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Entries in diversity (17)


Foot in the Jackfruit - a guest post from Kristie Cobb-Hacke

Where in the world are you when the expression “foot in the jackfruit” makes sense?  Brazil. Recognizing that this euphemism “Pé na Jaca” loses some of its finesse in English, it is nevertheless something that makes travel beautiful.

My goal during this adventure is to avoid “ na jaca.” Yesterday in our travels from Vitorio to Nova Viçosa throughout the drive we were able to see coffee plantations, sugar cane and eucalyptus farms. All of these farms were on formerly-forested areas, so interspersed we were able to spot the pink mangos, purple mangos and many other varieties of native plants. Although the jack fruit thrives in this environment, it is an invasive species. It is originally from India and archeologists have revealed it was first cultivated there 3,000 years ago. This tree has the largest tree-borne fruit and has spread quickly throughout areas of Brazil as birds and animals eat the seeds of fallen fruit and deposit them elsewhere. In recent years there have been some forestry management efforts to rid the national parks of saplings as these fruit are thought to have contributed to the decline of certain bird species. 

 During our drive we discussed the cultural challenges that come with conservation efforts. The mere idea of discussing the lack of conservation in an area may be a time where I could certainly have been through of as insensitive. I certainly don’t want to be considered as an invasive species to the crew and scientists on the Abrolhos expedition.  We discussed the change in the landscape and the growth in the farming industry, particularly eucalyptus.

This area of the world is considered a biodiversity hot spot by conservation international. This is an overview:

The Atlantic Forest or Mata Atlântica stretches along Brazil’s Atlantic coast, from the northern state of Rio Grande do Norte south to Rio Grande do Sul. It extends inland to eastern Paraguay and the province of Misiones in northeastern Argentina, and narrowly along the coast into Uruguay. Also included in this hotspot is the offshore archipelago of Fernando de Noronha and several other islands off the Brazilian coast.

Long isolated from other major rainforest blocks in South America, the Atlantic Forest has an extremely diverse and unique mix of vegetation and forest types. The two main ecoregions in the hotspot are the coastal Atlantic forest, the narrow strip of about 50-100 kilometers along the coast which covers about 20 percent of the region. The second main ecoregion, the interior Atlantic Forest, stretches across the foothills of the Serra do Mar into southern Brazil, Paraguay and Argentina. These forests extend as far as 500-600 kilometers inland and range as high as 2,000 meters above sea level. Altitude determines at least three vegetation types in the Atlantic Forest: the lowland forest of the coastal plain, montane forests, and the high-altitude grassland or campo rupestre. (

The Atlantic Forest of Brazil

But in a place like Brazil that is growing and actively developing their resources, it is important to understand the ranking of conservation among the needs and challenges of a country that is home to approximately 3% of the world’s population: over 190 million people ( the vast majority living in urban cities. In many cases large numbers of citizens face much less complicated but much more personally critical decisions like food, clothing, water, waste management and health come long before thoughts of the care of the surrounding environment.

So for our bright and inspired scientists on this expedition it is going to be critical for them to be clear with their efforts and decisive with their results so that they can avoid sticking their ‘foot in the jack fruit” and they can begin the process of educating their fellow Brazilians and affecting change to preserve their native and incredibly diverse environment. On its own nature can maintain a diverse and complex system of life including production, consumption and disposal of waste. These processes are all seamless in a well-balanced system. If at any point a part of the system is disrupted the natural web may become imbalanced and threaten the health and loss of species at a minimum and, at a maximum, could be catastrophic.

Unfortunately, sometimes it takes catastrophe to serve as a wake-up call. One of our travel companions, Nina Bilton, is from the state of Rio de Janeiro and she shared that the recent torrential rains and the subsequent mud-slides have drawn tremendous attention to the environment and have activated the concern of a nation. So in all of this devastation one bright light is that dedicated committed scientists, organizations and corporations can occasionally come together to start the process of understanding the environment. At the core awareness is the science behind understanding the natural environment around us all.

