A Dottyback in Damsel Clothing: Color Mimicking in Fish

I was looking around for a study and stumbled upon one about fish mimicry in Current Biology. What first caught my attention was its use of a video abstract. What a cool idea amped up a few notches by beginning with music reminiscent of Game of Thrones. Then I started to think back about posts I've done on predator-prey relationships and could only come up with 1, the One-Third for the Birds post back in 2012. Clearly it is time to revisit that topic. Oh, and while we’re at it, we’ll throw mimicry into the mix.

Different prey species employ various options in predator avoidance including mimicry. Generally, mimicry is a strategy of looking, acting, smelling, or sounding like something else as an act of deception to gain protection. But prey species are not the only ones that mimic. Predators use it to get close enough to catch their prey. Blending into the background or looking like something familiar can be very useful in sneaking up on an unsuspecting prey animal. However, in both predator and prey, there is a huge caveat to mimicry - numbers. The mimic must be rare compared to their model. If the mimics are encountered too often then the predator/prey learns of this cunning deception and the mimicry becomes ineffective.

This month Cortesi et al. published a short paper looking at body color and predatory behavior in dusky dottybacks (Pseudochromis fuscus). This small species (8 cm) is a generally solitary and aggressive predatory reef fish native to the southwestern Pacific Ocean and eastern Indian Ocean. The fish are usually found in association with branching corals (e.g. Cauliflower corals [Pocillopora]  and Staghorn corals [Acropora]), setting territories where they love to hunt and eat juvenile coral reef fish, particularly the similar-looking damselfish. Individuals range in color from yellow to a “dusky” purple/brown. The researchers based their experiments on 3 interesting facts: 1) when the dottybacks matched the color of other reef fish they increased their hunting success, 2) dottybacks have been shown to change body coloration within 2 weeks when translocated to a different, dark colored reef and 3) dottybacks aggressively mimic similarly colored adult damselfishes. Does one color work better than another? Are there cues that drive the color change?

Figure 1 (A and B) from Cortesi et al (2015) Current Biology 

To test this, they set up sites at Lizard Island, Great Barrier Reef, Australia. Ya know, given the option, that's probably where I’d do my research too. They collected dottybacks and adult damelfishes and assessed the home ranges of the yellow and brown dottyback color morphs. Then, to look at the genotypes associated with different color morphs, they used microsatellites on fin clips from fish from three lagoon locations. Next, they conducted a translocation experiment. They found an open area and created a small patch reef using pieces of live or rubble coral. A total of 15 yellow damselfish (Pomacentrus amboinensis, P. moluccensis) and 15 brown damselfish (P. chrysurus) of all size classes were placed on the patch reefs. Once the damselfish were adjusted to their new home, the dottybacks (tagged unique fluorescent elastomer markers) were added in a 2 x 2 x 2 design (dottyback color x damselfish color x habitat type, each with 2 levels: yellow/brown dottyback, yellow/brown damselfish, live coral/coral rubble). Once all of the fish were on the patch reef, they were observed for predation and body color (using spectral imaging, skin biopsys for histology, and lots of mathematical models).

The researchers also conducted a very similar experiment using controlled conditions. Damselfish and dottybacks were caught and placed into experimental aquarium tanks containing live and rubble corals. Both juvenile and adult damselfish were acclimatized to a tank before a dottyback morph was introduced. Then strike rates of dottybacks directed at the damselfish were recorded. Then they conducted a prey color choice experiment to examine if dottybacks had a preference for a particular colored prey fish, again in the experimental aquariums. Considering that dottybacks aren't just predators but also prey for larger fish, the researchers tested to see if dottybacks also benefit from matching the color of the habitat using coral trout (the predator) in controlled choice tanks.

Whew! That’s a lot of experiments for one little report paper. In the field, they found that yellow dottybacks associated themselves with live coral and yellow damselfish, and brown dottybacks associated with coral rubble and brown damselfish. The translocation experiment showed how the color of resident adult damelfish induced color change in the dottybacks in patches where their colors were mismatched, independent of habitat type. The skin biopsies showed that unlike other species of fish, the dottybacks did not achieve this change by altering the number of chromatophores (pigment containing cells that reflect ligh) but, rather, the ratio of xanthophores (yellow pigment cells) compared to melanophores (black pigment cells) alters.

In the aquarium experiments, they found that dottybacks were three times more successful in capturing juvenile damselfish when their color matched that of the adult damselfish. This bit of deception works on the fact that the juveniles are less vigilant when they perceive all bigger fish as harmless adult damselfish. The strike rates showed that dottybacks prefer to go after prey fish of the same coloration to themselves, but, when mismatched, brown dottybacks are more likely to have successful strikes than yellow ones. When the dottybacks became the prey species, coral trout were found to strike more often at fish that were color mismatched to the background. This means that the color change has a secondary camouflage benefit and possibly a dilution effect when they are associated with similarly colored damselfish.

Graphical Abstract from Cortesi et al (2015) Current Biology

Collectively, these experiments uncovered a novel mechanism of the mimicry game: phenotypic plasticity. Phenotype is an organism’s observable characteristics (how it looks), and plasticity describes a quality of being easily shaped or molded. Phenotypic plasticity is one of those rare scientific words that means exactly what it sounds like: the ability or an organism to change its characteristics in response to the environment. This plasticity allows the dottybacks to deceive their prey using multiple guises and thereby increase their hunting success with the added benefit of hiding from their own predators.


F. Cortesi, W.E. Feeney, M.C.O. Ferrari, P.A. Waldie, G.A.C. Phillips, E.C. McClure, H.N. Sköld, W. Salzburger, N.J. Marshall, & K.L. Cheney (2015). Phenotypic Plasticity Confers Multiple Fitness Benefits to a Mimic Current Biology, 25 (1-6) : 10.1016/j.cub.2015.02.013


Write-up by the authors on The Conversation: "The dusky dottyback, a master of disguise in the animal world."



(image via the Australian Museum)

Small Things, Big Problem: Microplastics Uptake in Shore Crabs

Lately I've been gearing up for some nano-particle research, and so I've been doing a lot of reading about very small things. While perusing the literature, I came across a paper published online in Environmental Science and Technology that takes a look at microplastics.

Let’s start with the Great Pacific Garbage Patch, a very good example of this type of marine pollution. This huge collection of marine debris in the North Pacific Ocean is created by an ocean gyre, a stable circular ocean current that draws in debris where it is trapped and builds up. The collected debris is our litter – plastics and other material that are not biodegradable. They can’t escape the gyre, they just collect. And as they sit out there swirling around, they break down into smaller and smaller pieces called microplastics.

Microplastics are defined as those plastic particles less than 5 mm in length, and these small particles are a huge marine pollution problem. They are classified into two groups: (1) primary microplastics that are created at the microscale for use in products like cosmetics and drugs and (2) secondary microplastics that are products of the breakdown of larger items. As a whole, they are persistent and widespread – we’re talking worldwide, the Great Pacific Garbage Patch is just the most well-known aggregation. These microplastics are very abundant, we’re talking 1,000-100,000 particles per cubic meter of seawater! And there is growing evidence of the danger these tiny materials are having on marine life, everything from turtles to sea birds to fish and even zooplankton.

A new study by Watts et al. takes look at the uptake of these microplastics in the shore crab (Carcinus maenas). Previous studies have shown that an important prey species of the shore crab, the common mussel (Mytilus edulis), accumulates microplastics as it filters the water for food (“ventilation”). In laboratory conditions, the direct transfer of microplastics from mussels to crabs has been shown, but then again, it has also been shown that crabs uptake microplastics as they pull water through their gills. So what exactly is going on here? How are these crabs exposed and are they able to clear the microplastics from their bodies?

This is one of those studies where I just love to describe the methods. The first thing the researchers had to do was to assess the ability of the crabs to uptake microplastics (in the form of 8-10 um polystyrene microspheres) through their gills. To do this, they fitted the crabs with masks designed to allow measurements of ventilation. Yep, they put little masks on crabs. Picture that. I love science. Next they assessed the ability of the crab to take up microspheres in their food by exposing mussels and then turning them into “jellified mussel homogenate” to then feed to the crabs. I wonder which undergrad had the lovely job of making gelatin mussel popsicles? To see if the microplastcs were cleared, they let the crabs sit in their tanks and tested the abundance of microspheres in the water during water changes every 2 days for 22 days, sampling periodically. During each stage of the experiment, they measured the abundance of microspheres in the gut and gill tissues, fecal material, and hemolymph (like blood). Using fluorescent microscopy and Coherent Raman scattering microscopy (CRS; a multiphoton microscopy that produces label-free contrast of both the target sample and the surrounding biological matrix), they were able to look at the location of the microplastics within the tissues.

