28 October 2014

Celebrate diversity: Big babies

The latest additions to “creatures we thought reproduced sexually but turn out to be able to reproduce asexually” is a pretty spectacular one, because one of the two species is one of the biggest snakes in the world.

A paper published back in June by Booth and colleagues is suddenly making the rounds on news and social media. It describes research on two python species, the reticulated python (pictured, record holder for longest snake), and the royal python. While the news is focusing on “snake gives virgin birth!” angle, this paper is far more interesting.

The major question in this paper is: how do animals switch, genetically, from sexual to asexual reproduction? In most vertebrates - including the two in this paper - the answer is “terminal fusion automixis.”

In most female vertebrates, gametes divide unevenly in meiosis, with one large cell set to become the egg, and the other becoming a “polar body,” which normally dies. Some species are able to take the polar body and have it act like a sperm cell. The offspring that result are not genetically identical to their mother, because there is a a random element in meiosis.

There’s been one apparent exception: a Burmese python reproduced without sex, and the offspring were clones of the mother. If so, the offspring could not have been generated by terminal fusion automixis. This would be weird, given that this is out of step with an increasingly large number of cases.

Booth and colleagues, however, describe some unpublished data from another Burmese python laying eggs without sex. Here, the offspring are apparently not clones of the mother, which is in line with other species, but not the one previous account. Because of this, Booth and company suggest the previous paper be “viewed cautiously.”

This would be the normal translation from academese:

Booth and colleagues suggest that the first clone python report is not due to an error. Instead, they suggest that an individual, which had been created by parthenogentic reproduction, reproduced again by the same means. They write:

If this is indeed the case, this would represent the first documentation of such reproductive competence of (facultative parthenogensis) in vertebrates.

Only time (and a few more replications) will tell if there are indeed clone snakes. If there are, they seem to be rare.

Hat tip to Jason Goldman.


Booth W, Schuett GW, Ridgway A, Buxton DW, Castoe TA, Bastone G, Bennett C, McMahan W. 2014. New insights on facultative parthenogenesis in pythons. Biological Journal of the Linnean Society 112(3): 461–468. http://onlinelibrary.wiley.com/doi/10.1111/bij.12286/full

External links

Virgin Birth Discovered In The World's Largest Snake
Python babies the result of 'virgin birth,' zoo confirms

Photo by Ryan Somma on Flickr; used under a Creative Commons license. Graffiti picture from here.

12 August 2014

Mestre and colleagues, 2013

Mestre A, Aguilar-Alberola JA, Baldry D, Balkis H, Ellis A, Gil-Delgado JA, Grabow K, Klobučar G, Kouba A, Maguire I, Martens A, Mülayim A, Rueda J, Scharf B, Soes M, S. Monrós J, Mesquita-Joanes F. 2013. Invasion biology in non-free-living species: interactions between abiotic (climatic) and biotic (host availability) factors in geographical space in crayfish commensals (Ostracoda, Entocytheridae). Ecology and Evolution 3(16): 5237–5253. http://dx.doi.org/10.1002/ece3.897


In invasion processes, both abiotic and biotic factors are considered essential, but the latter are usually disregarded when modeling the potential spread of exotic species. In the framework of set theory, interactions between biotic (B), abiotic (A), and movement-related (M) factors in the geographical space can be hypothesized with BAM diagrams and tested using ecological niche models (ENMs) to estimate A and B areas. The main aim of our survey was to evaluate the interactions between abiotic (climatic) and biotic (host availability) factors in geographical space for exotic symbionts (i.e., non-free-living species), using ENM techniques combined with a BAM framework and using exotic Entocytheridae (Ostracoda) found in Europe as model organisms. We carried out an extensive survey to evaluate the distribution of entocytherids hosted by crayfish in Europe by checking 94 European localities and 12 crayfish species. Both exotic entocytherid species found, Ankylocythere sinuosa and Uncinocythere occidentalis, were widely distributed in W Europe living on the exotic crayfish species Procambarus clarkii and Pacifastacus leniusculus, respectively. No entocytherids were observed in the remaining crayfish species. The suitable area for A. sinuosa was mainly restricted by its own limitations to minimum temperatures in W and N Europe and precipitation seasonality in circum-Mediterranean areas. Uncinocythere occidentalis was mostly restricted by host availability in circum-Mediterranean regions due to limitations of P. leniusculus to higher precipitation seasonality and maximum temperatures. The combination of ENMs with set theory allows studying the invasive biology of symbionts and provides clues about biogeographic barriers due to abiotic or biotic factors limiting the expansion of the symbiont in different regions of the invasive range. The relative importance of abiotic and biotic factors on geographical space can then be assessed and applied in conservation plans. This approach can also be implemented in other systems where the target species is closely interacting with other taxa.