As I write I am witnessing, for the first time, a completion of a submersible dive. I am excited to hear about what our researchers are seeing and learning and I’m looking forward to seeing the results. The data they have collected today is just one small piece to understand and protect the integrated web of life in the Abrolhos area.

(Kristie Cobb-Hacke is a vice president at Georgia Aquarium)


Five of the biggest marine science stories in 2010

Yes, I caved to the impulse and joined the inevitable cavalcade of “lists” that come at the end of every year.  Why?  Because these lists actually serve an important purpose: they cement the events of the past 12 months in our psyche and provide context about where these events fit into the grand passage of time.  They also give us something to read when we want to procrastinate shoveling snow off the driveway or vacuuming pine needles from behind the couch.  So here they are: five of the biggest marine science news stories from 2010.

5. National Ocean Policy.  Starting off sexy, right? Policy, yeeeahh baby!  No really, it IS a big news story that in July of this year the Whitehouse announced that the US finally has a comprehensive Ocean Policy.  That’s because such a document - and the institutions it enhrines - recognises the critical role that the oceans play in the lives of every American, even those that live far removed from the coasts.  As the biggest per capita consumers (and polluters) on the planet, the absence of a national policy to protect the oceans had long been lamented by marine scientists and consrvationists alike.  Now we have a National Oceans Council and a set of guiding principles for governing the use (and abuse) of coastal oceanic resources.  Its about time!  Read the Executive order here, and the Final Recomendations of the Ocean Policy Task Force here

4. What a load of garbage.  2010 marked the year that the concept of the “great ocean garbage patches” entered the public consciousness.  If you’ve been living under a rock and have no idea what that is, well, it’s the idea that millions of tons of plastic pollution have found their way down urban drains, to creeks, rivers and estuaries and thence to the centers of the great circular oceanic currents called gyres.  There becalmed, these floating fields of plastic debris form giant rafts of death, entering food webs and silently choking millions of animals.  The truth is slightly less dramatic; while the grabage patches are almost mind bogglingly large, the density of plastic particles within the patches is actually pretty dilute.  In fact, you have to sift a lot of water to recover appreciable quantities of the stuff; it’s just that, even then, they have vastly higher concentrations than parts of the ocean more well-mixed by large scale currents.  2010 was the year that scientists recognised that there is not only one patch (in the north Pacific) but probably a patch of sorts in the center of every gyre and that therefore this is a global problem.  Its also the year that the concept hit pop culture, partly from the well-publicised efforts of the Plastiki cruise, but mostly in the form of a new album from progressive UK hip hop outfit Gorillaz called “Plastic Beach”, a theme album conceived when the lead singer was sitting on a beach and realising how much of the sand was actully composed of tiny bits of plastic.  The garbage patch story also added the most excellent word “nurdle” to the lexicon, reason enough for it to appear on this list.  Read more about the adventures of a bona fide garbage patch researcher by following Miriam Goldstein at DeepSeaNews

3. To hack, or not to hack?  It’s pathetic, but perhaps not surprising, that the worlds leaders have not been able to agree on a binding plan of action to reduce carbon pollution and its two biggest impacts on the planet: global warming (both the atmosphere and the oceans) and ocean acidification.  First at the COP15 Copenhagen conference in late 2009 and, more recently, at the 2010 United Nations Climate Change Conference in Cancun, Mexico in December, politics consistently trumped the urgent need to reconstruct our industries and economies to prevent exacerbation of the problem (we’re already committed to a certain level of globe-changing temperature and pH shift).  While these “front end” solutions are desperately needed, a number of climate/ocean researchers around the world have been studying “back end” solution, the most familiar of which is carbon sequestration - the idea of catching CO2 from fossil fuel burning and burying it or otherwise preventing it from entering the atmosphere/ocean.  Perhaps the most controversial suggestion is to fertilise the oceans with nutrients that usually limit the growth of plankton (Iron is the best-studied), thereby causing huge plankton blooms that suck CO2 out of the air/water and, ultimately, export it to the bottom of the abyssal oceans.  The controversy of these sorts of planet-level solutions, collectively called “geo-hacking”, arise because they are designed to affect the whole earth ocean/climate system and take place in international waters, so arguments arise about who gets to decide on these sorts of things.  No sooner had I interviewed an expert on ocean fertilisation on this very blog than a UN moratorium was issued preventing any future research on this kind of solution until the risks and impacts are better understood.  C’mon UN - you can’t have it both ways: either make an internationally-binding decision about reducing carbon pollution, or allow people to move forward with alternative solutions, preferably both.  As it stand currently, we’re a boxer with both arms tied behind his back, and that’s never good.

