Pre-print power

Pre-prints are, of course, yesterday’s news in some circles. They are nothing new for the physics community, which has been using the arXiv pre-print server for more than two decades now. Several fields, including biology, have been reluctant to follow that trail. There is still a lot to talk about with pre-prints.

Pre-prints have been in the news a little more than usual lately, with a string of articles and editorials and blog posts about the potential benefits for pre-prints. (List of recent links at the bottom.) They’ve also been on my mind since a recent manuscript by Vogt and colleagues was the first in the Marmorkrebs research community to go up on a pre-print server, BioRxiv.

I asked two of the authors about what motivated their decision to post a pre-print, and how they thought this worked out for them.

Frank Lyko wrote:

We were a bit frustrated by the reviewing process. It takes time as it often takes some unexpected twists and turns. Also, it’s not uncommon that reviews or editorial decisions are completely off the mark. Posting provides you with an opportunity to let the community be the judge and not worry about the hidden agendas of reviewers or editors.

We wanted this story to be out in the open. Peer review can take an inordinate amount of time. BioRxiv promises to be fast, and indeed, 5 hours(!) after the initial submission, the screening process was completed. The paper was then instantly posted with a doi and thus became a citable reference.

And another point (even if it was not relevant in our case). The publication fees for some of the good journals now amass to several thousand euros. We are usually in the €5000 range if we want to include open access, which is egregious. BioRxiv posting is for free.

Günter Vogt wrote:

In the days after posting one of the staff writers of Science came across the paper and wrote a small article for the Science News. This small article was then discussed in the net and we have addressed some of the critical issues in our final paper in Biology Open, for example, the important question when a parthenogenetic lineage should be considered as an independent species and when not. The abstract of the BioRxiv version was clicked 1627 times already and the full paper was downloaded 666 times. This is a quite good distribution of knowledge in six weeks.

bioRxiv is still a developing resource. The site  recently started showing tweets about the paper. While more people are posting to the site (right), though, the number is a tiny fraction of biological publishing. This page indicates over 806,636 articles were added to PubMed in 2013, which works out to 67,000 papers a month. A couple of hundred bioRxiv papers per month pales in comparison.

As noted in the quotes above, the manuscript by Vogt and colleagues has been accepted for publication in a standard journal. I will be interested to see if interest in journal article tracks that of the pre-print. My own experience, with the PeerJ pre-print server, has been that while pre-prints are nice, the final journal article gets more attention.

References

Desjardins-Proulx P, White EP, Adamson JJ, Ram K, Poisot T, Gravel D. 2013. The case for open preprints in biology. PLOS Biology 11(5): e1001563. http://dx.doi.org/10.1371/journal.pbio.1001563

Pennisi E. 2015. Crayfish create a new species of female ‘superclones’. Science News ScienceShots. http://dx.doi.org/10.1126/science.aad1673

Shuai X, Pepe A, Bollen J. 2012. How the scientific community reacts to newly submitted preprints: article downloads, Twitter mentions, and citations. PLOS ONE 7(11): e47523. doi:10.1371/journal.pone.0047523

External links

Peer review, preprints and the speed of science
A PeerJ PrePrint – so just what is that exactly?
Preprints in paleontology: really that radical?
Preprints in science
Accelerating Scientific Publication in Biology
Four different reasons to post preprints
The science of asking

Kato and colleagues, 2015

Kato M, Hiruta C, Tochinai S. 2015. Androgenic gland implantation induces partial masculinization in Marmorkrebs Procambarus fallax f. virginalis. Zoological Science 32(5): 459-464. http://dx.doi.org/10.2108/zs150028

Abstract

The androgenic gland in malacostracan crustacean species produces and secretes androgenic gland hormone, which is responsible for male sexual differentiation, such as the induction and development of male sexual traits, and in turn the suppression of female sexual traits. Marmorkrebs, Procambarus fallax forma virginalis, which was identified as the first parthenogenetic species in decapod crustaceans, produces only female offspring. In this study, in order to reveal whether the Marmorkrebs crayfish is sensitive to androgenic gland hormone, we transplanted an androgenic gland from a related congener, P. clarkii, to P. fallax f. virginalis. In androgenic gland-implanted specimens, partial masculinization was confirmed: the masculinization of several external sexual characteristics (i.e., thickening of the first and second pleopods; formation of reverse spines on the third and fourth pereopods) was detected, whereas that of internal sexual characteristics (e.g., the formation of ovotestes and male gonoducts) was not. Our results imply that P. fallax f. virginalis still has sensitivity to the androgenic gland hormone and, at least partly, the hormone should be able to induce male characteristics, even in parthenogenetic Marmorkrebs.

Keywords: androgenic gland • masculinization • parthenogenesis • implantation • Marmorkrebs

Shen and colleagues, 2015

Shen H, Braband A, Scholtz G. 2015. The complete mitogenomes of lobsters and crayfish (Crustacea: Decapoda: Astacidea) reveal surprising differences in closely related taxa and convergences to Priapulida. Journal of Zoological Systematics and Evolutionary Research 53(4): 273–281. http://dx.doi.org/10.1111/jzs.12106

Abstract

We sequenced the complete mitogenomes of three species of Decapoda, Astacidea, comprising Astacida (freshwater crayfish) and Homarida (marine clawed lobsters): 1. Procambarus fallax f. virginalis (Astacida, Astacoidea), 2. Homarus gammarus (Homarida, Nephropoidea) and 3. Enoplometopus occidentalis (Homarida, Enoplometopoidea). Together with the available species in GenBank, the taxon Astacidea is covered with at least one representative for each of the four main subtaxa. Astacidea show unexpectedly diverse genomic organizations. Ten different gene arrangements have been observed in the 28 investigated species. Compared with the decapod ground pattern, a huge inversion, involving more than half of the mitogenome, has been found in four freshwater crayfish species of Astacoidea and convergently in one lobster species. Surprisingly, this inversion can also be observed in the distantly related Priapulida. This multiple convergent evolution suggests a relative ease in the evolution of great similarities in mitochondrial gene order. In addition, a partial or complete loss of the protein-coding gene nad2 has been found in E. occidentalis and H. gammarus but not in Nephrops norvegicus, Homarus americanus and Enoplometopus debelius. A reversal of the strand asymmetry has been found in five astacideans which is supposed to be caused by the inversion of a replication origin in the control region.

