This is not a true “Behind the Paper” post. Why? Because I cannot write a behind the paper post when I cannot publish a paper*. How did I get to the point of writing an unpublishable paper; well, I genotyped with microsatellites. After submitting my paper I received a number of kind reviews that said there was nothing wrong with my paper (questions, sampling design, analyses, interpretations) except for the genetic marker.
So what’s wrong with microsatellites?
The first argument (and the strongest in my opinion for population genetic studies) is that microsatellites do not represent full genome coverage. In an age where so many papers have full genome coverage (obtaining data from RADseq, transcriptomics, or resequencing), it’s a fair critique to highlight that microsatellites have less power to detect differences especially subtle genomic changes.
A second argument is that readers are not interested in reading microsatellite studies. Certainly some readers are totally over the marker, but others are not. This perspective may depend on individual readers subdiscipline and industry. I don’t have any data on this but I have a feeling that evolutionary biologists turn their noses up at microsatellites; whereas conservation biologists still see the marker as a useful tool for answering their questions. Relatedly, academics may prefer genomics where applied scientists (and academics with an applied focus) prefer genetics. The dichotomy between academics and applied scientists is well discussed in this paper by Shafer et al. But of course it is often academics and not applied scientists reviewing papers, which may account for fewer microsatellite papers in high profile journals.
How many microsatellite papers are getting published?
So a journal rejected my microsatellite paper; okay, I can deal. But what about everyone else’s microsatellite papers. Again, people are still using these markers for all types of studies, including: population delineation, genetic mark-recapture (to estimate census size), gene flow, relatedness among individuals, etc. And the use of molecular ecology appears to be growing, as more people add small or large molecular components to existing projects (although I admit I may have a bias towards seeing this being in a molecular ecology lab).
To understand the number of microsatellite studies being published I downloaded data from four journals I would expect to publish genetic studies: Molecular Ecology**, Molecular Evolution and Biology (MBE), Conservation Genetics, and Journal of Heredity. I used Scopus to record the number of papers each journal published per year from 1995 to 2014, and the number of those papers that had “microsatellites” in either the title, abstract, or keywords. The results are below.
I had a couple of takeaways from the figure. The first simply relates to the growth of number of publications. While MBE and J Heredity appear to have loose caps on the number of papers they will publish each year, Molecular Ecology grew significantly until 2009 then placed a cap on their publications. The story with Conservation Genetics may be similar, although Conservation Genetics Resources started in 2009 so it’s possible that some of the volume that may have gone to Conservation Genetics was shuttled to Conservation Genetics Resources which represents the drop in total publications after that time.
Now related to the publishing of microsatellite papers, there were very journal specific stories. MBE never had a high proportion of total publications coming from microsatellite studies (4% over the 20 years of data), where 50% of Conservation Genetics studies used microsatellites. The growth of microsatellite studies in J Heredity has grown from 3% in 1995 to 40% in 2014. Molecular Ecology also saw a lot of growth in the proportion of microsatellite studies (9% in 1995 to 60% in 2009) until 2010 where there was a precipitous drop, down to 20% in 2014.
Why do I care which journals publish papers with microsatellites?
On the one hand, my rejection was a wake-up call to the realities of academia. I will give significant pause before using microsatellites in another study, knowing that I will have a hard time publishing in the top tier journals of the field. Despite the segments of the community that want others to eschew thinking about journal impact factors when publishing, that is not a realistic approach for students and post-docs looking to advance their academic careers. Moving away from microsatellites may be a necessity for many academics to stay current and competitive. As Shafer et al. point out, collaborations between academics and conservation professionals may be needed as projects transition to genomics, and I would add that applied researchers need to understand why academics are moving away from microsatellites at a time when applied researchers appear very comfortable with the data these markers provide. That said, of course microsatellite studies are publishable, just not in the same journals as before. The growth of molecular studies, and science more generally, has been accompanied by growth in the number of journals so there are more places to publish microsatellite studies, they may just not have the readership and influence of the journals that people were once able to publish these studies.
*- Okay, I’m being a little dramatic here; I could have found a home for this paper at a very low impact factor journal. I chose not to because I had the data to change my paper into a genomics paper.
**- UPDATE- November 25, 2015- I was reviewing this data and noticed that “Molecular Ecology” included Molecular Ecology, Molecular Ecology Notes (before 2009), and Molecular Ecology Resources (after 2009). The drop in publications at 2009 may be better attributed to the change in number of papers published between the Notes and Resources.