2. BP/Macondo/Deepwater Horizon Oil Spill.  Bet you thought that would be number 1 right?  By volume, the largest oil spill in US history, affecting huge areas of the Gulf of Mexico in the peak of seafood season and threatening hundreds of miles of fragile coastal wetlands, surely it should be.  Nope.  Why not?  Well, largely because - disastrous though it was/is - it is both temporally and geographically restricted in its impact.  In other words, its effects will be found primarily in one place and for a limited (albeit relatively prolonged) time.  I argue that it is NOT these events that we (the world) need to be concerned about, but the long-term, chronic, death-by-a-thousand-cuts kind of problems.  The biggest of those are global warming and ocean acidification (see number 3).  It’s like the difference between a big financial windfall and the power of investment returns.  The local factory worker who wins a hundred million on the latest Powerball gets the news story, while tons of investors accumulate vast wealth in relative silence due to the inexorable influence of compounding interest and capital gains over time.  The BP spill was an absolute disaster that got a LOT of press and will keep many marine scientists and environmentalists busy for a long time (great coverage of both is at DeepSeaNews), but it’s a one-off event and not even on the radar in terms of the global health of the oceans.

1. Census of Marine Life.  The biggest marine science news of 2010 has to be the completion of the first Census of Marine Life; a phenomenal decade-long effort by thousands of marine biologists around the world to answer one simple question: What lived, lives and will live in the worlds oceans?  The brainchild of Rutgers marine scientist Fred Grassle, the scope was truly gargantuan: over 500 research expeditions covering every ocean, over 2,500 scientists and the discovery of over 6,000 species new to science and published in over 2600 peer-reviewed papers.  It revealed the chronic undersampling of the deep-pelagic realm and the incredible diversity of seamounts and the tropical, arctic and antarctic depths.  It also brought us some of the most stunning and engaging images of marine diversity ever captured.  The final estimate? Based on extrapolations of survey data, easily 1 million or more eukaryote species and perhaps as many as 10 million bacteria and archaea.  But CoML is so much more than numbers, it’s a peek into a treasure trove of new life, a testament to the phenomenal diversity of the oceans, and an enduring snapshot of the precious biological legacy we are lucky to be part of.  It’s often said that you don’t know what you’ve got til it’s gone.  Well, thanks to CoML we have a better idea of what a priceless gift of diversity we’ve got at our fingertips.  Now what are we going to do about it?

I’d love to read your feedback in the comments.  Did I miss anything?


There it is again!

That awesome feeling when you discover a species you never knew existed!  I just wrote about this in my last post, but it happened again today when I came across this video (cap tip to @support4oceans on Twitter) of Stygiomedusa, a giant jellyfish, seen for the first time in the Gulf of Mexico.  There’s not much to say because Mark Benfield from LSU says it all, but just consider that this thing has a bell the size of a beach umbrella and tentacles as long as a school bus!


