19 January 2017

Falckenhayn, 2016

Falckenhayn C. 2016. The methylome of the marbled crayfish Procambarus virginalis. Doctoral dissertation, Combined Faculties for the Natural Sciences and for Mathematics, University of Heidelberg, Heidelberg. http://archiv.ub.uni-heidelberg.de/volltextserver/22489/1/Falckenhayn_Cassandra_PhDThesis.pdf

Abstract

DNA methylation in invertebrates seems to play a different role as in mammals and its evolutionary conservation among invertebrates is unclear. Only two studies describe crustacean methylomes giving just a small overview. The parthenogenetic reproducing marbled crayfish display a high environmental adaptability besides its genetic uniformity and thus, possess the necessary attributes of a laboratory model organism. The aim of this work was to characterize the methylome of the marbled crayfish at single-base resolution using whole-genome bisulfite sequencing in an attempt to give new insights into DNA methylation in crustaceans and thus, in the evolutionary conservation among invertebrates. Analysis of the mitochondrial DNA of different marbled crayfish strains revealed a single origin and suggests to consider the marbled crayfish as independent asexual species Procambarus virginalis. Furthermore, since the P. virginalis possess a large genome size, the transcriptome was assembled and comparison to other species revealed a relative good quality of the first draft transcriptome as well as the presence of a conserved DNA methylation system in P. virginalis. Analysis of the CpG depletion in protein-coding sequences and mass spectrometry confirmed historical germline and current DNA methylation in various tissues of P. virginalis. The methylome was characterized by the key features of animal methylomes with methylation targeted to gene bodies. The gene bodies displayed the typical pattern of a mosaically methylated invertebrate genome and a bimodal distribution of their methylation levels. Targeted gene bodies were annotated as housekeeping genes and methylation showed a parabolic relationship to housekeeping gene expression suggesting that the DNA methylation of housekeeping genes might fine-tune their expression. Additionally, repeats were generally hypomethylated and the methylation of repeats depended on their position to gene bodies. Finally, inter-individual and inter-tissue comparison of gene body methylation revealed a high reproducibility of the methylation patterns, while inter-species comparison between P. fallax and P. virginalis displayed an overall hypomethylation in the P. virginalis genes which however, could not explain the by mass spectrometry detected global hypomethylation in P. virginalis. These findings uncovered that the P. virginalis methylome is characterized by tissue-invariant housekeeping gene methylation. This thesis describes novel insights into the evolutionary conservation of gene body and repeat methylation in invertebrates, especially crustaceans, and the preferential methylation of housekeeping genes highlights a functional difference to the tissue-specific methylation in mammals.

Keywords: None provided.

Patoka and colleagues, 2016

Patoka J, Buřič M, Kolář V, Bláha M, Petrtýl M, Franta P, Tropek R, Kalous L, Petrusek A, Kouba A. 2016. Predictions of marbled crayfish establishment in conurbations fulfilled: Evidences from the Czech Republic. Biologia 71(12): 1380–1385. https://doi.org/10.1515/biolog-2016-0164

Abstract

The marbled crayfish (Procambarus fallax f. virginalis) has become one of the potentially most dangerous nonindigenous crayfish species spreading in European countries and elsewhere. This taxon reproduces parthenogenetically and recently has been verified as a vector of the crayfish plague pathogen. Here, we report on two established populations of marbled crayfish in the Czech Republic. The marbled crayfish was observed during autumn 2015 in an urban pond connected by sewer piping with the Rokytka brook near its mouth to the Vltava River in Prague. Subsequently, three adult females, two of them having well-developed glair glands and oocytes, were captured in this pond during spring 2016, suggesting successful overwintering of the local population. Furthermore, four adult females were captured in an artificial pond at the Radovesická lignite spoil heap in the vicinity to the industrial conurbation of Bílina in summer 2016; one of them carried eggs. We tested these for the presence of the crayfish plague pathogen Aphanomyces astaci, with negative results. The introduction pathway for both populations is most likely a release from private aquaria, as these sites are popular for recreation activities. Our findings substantiate previous predictions that conurbations are likely to be the primary areas for marbled crayfish introductions.

Keywords: Procambarus fallax f. virginalis • biological invasion • first record • pet trade • Marmorkrebs • urban pond • postmining site

10 January 2017

Awards and scholarships for crustacean research, 2017

The Crustacean Society (TCS) has multiple scholarships and travel grants for its members.