Keywords: biological invasions • BAM diagrams • ecological niche models • host availability

Note: Co-author Menno Soes confirmed that the “Procambarus fallax” studied in this paper is indeed P. fallax f. virginalis, or Marmorkrebs.

First look at Freshwater Crayfish: A Global Overview

A new book on crayfish is now up at the publisher’s website. Here is the publisher’s description, with my emphasis added:


  • Provides an up-to-date reference work on commercially important crustaceans
  • Covers conservation status and biology of all endangered species, taxonomy, and distribution of crayfishes worldwide
  • Introduces a new model aquatic organism—a parthenogenetic freshwater crayfish


For their great commercial importance as a human food delicacy, crayfish are now becoming of wider interest to molecular biologists, and also to conservationists due to the fact that in some countries many of the native crayfish species are under threat from human activity, disease, and competition from other introduced crayfish species. Helmed by three editors in Japan, Europe, and the US, this book invites contributions from experts around the globe, covering the conservation status and biology of all endangered species, taxonomy, and distribution of crayfishes worldwide

It is slated for publication 15 April 2015.

04 August 2014

Verschueren, 2013

Verschueren H. 2013. Tracing endangered and invasive animal species in water using eDNA detection methods. Master’s thesis in Forensic Science: University of Amsterdam. http://dare.uva.nl/document/497579


In the Netherlands several protected animals that live in surface waters are monitored to meet Dutch directives or laws. Current animal monitoring is mainly based on visual observations which can be time consuming and labor intensive. These methods are also not always effective for animal species that are rare, have a hidden lifestyle or have ambiguous morphological characteristics. Alternative monitoring methods were introduced for animal species that live (partly) in water based on detection of DNA - traces excreted into the environment (eDNA). Due to the fact that this method detects
DNA, it is not required to catch or even observe the target organisms. eDNA can be detected and quantified using quantitative polymerase chain reaction (qPCR). This project aimed to develop and validate eDNA detection methods for protected weatherfish (Misgurnus fossilis) and great crested newt (Triturus cristatus) species, and for seven invasive freshwater crayfish species (Astacidae & Cambaridae). Target species are selected because they are rare (T. cristatus and M. fossilis) or have a hidden lifestyle (all). Besides, early detection of exotic and invasive species (Astacidae & Cambaridae) is essential for success of a control plan. Furthermore was examined under which circumstances eDNA detection method provide better results. Finally, two different sample processing procedures were compared for DNA yields and detection probability.

eDNA detection methods require robust qPCR-protocols for amplification and quantification of target species DNA. Specific primers were developed targeting COI, CytB and 16S genes present on mitochondrial DNA. Mitochondrial DNA (mtDNA) is known for its high copy number which increases detection chance. Besides, these DNA regions are variable between species but conserved within species. Both properties make mtDNA a suitable target for species specific detection methods. Species specific qPCR-protocols were proposed after extensive in silico and in vitro analysis. Primers and probes were analyzed for amplification efficiency of target- and reference species DNA. Specific M. fossilis and T. cristatus assays were successfully developed targeting a region in the COI gene. Assays for invasive Astacidae & Cambaridae species were not successful yet.

The sensitivity of the methods was successfully determined by analyzing samples taken from locations where target species were present. Developed eDNA methods were validated in a field study. Twelve locations were sampled in triplicate at several water bodies in the Alblasserwaard polder during early spring and late spring. Results were compared to conventional screening data from the same period. In general M. fossilis and T. cristatus DNA was detected in all samples taken from locations where species were observed. Moreover, DNA was amplified in more samples if collected during late spring than during early spring. This is most likely due to inactive M. fossilis species or absent T. cristatus species during colder periods. Finally, two different sampling methods and procedures were applied: 1 L filtration versus 15 mL precipitation. Sample filtration results in extraction of merely cellular DNA while sample precipitation results in extraction of both cellular- and extracellular DNA. Comparison of the results slightly indicated that precipitation of 15 mL volumes give higher DNA yields and filtration of 1 L volumes give higher detection probability. In conclusion, eDNA detection methods designed for Misgunrus fossilis and Triturus cristatus species show potential to be sensitive and specific tools in species monitoring but more research is needed before it can be applied.

Keywords: None provided.