One of the best things about marine biology

To me, the best bit about working in marine biology is the terrific moment of surprise when you discover a new expression of natural diversity.  Little kids know this - you can see it on their faces every time they turn over a rock in a stream or rock pool.   I think one of the reasons I enjoy it so much is that it almost takes you back to a state of childish wonder, and you get to appreciate something with truly fresh eyes, even if only for a moment.   In my early career in taxonomy, I became completely addicted to the idea of seeing a species that no-one else has seen before (of course, then you have to describe it, and some of the gloss wears off by the time you submit!).  These days, I get the same buzz just from learning about a species I didn’t know existed, and so it was when I recently read a story about an hourglass dolphin (Lagenorhynchus cruciger) that had washed up on a beach in New Zealand for the first time in a century.  Now, I’m not much of an expert on marine mammals, but I had never heard of or seen this animal before, and it was surprising to me because I usually expect the unknowns to come from among the other 95% (invertebrates), and not the more familiar mammals.  It was all the more surprising to me because of the stunning and bold markings of the animal, which are so distinctive, you’d think it would be more well-known (hey, maybe its just me).  Anyway, on the off chance that perhaps you, too, have never met this beautiful creature, I give you the hourglass dolphin, Lagenorhynchus cruciger:

Hourglass dolphins in the Great Southern Ocean. Image: South Georgia Heritage Trust (click for more)

Beautiful, aren’t they?  Have you ever had the feeling I’m talking about?  If so, what was the animal?


Cut to the CoML chase

Skip the press: read the official Census of Marine Life summary here: and the full report here: After 10 years and 500 research crusies, scientists conclude the obvious - we still don’t know that much about life in the oceans! Exciting that there are still such unexplored frontiers, isnt it?

Image: Enric Sala/CoML


When acute gives way to chronic, Deep concerns for the Gulf set in

Just five days before the Deepwater Horizon oil rig exploded in the Gulf of Mexico, I wrote a piece for this blog about a different oil spill in Australia, when a Chinese coal ship called the Shen Neng1 ran aground in Queensland and spilled thousands of gallons of fuel oil onto a section of the Great Barrier Reef.  The gist of that post was that, horrible though they may be, there's no great cause to worry about acute events like that, because many marine ecosystems show remarkable resilience in the face of singular disturbance events.  About a week later when the BP spill started, therefore, I had confidence that the well would swiftly be capped, the oil would dissipate, Gulf life would return to normal and folks would all move onto the next media-hyped panic-fest.  But, as the days have dragged into weeks and the weeks are now dragging into two months and counting, and as the estimates rise of the amount of oil that continues to leak, and as successive attempts to cap the thing have failed, that confidence that the Gulf can recover to the same state it was in before the spill has started to get ever more shaky.

Now, I like to be a positive person; I try to see the upsides in most situations and not get caught up in negativity, which I consider one of the greatest and most utterly pointless malignancies of modern society.  But, following the coverage in the mainstream news and on excellent blogs such as DeepSeaNews and Observations of a Nerd and thinking about the problem in terms of ecological processes, it seems to me that we may well have passed a tipping point and that the ecosystems of the water column, benthic (bottom) habitat and coastal marshes may never return to their former states, even if they could stop the flow right now.  This principle has been elegantly captured by the "rolling ball" analogy, wherein an ecosystem has, by virtue of its structure and complexity, a sort of "potential energy" like a ball on a hill and that, if disturbed hard enough, you can start cascades that see the system diverge - the ball rolling down hill - until it settles in a new organisation - a dip in the hillside.  The important point is that getting the ball back up the hill to the former state is next to impossible, or at least requires inordinate amounts of energy and a thorough knowledge of the organising principles, which we lack.

What does all that mean for the Gulf, though? If a Spartina marsh isn't, then what is it?  What happens in the water column?  On the bottom?  That's where research comes in, and I was encouraged to read on the NSF website and by conversations I had with NSF and NOAA Fisheries Service program officers yesterday that they have spent all available money on rapid response grants, most recently an NSF multi-institutional cruise coordinated by UGA to study microbial responses in the water column.  Its not enough though, and the slowness of the peer review-based funding systems we have just can't meet the needs of a crisis of this magnitude fast enough, once the rapid response fund is tapped out.  It really needs executive intervention: if the White House can propose a Wall Street or Auto industry bail-out, why not a rapid response research and rehabilitation fund?  We can bill BP later!