Scholarships in graduate studies

The Crustacean Society annually awards up to six US$1000 scholarships in graduate studies on crustaceans in any of the following fields:

  • Biology of large branchiopods (Denton Belk Memorial Scholarship)
  • Physiology and reproductive biology
  • Ecology and behavioural ecology, population genetics, and behavior
  • Eystematics, biogeography, and evolution
  • Larvae and development
  • Anatomy or paleobiology

Applicants and their faculty sponsor must be a member of The Crustacean Society and be enrolled in an undergraduate or graduate degree program.

Student travel awards


The Crustacean Society awards up to ten US$450 awards to support student attendance at Crustacean Society meetings (Society for Integrative and Comparative Biology, mid-year society meeting, or the International Crustacean Congress). Applicants and their faculty sponsor must be a member of The Crustacean Society, be enrolled in an undergraduate or graduate degree program, be the presenter of an oral or poster presentation at the Crustacean Society meeting they attend and demonstrate financial need for society support of travel to the meeting.

Early-career, post-Ph.D. travel awards

The Crustacean Society will award up to three US$1500 travel grants for early-career researchers with a Ph.D. awarded within 5 years of the application deadline. Extension of up to 8 years post-Ph.D. will be considered at the discretion of the Program Officer for applicants having taken a career break for family reasons. The grants shall cover travel to present results of their research in any field of study involving crustaceans at a Crustacean Society meeting (Society for Integrative and Comparative Biology, mid-year society meeting, or the International Crustacean Congress). The applicant must be a current member of The Crustacean Society at the time of application.

The closing date for all awards is 31 March 2017. Contact Dr. Joanne Taylor (jtaylor@museum.vic.gov.au) for more information. She is traveling until about Jan. 20, 2017; in the meantime, contact Mary Belk for forms (tcs1921@hotmail.com).

09 January 2017

Chucholl and Wendler, 2017

Chucholl C, Wendler F. 2017. Positive selection of beautiful invaders: long-term persistence and bio-invasion risk of freshwater crayfish in the pet trade. Biological Invasions 19(1): 197-208. http://dx.doi.org/10.1007/s10530-016-1272-5

Abstract

After interest in keeping crayfish (Crustacea, Decapoda, Astacida) in home aquaria peaked in the mid-2000s, the aquarium trade has become a novel introduction pathway for non-native crayfish species in Germany. Here, we provide an update on the ornamental crayfish trade approximately one decade after the ‘crayfish hype’ to explore the long-term implications in terms of bio-invasion risk. Specifically, species’ availability in e-commerce and potential invasiveness were assessed and compared to previous studies. Morphological and ecological traits of the offered species were compiled and related to their long-term availability (covering 2005–2015). In July 2015, a total of 31 online shops offered 28 crayfish species, which represents a decline of 24% in species diversity compared to the late 2000s. The estimated rate of import of new species has considerably flattened and approaches pre-hype values (<1 species year−1). However, the risk associated with the offered species, as assessed by a risk screening tool, has not decreased compared to the late 2000s. Long-term availability in the trade was primarily determined by bright coloration, the ability to reproduce under warm aquarium conditions, and a preference for lentic habitats. Species featuring such traits are likely to persist in the aquarium trade and include four high-risk species, most notably invasive and crayfish plague-carrying red swamp crayfish (Procambarus clarkii) and Marmorkrebs (Procambarus fallax f. virginalis). Persistent propagule pressure from aquaria has substantially contributed to the establishment of both species in Germany, stressing the need for more effective pathway management.

Keywords: aquarium trade • Crustacea • risk assessment • pre-introduction selection

31 December 2016

2016 was the best year ever for Marmorkrebs research

And it was the best by a long, long ways.

There are not only more papers, but they are coming from more places, too. In the early 2000s, papers were almost exclusively from western Europe and particularly Germany. Now, eastern Europe and Japan are regularly publishing Marmorkrebs papers in addition to the more established western European and American research programs. And the mix of papers is broad, too, with research on Marmorkrebs as invasive species, cellular biology, and behaviour.

Since I started this blog, it’s been a tradition for me to have a graph showing how many papers on Marmorkrebs were published compared to previous years. But making this year’s graph was trickier than before, because there are more kinds of research products out there than before.

In the past, I’ve included journal articles and book chapters. But by this year, I’ve been blogging pre-prints, master’s theses, and conference abstracts in addition to regular old articles and chapters. I’ve thought about whether to include these research products, and decided to include journal articles and book chapters only. In theory, pre-prints and master’s theses should be published later, so excluding them avoids the problem of inflating the publication rates.

As I noted last year, I also had the confusion of a book published in 2015 that had a 2016 cover date (Freshwater Crayfish, which I was involved with). Those book chapters are included in 2016, which bumps up the total for the year considerably. But 2016 would still be the best year ever for Marmorkrebs research even if if you removed the seven Freshwater Crayfish chapters from the total.

