World of Crayfish™ database and website

World of Crayfish™ is an ambitious new website that shows the geographic distribution of crayfish species in near real-time.

Of course, I checked for whether there was a Marmorkrebs map. There is! Click to enlarge!

 

It’s clearly out of date in some ways. I expected to see records from Madagascar, as several localities published in peer-reviewed journals have been available for some time. On the other hand, there seem to be new records that I have not found yet, like in southern France.

Nevertheless, this seems like a much more organized effort that might eventually supplant my own map of Marmorkrebs introductions.

External link

https://world.crayfish.ro

Reference

Ion MC, Bloomer CC, Bărăscu TI, Oficialdegui FJ, Shoobs NF, Williams BW, Scheers K, Clavero M, Grandjean F, Collas M, Baudry T, Loughman Z, Wright JJ, Ruokonen TJ, Chucholl C, Guareschi S, Koese B, Banyai ZM, Hodson J, Hurt M, Kaldre K, Lipták B, Fetzner JW, Cancellario T, Weiperth A, Birzaks Jn, Trichkova T, Todorov M, Balalaikins M, Griffin B, Petko ON, Acevedo-Alonso A, D’Elía G, Śliwińska K, Alekhnovich A, Choong H, South J, Whiterod N, Zorić K, Haase P, Soto I, Brady DJ, Haubrock PJ, Torres PJ, Şadrin D, Vlach P, Kaya C, Woo Jung S, Kim J-Y, Vermeersch XHC, Bonk M, Guiaşu R, Harlioğlu MM, Devlin J, Kurtul I, Błońska D, Boets P, Masigol H, Cabe PR, Jussila J, Vrålstad T, Beresford DV, Reid SM, Patoka J, Strand DA, Tarkan AS, Steen F, Abeel T, Harwood M, Auer S, Kelly S, Giantsis IA, Maciaszek R, Alvanou MV, Aksu Ö, Hayes DM, Kawai T, Tricarico E, Chakandinakira A, Barnett ZC, Kudor ŞG, Beda AE, Vîlcea L, Mizeranschi AE, Neagul M, Licz A, Cotoarbă AD, Petrusek A, Kouba A, Taylor CA, Pârvulescu L. 2024. World of Crayfish™: A web platform towards real-time global mapping of freshwater crayfish and their pathogens. PeerJ 12: e18229. https://doi.org/10.7717/peerj.18229

Global Register of Introduced and Invasive Species

Pagad and colleagues (2018) have a new paper about the Global Register of Introduced and Invasive Species. Naturally, I went looking for Marmorkrebs.

The first interesting thing is that Marmorkrebs appeared in the database with four different species name variations:

• Procambarus fallax (incomplete)
• Procambarus fallax f virginalis (missing period)
• Procambarus fallax f. virginalis (correct)
  
• Procambarus fallaxformvirginalis (even if spaces were added, would be wrong: “form” should be “forma”)
  

You can’t search for common names, for the looks of things, just Latin ones. We will have to wait and see whether the proposal to change the name of Marmorkrebs to Procambarus virginalis will reduce the number of variations in lists like these, or just be one more variant to search for.

The second interesting thing is that are only four countries on the list: Germany, Sweden, Croatia, Ukraine. The map of Marmorkrebs introductions that I curate has six more: Madagascar, Japan, Italy, Hungary, the Czech Republic, Slovakia, and the Netherlands. It will be interesting to check in from time to time to see how long it takes for this to be updated.

References

Pagad S, Genovesi P, Carnevali L, Schigel D, McGeoch MA. Introducing the Global Register of Introduced and Invasive Species. Scientific Data

External links

Global Register of Introduced and Invasive Species 5: 170202. https://doi.org/10.1038/sdata.2017.202

The CABI datasheet

The Centre for Agriculture and Biosciences International (CABI) Invasive Species Compendium has “datasheets, maps, images, abstracts and full text on invasive species of the world.”

