A lot of people don't know this about me, but in addition to my computational work I maintain a field research program studying various and sundry aspects of the evolution, ecology, and behavior of coral reef fishes.  As part of this work, I have been doing several weeks’ worth of diving in the southern Caribbean each year for the past six years, mostly in Curaçao.  During this time, I and my fellow researchers have been witness to an amazing and terrible biological invasion: the lionfish.

Lionfish are Scorpaeniforms, and are arguably the prettiest of the bunch.  They have long, beautiful, flowing fins with sharply contrasting patterns of brownish-red and white, and they get to be up to around 18” long.  Those beautiful fins conceal extremely sharp spines that can inject any fish (or person) that is unlucky enough to touch them with a venom that, while not as life-threatening as the venom of many scorpaeniforms, is nonetheless said to be exceedingly painful.  They seem quite keenly aware of their general badassery, too; rather than retreating when a diver approaches, they will spread their fins wide and shimmer their spines in what may be the world’s most intimidating display of jazz hands.

Lionfish are native to the tropical Indo-Pacific, which is thousands of miles away and on the other side of some fairly substantial land masses, so how did this happen?  Although it’s not known exactly when lionfish were first introduced to Caribbean waters, it seems to generally be agreed that it happened no more than two decades ago and was most likely at least partly due to irresponsible aquarists releasing captive fish they no longer wanted.  It’s likely that the original intent was not malicious, but the result has been devastating.  The lionfish is not just any old fish.  It’s a highly efficient and prolific predator, and looks and hunts like nothing else in the Caribbean.  The native fish just don’t seem to have much defense against it, and as a result the lionfish are having a field day.  They’ve spread southward from Florida through the Caribbean, and are now almost everywhere.

When we first dove in Curaçao in 2005, no lionfish had yet been seen there.  The first one we ever saw on a dive was two years ago, and they were something we would see maybe once every three or four dives.  On our trip this past September, however, we saw them on nearly every single dive.  Not just one or two, either – dozens of them!  These guys are under almost every overhang or boulder, just hanging there and eating anything they can get into their mouths.  And that’s one of the most amazing things about lionfish – they are just relentless eating machines.  As someone who spends a lot of time underwater (as much as I can, really), I can attest to the fact that predation in the reef environment is something that you don’t really see that often.  It happens, of course, but you really have to be in the right place at the right time to see it.  With the lionfish, though, we saw them eating native fish all the time.  I’ve been diving for my research for seven years now, but if I were to sit down and count up the number of successful reef fish predation events I’ve seen in the wild, well over half of them would be from the thirty or so dives we did in Curaçao this last September.

Unfortunately, even NOAA officials say there’s not much chance that we’ll ever completely eliminate the lionfish from the Caribbean.  People are trying really hard to respond, however.  In Bonaire, officials lifted a 40-year ban on spearfishing specifically for lionfish.  In the Florida Keys, the REEF foundation has started running “lionfish derbies”, offering substantial cash prizes for people bringing in the most, the largest, or even the smallest lionfish.  And across the Caribbean and elsewhere, there has been a push to get the lionfish recognized as a tasty dinner option.  It’s one thing to find a fish you can eat guilt-free in this day and age when so many species are in trouble.  It’s another thing entirely to find a delicious species that you can actually eat with a nice, satisfying sense of spite.

Pictures from Wikipedia, jason.nocks.com, and ipmsouth.com

Just found some newly available climate layers useful for modeling, thought I'd share in case anyone hasn't seen this yet. This post topic might be expanded when our group gets together and discusses this resource.

Here's the link to the website:  CliMond 

The publication that goes into more detail is: Kriticos, D.J., Webber, B.L., Leriche, A., Ota, N., Macadam, I., Bathols, J. & Scott, J.K. (2012) CliMond: global high resolution historical and future scenario climate surfaces for bioclimatic modelling. Methods in Ecology and Evolution

CliMond is a set of free climate data products consisting of interpolated surfaces at 10' and 30' for recent historical climate and relevant future climate scenarios. The data is available as monthly climate data, 35 Bioclim variables, in CLIMEX format, and as the Köppen-Geiger climate classification scheme. 

Lozier et al. (2009)  do good marketing with this paper, cleverly bringing up a point that has been mentioned by many, but not in such a catchy way.  Here's an excerpt from the paper that sums up the main point as we see it:

What did they do?  They  used "putative sightings and footprints for Sasquatch in western North America" to build a convincing species distribution model, and then compare that model to one constructed for a black bear, concluding that the two models were ecologically similar and that sightings of the Sasquatch (aka bigfoot) must be mistaken identity. Now, our group thought of many confounding factors that could have caused the model of the black bear to be ecologically similar to the Sasquatch model besides mistaken identity, but their overall point, and the reason for the paper, is a good one.

