 

A nice ventral view of D. parri, showing the light organs arrayed on the skin

So far his results are showing that the deep pelagic zone is not as homogenous as previously thought.  It seems that lanternfish distribute themselves into biogeographic zones somewhat according to latitude, but more so according the oceanographic features like major currents and landforms like islands.  He’s had a couple of real eye opening results too.  In one case, they observed - for the first time in Australia - a lanternfish spawning aggregation, off the coast of Cairns in far north Queensland.  That’s cool, but what was a real trip was that the laternfish in question (the Dana lanternfish) was a species known only from Tasmania, almost 2,000km away!  How did they get up there?  How will their young get back again?  On another expedition, they found lanternfish close to the surface at Macquarie Island, a remote rock in the Great Southern Ocean.  The island juts up into the prevailing currents, causing upwelling that brings nutrients and lanternfishes alike well within the foraging range of penguins and seals/sea lions that nest on the island.  It looks like lanternfish in this unique location are an important part of the diet of at least three penguin species as well as the pinnipeds (seals), and that’s a pretty novel discovery.

A Parasite a Day, keeps the Doctor in pay

My colleague Susan Perkins at AMNH has a most excellent blog that features a different parasite every day for a year.  Since the oceans have more parasites than anywhere else by far, many of her feature critters are marine.  Check out some of these marine beasties, then enjoy the rest of the collection.  There's a new one every day.

Crepidostomum cooperi - a digenean (fluke) parasite of fish
Nasitrema globicephalae - a digenean parasite of the sinuses of whales
Cyamus ovalis - isopod parasites often called "whale lice"
Maritrema novaezealandensis - an important model digenean from New Zealand mudflat animals
Polypodium hydriforme - a weird parasitic jellyfish relative that lives on sturgeon eggs, and:
Dolops sp., -  a type of Branchiuran (related to crustaceans) parasitic on piranha

While we're talking genomes...

...here's something distinctly more marine. 

A little while ago I drew attention to Andrea Marshall's paper showing that there's not one but possibly three species of manta ray (see Whats A Manta Do?).  In the preamble for that post, I drew analogy between mantas and killer whales as monotypic species; that is, the only members of their genus, a taxonomic one-of-a-kind.  Well blow me down if some new genomics work with killer whales doesn't suggest that there's more than one species of those, too!  Morin and colleagues used a different approach than Marshall, whose work was mostly based on colors and patterns and tooth shape.  Instead, they used "massively parallel pyrosequencing" (try saying that with a mouth full of marbles) to show genetic differences in the mitochondrial genome.  So what the heck does that mean?  Well, lets just say its sequencing a whole bunch of DNA at once, using DNA not from the nucleus of the cell, but from its engine room: the mitochondrion.  The technology is actually a really, fantastic example of miniaturisation; perhaps I'll write about it one day.  But, I digress...  Morin and friends recommend three species of Orcinus orca, with two more subspecies as well.  Subspecies are not required by the taxonomic code, but they are eligible for separate protections under the Endangered Species Act, so its a meaningful result for conservation biologists too; they'll now have to make assessments of each species and subspecies to see which, if any, require additional protections.

To the experts, its not a total surprise that there are multiple species in either of these groups.  You can bet your bum that they set out to confirm a hunch that there are more than one, leaving the surprise for the rest of us less familiar with these beasties and who never saw the subtle differences.  That's OK, I like surprises, especially when they involve new and unexplored diversity, right under our noses.  Maybe we should take a harder look at a few more monotypics, for the inevitable species flocks hiding in the details or the DNA.  Whale sharks, basking sharks, Mola, anyone?

Morin, P., Archer, F., Foote, A., Vilstrup, J., Allen, E., Wade, P., Durban, J., Parsons, K., Pitman, R., Li, L., Bouffard, P., Abel Nielsen, S., Rasmussen, M., Willerslev, E., Gilbert, M., & Harkins, T. (2010). Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species Genome Research DOI: 10.1101/gr.102954.109

The Type Room

This is one of the rooms at AMNH where type series are kept, in this case for fish. A type series is that original set of specimens lodged at a museum when a new species is first described. These are therefore very valuable specimens, in a sense irreplaceable!  Its hard not to feel the gravitas of the mission of museums when faced with something as fundamental as a type series.  We also had a chance to see real coelacanths (they're bigger than I thought!), which was very exciting.