Their page on Marmorkrebs is generally very thorough!

Their distribution map seems a little out of date, and has a couple of oddities. For instance, there is one dot right in the middle of the continental United States (roughly in Kansas or Nebraska). This is supposed to represent that Marmorkrebs are available in the pet trade throughout the country, and cite Faulkes (2010) as a resource. Strangely, that paper also found Marmorkrebs for sale as pets in Canada... but there is no dot on the map for Canada.

External links

Invasive Species Compendium - Procambarus fallax f. virginalis (Marmorkrebs)

Might we finally get a crayfish genome?

I just learned of a new project, Arthropods Genomes, which aims to sequence 5,000 arthropod genomes. The project wiki is here, which includes a form to suggest species to include for sequencing.

No need to rush. I suggested Marmorkrebs for sequencing before I started writing this post.

This should be no surprise, given that a crayfish genome is something I’ve been asking for for years. Indeed, every time someone mentions how bored they are with yet another genome being sequenced, or how hard it is for the poor genome researchers who are drowning in so much data, it’s become a running joke for me to say, “Yeah, yeah... So where’s my frickin’ crayfish genome‽”

As of this writing, four decapod species are in the draft list. The Lousisiana red swamp crayfish, Procambarus clarkii, is on the draft list of species. This is a good choice, as we know more about its biology than probably any other crayfish.

I hope this pans out.

Related posts

Olivia’s fantasy genomes
Genome research: Good idea, bad idea
The first crustacean genome

Hat tip to Ed Yong and Alex Wild.

Timeline

When I wrote my post on the Scientific American Guest Blog, “The decade the clones came,” I was sort of fumbling around for something like this without quite realizing it:

Marmorkrebs on Dipity.

Like the Google Earth map of Marmorkrebs introductions, this will be an ongoing project. I will update it as news becomes available. I’m also still tinkering with what level of detail to provide. Currently, I don’t think it needs to contain every research paper or blog post or tweet or YouTube video featuring Marmorkrebs. But maybe with a little tweaking, it can include those without loosing the “main events” that I’d like to emphasize.

If you have suggestions, let me know!

This Dipity timeline was inspired by Ed Yong’s stem cell research timeline, who was in turn inspired by John Rennie. If anyone out there would like to pay me, sorry. It’s all about the science, not the money.

Texas crayfish distribution

For a project I was working on, I had reason to compile the county records of crayfish contained in the very good and useful book Texas Crawdads (self-published, but still available for purchase online). The book shows a map with all the Texas counties that have crayfish, but I wanted to see the biodiversity “hotspots.” Because the book has county maps for most of the species, I was able to extract the information from them and compile it into a quick and dirty choropleth map:

The spreadsheet with all the data is available here: https://spreadsheets.google.com/ccc?key=0ApOCD9JZBwq0dGx1T3NfTFRIa05wUnBZMmxyM3k5Y0E&hl=en

The county with the most species, Brazoria, has ten different crayfish species. Van Zandt county (the one white patch in the north east) is shown in a summary map as having a crayfish record, but none of the genus or species maps show anything there.

This map underestimates the number of crayfish species in some counties, particularly in North and West Texas. There are seven (out of 39) species that the authors don’t give county maps for, though where they do mention specific counties in the text, I put that in my spreadsheet).

In particular, there are two very wide-ranging gray crayfish, Procambarus curdi and P. simulans, that didn’t warrant their own county maps, just a combined map with a third species (which did get its own separate map). P. simulans is described as having the widest distribution, so every county that is shown in Texas Crawdads as having “grays” with is assumed to have P. simulans. Those entries are marked with an asterisk.

What does this have to do with Marmorkrebs? It’s sort of related to a paper that’s in press right now about potential distribution of Marmorkrebs in the United States and elsewhere. But mainly, I just wanted to share the compilation in case someone else finds it useful.