Where is this all headed, and what should we expect to see in a "new" and different ecological regime in the Gulf of Mexico?  No-one can be certain at this point, but a hall-mark of such reorganisations is loss of diversity, and in any worldview, that is something to be lamented.  Lets hope it doesn't come to that, but at this point any concerns you may have that the damage to the gulf is irreparable could be forgiven, which is more than I can say for those responsible for this mess.


I'm baaaa-aaaaack...

Just returned from two weeks on the road, so I've got mounds of work to catch up on.  In the meantime, check out this interesting post over at Thomas' Plant Related Blog.  Its about Neutral Theory and why there are so many species distributed the way they are.  The ecology of diversity is one of my pet research areas, or at least, I like to think about it a lot (see earlier DTF posts about it here and here)


The water is ALIVE!

Its easy to get discouraged about the plight of marine ecosystems and the future of all those incredible marine species that we love so much. This is especially so of late, with all the bad news about the oil spill in the northern Gulf of Mexico and the impacts that it may well have on several habitats. Consider this post, then, as your good news story for the week. I am here to tell you that there is still amazing stuff to see in the ocean. Incredible stuff. Stuff that will blow your mind. I can tell you this with supreme confidence, because for the last two days, that’s exactly what I have been seeing. As part of the research program at Georgia Aquarium, I am with colleagues in Quintana Roo, Mexico, studying whale sharks and other species that live in the azure waters of the Yucatan peninsula. Jeff Reid, who is the aquarium’s dive safety officer, is here and our main colleague in Mexico is Rafael de la Parra of Project Domino, who has been working on whale sharks and other marine species in the area for many years. This is a remarkable part of the world, with a lot of great terrestrial activities (can you say Cenotes, anyone? No? How about Mayan ruins?), exceeded only by the marine life, which is truly spectacular.

Yesterday Jeff and Raffa and I spent the day boating around the northeastern tip of the Yucatan along with videographer Jeronimo. Now, when you’re on a boat, you can only see a small strip of ocean either side of the vessel, and yet over the course of the day we saw lots of mobula (devil rays), turtles, flying fish, manta rays, spotted dolphins and whale sharks. We snorkeled alongside some of these animals and, in the case of whale sharks and mantas, took samples of their food for later analysis. They dine on the rich plankton soup of this tropical upwelling area, much of which consisted of fish eggs, which hints at other fish species – yet unseen – taking advantage of the plankton to start their next generation by spawning in the surface waters. Snorkeling next to a whale shark in the natural setting was a special thrill; I’ve been lucky enough to work with the animals in the collection at Georgia Aquarium since 2006, but this was my first encounter with them in the wild. Except for the slightly different “faces” (we do get to know our animals pretty well) and the parasitic copepods visible on the fins of the wild animal, it could have easily been the very same sharks Jeff and I have been working with in Atlanta.

Today, Jeff and Raffa and I joined Lilia (from the Mexican department of protected areas CONANP) and pilot Diego for an aerial survey of the waters around the northeastern tip of the Yucatan. In contrast to the boat, you can’t get in the water from a plane (its not advisable anyway), but you can see a whole lot more at once and cover a much greater area in a relatively shorter time. From the air, lots of sharks, cownosed rays, manta, dolphins, fish schools and whale sharks were all visible, and I am told that flamingos and manatees can be seen at other times too. The manta rays, which numbered in the hundreds, were especially impressive and included at least two species (see my post about taxonomy of mantas). The sheer number of cownosed rays, called chuchas in the local slang, was staggering (muchas chuchas, if you will). They formed huge schools that looked for all the world like the rafts of sargassum weed that accumulate on the wind-lines at the water’s surface offshore. Many of the turtles and mobula seemed to be in the mood for love; most turtles were in pairs (or a pair being followed by other hopeful males), whereas the mobula followed each other in lazy tandems, their wingtips breaking the surface with every stroke. Whale sharks were also there – lots of them – with their attendant flotilla of tourist boats and tiny orange specks of snorkelers in life-vests, doing their best (and largely failing) to keep up with the gentle giants.