AMNH the reprise

It was a long but fantastic day at the Museum yesterday.  After Bento boxes with the grad studets, I met with folks from their comparative genomics and conservation genetics group including George Amato and Rob deSalle.  Then out for refreshments with the leech lab folks and their intrepid leader and old colleague of mine Mark Siddall. We gasbagged about everything from progressive metal to the latest leech they described, Tyranobdella rex, from up the nose of an unfortunate Peruvian child. What an awesome name. You can read more about it on Mark's blog Bdella Nea, linked from my blog roll somewhere hereabouts.
I didn't get to do everything on the agenda yesterday, so its back to the museum today to meet with people from Ichthyology and take a look at the fish type collection (drool). I might just snag some bit-o-critter pics from among the jars...

SAC's revisited

A little while back I wrote about how we can use Species Accumulation Curves to learn stuff about the ecology of animal, as well as to decide when we can stop sampling and have a frosty beverage. There’s a timely paper in this month’s Journal of Parasitology by Gerardo Pérez-Ponce de Leon and Anindo Choudhury about these curves (let’s call them SACs) and the discovery of new parasite species in freshwater fishes in Mexico. Their central question was not “When can we stop sampling and have a beer?” so much as “When will we have sampled all the parasites in Mexican freshwaters?”. They conclude, based on “flattening off” of their curves (shown below, especially T, C and N), that researchers have discovered the majority of new species for many major groups of parasites and that we can probably ease up on the sampling.

Trying to wrap your arms (and brain) around an inventory of all the species in a group(s) within a region is a daunting task, and I admire Pérez-Ponce de Leon and Choudhury for trying it, but I have some problems with the way they used SACs to do it, and these problems undermine their conclusions somewhat.

In their paper, the authors say “we used time (year when each species was recorded) as a measure of sampling effort” and the SACs they show in their figures have “years” on the X-axis. Come again? The year when each species was recorded may be useful for displaying the results of sampling effort over time, but its no measure of the effort itself. Why is this a problem? For two reasons. Firstly, a year is not a measure of effort, it’s a measure of time; time can only be used as a measure of effort if you know that effort per unit of time is constant, which it is clearly not; there’s no way scientists were sampling Mexican rivers at the same intensity in 1936 that they did in 1996. To put it more generally: we could sample for two years and make one field trip in the first year and 100 field trips in the next. The second year will surely return more new species, so to equate the two years on a chart is asking for trouble. Effort is better measured in number of sampling trips, grant dollars expended, nets dragged, quadrats deployed or (in this case) animals dissected, not a time series of years. The second problem is that sequential years are not independent of each other, as units of sampling effort are (supposed to be). If you have a big active research group operating in 1995, the chances that they are still out there finding new species in 1996 is higher than in 2009; just the same as the weather today is likely to bear some relationship to the weather yesterday.

OK, so what do the graphs in this paper actually tell us? Well, without an actual measure of effort, not much, unfortunately; perhaps only that there was a hey-day for Mexican fish parasite discovery in the mid-1990’s. It is likely, maybe even probable, that this pattern represents recent changes in sampling effort, more than any underlying pattern in biology. More importantly, perhaps, the apparent flattening off of the curves (not all that convincing to me anyway), which they interpret to mean that the rate of discovery is decreasing, may be an illusion. I bet there are tons of new parasite species yet to discover in Mexican rivers and lakes, but without a more comprehensive analysis, it’s impossible to tell for sure.

There is one thing they could have done to help support their conclusion. If they abandoned the time series and then made an average curve by randomizing the order of years on the x-axis a bunch of times, that might tell us something; this would be a form of rarefaction. The averaging process will smooth out the curve, giving us a better idea of when, if ever, they flatten off, and thereby allowing a prediction of the total number of species we could expect to find if we kept sampling forever. Sometimes that mid-90’s increase will occur early in a randomised series, sometimes late, and the overall shape for the average curve will be the more “normal” concave-down curve from my previous post, not the S-shape that they found.  After randomizing, their x-axis would no longer be a “calendar” time series, just “years of sampling” 1, 2, 3… etc.  There's free software out there that will do this for you: EstimateS by Robert Colwell at U.Conn.

The raw material is there in this paper, it just needs a bit more work on the analysis before they can stop sampling and have their cervezas.