The researchers found that the masked crabs took up 31,000-62,000 microspheres (0.39-7.7% of the initial exposure concentration) into their gills after only 16 hours. But this uptake was not even across the gills, with greater uptake in the posterior gills. The crabs where able to expel some of the spheres, but slowly, still expiring microspheres 21 days after being exposed. Imaging the gills showed the microspheres to be associated with the gill epidermis. The feeding experiment showed all crabs to have microspheres in their foregut and later in their fecal material. The residence time of these microspheres was short, but still took longer to excrete than regular food waste, up to 14 days. Microscopy showed microspheres associated with the internal setae of the foregut lining. But, neither the ventilation experiment nor the feeding experiment showed any microspheres in the hemolymph.

Back to the question of what’s going on here? The shore crabs did take up microplastics in both types of exposure, but residence time is the key. They were able to clear the microplastics they got through dietary means, but they were still trying to clear microplastics they took up during ventilation almost a month later. The authors constructed a model to explain the mechanism of the movement of the microplastics. They found that the crabs tended to exhibit an asymmetry in microplastic uptake in the gills, which they attributed to the pumping mechanism of the scaphognathite being more dominant on one side of the gill chamber. Also, the posterior gills have a larger surface area than the anterior gills so they are more likely to take up microplastics into their lamellae. The crabs were unable to dislodge the tiny particles by normal gill cleaning actions. It is interesting that no microspheres were found in the hemolymph at any of the sampling points in either experiment. That suggests that there is no movement of the particles. It is likely that the particle size they used (10 um) was a little bit too large as it has been shown that sizes of 0.5 um are able to translocate in these crabs. This idea of particle size is something I’ve been seeing with increasing frequency within the nano-particle literature, along with polymer type, shape, and coatings. To that I would add that species is probably also in the mix as gills in crabs and fish are structured differently, and nano-particles have been shown to move in to organs like the liver in fish.

Studies like this are interesting because they show how very small things can become a very large problem affecting multiple tissues of the same organism up to multiple levels of a trophic cascade. I mean, think about it, even we humans could be affected. After all, we consume a lot of crab. How many microplastics are you ingesting when you stop at the crab shack for a quick lunch?


Watts AJ, Lewis C, Goodhead RM, Beckett SJ, Moger J, Tyler CR, & Galloway TS (2014). Uptake and Retention of Microplastics by the Shore Crab Carcinus maenas. Environmental science & technology PMID: 24972075


I know I used some technical terms, if you need some help with crustacean anatomy check out Invertebrate Anatomy OnLine.

(image via UGA Evolution 3000H)

Eating and Evolution: Are Prey Preferences Causing the Evolution of Killer Whales?

When I was an undergrad, a lowly freshman who just knew she wanted to study biology, I took an internship at SeaWorld Orlando. I was excited that I got to participate in a real research project doing actual sciency stuff. The project was on the nursing behaviors of captive baby killer whales. Really cool right? Little did I know that actual science is composed of hours upon hours of tedious observation and documentation (2:00pm – melon bumping, 3:00pm – melon bumping, 4:00pm – melon bumping…). Despite that (or, who knows, maybe because of it), it was an neat project that boosted my interest research biology. And I got to watch killer whales for hours every week. So when I came across the paper for today’s post it really reminded me those times.

A new study published in the Proceedings of the Royal Society B, Biological Sciences looks at niche variation within sympatric killer whale populations in the North Sea. Those of you familiar with the terminology I just used might want to skip to the next paragraph. Otherwise, let’s hit a few terms first. We’ll start with the niche variation hypothesis. In the simplest terms, a niche describes where a species lives and the roles it plays in its habitat. The niche variation hypothesis describes differences within a species that are correlated with the variety of foods and habitats that are used by various populations. For example, why do island birds of the same species have different bill sizes? Likely because their bills adapt to the food items they are exploiting on their own island. It conveys a competitive advantage which results in a reproductive advantage that will lead, eventually, to an evolutionary change. This change will likely be a speciation event. This is a lineation-splitting event that produces two or more separate species from one (think about the branching on the tree of life). Usually we think of speciation as occurring via a geographic isolation (birds on different islands, populations separated by a mountain range, etc.), but the niche variation hypothesis allows for sympatric speciation because the exploitation of different resources splits a population within the same habitat. Admittedly, this type of selection would need to be really strong and stable over a long period of time to cause speciation. Now on to the study!

Killer whales (Orcinus orca) are actually members of the dolphin family (Delphinidae). They are the most widely distributed cetacean species in the world and are top marine predators. Males typically live about 30 years on average, and females about 50 years. The diet of killer whales is often geographic or population specific. Populations of orcas are usually defined as either “residents” or “transients.” As the name suggests, residents tend to stay in a more localized area whereas transients travel over large distances, sometimes overlapping with the ranges of resident populations. It has been documented that these different types of populations vary greatly in their diets, each consuming a narrow range of prey. Residents feed primarily on fish while transients feed nearly exclusively on other marine mammals. Considering this, and what we know of how the niche variation hypothesis cause speciation, have or are killer whales branching in to two species?

One of the problems in answering this question is the long-lived nature of these animals. It’s difficult to see a long-range change on a long-lived species. Most evolutionary studies use either comparisons at a single point in time or over timescales representing one to a few generations. Okay, that’s pretty good, and these snapshots have been very informative, but to get a real-time view in a long-lived species you really need to go small. And by that I mean molecular. Ancient DNA (aDNA) and stable isotope data from subfossil (remains that have not completed the fossilization process) specimens can be used to track niche and evolutionary history. The scientists in this study used these methods to look at the evolution in sympatric killer whale populations in the North Sea. First, they sampled 23 subfossil killer whale bones and teeth recovered by dredging or trawling the Southern Bight of the North Sea or from archaeological sites in Southern Scandinavia. Then they dated their samples using radiocarbon techniques or archaeological context. Next, they used stable isotope ratios to provide a long-term measure of what the animals ate during their lifetimes and thereby estimate the orcas’ niche width (it is argued that populations in wider niches are more variable than populations in narrower niches). Additional evidence of these dietary habits was gathered from examining the wear-patterns on the teeth (for example, feeding heavily on herring badly wears down the teeth). Then mitochondrial DNA (mtDNA) sequencing was used to determine the degree of linage sorting (separate populations carry their genetic diversity with them) based on isotopic (prey) niche. And finally, they biopsied the skin of modern orcas, sampling either while the animals fed on fish or on stranded remains with known stomach contents. From this they were able to extract high-quality DNA and conduct an individual-based analysis of population structure. This, combined with the aDNA data, effectively gave them a map of the evolutionary outcome of niche variation.

This is one of those studies where the results are all variable. *sigh* ‘Tis science. From the isotopic analysis, the researchers found  a lot of overlap in the results, mostly likely explained by among-individual differences. Because this type of analysis represents what an animal ate over its lifetime, differences in prey items within the diets of individuals are not apparent. This and the analysis of tooth wear suggests some overlap either in the diet and/or foraging method of the specimens studied. The result is consistent with the observations of the modern whales. Fish eating pods are often found with mammal remains in their stomach contents. Lineage sorting of mtDNA sequences based on the isotopic values revealed that there “has been multiple diversifications [sic] in isotopic niche” and “an indication there was relatively stable transmission of isotopic niche along matrilineal lines within some clades, in particular those that were dominated by samples from Norway.” The incomplete lineage sorting they found seems to be consistent with relatively recent divergences in niches, and their models indicate panmixia (random mating) between at least some groups that feed on fish and some groups whose diet includes seals.

To sum up, we know that there is niche variation in populations of killer whales. But all of that variation and overlap that the researchers found suggests that any speciation is still at an early stage in this system. And while the results of this study seem to be all over the place, it does add more information to the story while providing a useful long-term evolution study methodology. It also strengths the argument that sympatric speciation is difficult to achieve.

Also check out this great presentation on this study!