References

Johnson SK, Johnson NK. 2008. Texas Crawdads. Crawdad Club Designs, College Station, Texas. http://www.texascrawdads.com

Johnson SK, Johnson NK. 2009. Texas Crawdads Supplement. http://texascrawdads.com/yahoo_site_admin/assets/docs/2009_Texas_Crawdads_Supplement.73195937.pdf

A new garden for research

You’ve heard of evo-devo? Passé. The new thing is evo-devo-eco.

Cassandra Extavour has started a project for people interested in the interface of these three disciplines. It’s the Evo-Devo-Eco Network, naturally. Or, if you prefer, EDEN.

Ah, we scientists do love our acronyms.

This network would seem to be one of interest to the Marmorkrebs community, given that some of main prongs of research around the species revolve around the three prongs of evolution (“How did Marmorkrebs originate?”), development (“How much developmental variation can you have?”), and ecology (“How are these going to affect indigenous species as Marmorkrebs are introduced around the world?”).

I’ve joined the EDEN network, and you can see the lab profile here. And, if there are any undergraduates interested in this, note that while I put that I am not seeking undergraduates does not mean an automatic “No.” It’s just that I’m at a large undergraduate university, and I usually enough students from my home institution to look after. But don’t let that deter you. Let’s talk.

Hat tip to Steffen Harzsch for bringing this to my attention.

North American crayfish diversity threatened

When I recently attended the International Association of Astacology meeting, it was ground into my face how bad things are for crayfish.

In Europe, crayfish are being beaten up by exotic North American species. If competition doesn’t get them, the crayfish plague that the exotics carry will.

In North America, the home to the greatest diversity of crayfish species in the world, non-indigenous species are playing a role in some regions, but habitat degradation is the bigger concern. At the Astacology meeting, we were treated to scenes like this:

Mountains are being flattened to remove coal.

Strangely, the same factors that lead to the wonderful high diversity of North American crayfish are the same factors that make them vulnerable, mainly geographic isolation. Because crayfish need to stay wet, and are not terribly mobile, they often don’t disperse very well on their own. Consequently, many species have a limited range, often falling within a few locations in a single American state.

Taylor and colleagues provide a summary of just how bad things are in North America. The take home message that every crayfish biologist and every crayfish pet owner should have burned into their brain is this:

Almost half of North American crayfish species are under threat.

I don’t use the phrase “under threat” in any sort of technical way, but just indicating some sort of conservation concern.

On a per species basis, crayfish are the second third most threatened kind of animal in North America, behind freshwater mussels and snails, which obviously have many of the same issues as crayfish: small geographic ranges, limited mobility (though crayfish are more mobile than snails and mussels), vulnerable to competition and habitat degradation.

Taylor and colleagues provide other useful information, including a list of all known species and a standard common name. The article is rather nicely illustrated with a few crayfish pictures, too (not for every species, however).

All of this makes the prospect of Marmorkrebs being introduced into North American waters a veritable nightmare scenario. Competition between Marmorkrebs and a local species could be enough to push a species into extinction.

Reference

Taylor, C., Schuster, G., Cooper, J., DiStefano, R., Eversole, A., Hamr, P., Hobbs, III, H., Robison, H., Skelton, C., & Thoma, R. (2007). A Reassessment of the Conservation Status of Crayfishes of the United States and Canada after 10+ Years of Increased Awareness Fisheries 32(8): 372-389. DOI: 10.1577/1548-8446(2007)32[372:AROTCS]2.0.CO;2

Photo by ddimick on Flickr. Used under a Creative Commons license.

Olivia’s fantasy genomes

The always articulate Olivia Judson looks at genome projects in her recent New York Times column, and asks what organisms should be on the list to have their genome sequenced. She makes a persuasive case for the famous “living fossil,” the deep sea coelacanth.

The reader comments contain many good nominees (whales, naked mole rats, potato blight, and more), but I’m afraid I was not selfless. I wrote in the comments:

Coelacanth is an excellent choice. It could be difficult to get enough tissue, given that they are such elusive creatures.