Perez-Ponce de León, G. and Choudhury, A. (2010). Parasite Inventories and DNA-based Taxonomy: Lessons from Helminths of Freshwater Fishes in a Megadiverse Country Journal of Parasitology, 96 (1), 236-244 DOI: 10.1645/GE-2239.1

Today's Fishbase fodder

The aristocratic bunquelovely, Symphysanodon typus

I don't mean to say "I told you so"...

This morning I posted about how taxonomy underlies all else in biology, with respect to manta rays.  As if to make my point, an article is just out in Nature suggesting that the genus Drosophila - better known as fruit flies - may be revised such that one of science's best known model species - Drosophila melanogaster - gets kicked out of its genus!  The split hasn't taken place just yet, but the door is open, and if it were to happen, D. melanogaster might well become Sophophora melanogaster during the reorganisation.  Of the implications for the enormous literature and the many genetic databases that are heavily built on the current taxonomy, one Drosophila scientist is quoted in Nature as saying simply (but most unscientifically) "Oh my God".

What high drama!  And you thought taxonomy was only arcane monographs penned by bespectacled formalin-smelling old men in the basements of museums...

Dalton, R. (2009). A fly by any other name Nature DOI: 10.1038/457368a

What's a Manta do?

Manta rays (Manta birostris) surely vie for the title most spectacular among the large animals in the ocean. Not only do they grow to enormous sizes, but they are placid, graceful, and generally unafraid of humans, which means we can get close to them in the water and really appreciate how incredible they are, up nice and personal. I always thought that mantas were a one-of-a-kind species - the only member of its genus - like humans, whale sharks, koala bears or killer whales. Luckily, Andrea Marshall is not like me. She and her colleagues took a closer look at the body features, colours and patterns on lots of mantas from all around the world and they concluded that there are at least two, and possibly even three, manta ray species. They’re not the first people to propose this, so technically what they have done is “resurrect” the name Manta alfredi, the Prince Alfred manta, which had been made a synonym of Manta birostris some time ago (read the paper for the full sordid taxonomic history of mantas). The differences between the two species are subtle and mostly to do with the colour of the lips, wings and shoulders, the spots on the belly and the presence or absence of a bony mass near the base of the tail, but nonetheless they probably reflect real differences between the animals and, under the current definition of “species”, they probably cannot successfully interbreed. The third potential species they call “Manta sp. cf. birostris” which is taxonomist shorthand for “as-yet undescribed manta species sort-of like M. birostris”.

If you have ever been to the Georgia Aquarium, you may have seen one or both of their mantas in the Ocean Voyager exhibit. If you look closely at these and compare them to the Marshall paper, you’ll see that one (called “Nandi”) is Manta alfredi and the other (“Tallulah”) is more like Manta sp. cf. birostris. Its slightly ironic that in light of this new paper, neither of them is the “actual” or original “manta ray”.  Of course, they are both still spectacular animals!

Who cares about all this anyway? What does it matter if there’s one or three or a dozen manta species? As it happens, it matters a great deal! Taxonomy underlies everything else in biology. What good is a population estimate, for example, if that estimate confuses two species? We would grossly overestimate both, potentially leading to overexploitation. More generally, how can we understand migration patterns, breeding grounds, diets, ecological roles or behaviour, if we are constantly confounded? These are, of course, somewhat self-centered concerns about the quality of our science or management decisions; a species count is about the most fundamental measure of nature that we have, and those sorts of diversity stats are predicated on a decent taxonomy. Consider this: how much of a ginormous “oops!” would it be if we were to protect a species in one area of ocean, only to learn that the animal in the area we didn’t protect was actually a different species?   Perhaps a more important reason it matters is for the mantas themselves and the rest of their ecosystem.  Each species has an intrinsic right to exist and a value to the ecosystem its part of. 

I just love the idea that even for familiar, charismatic mega-animals like mantas, if we look a little closer, nature shows us hidden diversity: surprising, unexpected, and exciting.

Marhsall, Andrea D., Compagno, Leonard J.V., & Bennett, Michael B. (2009). Redescription of the genus Manta with resurrection of Manta alfredi (Krefft, 1868) (Chondrichthyes; Myliobatoidei; Mobulidae) Zootaxa, 2301, 1-28

Explosive radiation (in) rocks!