Foote, Andrew D., Newton, Jason Newton, Ávila-Arcos, María C., Kampmann, Marie-Louise, Samaniego, Jose A., Post, Klaas, Rosing-Asvid, Aqqalu, Sinding, Mikkel-Holger S., & Gilbert, M. Thomas P. (2013). Tracking niche variation over millennial timescales in sympatric killer whale lineages Proceedings of the Royal Society B, Biological Sciences, 280 (1768) DOI: 10.1098/rspb.2013.1481

Science's article "North Atlantic Killer Whales May Be Branching Into Two Species"

For more information and explanation of some of the evolutionary terms discussed this post see:
Understanding Evolution via Berkeley, particularly the page on sympatric speciation
and for a nice description and examples of niche variation see
Soule, M. and Stewart, B.A. (1970) The "Niche-Variation" Hypothesis: A Test and Alternatives. The American Naturalist, 104(935): 85-97. (LINK)

Some useful resources for information on killer whales:
NOAA Fisheries Office of Protected Resources page on Killer Whales
National Marine Mammal Laboratory's page on Killer Whales
Cascadia Research Collective's "Studying the diet of fish-eating killer whales"


(image via National Geographic, photo credit Gerard Lacz/Animals Animals—Earth Scenes)

They're All Alike: The Giant Squid Conundrum

I wasn’t going to post on another paper this week but then two things happened: I saw the video of the first giant squid filmed in its natural habitat (those scientists get so excited!), and I saw the study about giant squid diversity. I posted the first above and now we'll take a look at the second.

The giant squid (Architeuthis spp.) is one of the largest invertebrates and lives in the deep sea. It was first described as Architeuthis dux in 1857 by Danish naturalist Japetus Steenstrub, but since then, as many as 21 nominal species of Architeuthis have been described. The descriptions of this creature have primarily come from remains found washed up on beaches, found floating on the ocean surface, caught by deep-sea trawling activity, or in the stomachs of sperm whales (Physeter macrocephalus). It wasn’t until 2004 that a live specimen was observed in its natural habitat, and earlier this year that the first video footage was published (although not the in-the-natural-habitat version above). It is estimated that female squid reach a total length of 18m (59ft) and males reach slightly smaller sizes. The giant squid is globally distributed, with the exception of polar regions. They feed primarily on fish and smaller cephalopods. Studies of carbon and nitrogen isotope profiles of the upper beaks suggest ontogenetic diet shift earlier in life (smaller to larger prey items), and carbon isotope composition remains constant in food sources indicating that the squid inhabit relatively small, well-defined and productive areas. The predation of adult squid by sperm whales suggests that squid population size must be large enough to support such a large whale population, although this has never been proven.

There are some rather obvious difficulties in studying giant squid using conventional, observational techniques. So other techniques must be utilized. Enter, DNA. Recent advances in DNA sequencing techniques have made it easier, quicker, and more economical to sequence long stretches of DNA. The role of DNA sequencing is becoming more and more important in phylogenetic and population biology studies. It allows you to assess the number of species, examine the amount of genetic variation, and describe population structure.

In a new paper in the Proceedings of the Royal Society B: Biological Sciences, researchers collected 43 Architeuthis soft tissue samples from the carcasses of dead animals across their known range. They extracted DNA samples from the specimens to analyze the mitochondrial genomes (mitogenomes) and levels of nucleotide variation. They generated mitogeome datasets using several strategies, depending on the quality of the DNA in each sample. I’m not going to go into their sequencing methods – if you are a molecular biologist then you already know them, and if you aren’t then I’ll just bore you. To look at the population level of the genetic variance, they wanted to compare their samples with the fossil record of coleoid cephalopods. This is challenging considering the extremely limited fossil record for these organisms. So they used four different mutation rates to tentatively estimate a time of expansion and upper and lower bounds for the time of divergence of Achiteuthis from other squid families.

They were able to complete 37 complete and 6 partial mitogenome sequences. Remember up at the top of the post where I said “21 nominal species of Architeuthis have been described?” One pretty strong conclusion of this study is that there is only one species of Architeuthis that exists, namely Architeuthis dux (Steenstrub, 1857). The researchers found the haplotype diversity of these giant squid to be high at the mitogenome level, but the level of nucleotide diversity in these sequences was found to be extremely low, with only 181 segregating sites of a 20,331 base pair long sequence. Only the basking shark (Cetorhinus maximus) has a similarly low diversity, which is the result of a recent bottleneck. This diversity for giant squid is much lower than is seen in other squid, 44 times lower than Humboldt squid (Dosidicus gigas) and 7 times lower than the recently restricted population of oval squid (Sepioteuthis lessoniana). The high haplotype to low nucleotide diversity relationship is interesting because it shows that out of a very diverse phyla of animals, the giant squid is the odd one out. Looking at the species across its range, there was no evidence of any phylogeographic structure, which is odd considering the global distribution.

So how do you explain the low genetic diversity in comparison to the global distribution (and potentially large population size)? The authors hypothesize that it could be a low rate of mitochondrial DNA evolution, something that has been observed in other marine organisms. But a low mutation rate does not explain why mitogenome duplications maintain near 100 percent identity. The authors suggest that “perhaps the duplicated sequences form stable secondary structures, which are somehow selectively beneficial, thereby causing mutations to be under negative selection,” which would lead to “a decreased rate of divergence in the duplicated regions relative to the rest of the genome, which does not appear to be the case.” Alternatively, it could be a recent selective sweep such as a bottleneck. Bottlenecks are events that greatly reduce the size of a population, usually resulting in a large reduction in the genetic diversity of that group. If this bottleneck were followed by an expansion in the number of individuals in that population then you would see that low diversity spread amongst a large population. Modeling and analysis of data support the latter hypothesis over the former.

Unfortunately, genetic data alone can’t provide an answer as to why this might have happened. Whatever event it was, climatic or biological, it would have had to been wide ranging enough to affect a global population. Perhaps it was a sudden inflation of a population that was historically smaller. It is known that cephalopods tend to be subdominant predators, and as such, are affected by the changes in population of predators and competitors. If this small size was due to restraints on predators and/or competition and that restraint were released then you would expect such an inflation in squid numbers. Considering the effect of industrialized whaling in the 1700s to late 1800s, this is a likely explanation, but still too recent to explain it entirely. This change in predators and/or competitors could have been the result of climatic effects such as the last ice age changing. Such changes could have altered the abundance and distribution of competitors such as predatory fish. Or perhaps, rather than a bottleneck, A. dux existed historically as a single, small, geographically isolated population that then expanded globally. This expansion would have had to been in a non-ordered fashion with either nomadic adults or dispersing juveniles and small pelagic paralarvae capable of using currents to travel long distances. But if they can disperse really far then why would they have been restricted historically? The authors hypothesize that a global population existed for a considerable time, and that an average of just one individual exchanged between two populations per generation will be enough to prevent genetic differentiation between them. They believe that the wide ranging dispersal of paralarvae and juveniles on the currents of the upper layers of the oceans could achieve this. These young life stages float along with the currents feeding on zooplankton and such until they reach a sufficiently large size, after which they descend to the closest nutrient-rich deep habitat where they remain until maturation.

I think that’s a pretty good explanation. What about you?


Winkelmann, I., Campos, P., Strugnell, J., Cherel, Y., Smith, P., Kubodera, T., Allcock, L., Kampmann, M., Schroeder, H., Guerra, A., Norman, M., Finn, J., Ingrao, D., Clarke, M., & Gilbert, M. (2013). Mitochondrial genome diversity and population structure of the giant squid Architeuthis: genetics sheds new light on one of the most enigmatic marine species Proceedings of the Royal Society B: Biological Sciences, 280 (1759), 20130273-20130273 DOI: 10.1098/rspb.2013.0273


ScienceNOW article: "Giant Squid Worldwide Are One Species"
ScienceDump: "The search for the giant squid"
Vido via Nature's: "Giant squid filmed in its natural environment"

Google Goes Underwater

If you have been online ever then you are probably familiar with Google Street View, the interactive panorama feature within Google Maps. Over the past couple of years Google Maps has expanded past the terrestrial roads we drive everyday to more exotic locales such as eye-level images of Antarctica, inside NASA's Kennedy Space Center, floating down the Amazon, and through the halls of famous museums.

Now Google Maps is going underwater. On Wednesday, the site added panoramic undersea images of the Great Barrier Reef in Australia, visages of the waters off the Apo Islands in the Philippines, and the wonder that is the underwater life around the Hawaiian islands. It even has zoom features that allow you to get close up looks of coral and fish. These photos are part of a partnership with the Catlin Seaview Survey, a project working to document the world's reefs in 360-degree images so that scientists can study them. Their partnership with Google is an attempt to get people involved in the fate of these ecosystems and to understand how oceans play a role in the health of the planet.