When you have experiences such as those I have shared with my colleagues over the last two days, you are reminded why we do this stuff in the first place. Its not just for the papers, or the salary or the glory of new discovery (yeah, right!), its for those moments working with animals when you and a colleague become friends because you shared an experience of the oceans that most folks will never have. We should seek to share and recreate those moments with everyone we can, whether its in an aquarium or on the open ocean. I am pretty sure that if we could all do that, then public empathy for the plight of the oceans would skyrocket, and many of the threats that face them would be addressed quick smart.


12,081ft - The oceans, by the numbers

I was inspired by recent articles highlighting a revised calculation of the ocean’s average depth as 12,081ft, to consider the seas in a numerical light today. To that end, here’s a few random, sourced numbers and back-of-the-envelope calculations that might be food for thought:

0.87% = Amount we can see by diving from the surface (about 100ft) over the average depth
0.28% = Amount we can see by diving over the deepest part (Challenger Deep, Marianas Trench off the Philippines)
2.9 = Number of times deeper the deepest part is, compared to the average.
5,400 = Number of mammal species in the world
25,000 = Number of fish species in the world
Millions? = Number of marine invertebrates species in the world (no-one really knows)
2.3 Million = The number of US citizens directly dependent on ocean industries (source: NOAA)
$117 Billion = Value of ocean products and services to the US economy (yr 2000, source: NOAA)
50% = US population living in coastal zones
48% = The proportion of all human-produced CO2 absorbed by the oceans in the Industrial era (NatGeo)
0.1 = The pH drop in the surface oceans since 1900
0.35 = Expected pH drop by 2100 (source)
18 = The number of times more heat absorbed by the oceans than the atmosphere since 1950 (source - TAMU). Global warming is an ocean process far more than an atmospheric one.
3.5 Million = Estimated tons of plastic pollution circling in the Great Pacific Garbage Patch, and growing.

And yet:

30 = Number of times thicker the atmosphere is (out to the “edge of space” about 60 miles) than the average ocean. That would be the atmosphere that astronauts describe as a “thin veneer” on the planet…
0.06% = Thickness of the average ocean, compared to the radius of the earth. I think we can argue that the water is the veneer, not the air
$4.48 Billion = NOAA’s 2010 budget, including the National Ocean Service, Weather Service and Fisheries Services. (source NOAA)
$18.7 Billion = NASA’s 2010 budget, i.e. 4 times the size of the agency that looks after our own planet (source NASA)
$664 Billion = Department of Defense base budget 2010, not counting special allocations (source DoD)
0.6% = The amount you would need to cut Defense in order to double the NOAA budget

Some sources:  