The book publication does mean that it will be hard for 2017 to top 2016 in the number of crayfish papers. The overall trend, however, shows no signs of flattening.


Related posts

2008 was the best year ever for Marmorkrebs research
2009 was tied for the best year ever in Marmorkrebs research
2010 was the best year ever for Marmorkrebs research
2011 was not the best year ever for Marmorkrebs research
2012 was an average year for Marmorkrebs research
2013 was the second best year ever for Marmorkrebs research
2014 was a good year for Marmorkrebs research
2015 was the best year ever for Marmorkrebs research

14 December 2016

By “invasive species,” do you mean crayfish or Daleks?

When you’re a scientist, sometimes you forget that other people see the world through different lenses than you do. And sometimes you have that point hammered home in no uncertain terms.

Last week, the American White House released an executive order from outgoing President Barack Obama about invasive species.

As someone who has written about invasive species, I thought, “Ho hum, routine sorts of stuff.”

But because I had shown interest in invasive species, Google suggested this page to me:

NO JOKE! Obama signs executive order to ‘Safeguarding the nation from an INVASIVE SPECIES’


Wait, what? Why is this page showing the American president and a SF style alien? My emphasis:

Obama has pushed through an act called “Safeguarding the Nation from the Impacts of Invasive Species.” The interesting thing about this presidential order (see full text below) is the legal wording of the document leaves a lot up for suspicion. The article was left purposely vague, it seems.

There are a few reasons for this. The first could be simply so the article can be interpreted for years to come. The second is a little more malicious and slightly terrifying. An invasive species in the document is vaguely defined as an organism that disrupts an ecosystem. Because of this, some are speculating that this last order of 2016 is meant to protect from alien invasions, and purposely set some guidelines for the next presidency.

It has been shown in the news that the government is getting closer to telling its people what is actually out in space. If the planet needs protection for these beings, it will make sense that they would be motivated to tell the people, and also motivated to write an article to set up pretenses to protect the Earth. This is only my opinion, but I hope that some of my readers will do some investigation. Something strange is happening within the government.

Now I wonder: when I have said, “invasive species,” how often have non-scientists heard, “alien invaders”? It kind of makes sense to me now. Anyone who watches science fiction will probably heave heard aliens described as “difference species.” Indeed, there’s a horror movie franchise whose name plays around with that ambiguity:


But despite that, it never occurred to me that someone might think “species” is synonymous with “extraterrestrial” rather than meaning “type of organism.”

Now, when I write about potential negative impacts of crayfish introductions, I have to think of other phrases to use so that when I say “invasive species,” people don’t automatically leap to this:


Related posts

Crayleks!

External links

Executive Order -- Safeguarding the Nation from the Impacts of Invasive Species
NO JOKE! Obama Signs Executive Order To 'Safeguarding The Nation From An INVASIVE SPECIES'


09 December 2016

Listing a species as “injurious”


The Center for Invasive Species Prevention was about to ask the US Fish and Wildlife Service to add Louisiana red swamp crayfish (Procambarus clarkii) to a list of “injurious” species.

In the petition, the CISP says the red swamp crawfish does not provide any essential economic or other benefits that outweigh their current and potential harm to the United States. ...

If the proposed changes are adopted then it could limit or prohibit the sale and export of crawfish across state lines.

But the day after I read the news article announcing that, the Center backed off. Judging from the news story and memo, it looked like the petition caused a bit of a freak out among people who sell the beast for food.

I think it’s a very interesting window into regulation. Biologically, there is no question that P. clarkii is a problematic invasive. It’s caused problems worldwide, from being farmed for aquaculture and is one of the most widely distributed crayfish in the pet trade (one of the “big six” worldwide). I think you would be hard pressed to find any biologist specializing in crayfish or invasive species that wouldn’t consider P. clarkii an extremely successful and problematic invasive species.

But there is so much established trade already within the U.S. that it is completely unsurprising that there would be pressure to not change anything.

The food industry is large and powerful. So is the pet industry, the other main mover of crayfish today. And the trade is largely unregulated, particularly for invertebrates. Although crayfish are not particularly popular in the US as pets right now, the European experience in the 1990s shows that there could easily be a “boom” in interest.

External links

Are crawfish an invasive species? Warning: contains annoying auto-play video
Statement of the Center for Invasive Species prevention on withdrawing its proposal to the U.S. Fish and Wildlife Service to add the red swamp crayfish to the Lacey act for further analysis

Picture by Michael Bok on Flickr.