The images you see were taken by a camera called SVII that was custom-designed for the Catlin Seaview Survey. The design of the camera was inspired by sharks, and it is a rapid-fire camera that can be controlled by a tablet in a watertight housing. When a picture is taken it also records GPS data along with the exact angle at which the photo was taken. However, taking images at greater depths (30-100m or 98-328ft) becomes a little more complicated. The Survey crew will need to send down a special remotely operated vehicle outfitted with remote-controlled digital single-lens reflex cameras. Right now you can browse through the 15,000 available panoramic photos. And keep a look out for more photos in the future. The team would like to have between 50,000 and 100,000 pictures by the end of next year, expanding to sites like Bermuda, the Caribbean, the Indian Ocean, and the Coral Triangle.

Learn more here:
World Wonders Project
Google article: "Dive into the Great Barrier Reef with the first underwater panoramas in Google Maps"
CNN Tech article: "Stunning undersea panoramas now on Google Street View"

Perpetual Ocean

The wind map I posted a couple of months ago was pretty popular. If you liked that then you'll love this.

NASA's Scientific Visualization Studio has created an animation called Perpetual Ocean. The visualization shows ocean surface currents around the world during the period from June 2005 through December 2007. The goal of this project was to use ocean flow data to create a simple, visceral experience. Mission accomplished.

These visualizations were "produced using model output from the joint MIT/JPL project: Estimating the Circulation and Climate of the Ocean, Phase II or ECCO2. ECCO2 uses the MIT general circulation model (MITgcm) to synthesize satellite and in-situ data of the global ocean and sea-ice at resolutions that begin to resolve ocean eddies and other narrow current systems, which transport heat and carbon in the oceans. ECCO2 provides ocean flows at all depths, but only surface flows are used in this visualization. The dark patterns under the ocean represent the undersea bathymetry. Topographic land exaggeration is 20x and bathymetric exaggeration is 40x." The videos I've posted here are grabbed from YouTube. I highly recommend clicking the links below each video and going to the NASA webpages. There you will find more videos, all designed for a very wide, high resolution display.

This first Perpetual Ocean visualization is of some of the world's surface ocean currents.



Learn more at NASA's Perpetual Ocean website

This next visualization shows the Gulf Stream stretching from the Gulf of Mexico all the way over towards Western Europe. The colors indicate sea surface temperatures in degrees Celsius (blue is < or = to 0, yellow is 17, and red is > or = 33).



See more at the Gulf Stream Sea Surface Currents and Temperatures webpage.

This animation shows "ocean current flows in the Mediterranean Sea and Western Atlantic. The time period for this visualization is 16 Feb 2005 through 16 January 2006. For each second the passes in the visualization, about 2.75 days pass in the simulation. The colors of the flows represent their depths. The white flows are near the surface while deeper flows are more blue." Click the picture to be transported to the video.

These animation can be found in various video forms at the Ocean Current Flows around the Mediterranean Sea for UNESCO webpage

This animation shows sea surface current flows. The flows are colored by corresponding sea surface temperature data. The global sea surface currents have been colored by temperature in the same way as the Gulf Stream video above.



The webpage for this visualization has several videos, many of which are cropped to show only certain parts of the Earth. They can be found at the Global Sea Surface Currents and Temperature webpage and the Flat Map Ocean Current Flows with Sea Surface Temperatures (SST) webpage.

A Lionfish of a Problem

Lionfish are beautiful but venomous. Very recently these fish have become quite a large problem in the Caribbean, the fastest invasion documented for a marine fish. The Indo-Pacific lionfish (Pterois miles and P. volitans) are native to the reefs of the Indian and Pacific Oceans. They are also very popular aquarium fish. Whether through accidental or purposeful releases in the late 1970’s through the present, lionfish have made their way into the Caribbean. It started out as not-so-bad (as such things do) with only 5 or 6 individuals, but the problem has grown (as such things do) to a self-sustaining population that reaches over 1,000 lionfish per acre in some locations. P volitans seems to have taken up all of the reef real estate south of the Bahamas, while both species can be found north of Florida extending to Bermuda and out in the Sargasso Sea. But what makes lionfish such a problem? Well, mainly their appetite. Lionfish are generalist carnivores with voracious appetites, consuming more than 56 species of fish and many invertebrates. They have evolved to food availability in the Pacific, which may be patchy, and so they eat as much as they can whenever they can. Using this appetite, they have been known to reduce their fish prey by up to 90 percent. They are capable of permanently impacting native fish reef communities across multiple trophic levels. Another problem? They have a very high rate of reproduction. Lionfish become sexually mature at about 7 months to 1 year old and spawn in pairs. Females will release 30,000 eggs every spawning cycle, adding up to about 2 million per year in some cases. These eggs settle out as baby fish in about 30-40 days. Are you doing the math? Because that’s a lot of fish and a really big invasion problem. Today I’m going to take a look at two papers (out of an ever-growing number) that ask why lionfish are successful invaders and which habitats within their invasion zone they flourish.

The first paper looks at why lionfish are successful by comparing Kenyan and Bahamian lionfish populations. This is not an uncommon type of comparison. However, it is seldom studied in marine invaders as a whole, and since marine predatory vertebrate invaders are rare it is even less common in this realm. The idea is relatively simple: Invasive species are not a problem in their home ranges, they are kept in check by other components and members of their ecosystem. Comparing invasive species to their native counterparts can reveal shifts in ecology and behavior and can shed light on the factors contributing to a successful invasion and even some potential control methods. This study tested if lionfish on invaded Caribbean reefs have reached greater abundance than they normally reach on their native reefs, and they tested potential ecological differences by measuring lionfish body size and activity levels between the native and introduced fish. To see if lionfish are in greater abundance and/or size in introduced areas, the researchers conducted underwater visual surveys of lionfish in both their native (Kenya) and introduced (Bahamas) ranges, recording numbers of fish and total length of each fish. During these surveys, they also recorded lionfish behavior as active (i.e., either hunting, swimming, hovering in the water column or moving over the substratum) or inactive (i.e., resting motionless on the substratum).

This study found that invading Bahamian lionfish reached a higher abundance than their ecological equivalent in Kenya. However, it is important to note that when they combined the density of all five Kenyan lionfish species they were similar to Bahamian P. volitans, and that some Bahamian reefs had much greater densities than others. The Bahamian lionfish were also about 50 percent longer and had an overall biomass that was 13 times higher than Kenyan equivalents or the Kenyan lionfish species assemblage. There are several hypotheses as to why including lack of exploitation, low predation, low predator diversity and abundance, low fishing pressure, and a release from congeneric competitors. They are so numerous that they now make up a significant portion of the fish biomass on invaded reefs.

The second paper looks at the progression of lionfish into different habitats. In their native range, P. volitans and P. miles are predominately found on coral, rock, and sand substrates from <1 to 50 meters underwater. Their invasive range has been observed to be much broader, extending into habitats that include reefs, seagrass, mangroves, and in depths from 1 to >600 meters of water. Two previous studies that have looked at this habitat question have found that mangroves supported higher densities of smaller-sized individuals than nearby reefs and that lionfish in seagrass were smaller than those on reefs (both suggesting a nursery function). And while there is an international effort to document the spread of the lionfish, there has been less emphasis placed on how a new location becomes colonized. This study looks the invasion history as well as this colonization. The study area was located around South Caicos (a small island in the Turks and Caicos Islands) and Long Cay (on the eastern edge of the Caicos Bank). Five different marine habitat types were distinguished: mangrove, seagrass, sheltered shallow reef, exposed shallow reef, and deep reef. Using surveys consisting of timed swims, relative density of lionfish (number of individuals seen per observer and per unit effort) was calculated within these habitat types from 2007 to 2010. To look at size frequencies of lionfish within these habitats, individuals were caught and depth, habitat, type of shelter used, and total length were recorded. The age of individuals was estimated from total size.

 They found that by the end of 2010, lionfish had been observed in all five habitats with relative densities consistently rising throughout the course of the study period. Back-calculation of settlement dates indicated that lionfish may have started settling there as early as 2004. Sightings during their surveys initially showed that the density of lionfish in seagrass was 20 times higher than on deep reefs, but as the study went on the relative densities became similar across the habitat types with the concluding year showing the deep reefs to have over an order of magnitude higher lionfish density than any other habitat. There was also a significant difference in the sizes of lionfish caught in different habitats. Lionfish in deep reef habitats were significantly larger than those in seagrass and sheltered reefs, but they found no size differences in individuals from shallow habitats. Individuals found in these shallow habitats were younger than those found on deep reefs. Most of the lionfish were found to shelter on, in, under, or around other structures (corals, rocks, seawalls, trash, etc.). Observations of exposed reef habitats found lionfish to be conspicuously absent until 2010. They were found preferentially (but not exclusively) to settle in shallow habitats (seagrass, sheltered reefs, mangroves) before moving to deeper water once they had grown larger. However, they would have had to pass through these exposed reefs on their way to the deep reefs. The few individuals found on exposed reefs may be a result of this movement combined with the turbulent conditions associated with this habitat type. This evidence supports the idea that seagrass, mangroves, and sheltered shallow reef areas may serve as nursery habitats and adult fish move to deeper reef habitats later.