Another way to put this: Garbage in Garbage out.  

So nothing not known by many doing this kind of modeling, or any modeling for that matter. Many of our group thought that the point was so obvious, they were surprised by the acceptance of such a tongue-and-cheek article with that as it's motive. I for one believe that many scientists understand this "garbage in garbage out" idea in theory, but when in comes to number crunching and analysis time, all is fair game and the more data the better regardless of quality.  I applaud the efforts of this group to shed a bright light on the subject. 

I am employed by a natural history museum that prides itself on a high level of quality control in its collection and maintains one of the highest quality fish occurrence databases in the world (www.fishesoftexas.org) in my opinion.  SOOOO much under appreciated effort is put into this and other databases maintained by public institutions, and we still see errors and misuse all the time.  With the advances of information technologies that are permitting digitation of museum and natural history databases, techniques such as species distribution modeling have a bright future.  But inevitably there will be a lot of trash produced along the way.  Hopefully, publications like this one can remind researchers to mind their data, and therefore limit the litter.

The gist is that researchers should carefully consider what kinds of records and databases they use in model construction, taxonomy is slippery and important to validate, exclude questionable specimens or outliars, and call an expert!  

Brackenridge Field Laboratory, 2907 Lake Austin Blvd.

Arrive early for refreshments and kids activities.

Tell your family & friends!

Jacob Soule, Graduate Student in Ecology, Evolution & Behavior at the University of Texas at Austin, will explain the many strange relationships that pollination produces.  

http://scienceunderthestars.org/2012/02/01/february-9-2012-jacob-soule/ 

I love bats and considered studying bat parasites back when I was trying to make up my mind about what to focus on for my dissertation. They are amazing spreaders of mammal pathogens and parasites, things like Nipah, Hendra, rabies, SARS and potentially Ebola. Our own human parasite, the bedbug, Cimex lectularius, is thought to have evolved from bat bugs!

But bats are not all bad from an anthropocentric viewpoint, they also provide important ecological services like pollination and pest control. Plus, I love watching them fly around the steeples in Austin at night and I hear they also fly out from under the Congress bridge, photo from Talke Photography. I'm a bad Austinite, I haven't actually been to see them yet!

Our furry flying friends are in danger! A highly fatal disease known as White Nose Syndrome or WNS is killing them off in droves.  WNS was first discovered in hibernacula in New York state in February 2006. Since that initial finding it has spread more than 2,000 kilometers into western Oklahoma.  A Nature paper published in December 2011 demonstrates that the fungus, Geomyces destructans, causes WNS: http://www.nature.com/nature/journal/v480/n7377/full/nature10590.html

WNS disrupts the hibernation schedule of bats and causes "abnormal arousals." Infected bats will fly at daytime in winter when they should be hibernating and also tend to cluster near the colder front portion of their caves. Many of the bats found with the parasite are emaciated [from using up their winter fat] and have fungal lesions on their muzzles and wings. I, of course, wonder if there is some way that this behavior might be beneficial for parasite dispersal. I don't want to make an adaptationist assumption, the behavioral changes could also just be a terrible side-effect with no fitness benefit for the pathogen. However, the parasite does prefer cold temperatures.

Thus far WNS has killed somewhere around 6.5 million bats and 80-97% of the bats in some caves and mines the northeast. I could ramble on and on about the damning statistics but instead I will present a link for you from USGS about the fungus: http://www.fort.usgs.gov/wns/ and a very well written article found here:  http://www.examiner.com/biology-in-hartford/geomycosis-the-cause-of-white-nose-syndrome-bats 

The big question on my mind is will it spread to Texas and what can we do about it?
The parasite seems to favor hibernating Myotis species as opposed to our migrating Mexican Free-tails, Tadarida brasiliensis. However, Texas is home to 32 species of bats and is located at a central overlapping position of migrating and hibernating species. One concern is that species not prone to infection will still transport the pathogen to susceptible and naive hosts far beyond northeastern North America. My hope is that because it is hot here and our winters are mild we will be spared the bat plague due G. destructans preference for cold temperatures. However, portions of the Panhandle might be at higher risk climatologically because of the colder temperatures experienced there. Colorado is apparently on high alert and has already taken precautionary measures such as closing public caves the year after WNS was found in Oklahoma. Luckily it hasn't spread further than OK since 2010.