I want to argue for a crayfish genome.

Crayfish (and their relatives, lobsters and other decapod crustaceans) are commercially important. They are harvested for food and cause ecological and economic damages as invasive species to name just two reasons.

Crayfish are important model organisms for research, particularly neurobiology. Discoveries made in crayfish include electrical synapses, presynaptic inhibition, and neuromodulation of aggression.

Crayfish are the current record holder for highest number of chromosomes in an animal (Pacifastacus leniusculus: 2n=376).

There is only one crustacean genome (a small freshwater one, Daphnia pulex). In comparison, about a dozen insect genomes are complete and more are on the way.

Probably the best choice of species would be Louisiana red swamp crayfish (Procambarus clarkii), because it is common, spread across the globe, and well studied.

The mysterious crayfish Marmorkrebs could be an interesting second choice, because their origins are unknown, and they are the only known decapod crustacean where all the individuals are female.

Map of the world

View Marmorkrebs introductions in a larger map.

The main Marmorkrebs.org page lists an in-press paper describing a case of Marmorkrebs being found in a natural ecosystem. I’ve mentioned Madagascar before, and now Italy has been added to the list. The Italy article hasn't been posted in the blog yet, because I like to include articles here only once they have final pagination and so on.

It seems reasonable to expect more such reports in the future. I’ve created a Google map to start documenting where Marmorkrebs are reported. I will update it as often as I get information.

23 Squidoo

Marmorkrebs are now featured on a Squidoo lens and The Aquarium Wiki.

I find it fascinating how the picture I uploaded for Wikipedia makes its way elsewhere around the web.

The new phonebook is here!

This blog is now listed in the Nature.com blog list. Right below the more imaginatively named, "Monday Begins on Saturday" (a sentiment I fully appreciate, by the way).

I know blogging about being listed in a directory is a bit like Steve Martin's joy over the new phonebook in The Jerk (below), but this is about as close as I'll probably ever get to having something in Nature, so I shall enjoy it.

Glorious movies of zebrafish development

This week, Science published an article about zebrafish development. The article, however, does not do justice to the joyous, glorious movies that it is about. Single frames don't do -- you really have to see these things in motion.

Check it out here. I think many people will find them fascinating, even non-biologists. The early stages show near-simultaneous cell divisions making the embryo pulse, while the later stages show cells rolling around the embryo like fireworks obeying some strange alternate laws of gravity.

Since zebrafish represent the kind of work that Marmorkrebs are very good for -- development -- the natural question to ask is, can similar approaches be applied to Marmorkrebs eggs? Hard to say. Zebrafish embryos are quite transparent, whereas Marmorkrebs embryos are more yolky and therefore opaque. But many things are possible, and this technology might be able to visualize at least parts of what's going on.

The follow-up question might be, "Can I play with those great toys?" The "toys" in this case is their modified confocal microscope that made this possible. Alas, not possible for me, since the team hails from Germany.

Wiring the -ome

NeuronBank is a project I have been offering moral support to, mainly in the form of links here and there around the Marmorkrebs websites I run. The goal of NeuronBank is to compile the "neurome" for organisms, mainly invertebrates.

Most people are familiar with the concept of a genome: the sum total of all the genes in an organism. Since the success of the Human Genome Project, other "-ome" projects have been slowly creeping into scientific awareness. Arguably proteomics is one of the most common new -omes in the scientific news. Neuromes -- a description of all neurons in an animal -- are not in that league yet, but that may start to change.

A forthcoming new review by Lichtman and Sanes in Current Opinion in Neurobiology goes one step further, discussing not only neuromes, but connectomes: a description of not only all the neurons in a nervous system, but their anatomical and physiological connections, too.

If that sounds difficult, it is, but it's already been done in one animal: the little nematode worm C. elegans. The C. elegans project is discussed in some detail -- which it has to be, seeing how it's the only animal in the connections between all 302 neurons in the wild-type animal has been described.