From all I’ve gone through today, the story looks pretty bleak. And I’ll be the first to admit that it doesn’t look optimistic. But there is good news. There are several lionfish research programs and international efforts to control or even eradicate these fish from the Caribbean (see some links below). And another bonus? Apparently they taste great!

Emily S. Darling, Stephanie J. Green, Jennifer K. O’Leary, & Isabelle M. Coˆte (2011). Indo-Pacific lionfish are larger and more abundant on invaded reefs: a comparison of Kenyan and Bahamian lionfish populations Biological Invasions, 13 (9), 2045-2051.: 10.1007/s10530-011-0020-0
 
John Alexander Brightman Claydon, Marta Caterina Calosso, & Sarah Beth Traiger (2012). Progression of invasive lionfish in seagrass,mangrove and reef habitats Marine Ecology Progress Series, 448, 119-129.: 10.3354/meps09534


Here are a couple of  websites to get you started looking in to this problem:
CCFHR: Invasive Lionfish
REEF Lionfish Program
Interview with Chris Flock from Ocean Support Foundation

Challenger Deep Expedition

What do you do when you are the most successful filmmaker in recent history? You dive to the deepest point on the planet. Duh.

James Cameron was born in Canada and moved to the U.S. in the early 1970's, majoring in physics at California State University. After school, he quickly rose in the film industry, making such well known films as The Terminator (1984), Aliens (1986), The Abyss (1989), Terminator 2: Judgement Day (1991), True Lies (1994), Titanic (1997), and Avatar (2009). That's just to name a few. These movies have broken all kinds of box office records and racked up several Academy Awards. Today, he is one of the most sought-after directors in Hollywood. As you may have noticed, many of Cameron's films have water or the ocean as a central theme, and many of them use machines as an important plot point or weapon. To say that Cameron has a fascination with the ocean and it's depths would be an understatement. He is an avid explorer, with 72 submersible dives to his credit.

“I’ve always dreamed of diving to the deepest place in the oceans. For me it went from a boyhood fantasy to a real quest, like climbing Everest, as I learned more about deep-ocean exploration and became an explorer myself in real life. This quest was not driven by the need to set records, but by the same force that drives all science and exploration … curiosity. So little is known about these deep places that I knew I would see things no human has ever seen. There is currently no submersible on Earth capable of diving to the ‘full ocean depth’ of 36,000 feet. The only way to make my dream a reality was to build a new vehicle unlike any in current existence. Our success during seven prior expeditions building and operating our own deep-ocean vehicles, cameras, and lighting systems gave me confidence that such a vehicle could be built, and not just with the vast resources of government programs, but also with a small entrepreneurial team. It took more than seven years to design and build the vehicle, and it is still a work in progress. Every dive teaches us more, and we are continuing to improve the sub and its systems daily, as we move through our sea trials.” —James Cameron

Most recently, Cameron has made history with National Geographic's DEEPSEA CHALLENGE Expedition. DEEPSEA CHALLENGE, a joint scientific expedition by Cameron, National Geographic and Rolex to conduct deep-ocean research and exploration. Scripps Institution of Oceanography is the primary science collaborator, working explore and study the deep sea and its marine life. It has been 50 years since man has descended 35,800 feet (10,912 meters) to the deepest point in the ocean, known as the Challenger Deep in the Mariana Trench. With a team of engineers, Cameron co-designed a submersible that incorporated the newest technologies, designs, and material available that could carry a human pilot to the deepest sites in Earth's oceans and perform work with significant bottom time for research activities. This submersible was also designed to dive repeatedly to gather data, samples, and imagery of the deep oceans.

The submersible was launched into the Pacific Ocean some 200 miles (322 km) southwest of Guam on Monday, March 26. The voyage down to the Challenger Deep took 2 hours and 36 minutes, the stay at the bottom lasted about three hours, and the return trip took only 70 minutes. During the time at the bottom they were able to collect research samples, still photographs, and moving images. This amazing trip makes James Cameron the first person since 1960 to reach the very bottom of the world. And he wouldn't be the filmmaker he is without documenting this for a new 3-D feature film, which will be broadcast on the National Geographic channel in the future. Look for it. I know I will!

One of the first images from the expedition

Visit National Geographic's DEEPSEA CHALLENGE website for more information, updates, videos, and great pictures.

Read more at National Geographic's Press Release Detail about the expedition.

Scripps Institution of Oceanography's webpage about the dive.

(images via the DEEPSEA CHALLENGE website and Live Science)

One-Third for the Birds

For this post I was looking for something a little different. Not so much a weird topic, but more like a topic that I haven't really posted on before. I came across an interesting article about predator-prey relationships as they relate to population sizes. It is one of those basic dynamics that is taught in almost every biology and/or ecology class there is, and rightfully so, because when you get down into it it is actually pretty interesting, no to mention really important.

Most people think they know predator-prey relationships. One thing eats another thing. The organism doing the eating is the predator and the one that is eaten the prey. That is perfectly true. Now think about it in terms of evolution. The predator and the prey evolve together, what is usually referred to as the "evolutionary arms race." If the predator does not catch any food then it does not survive; those that evolve better ways to catch food survive (speed, stealth, smell, sight, etc.). If the prey gets caught by the predator then it (obviously) does not survive, and so it evolves better ways to evade predators (camouflage, speed, poison, etc.). It is important to point out that both the predator and they prey are both adapting, a type of co-evolution. Next, think about the system in terms of population. The interaction of predators and prey greatly affect their population sizes, often on several levels within the food chain/web (or tropic pathway/cascade). When predators eat prey they: (1) decrease the population size of the prey, (2) survive, thereby not decreasing their own population, and (3) are healthy, and alive, enough to breed additional predators, increasing their population. So when there are lots of predators you see a big dip in the size of the prey population. You will can make the same types of conclusions when you take the point of view of the prey. When prey is eaten by the predator: (1) they are removed from the population, decreasing population size, (2) are no longer healthy and alive to reproduce, (3) release their food source (if there is one) to increase their population, and (4) by decreasing their population there is that much less food for their predators. These interactions can result in very predictable, natural boom and bust cycles within these populations and is more the focus of today's topic. If you want pictures and graphs then check out the classic lynx-hare relationship and the Lotka-Volterra Model.

A new paper published in Science takes a look at the role of top predators in marine ecosystems. These upper tropic level (UTL) species include seabirds, marine mammals, and large predatory fish. All groups that have been depleted due to human activities. Fisheries impacts cause direct mortality in the targeted species and indirect, often more subtle, mortality lower down in the food chain/web. Fisheries that specifically target lower tropic level (LTL) species (small fish, squid, crustaceans, etc.) threaten those higher tropic level species by directly removing their food sources. However, it can be very challenging to assess the impacts of fishing on food webs, an ecosystem level approach. Think about it: all those predator-prey interactions in the ocean. That's tough. Often what you see is studies, even large ones, taking on a big chunk of the system, modeling how it works based on gathered data, and drawing conclusions or feeding it into an even bigger model. This study in Science specifically looks at seabirds.

Figure 1: A map of the distribution of
seabird and prey species. (click for
larger view)

Seabirds are a good system because they are conspicuous members of the marine ecosystem globally, have been studied and measured for decades, can reflect change at several scales, long-term breeding datasets from several species in several environments exist, and data from systems where prey availability has been measured suggests that seabirds can be used as indicators for forage fish population fluctuations. This study looked at the response between seabird breeding success and forage fish abundance across various species and ecosystems. The modellers compiled 438 data points spanning 15 to 47 colony-years per breeding site, in a total of seven marine ecosystems spanning 19 time series, 14 seabird species and their prey. They crunched a whole lot of numbers, using statistical methods that I'm not going to mention here, to quantify the fluctuations in food abundance and breeding success.

They found something that you usually don't see when you crunch that much data - all their species showed the same response. The results showed that the number of fledglings per breeding pair started to decline and was more variable when their forage fish food source dropped below one third of its maximum observed amount. The prey becomes scarce and as a result the hunting becomes more inefficient. The birds do not have enough food to successfully raise that many young.