Keywords: gene order • convergent evolution • gene inversion • nad2 • strand reversal

Vogt, 2016

Vogt G. 2016. Research on stem cells, aging, cancer resistance, and epigenetics in marbled crayfish and relatives: potential benefits for human biology and medicine. In: T Kawai, Z Faulkes, G Scholtz, eds. Freshwater Crayfish: A Global Overview, pp. 115-157. Boca Raton: CRC Press. https://www.crcpress.com/Freshwater-Crayfish-A-Global-Overview/Kawai-Faulkes-Scholtz/9781466586390

Excerpt

Freshwater crayfish and their relatives have not yet been taken into the focus of stem cell biology, biogerontology, cancer biology and epigenetics although research of the last decade suggests a promising potential. In this chapter, the state of the art in these emerging fields of astacology, emphasizing contributions made by the parthenogenetic marbled crayfish as an emerging model organism have been reviewed.

Keywords: None provided.

Related posts

Kawai and colleagues (editors), 2016

Chucholl, 2016

Chucholl C. 2016. Marbled crayfish gaining ground in Europe: the role of the pet trade as invasion pathway. In: T Kawai, Z Faulkes, G Scholtz, eds. Freshwater Crayfish: A Global Overview, pp. 83-114. Boca Raton: CRC Press. https://www.crcpress.com/Freshwater-Crayfish-A-Global-Overview/Kawai-Faulkes-Scholtz/9781466586390

Excerpt

In this chapter, knowledge on this novel and on-going pathway for alien crayfish species introductions will be reviewed. In line with the other chapters in this section, emphasis will be placed on the marbled crayfish (Procambarus fallax f. virginalis Martin et al. 2010). The history of the marbled crayfish is inseparably tied to the aquarium trade, which introduced this species to the scientific world and which, at the time of this writing, is still the only known ‘natural habitat’ of marbled crayfish.

Keywords: None provided.

Related posts

Kawai and colleagues (editors), 2016

Martin, 2016

Martin P. 2016. Parthenogenesis: mechanisms, evolution, and its relevance to the role of marbled crayfish as model organism and potential invader. In: T Kawai, Z Faulkes, G Scholtz, eds. Freshwater Crayfish: A Global Overview, pp. 63-82. Boca Raton: CRC Press. https://www.crcpress.com/Freshwater-Crayfish-A-Global-Overview/Kawai-Faulkes-Scholtz/9781466586390

Excerpt

This chapter deals with the question of what is behind the often misinterpreted term parthenogenesis and what effect it has on marbled crayfish. It starts with a general overview about the mechanisms and genetic consequences of sexual reproductive systems and several different asexual ones. This is followed by a section on the origin of parthenogenesis in animals, its short-term benefits and long-term disadvantages, from the perspective of the evolutionary theory of sex. Then, the current state of knowledge on the extraordinary reproduction mode of marbled crayfish and the presumed cause for its emergence is described. Finally, the possibilities for this crustacean as laboratory animal and its ecological impacts resulting from parthenogenesis are discussed.

Keywords: None provided.

Related posts

Kawai and colleagues (editors), 2016

Vogt and colleagues, 2015

Vogt G, Falckenhayn C, Schrimpf A, Schmid K, Hanna K, Panteleit J, Helm M, Schulz R, Lyko F. 2015. The marbled crayfish as a paradigm for saltational speciation by autopolyploidy and parthenogenesis in animals. BioRxiv: 23 August 2015. http://dx.doi.org/10.1101/025254

Abstract

The parthenogenetic all-female marbled crayfish is a novel research model and potent invader of freshwater ecosystems. It is a triploid descendant of the sexually reproducing slough crayfish, Procambarus fallax, but its taxonomic status has remained unsettled. By cross-breeding experiments and parentage analysis we show here that marbled crayfish and P. fallax are reproductively separated. Both crayfish copulate readily, suggesting that the reproductive barrier is set at the cytogenetic rather than the behavioural level. Analysis of complete mitochondrial genomes of marbled crayfish from laboratory lineages and wild populations demonstrates genetic identity and indicates a single origin. Flow cytometric comparison of DNA contents of haemocytes and analysis of nuclear microsatellite loci confirm triploidy and suggest autopolyploidization as its cause. Global DNA methylation is significantly reduced in marbled crayfish implying the involvement of molecular epigenetic mechanisms in its origination. Morphologically, both crayfish are very similar but growth and fecundity are considerably larger in marbled crayfish, making it a different animal with superior fitness. These data and the high probability of a divergent future evolution of the marbled crayfish and P. fallax clusters suggest that marbled crayfish should be considered as an independent asexual species. Our findings also establish the P. fallax-marbled crayfish pair as a novel paradigm for rare chromosomal speciation by autopolyploidy and parthenogenesis in animals and for saltational evolution in general.

Keywords: None provided.