Thursday, April 29, 2010
Wednesday, April 28, 2010
These days, disease studies are becoming a lot more nuanced, and its revealing a whole new world of how diseases start and stop. Rocco Cipriano, a microbiologist colleague of mine at the National Fish Health Labs in Leetown WV, has been promoting a model lately where an infectious disease of fish (furunculosis) is caused by a disruption to the natural community of bacteria on the skin of fish; a community in which pathogens have no place normally. The furunculosis agent (Aeromonas) is excluded from these communities by bacteria better adapted to living in normal fish skin and its associated mucus layer. That is, until an environmental modulator, like a temperature spike or pollutant, shakes things up a bit; what ecologists would call disturbance. And what is the first outcome of disturbance in most systems? Loss of diversity, in this case among the normal bacterial community. Some bacteria disappear from the skin of the fish, freeing up resources (space, food) that are exploited by other bacteria - opportunists that can come in and pounce on the new space or food. When that space and food consists of the fish itself, we call those bacteria pathogens. This same process happens after any ecological disturbance, like a hurricane on a reef or a tree falling in a rainforest: opportunists come in and pounce on a newly-available resource; then as things settle down a succession takes place, until the early colonisers are displaced by more typical fauna. In this view, disease is nothing more than a byproduct of disturbance and loss of diversity in the normal microbial community.
Which brings me back to corals and to the recent paper by Mao-Jones and colleagues in PLoS Biology. These folks used a mathematical model to show that much the same holds true for the diseases of corals, which, like fish, rely heavily on a surface layer of mucus as their first line of defence. It seems that in both corals and fish, the mucus is important, but even more important are the normal bacteria that live there, continually excluding pathogens and acting as a protective guard against disease. In a very anthropomorphic sense, the corals (and fish) are using the surface bacteria as a biological weapon against the potential pathogens, at the expense of having to produce all that mucus for the bacteria to live and feed on. Importantly, Mao-Jones and friends show us that the derangement of the mucus community can persist for a really long time after the initial disturbance. This is important, because you often come along and see disease starting, but you may well have missed the initial insult that got the ball rolling, which may have occurred some time ago.
I really like this idea of infectious disease as an ecological disturbance and of many pathogens as simply early colonisers in the succession back towards health (or towards death, if the disturbance was too severe). As a model, it doesn't work for everything, though. There are many "primary pathogens" that are specifically adapted to invade healthy animals, but its not in the best interests of those organisms to invest so much energy in adaptations to invasion, only to kill the host, thus many of those are fairly benign. For more "opportunistic" agents, however, I suspect it holds true much of the time, and that group includes many or most of the really virulent diseases. I dare say many of the "emerging" diseases fall in this category, and we can expect to see more of this as the global climate continues to tilt the tango in favour of the pathogens.
Mao-Jones, J., Ritchie, K., Jones, L., & Ellner, S. (2010). How Microbial Community Composition Regulates Coral Disease Development PLoS Biology, 8 (3) DOI: 10.1371/journal.pbio.1000345
Tuesday, April 27, 2010
"The [Shen Neng 1] ship grounding, in the scheme of things, is not a major incident. It's bad if you happen to be one of the corals the ship parked itself on, but it's tiny in the face of the real problem: global warming."
"I am not worried in the slightest about this incident. Not that its a good thing - far from it - but this accident is nothing more than a tree, obscuring us from seeing one big and scary forest [burning fossil fuels]."
Terry, you're my Ambassador of Kwan.
Monday, April 26, 2010
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
Good on ya 'Gourney, you're OK!
Sunday, April 25, 2010
Having announced this great achievement (and it is) in their abstract, the authors go on to point out that this particular bacterium, a symbiont from the gut of an insect, is polyploid. In other words, it has multiple copies of the whole genome per cell - in fact, up to 900 copies! So, while its technically correct that they sequenced a genome based on a single cell, you'll forgive me for thinking they're gilding the lily a bit.
While we're at it, who is proofing manuscripts at PLoS One these days? The last sentence of the abstract reads: "This study demonstrates the power of single cell genomics to generate a complete, high quality, non-composite reference genome within an environmental sample, which can be used for population genetic analyzes." Huh?
Woyke, T., Tighe, D., Mavromatis, K., Clum, A., Copeland, A., Schackwitz, W., Lapidus, A., Wu, D., McCutcheon, J., McDonald, B., Moran, N., Bristow, J., & Cheng, J. (2010). One Bacterial Cell, One Complete Genome PLoS ONE, 5 (4) DOI: 10.1371/journal.pone.0010314
Thursday, April 22, 2010
I got a bit behind while I was in NY, but am back on deck today and will be back to posting a bit more regularly. Here's the solutions to the recent bit-o-critters.
Round 9 - Six-gilled shark, Hexanchus griseus
A big ol' slug of a shark, most common in the colder waters of the world. I picked it because it always seemed odd to me that six and seven gilled sharks manage to have one or two more than everyone else. Five seems kind of a fundamental number for gills.