So what can we do to minimize risk of spreading the pathogen? First, if you are a spelunker, wash your clothing and gear when caving in different caves. There is some evidence that humans have introduced the pathogen to virgin caves. Also, if you've seen it, report it to USGS National Wildlife Health Center and follow these guidelines: http://www.nwhc.usgs.gov/disease_information/white-nose_syndrome/USGS_NWHC_Bat_WNS_submission_protocol.pdf 

After conducting a Google Scholar search for "Geomyces destructans"/"white nose syndrome" and "ecological niche model"/"species distribution model" I found no hits. Perhaps some SDMs on the parasite's potential distribution are needed? Also, perhaps climate change will actually help our bat species out in Texas!

Author
Stavana Strutz is a doctoral candidate in the Parmesan Lab at the University of Texas studying disease ecology.
 

So the holidays took their toll on us modelers, but we're back in full form and ready to write again.  As a reminder, this slimy segment to the blog is dedicated to our friends under the water.

For this segment, a day late I know, I want to revisit Eels for a cool life history story as well as a prime example of how a life history can potentially throw off how we determine distributions and go about modeling them.  

First, a wiki reference for a description of the American Eel: "The American eel, Anguilla rostrata, is a catadromous fish found on the eastern coast of North America. It has a snake-like body with a small sharp pointed head. It is brown on top and a tan-yellow color on the bottom. It has sharp pointed teeth but no pelvic fins. It is very similar to the European eel, but the two species differ in number of chromosomes and vertebrae."  Here's a pic:

So even thought this critter has been researched to hell, with almost 10,000 publications and studied by Aristotle and Freud, we still know little about it.  And this is due to its crazy life!  The thing is, scientists and anglers never caught baby eels. Not until about 1900 did it come together.

You see, eels spend almost their entire life in freshwater. So it was a big surprise when scientists were raising these tiny transparent 2-inch worm-like things in captivity when they turned into juvenile eels.  At the time, these "glass eels" were considered their own species, Leptocephalus brevirostris.  To this day the larvae are called leptocephalus (should that be italicized when its a Latin common name??).   

So whats the story!  Quote from the interweb: "The eel lives in fresh water and only leaves this habitat to enter the Atlantic ocean for spawning.  The female can lay up to 4 million buoyant eggs, but dies after egg-laying. It takes 9 to 10 weeks for the eggs to hatch. After hatching, young eels move toward North America and enter freshwater systems to mature."

So that states it mildly.  These fish swim from sometimes hundreds of miles inland, to the middle of the Atlantic ocean, the Sargasso sea, breed and then die (much like Salmon but the opposite, sort of). The larvae hatch, then being 2-3 inches, swim back to land and up streams, growing into juveniles by the time they reach adulthood.   

There's much more to this eel story, they're economically important and threatened from dams and overfishing, but the main reason for this post is to bring up the point of the importance of life history when understanding distributions.  Just because habitat might be marginal to one life stage, doesn't mean another stage doesn't completely rely on it for various reasons. My research right now is being complicated with decisions on ecologically relevant thresholds, so the perspective of habitat utilization among and between life stages is important.

Ben Labay is a "fish-geek" and research associate for the Texas Natural History Collections at UT Austin

See his fish art at: www.inkedanimal.com

So I've built ecological niche models and then species distribution models for the past 3 years preferentially using Maxent. I chose Maxent based on Elith's 2006 Ecography review paper of the different statistical software programs available. Recently, I felt I was becoming too reliant on Maxent and decided to reevaluate the ecological theory behind my modeling choices. This is one of many reasons why I started our species distribution modeling reading group at UT along with Dan Warren. Additionally, the SDM literature is overwhelming in size! it's nice to have a forum to meet and discuss relevant papers we stumble across. There is no way to read every SDM paper published...there are just too many these days!

As a graduate student I've completed all the classes I need for my PhD but I'm a sucker for interesting classes where I think I'll learn new and applicable information. I also hate paying tuition money to sign up for research hours when I'm going to do the research anyway! So this spring semester I signed up for a graduate level course on ecological modeling with a focus on species distribution modeling offered by our geography department. The course is being taught by Dr. Jennifer Miller whose PhD advisor was Dr. Janet Franklin. The course is much more theory focused but also has some fun activities. I'm just happy to have another place where I can talk about SDM!

One of the activities of the class is a SDM competition to see who can build the best model. I don't know if the data we will be given is going to be simulated or real...but I do wonder how it will be evaluated. So one of my goals on this blog is to keep y'all updated on the competition and my different ideas for how to best model the species occurrence data I will eventually receive.

Author

Stavana Strutz is a doctoral candidate studying disease ecology in the Parmesan lab at UT Austin. 