While there is no complete neurome or connectome for a crustacean, there are neuromes and connectomes for parts of crustacean nervous systems. The stomatogastric ganglion in several species has about 30 neurons, and all the neurons and all the connections in the stomatogastric ganglion are known for some crabs and lobsters, thanks largely to work in Allen Selverston's lab. This has led to a massive amount of research on the stomatogastric ganglion. Literally entire books have been written on the subject (Harris-Warrick, 1992; a PDF of the first chapter is available here).

The crustacean cardiac ganglion, which usually has 9 neurons, may also have a complete circuit worked out for it, though I have been unable to confirm this in writing this post. In any case, it is well characterized (Cook, 2002).

But are other parts of the crustacean nervous system amenable to compiling a even a partial neurome, never mind a connectome? I think so, and suggest crayfish abdominal ganglia are ripe for creating a neurome.

The tail of a crayfish contains six clusters of nerve cells (a.k.a. ganglia). The first five from the front are very similar, and only the very last one, the terminal abdominal ganglion, is substantially different than the others. The abdominal ganglia of crayfish are widely used for electrophysiology, because the dissection is very simple. Wine (1984) estimated that there are about 650 neurons in each of the first five abdominal ganglia.

650 is not that big a number of neurons. And a reasonable number of them are already described. Given a few dedicated labs, creating a neurome for these ganglia seems at least feasible.

In one of my earliest posts on this blog: Every major model organism has earned that rank on the back of a massive descriptive project. I've already said there should be a crayfish genome project; a crayfish neurome project should be in the works, too.

References

Cooke IM. 2002. Reliable, responsive pacemaking and pattern generation with minimal cell numbers: the crustacean cardiac ganglion. The Biological Bulletin 202: 108-136. http://www.biolbull.org/cgi/content/full/202/2/108

Harris-Warrick RM, Marder E, Selverston AI, Moulins M (eds.). 1992. Dynamic Biological Networks: The Stomatogastric Nervous System. Cambridge: MIT Press.

Lichtman JW & Sanes JR. 2008. Ome sweet ome: what can the genome tell us about the connectome? Current Opinion in Neurobiology: In press. http://dx.doi.org/10.1016/j.conb.2008.08.010

Wine JJ. 1984. The structural basis of an innate behavioural pattern. The Journal of Experimental Biology 112: 283-319. http://jeb.biologists.org/cgi/content/abstract/112/1/283

Who's talking about Marmorkrebs

It's amazing what you can learn just by using a new search engine.

I was trying out the interesting new search engine Addictomatic, and naturally, typed in "Marmorkrebs." I'll have more posts on what I found later, but I thought I would start with this little YouTube gem...

Making something great

There's a thoughtful post on the Encyclopedia of Life (EOL) blog about the difficulties in creating an ambitious project like EOL.

Now that EOL is live and people have had a chance to look around, it is striking that 76% percent of visitors don’t return, and 44% of all visitors left in under 10 seconds. After the initial launch where, if anything, EOL was too popular, interest seems to have dropped off markedly. One possible reason for this is the relative lack of content. As I noted elsewhere, for many pages EOL compares unfavourably with other sites(.)

The blog mentions an interesting project called iSpecies. It's a sort of species-based multi-search. Luckily, it work from common names as well as scientific names. For Marmorkrebs, it brings up the English Wikipedia article (no surprise), but also several pictures.

ZipcodeZoo also looks interesting, although it's highly geared towards plants and vertebrates. But then, its target is naturalists, not scientists.

So despite the current content problems, Encyclopedia of Life still looks to have the best shot at becoming the point of call for scientists looking for research information on a species.

But I digress. The EOL project is struggling with high expectations and the curse of the internet age: impatience. People want a lot done instantly. I have to wonder if the prospect of spending years to make even a small dent in the problem of generating even a fraction of webpages needed could mortally wound the EOL venture. I think researchers need to see progress before they're willing to come on board in a significant way.

