Molecular Ecology Resources PGR Note FAQ

Last updated 1 December 2010

This FAQ is meant to accompany the MER author guidelines by giving additional details of and answering common questions about our manuscript types. For questions regarding this FAQ or other matters relating to the journal, please contact either the chief editor or managing.editor.Permanent Genetic Resource Notes PGR Note submissions are no longer published in Molecular Ecology Resources as individual papers. Instead, each issue now carries a summary article announcing the primers developed for various species by different research groups. The first author of these articles is “Molecular Ecology Resources Primer Development Consortium”, and contributing authors are then listed in alphabetical order. Example papers can be found in issues of the journal after 2009 at the Wiley Online Library site (except some special issues). PGR Notes typically describe novel polymorphic microsatellite loci or SNPs. When presenting new loci, a submission must describe at least eight novel polymorphic loci that have both a high heterozygosity and success rate when used to genotype individuals from natural populations. To show that the loci contain sufficient variation for individual discrimination, they must be tested on at least 20 diploid/polyploid individuals or 40 haploid genomes from a single population. PGR Notes may also describe the successful cross-amplification of existing loci in new taxa. These submissions must demonstrate that at least eight* of the tested loci are polymorphic and can be reliably amplified in the focal taxon. In addition, authors must also have sequenced all loci presented to demonstrate they are homologous to the original locus. To show that the loci contain sufficient variation for individual discrimination, they must be tested on at least 20 diploid/polyploid individuals or 40 haploid genomes from a single population. Common Questions   Should I submit my data to the database before I submit a manuscript? The place to start is the submission of a manuscript. Once the submission is accepted, then you will need to submit the primers to the database prior to final publication. How do other authors cite my loci with the new summary article format? Authors citing these summary articles in future papers are encouraged to consult the guidelines for the specific journal, but as an example we reproduce here the formatting following the Chicago Manual of Style: In text: … a panel of 13 polymorphic microsatellites (Molecular Ecology Resources Primer Development Consortium et al., 2009)… In references: Molecular Ecology Resources Primer Development Consortium, G.R. Almány, M.P. de Arruda, W. Arthofer, Z.K. Atallah, S.R. Beissinger, M.L. Berumen et al. 2009. Permanent Genetic Resources added to Molecular Ecology Resources Database 1 May 2009–31 July 2009. Molecular Ecology Resources 9: 1460-1466. How can readers find important details about my loci with the new summary article format? The author’s original manuscripts for the loci presented in a summary article are available on the Molecular Ecology Resources Primer database as a link from each locus entry (sample record). What if my markers deviate significantly from Hardy-Weinberg equilibrium? Loci showing strong deviations from Hardy-Weinberg equilibrium, high frequencies of null alleles and/or high levels of linkage disequilibrium may be discounted from the total number of loci presented in a manuscript, as these often prove to be less reliable in subsequent studies. There are biologically plausible explanations for loci not being in Hardy-Weinberg equilibrium (HWE) in a population, however, and authors may provide a rationale for their samples that could influence the editor’s decision on the manuscript. What about monomorphic loci? Loci that amplify successfully but prove to be monomorphic in population assays may be mentioned in the text and submitted to the Molecular Ecology Resources database, but they should not be included in the MS data tables. Does the word count include references? This word limit includes all text. In general, PGR Note manuscripts should include an Abstract (<100 words), main text, References, brief Acknowledgments, Figure Legends and Tables and Figures, in this order. Although not subdivided, the standard order of topics (Introduction, Materials and Methods, Results and Discussion) should be followed in the main text. Is there a resource I can use to get help if English is not my native language? The first choice should be collaborators or colleagues. If this is not an option, Wiley-Blackwells has a list of editing services that can be of use: Other groups have previously developed primers for this species. Can I still submit a manuscript? If other groups have been active in developing assays for a particular taxon/gene, the article should make clear why additional assays are needed. For example, if there is already a saturated microsatellite map for a species, adding in eight new loci may not be sufficient to warrant a new publication. If other researchers have previously published assays for this same species and/or gene, the new authors must be sure to check Genbank to see if any of the new assays overlap with the old. This is most easily accomplished by BLAST searches against the sequences from the old loci (you can limit searches in Genbank to specific taxa) to look for sequence similarity. The results of this test should be included in the cover letter if negative or mentioned in the text if positive. Can I submit more than one article if I develop more assays for this or another species? The short answer is yes, but with an important caveat. We see articles in MER as an important resource for the molecular ecology community, both to get these resources out and to help get initial publications for research projects. The health and status of the journal depend on citations of published articles, however, so we cannot just be publishing the development of assays for the sake of having more assays. This means that we need to take into account and balance the encouraging aspects and the detrimental aspects when considering multiple publications from one lab. We are concerned when we see that the development of assays by a group is occurring much faster than their implementation, and in some cases we reserve the right to suspend acceptance of manuscripts from these groups. If you have any concerns or questions about this policy, please feel free to contact the chief editor. My manuscript was rejected, what can I do? Manuscripts that receive a “reject encourage” decision may be resubmitted if they address the editor’s concerns. Please note that resubmissions of these manuscripts will either be accepted or rejected without the chance to resubmit, so care should be taken in their preparation. Does MER accept manuscripts describing variation using RAPD primers? No. I have already used these markers in a published paper, but I didn’t fully describe their development. Can I still submit them to MER? We regret that we cannot publish articles that report assays that have already been used in published studies. *In January 2012 this was lowered from 12 to 8