This is a combination Fish Friday and Parasaturday post. Basically, I was looking up recent news of parasites and this little gem popped up in the San Marcos Mercury:
http://smmercury.com/53183/invasive-snail-parasite-threaten-central-texas-fish-stocks/ 

An invasive snail species, Melanoides tuberculatus, from Asia is invading central Texas waterways. The species was originally adapted to warmer temperature water (above 64 degrees Fahrenheit) which had constrained its ability to spread from warm springs at the head of the Comal River to other cooler surface waters. Alas, as evolution would have it, or fortunately from the snail's point of view, the snail began to adapt to its new climate.

"In 2009, Huffman began finding snails thriving in the much colder waters of the Guadalupe River, and by 2011 they’d moved upstream as far as Gruene Crossing and downstream through Lake Dunlap and as far as one mile into Lake McQueeny. In January 2012, Huffman found hundreds of snails seemingly thriving near Dunlap Dam in water that had been between 11-13°C (51-55°F) for weeks—temperatures that should’ve killed the snails within two or three days."

I find this next part the most interesting though:
 "Because of the continuous, wild temperature swings at the confluence of the Comal and Guadalupe rivers in New Braunfels, Huffman predicted as far back as 2000 that if the snail were to ever make an evolutionary adaptation to colder temperatures, that’s where it would happen—and that prediction now seems to have been borne out." 

I also wonder how much the mild winter, hotter temperatures and drought has contributed to the invasive expansion of this snail. Shallower streams caused by drought would most likely be warmer as well, right? Huffman goes on to say that there aren't as many mature fish appearing in the Comal anymore, he attributes this to the trematode parasite carried by the snail which he doesn't name but I'm assuming is Centrocestus formosanus based on another paper he published, "Egg predation and parasite prevalence in the invasive freshwater snail, Melanoides tuberculata (Müller, 1774) in a west Texas spring system":
http://www.aquaticinvasions.net/2011/ACCEPTED/AI_2011_accepted_Ladd_Rogowski_correctedproof.pdf

The parasite actually damages the host's fitness in the following way:"Because the flatworm encysts on the gills of fish, it interferes with the fish’s ability to oxygenate the blood. With enough parasites, the effect would be like a person trying to run a race during an asthma attack. For fish, such infections would make them slow and sluggish, easy picking for predators long before the parasites killed them outright." 

The parasite has been found in west Texas springs but I don't see any evidence that is in central Texas from this paper or news article. Readers, is this parasite in our region? 

Does anyone want to build an SDM for this invasive species and its parasite, wink, wink, nudge, nudge? It could be fun!

Author

Stavana Strutz is a doctoral candidate studying disease ecology in the Parmesan lab at UT Austin.

This is going to be a fairly short reading group post compared to the previous few, as I'm rushing to get a bunch of things together before I head out of town for the holidays.

Anyway, the paper we read last week is a new one in GEB by Pagel and Schurr, entitled "Forecasting species ranges by statistical estimation of ecological niches and spatial population dynamics".  In the paper, the authors develop a Markov chain Monte Carlo approach to estimating a hierarchical Bayesian model from distributional data.  The modeling process is very interesting, as it involves the combined estimation of a niche model, a population dynamics model (including dispersal), and a model of observer behavior (the "virtual ecologist").  The authors demonstrate the value of their approach using simulated data sets of different levels of detail and quality.

The paper is fairly dense, but in my opinion the method demonstrates great potential.  It appears to deal fairly well with a lot of issues that are generally problematic for ENM/SDM methods, such as dispersal, species whose distributions are out of equilibrium with the environment, and stochastic population processes on a local scale.  The simulations show the dynamic range model beating the pants off of a more traditional SDM method in most cases.

However, it's not all sunshine and roses.  As far as I can ascertain, there's no readily available package or R code that makes the analysis available to the general public - you'll either have to program it yourself or bash something together in BUGS.  It also seems to be fairly computationally intensive, although for those of us with cluster access that's not a big concern.  More important than either of these issues, though, is that the method doesn't seem to work (or at least was not demonstrated to work) with presence-only data.  That's a shame, as that is by far the most plentiful type of data we have available to us.  

In summary, the method is very promising but it may be a while before there's an application that is ready for most end-users.  I'm all for the idea of a Bayesian MCMC approach to estimating ENMs/SDMs, as I think the level of information about uncertainty that these methods can produce would be a great step forward for the field in general.  I'm excited to see where this research program goes.

Luckily, these biologically iced sugar cookies were not cookies of death. I baked these for my preliminary examinations in the Ecology, Evolution, and Behavior PhD program at the University of Texas. Of course, had I not passed...they might have been. I kid, I kid!