In many ways, the problems of the highly visible EOL project are much like those facing the fledgling Marmorkrebs community. With this website, I am deliberately trying to raise expectations about Marmorkrebs as a model organism. But if progress is too slow, people feel their expectations are not met and lose interest. It's a fine line to walk.

What's in a name?

One of the many ways in which Marmorkrebs is an oddity is that it's extremely unusual for an organism to be the subject of multiple scholarly research papers... but have no name. It's even more unusual that nobody, as far as I know, is in any sort of hurry to give Marmorkrebs a proper scientific name.

Scientific names for organisms are also known as Latin names. Carl Linnaeus (pictured) started the naming scheme used in biology to today, with a few modifications. At the time, Latin was still a fairly dominant language of scholarship. So Linnaeus gave plants, and later animals, names in Latin. I think names based on Greek are also acceptable.

Today, for animals, the rules for names are handled by the International Commission on Zoological Nomenclature (ICZN). There are similar but separate organizations for plants and microbes and, I believe, fossils.

I'm going to do my best to summarize other people's arguments about giving Marmorkrebs a scientific name. (Some of these are based on half-remembered conversational snippets from conferences, so forgive me if I make errors.)

Marmorkrebs seems to belong in the genus Procambarus. The major crayfish taxonomist who described many of the members of this genus was a man with the wonderfully alliterative name of Horton H. Hobbs, Jr.. He based many of his species descriptions on the basis of the male sex organs... which Marmorkrebs, being all females, do not have.

The next plan of attack might be to use genetics. But there really isn't a lot of precedent for describing species on the basis of genes alone. I am not sure whether the ICZN code allows it. Regardless of whether it is permissible, there are strongly established traditions in taxonomy, and formal species descriptions are supposed to have detailed morphological descriptions, designate a type specimen for safekeeping in a museum, and so on.

And as you consider the problem of whether to give Marmorkrebs a scientific name, it leads to a very core question: What is a species? This is a question that has resulted in a lot of ink being spilled in scientific papers, and simply put, there is no consensus on how to define a species.

Based on some comments Keith Crandall has made, Marmorkrebs are genetically extremely similar Procambarus alleni... so following some species concepts that revolve around morphological separation, this might qualify as putting Marmorkrebs in with P. alleni.

But because Marmorkrebs reproduce asexually, they do not interbreed with sexual species... so following species concepts that revolve around interbreeding, this would suggest that Marmorkrebs should get its own species name.

As the preface to the latest edition of the code of zoological nomenclature notes:

One should always keep in mind that an important function of classifications is information retrieval.

So maybe it's not really critical to have a scientific Latin name immediately in these days of search engines and databases... but what is definitely important is to have a consistent name, one that can be found in databases.

For obvious reasons, I suggest "Marmorkrebs" be that name for use in titles and keywords.

A victim of its own success

The Encyclopedia of Life page, as I expected, was under huge server load yesterday. The webmasters have gone back to its old preview pages rather than its more advanced first release that I posted about yesterday.

Hopefully, it will be back soon so that we can really start to see what the website can do.

Encyclopedia of Life

The Encyclopedia of Life has finally moved past the preview stage.

It’s been very slow today, the server no doubt reeling under the load of people who have been eagerly awaiting it. But it’s a treat if you can get to it.

This particular database sprang from a TED prize for biologist E.O. Wilson, shown below.



This kind of project has been on the minds of a lot of people for a long time. There are various taxonomic databases out there. The Tree of Life was probably the first major one, and Wikispecies is another. And those projects have been very valuable, but I think it's fair to say they haven't revolutionized the science the way that GenBank did for DNA or that Wikipedia did for general knowledge.

Hopefully, Encyclopedia of Life can be that transformative resource.

No entry for Marmorkrebs – yet! – but there are plenty of crustaceans in the database already. Check out the crayfish page.