02 August 2014

van Oosterhout and colleagues, 2014

van Oosterhout F, Goitom E, Roessink I, Lürling M. 2014. Lanthanum from a modified clay used in eutrophication control is bioavailable to the marbled crayfish (Procambarus fallax f. virginalis). PLOS ONE 9(7): e102410. http://dx.doi.org/10.1371/journal.pone.0102410


To mitigate eutrophication in fresh standing waters the focus is on phosphorus (P) control, i.e. on P inflows to a lake as well as a lake’s sediment as internal P source. The in-lake application of the lanthanum (La) modified clays – i.e. La modified bentonite (Phoslock) or La modified kaolinite, aim at dephosphatising the water column and at reducing the release of P from a lake’s sediment. Application of these clays raises the question whether La from these clays can become bioavailable to biota. We investigated the bioavailability of La from Phoslock in a controlled parallel groups experiment in which we measured the La in carapace, gills, ovaries, hepatopancreas and abdominal muscle after 0, 14 and 28 days of exposure to Phoslock. Expressing the treatment effect as the difference of the median concentration between the two treatment groups (Phoslock minus control group) yield the following effects, the plus sign (+) indicating an increase, concentrations in µg g−1 dry weight: Day 14: carapace +10.5 µg g−1, gills +112 µg g−1, ovaries +2.6 µg g−1, hepatopancreas +32.9 µg g−1 and abodminal muscle +3.2 µg g−1. Day 28: carapace +17.9 µg g−1; gills +182 µg g−1; ovaries +2.2 µg g−1; hepatopancreas +41.9 µg g−1 and abodminal muscle +7.6 µg g−1, all effects were statistically significant. As La from Phoslock is bio-available to and taken up by the marbled crayfishes (Procambarus fallax f. virginalis), we advocate that the application of in-lake chemical water treatments to mitigate eutrophication should be accompanied by a thorough study on potential side effects.

Keywords: None provided.

25 June 2014

Kouba and colleagues, 2014

Kouba A, Petrusek A, Kozák P. 2014. Continental-wide distribution of crayfish species in Europe: update and maps. Knowledge and Management of Aquatic Ecosystems 413: 05. http://dx.doi.org/10.1051/kmae/2014007


Recently published astacological studies substantially improved available data on distribution of crayfish in various European regions. At the same time, spread of invasive species has been recorded, additional non-indigenous species became established in various countries, and losses of populations of native species due to crayfish plague and other negative factors were observed. We overview recent advances in this knowledge, and provide updated colour maps of the distribution of all crayfish species present in Europe. These maps are originally based on the data from the Atlas of Crayfish in Europe published in 2006 as a result of the CRAYNET project, and were further updated from more recently published reports, grey literature, and especially thanks to contributions and feedback of over 70 specialists from 32 countries. Separate maps are available for all indigenous crayfish species in Europe as well as for three most widespread non-indigenous crayfish species. Additionally, two maps give locations of known findings of crayfish species introduced to Europe after 1980. These newly established alien species have so far restricted distributions; however, the frequency of recent reports suggests that findings of such species resulting from releases of aquarium pets will further increase.

Keywords: crayfish distribution • indigenous species • invasive species • native range • maps

24 June 2014

Soedarini and colleagues, 2014

Soedarini B, van Gestel CAM, van Straalen NM, Widianarko B, Röling WFM. 2013. Interactions between accumulated copper, bacterial community structure and histamine levels in crayfish meat during storage. Journal of the Science of Food and Agriculture 94(10): 2023-2029. http://dx.doi.org/10.1002/jsfa.6519



Pollution in aquaculture areas may negatively impact edible species and threaten seafood quality and safety. The aim of this study was to determine the interaction between copper and bacteria in the aquatic habitat and their impact upon crustaceans. Marbled crayfish was chosen as a model of aquatic crustaceans and the influence of metal contamination on bacterial community structure in water used to culture crayfish and in crayfish themselves was investigated. Histamine, an allergen commonly formed by certain groups of bacteria in crustacean's edible tissue during storage, was also determined.


Copper exposure increased its concentration in crayfish meat by 17.4%, but the copper concentration remained within acceptable food safety limits. Elevated copper levels affected the bacterial community both in the water used to cultivate crayfish and in the marbled crayfish themselves. Cluster analysis of 16S rRNA-gene based microbial community fingerprints revealed that copper impacted the bacterial community in the water and in the crayfish meat. However, copper exposure reduced the formation of histamine in crayfish meat during storage by 66.3%.


Copper from the habitat appears to reduce histamine accumulation in crayfish meat during storage by affecting the bacterial community structure of the cultivation water and most likely also in the intestines of the crayfish. From a food safety point of view, copper treatment during the aqua culturing of crustaceans has a positive impact on the postharvest stage.

Keywords: copper • bacterial community structure • histamine • crayfish • storage