Behind the Paper: Are Microsatellite Studies Publishable?

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.

MicroPubs
Number of publications with (blue) and without (grey) microsatellites published from 1995 to 2014 in four journals.

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.

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11 Comments Add yours

  1. manuelinor says:

    Interesting post, thanks! I work in functional/community ecology & am not savvy with genetics, so apologies if I’ve missed the point. But I’m curious to know why you chose to transition to a genomics paper, instead of pursuing publication of the microsatellite paper with a mid-range impact journal when, as you say, that approach is still useful for an applied focus?
    I think a similar thing happens in most disciplines – the most specific level of ID/marker is often considered more useful for developing ecological theory, but less-specific ID levels are still extremely useful for other research areas, especially where there is an applied focus. For example, functional diversity is now thought to be a better indicator of community response to environmental change than species diversity, which has traditionally been used in those type of studies.

    1. EEPuckett says:

      Hi, thanks for your question. A couple of reasons: first, it was not a conservation paper, it was an evolution paper. I had a genomic data set with the same samples for another purpose, and was able to analyze a different way to answer the questions in the paper I’m talking about. If I did not have this data set, I would have made different choices. Second, impact factor is important to me, which is why I did a full rewrite instead of a minor one for a different journal.

      My main reason for writing the post really was to ask which journals are publishing microsatellite studies. I agree that they have utility, but papers that were published in Molecular Ecology 5 and 10 years ago cannot be published there now, and I don’t think that has fully filtered into conservationists understanding of the publishing landscape.

  2. Stacey Lance says:

    Emily I would love to know if your conclusions changed when you switched from msats to “genomics.” To me that is the key, if they did, then it would be really helpful to others to publish those differences…if they didn’t, well just as important to emphasize that.

    1. EEPuckett says:

      Great question Stacey. Yes, my interpretation of the data did change between the micros and SNPs. The paper is currently under review, but once accepted I’ll do an actual “Behind the Paper” post and emphasize those differences. The main change was a much finer scale resolution for the population structure including cluster identification, admixture proportions, and geographic distribution of inferred clusters. The main thing that did not change were the estimates of divergence times.

  3. Nicole says:

    I wonder how your numbers would change if you added “SSR”and “simple sequence repeat” to the search. I’ve noticed a shift in the language in some journals.

  4. Danielle Brown says:

    I had the ‘doh’ moment when, after spending 2 years of getting the microsatellites, Conservation Genetics Resources and Molecular Ecology Resources suddenly became very persnickety about how many markers you must have before you can even submit (rule changes as of March 2015). Which low-impact-factor journals are you referring to that will publish meats? At this point, my data will go unpublished, which is worse than appearing in a low-impact-factor journal.

    1. EEPuckett says:

      Have you tried taxa specific journals?
      Personally, I’m against primer notes. I think primer development should be in the methods or appendix of a paper that uses those markers to answer an evolutionary, ecological, or conservation question. By taking this route, you’ll have access to journals that want to publish the science not the primer sequences.

      Thanks for your comment. Very interesting that Molecular Ecology Resources says that Conservation Genetic Resources will take microsatellite primer notes; except Con Gen Res clearly states they will not.
      Mol Eco Res: “Papers that describe a small number of microsatellite or SNP primers (known as Permanent Genetic Resources Notes or Primer Notes) are no longer considered for publication in Molecular Ecology Resources in any form. These may be better suited to journals like Conservation Genetics Resources or Applications in Plant Sciences.”
      Con Gen Res: We no longer publish microsatellite DNA loci and primers in this section, but will consider notes on other genomic resources such as new SNP, Y-chromosome or plastid markers.

  5. Dee Ann Aye says:

    Conservation Genetics Resources does accept microsatellite notes per se, but now they bind all received notes for a period to a single Microsatellite Records type publication but, indeed, they put a threshold of a minimum of 20 “useful*” (i.e. HWE) loci. There is a lot of science and scientific reasoning behind characterizing, developing and validating primers.

    *If a locus is not conforming to HWE they usually assume it is a marker problem, such as null alleles, but in fact, many are catching population genetic effects, such as population substructuring at that genome portion, probably and should not be right away discarded, imho. There is a good discussion about this in the Conservation and the genetics of populations book by Allendorff et al.2012.

  6. tizgelmi says:

    ahhhhhhhhhhhh it was an evolution paper. I finally got the info after scrolling through all the comments. I was getting worried a bit about the SSRs but it makes sense now. I used them to understand gene dispersal at a local scale and they worked wonderfully. I could identify related individuals through parentage analysis and they perfectly mirrored the movement of my dispersal vector. I ended up here while looking for where to publish the primer note though, or better said, “characterization”. I combined it with a validation for a different sampling and storage method so I don’t know where to send it.

  7. EEPuckett says:

    It’s not that I think microsatellites are a poor marker or that they do not provide quality inference. My results were that the micro and SNP studies had the same inference (although clearer patterns with the SNPs). However, I had trouble publishing the microsatellite analysis. What was your experience? Did you get push back from the journals on marker type?

    If your paper was published without push back from reviewers on marker type (which is what should happen if micros answer the question of interest), will this be the case in 5, 10, 20 years? Will the field consider them obsolete, even though as you point out they are useful for answering evolutionary questions.

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