Like all cookies, these cookies underwent a baking metamorphosis. These cookies were once a much more delicious product: dough. Eating raw dough is my favorite part of cookie consumption! However, raw dough also poses one of the greatest risks to one's health when it comes to the entire process of cookie production/gourmandization besides exploded stomachs. Raw dough has raw eggs and these raw eggs sometimes have parasites that can kill you.

I'm a bit of a germaphobe but I like to tell myself that probabilistically there isn't that great of a chance of me contracting a horrible disease from dough because a) there is a low prevalence of germy eggs and b) my immune system could eradicate the pathogens. This post aims to investigate the first of these two justifications.

If you’re like me, you’ve no doubt been warned to not eat raw dough but then ignored the advice. There are several different salmonella species and they infect various animals such as cattle, chickens, amphibians and occasionally people. The species, subspecies and serotype we are interested in is Salmonella enterica enterica enteritidis or S. enteritidis (a discussion of the complication and controversies surrounding taxonomic classification of pathogens will undoubtedly ensue at a later date).  Before the 1970s most cases came from feces on the egg shell surface but now egg shells are sanitized. In the 1980s a new strain appeared that actually infects the ovaries of the hens and is passed down vertically within the egg itself. This is the strain we are worried about.

Most of the publications I found on the topic of S. enteritidis prevalence were from the 1990s. In the northeastern region of the United States, 45% of hen houses were contaminated with S. enteritidis while central and southeastern regions were lower, 17% and 3% contamination respectively.  This information made me feel a little better about my raw egg eating ways since the south has a lower prevalence rate but I was still concerned. The sampling was done on the ceca and not the ovaries. Would this detection method be sensitive enough to detect infection inside the eggs? I also found out that salmonella of some type was detected in 80% of egg-laying houses.  So then of course, I wondered if competitive exclusion took place between the different salmonella species and if infection with “good” salmonella prevented infection with “bad” types. (Ebel et al. 1992)

Hogue et al. also found the northern region of the US to have the highest prevalence of S. enteritidis in unpasteurized egg product and slaughtered hens, 40%. Other regions ranged between 10-12% (Hogue et al. 1997).  Another paper, however, only detected S. enteritidis in 1 out of 42 flocks from the southeast and Pennsylvania when sampling directly from ovaries, a 2.4% prevalence rate (Barnhart et al. 1991).  Aha, I thought, here is my vindication finally!   

And because this is a blog post and not a research paper, I’m going to wrap up the post now. Basically, it seems like if you live in the northern region of the United States, don’t eat raw eggs.  Nearly half the flocks/hen houses are contaminated with pathogenic salmonella. Other areas face a risk but depending on the sampling method, the prevalence will vary.  The real question is what prevalence rate are YOU willing to risk eating cookie dough for? Is 17% too high? Is 2.4% too high? And remember, these studies are dated, what is the actual prevalence now? I would also say that if you are immunocompromised or a young child you should definitely not eat raw dough. I don’t have an answer yet as to whether this information will change my behavior, most likely it will not. Maybe if I move to the east coast it will.

So as the holiday season reaches its apex, remember that not only must you beware of cookie dough but also beware of homemade egg nog, sunny side up eggs, bean sprouts, and frogs. Nothing says Christmas like a holiday tree frog. And apparently, even if your eggs are pasteurized and you buy dough from the store, you may still get sick…from E. coli contaminated flour! (http://well.blogs.nytimes.com/2011/12/12/beware-of-raw-cookie-dough/) 

Here is a great link from the CDC on how to reduce your exposure to salmonella: http://www.cdc.gov/Features/VitalSigns/FoodSafety/ 

Barnhart, H.M., Dreesen, D.W., Bastien, R. & Pancorbo, O.C. (1991). Prevalence of Salmonella enteritidis and other serovars in ovaries of layer hens at time of slaughter. Journal of food protection, 54, 488-491.

Ebel, E.D., David, M.J. & Mason, J. (1992). Occurrence of Salmonella enteritidis in the U.S. Commercial Egg Industry: Report on a National Spent Hen Survey. Avian Diseases, 36, 646-654.

Hogue, A.T., Ebel, E.D., Thomas, L.A., Schlosser, W., Bufano, N. & Ferris, K. (1997). Surveys of Salmonella enteritidis in unpasteurized liquid egg and spent hens at slaughter. Journal of food protection, 60, 1194-1200.
   

Author

Stavana Strutz is a doctoral candidate studying disease ecology in the Parmesan lab at UT Austin.