Round 11 - Loriciferan. OK, that was just mean. A truly obscure group of microscopic invertebrates that live between sand grains on the bottom of the ocean. A phylum unto themselves, they were only discovered in 1983. Not much to them except the lorica or house (the clear baggy bit on the right), some somatic and reproductive cells (pink) and the ring of tentacles around the oral cone (on the left).
Tuesday, April 20, 2010
Round 9 - One more than normal
Round 10 - Men are distinctly uncomfortable around this animal
Round 11 - This group not discovered until 1983
I will post the solutions when I get back to Atlanta tomorrow.
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...
Monday, April 19, 2010
Seminar at AMNH went well. Now meeting with graduate students in the new graduate program in comparative biology. What a great program and opportunity for students to take advantage of the collection and curatorial staff. Makes me kinda jealous.
Even though its a thoroughly modern museum, The place still smells of mothballs and that makes me smile.
Sunday, April 18, 2010
Saturday, April 17, 2010
Thursday, April 15, 2010
You may have followed some press in the last week or so about a Chinese coal ship, Shen Neng 1, that ran aground on the Great Barrier Reef and spilled some of its fuel oil. This has caused a regular frenzy in the Aussie media and the global conservation and environmental news-o-sphere. There have been all sorts of calls for prosecution of the shipping company and new stringent regulations for the transport industry and so on, along with dramatic accounts of the damage the ship did and the risky salvage operation that came next. But you know what? I am not worried in the slightest about this incident. Not that its a good thing - far from it - but this accident is nothing more than a tree, obscuring us from seeing one big and scary forest.
The main reasons I am not especially bothered by the Shen Neng accident are that (1) it affected a very limited area - the G.B.R. is really B.I.G. and one ship can only damage so much of it; and (2) it was a single event in time - this was not a process or an ongoing problem, but a singular disturbance. Science shows us that the GBR, and reefs in general, are amazingly resilient to violent disturbances like this; a decent cyclone can literally turn a reef upside down, and a couple of years later you'd never know the difference. Indeed, periodic disturbances may be really important for maintaining a healthy reef ecosystem.
No, the Shen Neng is just a tree, obscuring us from seeing the forest that really threatens the future of the GBR and all reefs. Its not the 2km gash that the hull cut in the reef, nor is it the tons of fuel oil leaked into the water; it's the very concept of burning that fuel oil, and burning the thousands of tons of coal that the Shen Neng 1 was carrying. When you consider all the other ships and all the coal and fuel they were carrying that day and every day, and all the cars in the world, the power plants and so on ... ach, you get my point. THAT'S what we ought to be worried about, because both of the main effects of increased atmospheric CO2 - warming and ocean acidification - will likely result in unrecoverable damage to All reefs. Everywhere. In our lifetime. Warming is directly linked to lethal bleaching events, while acidification disrupts the ability of reefs to lay down their skeleton and grow. Oh yeah, and lets not forget the drowning effects of sea level rise, too. The more I think about it, the more it seems that jumping up and down about the Shen Neng is hypocritical (coal is one of Australia's biggest exports, after all) and akin to complaining about the deck chair arrangements of another, even bigger, ill-fated ship. (Ironically, if Titanic sailed today, she probably wouldn't have to worry about icebergs...)
Of course, its a false dichotomy, we should be worried about BOTH the Shen Nengs of the world AND the global climate change/ocean acidification. But I only have so much energy/capacity for worrying about these things, so with a limited anxiety budget, I feel compelled to focus on the bigger issue and what (if anything) we can do about it - to try to reduce consumption and to try to make sensible decisions that are mindful of how much energy is involved and what the broader impacts might be.
In other words, to worry about the forests - and let the trees take care of themselves.
Wednesday, April 14, 2010
Tuesday, April 13, 2010
Of course, they also recommend pole-dancing.
Round 5 of bit-o-critter was the most competitive yet. Eventually Akira triumphed, recognising the sarcastic fringehead, Neoclinus blanchardi, which is a relative of the blennies, that lives in the cold waters of the Pacific northwest. If you've watched Life on Discovery, you may recognise this fish from an awesome sequence they had of fringeheads fighting. Here's some other footage from YouTube of the same.
Like I said, it's weird that a fish with such a ridiculously large mouth gets named after some wussy little fringes on its head. Perhaps that was the sarcastic bit...
Monday, April 12, 2010
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.
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
Sunday, April 11, 2010
Saturday, April 10, 2010
lobster holocaust that started in (well, before, if you ask me) 1999. When we were out on the RV Seawolf, the Throgs Neck bridge marked your entry into the East River and the start of one of the most unique and strangely beautiful urban research cruises around, right down the East side of Manhattan, past the Statue of Liberty and out into the Lower NY bays. We would pass through on our way to do winter flounder spawning surveys off the beach at Coney Island (its that or go around Montauk). Proof that not all interesting biology takes place in Peruvian rainforests...
In the comments, tell us about a field location YOU have loved and why. Post links if you can find them.
Friday, April 9, 2010
Thursday, April 8, 2010
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
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”.
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
Wednesday, April 7, 2010
Here we go. Easy one to start:
That's it, I'm leaving tomorrow. Just as soon as I take care of this thing, and some stuff....and that other junk...
Tuesday, April 6, 2010
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!)
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