Sure, there are the normal high and low cycles that I mentioned at the beginning, and those are natural. However, adding high rates of fishing from humans into it and, as with many other systems, we exacerbate the problem or collapse the system completely. The fish populations never recover from low seabird numbers because predation and habitat destruction by humans still puts a large amount of pressure on the fish, causing chronic food scarcity for the birds. And, as this study shows, this scarcity can have long-term affects on breeding success, can reduce survival in adult birds, and may affect the trajectory of their populations. The thresholds revealed by this study should inform management objectives in balancing predator-prey interactions, a "keep one-third for the birds" approach. If done well, these management decisions can sustain healthy UTL predator populations, maintain LTL fish populations, and could be applied to other marine ecosystems.

Read the paper here:
Philippe M. Cury, et al. (2011) Global seabird response to forage fish depletion -- One-third for the birds. Science: 334(6063), 1703-1706. (DOI: 10.1126/science.1212928)

And a write-up in ScienceNOW called "A Surprising Threshold for Seabird Survival"

Learn more about predator-prey interactions at
University of Michigan's Introduction to Global Change Curriculum's "Trophic Links: Predation and Parasitism"
New England Complex Systems Institute (NECSI)'s Predator-Prey Relationships page
University of Wisconsin-Madison's SSCC page on Predator-Prey Models (Warning: Contains potentially scary math)
A neat demo from Wolfram of a Predator-Prey Model of foxes and rabbits

Also, revisit my post called "To Eat or Not to Eat, That is the Fishy Question" to learn more about how to purchase seafood from green stores or restaurants and guides on choosing the correct seafood.

(image from readysetwhoa.wordpress.com)

To Eat or Not to Eat, That is the Fishy Question

I love seafood as much as the next person...well, ok, probably more. It is a healthy and delicious food source, but there is a limit to the fish in the sea. We tend to think of ocean fish and shellfish as just food on our plates, but they are wildlife. Wildlife that we hunt on a very large scale.

Humans have been fishing the oceans for thousands of years, but within the last half century technology has developed such that we are able to fish farther, deeper, and more efficiently. As such, more than 70 percent of the world's commercial marine fish stocks are either fully exploited, overfished, or have collapsed. Add to that illegal fishing, habitat damage, and bycatch and you have a serious worldwide problem. Over the past few decades aquaculture, or fish farming, has become an increasingly popular solution to the increasing pressures on marine resources. In fact, today, half of our seafood comes from farms. However, the ecological impact of farming depends on the species raised, the farm location, and how the animals are raised. What does that mean? Well, some species are easier to raise than others, some farms are closed-systems where wastes are controlled, some farms have higher escape rates which threaten native species with diseases, and some farms feed a vegetable- or soy-based diet while others feed with wild caught fish.

Alright, well, that's pretty bleak right? So what can you, the single lowly consumer, do about it? Actually, that is pretty simple. Ask questions and watch what you eat. First, there are a few ocean-friendly steps that you can take:

1. Purchase seafood from a green (or if unavailable, yellow list) or look for the Marine Stewardship Council blue eco-label in stores and restaurants. (see below about where to get and how to read seafood guides)

2. When you buy seafood, ask where it comes from and if it is farmed or wild-caught. Most reputable markets will label their fish. However, some stores and restaurants only give generic names and catch locations for their fish. Ask anyway and tell them why you care, it may prompt them to look into it. An alternative is to buy seafood through online retailers, such as EcoFish.com, who feature sustainable species and deliver right to your home.

3. Spread the word. The more people practicing safe seafood the better.

Seafood guides are a free and easy way to help you choose the right seafood. In general, the lists are broken up into three colors:

•  Green (Best) - abundant, well-managed and caught or farmed in environmentally friendly ways.
• Yellow (Good/OK) - an alternative to green but there are mixed records on how they are managed, the health of their habitat, or how they are caught or farmed.
•  Red (Avoid/Worst) - have one or more serious environmental problems such as overfishing, poor management, high bycatch, extensive habitat damage, or come from farms that allow widespread pollution, spread disease, use chemicals, or have a high escape rate.

No matter the country you live in you should be able to find a list that works for you. There are small pocket guides, larger lists, and even easy-to-use online searches. I've listed some great websites below where you can find more information about sustainable seafood and lists to help you choose wisely.

Monterey Bay Aquarium Seafood Watch
This is the best website I have found for information, guides, searches, and links.

Environmental Defense Fund's Seafood Selector
This is a great website that includes a lot of information about each of the species on each of the three lists. They also include great, free, downloadable guides.
Blue Ocean Institute's Seafood Page
This website includes a great FAQ page as well as a seafood and sushi guide.

Natural Resources Defense Council's Sustainable Seafood Guide
This guide delves more into the topic of contaminated seafood but includes a shopping guide, recipes, and health alert information.

Marine Stewardship Council
Find out what MSC products are available in your country. Find out about what it takes to get a product certified and even track a fishery.

Marine Conservation Society - FISHONLINE website
This is for you U.K. folks. You can search for a fish, get fish ratings and lists, get information on fishery/production areas and methods, and download seafood guides.

Australian Marine Conservation Society
This one is for the Aussies. They include all the information you could want about your oceans. There are downloadable seafood guides and also an iPhone app!

WWF Sustainable Seafood Consumer Guides
Not in the U.S., the U.K, or Australia? Not a problem. Check out the World Wildlife Fund's list of worldwide seafood guides. The is a link to your country's web page with link to download a seafood guide PDF. While you are there (no matter your country of origin) check out their information on fisheries and sustainable seafood.

End of the Line
This is the world's first major documentary about the effects of overfishing. It premiered at the Sundance Film Festival this year and is now out on DVD. Go to their website to watch the trailer, find or organize a screening, order a DVD, and/or find links for guides.


(image from envirothink.wordpress.com)

Settling Sediment

I found a nice paper on the coral reef environment in the Caribbean. But first, because I haven't introduced it yet, and so I can refer back to it in the future: Coral. What is it?

Coral is an animal that belongs to the phylum cnidaria (ni dare ee ah, that c is silent folks). This is a very diverse group that consists of jellyfish, corals, and other stingers. These animals sting because they are armed with stinging cells called nematocysts. If you've ever come face to tentacle with a jellyfish then you are aware of their painful potential. There are four major groups of cnideria: Anthozoa (true corals, anemones, sea fans, and sea pens), Cubozoa (box jellies), Hydrozoa (siphonophores, hydroids, fire corals, and medusae), and Scyphozoa (true jellyfish).

We will be concentrating on the first because it includes the corals that build the large reefs found in tropical waters, generally between 30 degrees N and 30 degrees S latitudes. Various types of coral species can be found at various depths, but reef-building corals are usually found at depths of less than 46m (150ft). This a warm depth that allows sunlight to get through to feed their zooxanthellae. Zooxanthellae (zoo zan thell ee) are a type of microscopic algae that have a symbiotic relationship with coral. This shallow water depth also tends to be close to shorelines where wave action is abundant and brings in food to these filter feeders. The temperature and salinity of these waters also allows for the precipitation of calcium which the corals use to build their hard skeletons. Within a skeleton lives an individual coral polyp. A polyp starts off life as a floating animal but when it reaches adulthood it becomes sedentary and its body changes to a tubular saclike shape with a central mouth surrounded by a ring of tentacles. These tentacles are used for defense and for moving food to the mouth, and they contain the nematocysts which are double-walled structures containing a folded, venom-filled thread with a barbed tip that can shoot out and penetrate prey. The wonderful colors of the coral reef come from the natural pigments of the coral tissue or the zooxanthellae. Coral reefs are formed as old coral dies and new coral builds on top of it, a process taking hundreds or thousands of years, and a reef is made up of millions of individual polyps. The corals within this ecosystem remove and recycle carbon dioxide, shelter and provide food for other reef animals, and can even offer some protection to the land.

Humans contribute to the deterioration of coral reefs in a number of ways. Physical damage caused by boats, recreational contact (touching coral kills it, so hands and fins off!), and over-fishing cause a lot of ecological stress to reefs. The runoff of sediments, contaminants and nutrients from agriculture, industry, sewage, and land clearing are also stressful. Additionally, coral bleaching is occurring at a rapid rate. This is when the environmental conditions no longer support the symbiotic relationship of corals with zooxanthellae. No colored zooxanthellae, no colored coral. No symbionts equals coral death.