Much like internal waves, I always loved the idea of explosive radiation.  Not the nasty, pernicious Chernobyl kind; I mean the rapid evolution of a whole bunch of species from a common ancestor, over a relatively short period of time.   There's a few textbook examples of explosive radiations, but none so well-worn (possibly even hackneyed) as that of the cichlid fishes in the rift lakes of eastern Africa.  The startling diversity of these little fishes in lakes Tanganyika, Malawi and Victoria has kept evolutionary biologists busy (and Africans fed) for years.  See for example, the paper by Elmer and colleagues cited below, which points out that due to the drying-out of Lake Victoria 15-18,000 years ago, either all the cichlids there evolved since then based on stock that re-colonised from Lake Tanganyika, or they sought refuge elsewhere during the dry spell and returned when the lake refilled.

Cichlids are nice and all, but if you look around, you start to see radiations all over the place.  Turtles, bivalves and salamanders in the US south-east; tetras in the Amazon, eleotrid gudgeons in Australia, and gobies on coral reefs are just a handful of aquatic examples that are still with us, but there are many others in the fossil record too (hence my title) including trilobites and ammonoids and lots more.  Presumably these are the sorts of patterns that led Stephen Jay Gould and Niles Eldredge to develop the concept of punctuated equilibrium back in the 70's: theirs was the idea that evolution proceeds not gradually, but in fits and starts, in response to dramatic environmental changes and chance events.  The way I see this idea, most of the species we observe around us are the dregs of explosive radiations past, whittled away by extinctions to just the most successful few, either gradually or equally punctuated.  Cases like the rift-lake cichlids are just ones in which relatively few have gone extinct yet (but see the effects of the introduced Nile perch!)

All of this was just a preamble for what I really wanted to post about, which was about a radiation I only heard about recently.  Late last year I was at a scientific exchange  of US and Russian fish health researchers organised by the National Fish Health Research Laboratories and sponsored by the Living Oceans Foundation, at which one of the Russian speakers  Maxim Timofeev introduced us the radiation of several groups, including amphipods, in Russia.  Amphipods are (usually) tiny shrimp-like animals that live on the bottom or among dense plants or algae; read more about them in the Väinölä paper cited below.  Well, in Siberia's Lake Baikal, the worlds oldest, largest and deepest freshwater lake, they underwent a remarkable radiation, to produce over 300 species (a third of the worlds entire fauna), including spectacular beasts such as the fish predator (!) shown here. I mean, HOW AWESOME IS THAT THING?  Freaks me almost as much as giant wetas used to do, when I was younger (if you don't dig on bugs, I recommend not clicking that link...).  Anyway, I had no idea these things existed until Maxim gave his talk.  Don't you just love discovering new critters you never knew about before?  And not just one, but hundreds.

(Check out this link about Baikal fauna too; the language is just terrific.  Try this turn of phrase on for size: "When it comes to tenderness and gustatory qualities of meat, the omul knows no rivals")

Elmer, K., Reggio, C., Wirth, T., Verheyen, E., Salzburger, W., & Meyer, A. (2009). Pleistocene desiccation in East Africa bottlenecked but did not extirpate the adaptive radiation of Lake Victoria haplochromine cichlid fishes Proceedings of the National Academy of Sciences, 106 (32), 13404-13409 DOI: 10.1073/pnas.0902299106

Väinölä, R., Witt, J., Grabowski, M., Bradbury, J., Jazdzewski, K., & Sket, B. (2007). Global diversity of amphipods (Amphipoda; Crustacea) in freshwater Hydrobiologia, 595 (1), 241-255 DOI: 10.1007/s10750-007-9020-6

Funny scientific names - Abra cadabra

I started my career in taxonomy.  Its a serious business, the naming of new species, and you're not supposed to make light or fun out of an animal (or plant) name.  After all, they are stuck with it for all time.  Nonetheless, people can't help themselves and from time to time, you get some real crackers!  A fella by the name of Arnold Menke at USDA put together a list of them, so did Doug Yanega.  Here's some of my favourites.  Which do you like best?

Agra vation (a beetle)
Colon rectum (another beetle)
Ba humbugi (a snail)
Aha ha ( a wasp)
Lalapa lusa (a wasp)
Leonardo davinci (a moth)
Abra cadabra (a clam)
Gelae baen, Gelae belae, Gelae donut, Gelae fish, and Gelae rol (all types of fungus beetles)
Villa manillae, Pieza kake and Reissa roni  (bee flies)
Ytu brutus (a beetle)

and my personal favourite (whenever possible):
La cerveza (a moth)

I'll drink to that - here's cheers to creative taxonomists!