Mountains of Pelagic Diversity

If you ever saw the dramatic seamount scene in Blue Planet (and if you haven’t, where ya been??), then you are probably familiar with the idea that submarine mountains can attract lots of animals; as Attenborough puts it, they “create oases where life can flourish in the comparatively empty expanses of the open ocean”.  In that spectacular BBC sequence, jacks and tuna swarm an Eastern Pacific seamount peppered with colourful schools of barberfish, Anthias and goatfish.  Then the sharks cruise in, including silkys and hammerheads, there for a clean from the faithful barberfish.
There’s a paper in the latest issue of PNAS that quantifies the richness of seamounts, so beautifully depicted by those geniuses at the BBC Documentary department.  The authors, led by Telmo Morato from the Secretariat of the Pacific Community in New Caledonia, analysed data gathered by longline fisheries in the western and central Pacific, close to and remote from seamounts .  In a sense, a longline is a standardized sort of sampling unit like a quadrat, so they can be analysed across locations to measure differences in diversity.  They accounted for differences between total catch per longline using the statistical process called rarefaction which is a practical application of one of my favourite fundamental biological patterns – the species accumulation curve - which I’ve discussed before (here and here).  It looks like a great dataset with great spatial resolution and pretty good coverage in the tropics, though the equatorial zones are less well-represented.
I don’t think anyone would be surprised by their result that, yes, seamounts are diverse places.  When they broke it down by species, about 2/5 (15 species) showed positive association with seamounts; this group included both sharks and fish.  Interestingly, 3 species (pelagic stingrays, albacore and shortbilled spearfish) showed negative associations with seamounts, while 19 showed no measurable association.  So, the net effect is positive, but there's clearly some structure in the data, depending on what species you look at.  Nor, I think , would most people be surprised by the distance effect they found, wherein sample diversity decreased with distance moved away from the peak of a seamount, and most sharply in the first 10 or so kilometers.  What was surprising, to me at least, was that both the absolute diversity and the distance effect they found were greater on seamounts (left) than they were for coastal zones (center). 
I would have thought that coastal zones, with their larger area, more complex topography and currents, coastal upwelling and inputs from the land, should have had higher diversity.  Indeed, it kind of goes against the island biogeography ideas, that as we go away from the largest habitat towards smaller more distant patches, diversity drops; if you think of seamounts as underwater islands and continental shelves as underwater mainlands, perhaps you’ll see what I mean.
There’s a couple of reasons I can think of to explain the observed difference.  Perhaps there is something intrinsic to seamounts, some feature of topography or productivity that makes them real magnets for diversity.  Under this scenario, they are true biodiversity hotspots.  Alternatively, perhaps coastal zones once were more diverse than seamounts but have been denuded by our actions, so that only the remote and submarine mountains remain as examples of what once was.  Perhaps it’s a bit of both, or some other concept (that you should propose in the comments).  Either way, Morato et al. show us that we may be successful at protecting widely roaming pelagic species by strategically preserving relatively tiny specks of submarine oases.  Since reading their paper, I have enjoyed thinking of schools of pelagics, hopping from mountaintop to mountaintop, skipping across vast plains of abyssal ocean, and as usual dreaming about diversity and all the fantastic forms of life in the 3D wonderland of the open ocean.  It just makes you want to down tools and grab the next slow boat bound for Cocos, doesn't it?

Morato, T., Hoyle, S., Allain, V., & Nicol, S. (2010). Seamounts are hotspots of pelagic biodiversity in the open ocean Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0910290107


Tilting the three-way tango - disease as a loss of diversity

ResearchBlogging.orgDisease is a funny old thing.  We're taught from very early on that disease agents are "bad" and that, by contrast, the infected are somehow poor and unfortunate victims of nasty evil bugs.  This is clearly a cultural bias, wherein we project our own concerns about getting sick onto all other animals; there's no real reason to think that a bacterium or virus has any less right to be here or any less important role in the ecological processes of the world than does the dolphin it infects, or the fish or the lobster.  We have all survived eons while avoiding extinction, which makes us winners in the great game of evolution, the microbes every bit as much (or more) than their hosts.

Still, biases run deep.  This is important because sometimes they cloud our perceptions of whats really going on.  Consider coral diseases for a moment.  What, you didn't know that coals get diseases?  That's OK, neither did most folks, including many scientists, until fairly recently.  Lets picture a nice reef coral, maybe a handsome Porites, infected with one of the many "band"-causing agents (diseases that march across the surface of the coral, destroying tissue along a coloured front that gives the disease its name).  Most folks would perceive that the coral (good) was quietly minding its own business when it was "infected" by the microbe (bad), causing disease.  But actually it took at least three players to tango in this case; the coral had to be susceptible to the pathogen, the pathogen had to be infectious to the coral, and the environment had to set the scene that made the interaction swing in favour of the pathogen.  This simple "disease triad" is the most basic model of how infectious processes take place, but its just that: a basic model.

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


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

ResearchBlogging.orgA 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