An older, but still relevant, paper published in the Bulletin of Marine Science reports on a project that monitored the effects of land development on a near-shore reef in St. Thomas, USVI. Land development in the Virgin Islands has rapidly increased, particularly up from the shoreline. This development means the removal of natural vegetation and construction of roads, increasing erosion rates. That means lots more silt and clay that gets into the water. As I mentioned above, sedimentation is very stressful and deleterious to coral. It is just dirt, you may think, so how is that bad? Well, sediments decrease light penetration (which reduces photosynthesis in zooxanthellae and coral growth), settling sediment contributes to tissue loss or mortality (it reduces larval settlement and it literally smothers the coral polyps), it increases coral energy costs (increasing respiration while decreasing photosynthesis), and chronic sedimentation may reduce the abundance and diversity of corals and other reef organisms (increasing susceptibility to diseases, bleaching, and predation and decreasing recovery rates after disturbances). Because of these detrimental effects the Virgin Islands Coastal Zone Management (CZM) has implemented a strict code for developers proposing building projects in sensitive shoreline areas, and academic and government organizations conduct reef assessments to quantify the impact of development on the coral reef environment.

This study's objectives were to measure the rates of sedimentation, monitor water quality, quantify changes in the abundance and diversity of sessile reef organisms, document the acute and chronic effects of sedimentation on coral condition, and develop management guidelines for evaluating the effectiveness of sediment control measures. The conducted their study a fringing coral reef in Caret Bay, on the northwest side of St. Thomas, particularly looking at the Caret Bay Villas construction site in relation to this reef. The conducted a sediment analysis using sediment traps at 5 and 12 meters, calculating sediment load and composition. They also did seawater analysis, collecting water along transects to look for suspended solids and turbidity. They also measured the percent cover of scleractinian (stony) corals, sponges, encrusting gorgonians (sea whips and sea fans), and macro algae. Using quadrants they identified and counted gorgonians and focus monitored individual coral heads of Porites astreoides and Montastrea annularis.

They found that the distribution of fine sediments along the reef were more concentrated in shallow depths, and that coarse sediments were only deposited in traps during months when large ground swells occurred.  The patterns of sedimentation relative to rainfall was related to the progress of the Villas' construction. The percent cover of living coral was found to have declined 14% over 18 months. This large decline may have resulted from dislodgement by large waves in the winter, smothering from sedimentation, or death due to pigment loss. They did document dislodgement but it is unlikely that that this was the sole mortality factor.  The authors also rule out much mortality due to direct smothering since they never actually observed it. They concludef that it is most likely that the majority of the mortality was related to the indirect effects of sedimentation and bleaching. They found strong evidence that the bleaching of corals was strongly correlated to sedimentation rates. So more suspended sediments equals an increased likelihood that corals will bleach. And this is in line with other studies.

This study is nice because it provides direct evidence that sedimentation (in this case from land development) cause stress to corals and may lead to their decline due to bleaching. It also provides good evidence for management practices along sensitive shorelines.

Here's the paper:
Nemeth, Richard S. and Joshua Sladek Nowlis (2001) Monitoring the effects of land development on the near-shore reef environment of St. Thomas, USVI. Bulletin of Marine Science: 69(2), 759-775. (LINK)

If you like this then I also recommend this more recent marine ecology survey:
Pittman, Simon, Ron Kneib, Charles Simenstad, and Ivan Nagelkerken (2011) Seascape ecology: application of landscape ecology to the marine environment. Marine Ecology Progress Series: 427, 187-190. (DOI: 10.3354/meps09139)

And here's some more info on corals:
U.S. Environmental Protection Agency's Page on Coral Reefs
Ocean World's Coral Page
Berkeley's Introduction to Cnideria
SeaWorld's Corals and Coral Reefs Page
Kansas Geological Survey's Biogeoinformatics of Hexacorals

(image from treehugger.com)

Citizen Science. Get Involved.

Citizen science is becoming more and more popular these days. And why shouldn't it? It is an opportunity for volunteers, who may or may not have specific scientific training, to contribute to ongoing scientific research. The volunteer gets the benefit of participating in a task they are interested in and the scientist gets the benefit of many people going through very large amounts of data, allowing them to accomplish their research objectives. It is just a great way to involve the individual as well as promoting public engagement in science.

Citizen science is not a new concept, it has been around for centuries. However, with advances in technology and the rise of the Internet it has become so much easier to get people involved, especially across large geographic areas. And in most cases the human brain is much better at analyzing images and other data than a computer. Add to that the number of replications you can have when multiple people classify the same image and you can see how errors can be decreased and new discoveries made.

So how does this whole thing work and how can you get involved? Well, first, think about a scientific topic that interests you: ornithology, astronomy, climate change, geology...whatever. The scope of science is so big that there is likely a project that fits your interests. Next, you need to find a project. They come in several varieties. First there is the scope: international, national, regional, or local. Next there is the type of activity you want to do: field work, image or data analysis, or just contributing some of your computer's power. And finally, how long do you want to spend working on this: years, months, or hours. That sounds like a lot but once you have figured these parameters out it will make it much easier to find a projects that suits you. Once you have found a project there is typically a short training session to get you familiar with the user interface and how the data should be analyzed/recorded. Then you are all set to do some science!

I've divided some of the most popular citizen science projects down by category, giving a short description of each. Each icon is linked to take you to the project described. At the end I've linked to a couple of general, easily searchable websites that will help you find the project you want.

ASTRONOMY

This is one of the most popular citizen science fields, and the projects that make up the Zooniverse are the most popular of these projects. There are several projects within the Zooniverse to choose from including:

• Ice Hunters
•  Help find the final target of NASA's New Horizons Mission! After passing Pluto (and pending NASA approval of an extended mission, of course) the spacecraft will retarget itself for an encounter with a Kuiper Belt Object (KBO). The target won't be selected until shortly before the Pluto encounter and there will be lots of images to go through to find out where to go next. This is where you come in. Look at pictures of never seen before objects to find out which one we should visit.
• Moon Zoo
• Explore the surface of the Moon! Look through images taken by NASA's Lunar Reconnaissance Orbiter and answer questions about what you see. Identify craters, boulders (called "Boulder Wars," LOL), or any interesting or weird features you come across.
• Galaxy Zoo: Hubble
•  There are hundreds of thousands of galaxies drawn from NASA's Hubble Space Telescope archive. In this project you get to look at the gorgeous imagery from this telescope and classify the galaxies. Are they elliptical, spiral, irregular? Or is there some new type out there waiting to be discovered?
• Galaxy Zoo: Supernovae
•  This project is similar to the project above, this time contributing data from an automatic survey in California, at the world-famous Palomar Observatory. Except here you are looking for supernovae. Exploding stars!
• Galaxy Zoo: Mergers
• Here you are looking for the merging of galaxies. From images you select simulations that look similar to the targeted merger, tuning your best matches. You can even decide which simulation wins in a series of tournament-style competitions.
• Planet Hunters
• Look for extrasolar planets (planets around other stars)! This project finds planets by identifying how the brightness of a star changes over time.
• The Milky Way Project
• This projects aims to sort and measure our galaxy. Using the beautiful infrared data from the Spitzer Space Telescope you are asked to find and draw bubbles. These bubbles identify the life stages of the stars in our Milky Way Galaxy. 
• Old Weather
• This project works to recover worldwide weather observations made by Royal Navy ships around the time of World War I. This will contribute to climate model projections, improve a database of weather extremes, and track past ship movements and the stories of the people on board.
• Solar Stormwatch
• Help spot explosions on the Sun and track them across space to Earth! Not only will you help to identify and classify activity on the Sun but you will also contribute to early warnings if dangerous solar radiation is heading toward astronauts. 

These scientists are seeking to understand a star that has been a mystery for many years. This star is epsilon Aurigae, it is located in the constellation Auriga, and it is a variable star (it changes in brightness over time). This change in brightness is called eclipse. It takes over 600 days, and it only occurs every 27.1 years. The project scientists will guide you through the process of how to observe epsilon Aurigae, how to send them your observations, and then how to see your results, analyze them, and even publish them in a scientific journal.

SETI@home is a scientific experiment that uses Internet-connected computers in the Search for Extraterrestrial Intelligence (SETI). You can participate by running a free program that downloads and analyzes radio telescope data. It is completely safe. All you need to do is download the program and it will run while your computer is on, not disrupting any of your other computing tasks.

CLIMATE SCIENCE

This project works to produce predictions of the Earth's climate up to 2100 and to test the accuracy of climate models. To do this, they need people around the world to give them time on their computers - time when they have their computers switched on, but are not using them to their full capacity. What do you do? Not much really. You to run a climate model on your computer. It runs automatically in the background, not affecting any other tasks for which you use your computer. It is completely safe and requires no more of your time than it takes to download the program. Read more by clicking the image link or go to download the program HERE.

Community Collaborative Rain, Hail and Snow Network (CoCoRaHS) works to measure and map precipitation. Each time a rain, hail or snow storm crosses your area, you take measurements of precipitation from as many locations as possible and report it on the website. These data are compiled and used to provide accurate high-quality precipitation data, increasing the density of precipitation data available throughout the country, and encourage citizens to have fun participating in meteorological science while heightening their awareness about weather.

This project aims to accurately record and analyze "ice on" and "ice off" events as well as snow depth, air temperature, and wildlife observations to learn how climate change affects our environment. You will receive instructions on how to properly IceWatch (even if you live in a warmer climate), you pick your location to observe over the winter (like a nearby lake, bay, or river), record your observations, and submit them online.



GENETICS AND MOLECULAR BIOLOGY

This project is great for gamers!

Genetic sequences are difficult to understand and decipher their structure, and this project aims to compare them to detect any similar regions they may have. So they have put together a website that abstracts the multiple alignment problem to a game where the goal will be to align words made by pieces of different color instead of letters representing the genetic code (A,C,G,T). You create columns of the same color and create gaps, ultimately finding the best tradeoff between aligning color and creating gaps. You can even choose a puzzle to solve from the disease you want to treat.

Another project that is great for gamers. This project is all about protein folding. Proteins are built from individual amino acids but they don't stay all stretched out in a strand, they fold into very specific shapes. Finding the shapes and the optimal folding is the hard part though and is what this project aims to do. Knowing the structures is important to things like drug development and disease research. The problem has been put into game form. You, as the player, solve a series of puzzles to optimally pack you protein, hide the hydrophobic bits, and clear any clashes. You can play individually or form teams, competing with other protein folders around the world.

OCEANOGRAPHY

The whale shark photo-ID library...its cool just saying it. This project uses photographs of the skin patterning behind the gills of each shark and any scars to distinguish between individual animals. This helps scientists to see where individual animals are going, the abundance of whale sharks, and their distribution. If you see a whale shark while out diving you can report all kinds of information about the encounter by filling out their online form, and you can submit pictures to the library.

Do you love whales? All kinds? This project is working to classify the sounds that whales make into distinct regions. "For example, in Orcas (Killer Whales) there are over 150 identified types of call. Every time you match a pair of Orca calls, you're casting a vote for those two calls to be considered 'similar'." The more this is done the better map the researchers get of calls that are alike. This allows them to identify patterns, groups of whales, and eventually get a better understanding of how whales communicate with each other. All you do is look at a spectrogram and listen to a call and then find a matching call. Simple.

This is a project for reporting jellyfish and other marine organisms. If you have seen jellyfish, red tide, or any other unusual marine life you just go online and fill out their form and submit it. They even have a list of similar projects around the world that you can participate in.

FishWatchers is a project out of the International Game Fish Association. This website allows you to  upload your fish observations and photos through the Internet. Any fish any time. This information will then be used to create current distribution maps to assist in monitoring trends in biodiversity

TERRESTRIAL PLANTS AND ANIMALS

This is a great project from a Dutch entomologist that lets motorists report the date, time, and location of their latest outing and the number of insects that get hit (and probably smushed) by their vehicle. Not only does it give an idea about how many bugs are killed by vehicles it provides insect presence in certain locations and information about their flight patterns.

This is a network of people across the United States who monitor plants as the seasons change. It is a national field campaign designed to engage the public in the collection of important ecological data based on the timing of leafing, flowering, and fruiting of plants (plant phenophases). You can send in regular observations or just a single report. Everything is usefull. They provide good identification keys and other tools you will need to start. Not in the U.S.? I'm sure there is is similar project near you.

This is a U.S. based citizen science project that is a national animal and plant phenology observation program. You find out the plants and animals near you on a provided list, learn to select a site and observe and record what is there, and submit your results.

 eBird is a real-time, online checklist program that reports and accesses information about birds. It provides information on bird abundance and distribution at a variety of spatial and temporal scales. It is amassing one of the largest and fastest growing biodiversity data resources in existence. You enter when, where, and how you went birding, fill out a checklist of all the birds seen and heard during the outing, and submit your observations into the eBird database. They even provide tools so you can maintain your personal bird records and even visualize your personal data with interactive maps, graphs, and bar charts.

Neighborhood Nestwatch is a project out of the Smithsonian National Zoological Park and the Smithsonian Migratory Bird Center. The idea is to find and monitor bird nests so scientists can compare how successful nests are in urban, suburban, and rural areas. All you have to do is keep a watchful eye out throughout the year and report your results.

 I know several people that participate in the Christmas Bird Count each year and have a really great time. From December 14 - January 5 volunteers brave the cold weather to do a little bit of bird counting. Anything from feeder-watching to active birding counts. It provides valuable information on migrating birds, bird abundances and distributions, and much more. There are many groups out there too that participate in the count and would love to have another person to help, regardless of your skillset.

 NestWatch, as you might gather from the name, is a nest-monitoring project. It aims to compile large, continent-wide databases tracking survival and reproductive success of a wide range of species and provide a unified nest-monitoring scheme to track reproductive success for all North American breeding birds. You "get certified" (meaning you learn how to properly observe a nest without jeopardizing the nest), look for active nests, monitor the nests and collect data, and enter the data online. The fact that you get to see baby birds should be a big selling point *wink*

The Backyard Bird Count is similar to the Christmas Bird Count in that it is an annual event that provides a real-time snapshot of where the birds are across the North America. The Count occurs from February 17 - February 20 and takes as little as 15 minutes on one day, or you can count for as long as you like each day of the event. When you are finished you enter your results on their webpage.

When it comes to doing science, watching the visitors to your bird feeder sure ain't bad. Project FeederWatch is a winter-long project of birds that visit feeders in backyards, nature centers, community areas, and other locales in North America. By counting birds at your feeder you help scientists to broadscale movements of winter-bird populations and long-term trends in bird distribution and abundance. You count birds at your count site that are there because of something you have provided (plantings, food, or water) and only report the highest number of individuals you see in view at one time, and then you report it online. Simple.

OTHER

 The Quake-Catcher Network (QCN )is a collaborative initiative for developing the world's largest, low-cost strong-motion seismic network by utilizing sensors in and attached to Internet-connected computers. The QCN obtains information about earthquake waves (seismic waves) by using computers that are connected to the Internet. Many laptop computers have built in sensors and desktop computers can utilize small USB sensors to collect the data. The data from these sensors are collected only when the computer is turned on and idle and is sent over the Internet. It is safe and easy. All you need to do is download the program.

 I used to take my ecology lab students out to cemeteries so we could collect data to make life tables. They were always a little squeemish at first but ended up loving the work. The Gravestone Project aims to map the location of a graveyards around the globe and then use marble gravestones in those graveyards to measure the weathering rate of marble at that location. The weathering rates of gravestones are an indication of changes in the acidity of rainfall between locations and over time and could be used as a measure of changes in climate and pollution levels. You go to your local graveyard and take a few measurements such as the lead lettering or headstone thickness.

The bodyLab is a project that researches the evolution of human body shapes and our ideas of attractiveness. All you have to do is go to the website and rate the silhouettes of women and/or men based on if you find that body shape attractive. It is so easy to do you don't even need to create an account.

The Sound Around You is building a sound map of the world as part of a new study into how sounds in our everyday environment make us feel. All you do is use your mobile phones (or another audio recording device if your phone is not compatible) to record 10-15 second clips from different sound environments, or ‘soundscapes’ from a family car journey to a busy shopping center, and to upload them to the virtual map, along with your opinions of them and why you chose to record it.

Dognition is a site that offers dog owners a series of science-based games that determine their dog's unique abilities and their relative strengths and weaknesses in various thinking skills. These skills range from empathy to cunning to memorization. As a user, you enter the results of your dog's behaviors, contributing to a data set that can be used by researchers studying dog cognition. It also offers the owners a "window into [their] dog's mind, offering a first step on the path toward improved behavior." You can tell how your dog sees the world and how they respond in different situations while at the same time contributing to science. Note: As of now this site/service has a fee.

WEBSITES FOR FINDING CITIZEN SCIENCE PROJECTS

This is the best website I have found for finding a project that suits you. It has a great search engine and describes the projects very well. It also includes many local projects as well as great projects for kids.

This site is less detailed and contains fewer projects but is still a good source for citizen science.


(top image from thisgreenblog.com)