Editorial 2012

We are pleased to report that the state of the journal continues to be strong. Molecular Ecology’s impact factor as calculated by ISI Web of Knowledge rose for the sixth year in a row, from 4.301 in 2005 to 6.457 in 2010. The journal currently ranks fifth in impact in both the Ecology (130 journals) and Evolutionary Biology (45 journals) categories tracked by ISI. When only journals publishing primary research articles are considered, Molecular Ecology ranks second and third among Ecology and Evolutionary Biology journals, respectively. The 414 articles published in Molecular Ecology in 2010 make it one of the largest journals in ecology and evolutionary biology as well, ranking third in both subject categories. The 2011 Molecular Ecology Prize was awarded to Professor Deborah Charlesworth of the University of Edinburgh for her pioneering studies of mating systems and the origin of sex chromosomes. A biography of Deborah and her contributions to molecular ecology can be found on page 23 of this issue. In 2012 the first Joint Congress on Evolutionary Biology (Evolution 2012) will be held in Ottawa, Canada’s capital city. This signal event will bring together five of the world’s largest academic societies devoted to the study of ecology and evolutionary biology: the American Society of Naturalists (ASN), the Canadian Society for Ecology and Evolution (CSEE), the European Society for Evolutionary Biology (ESEB), the Society for the Study of Evolution (SSE) and the Society of Systematic Biologists (SSB). 2012 also marks the 20th anniversary for Molecular Ecology. To celebrate the tremendous advances that have been made in this research area, as well as to brainstorm about the future of the field, the journal is sponsoring a Molecular Ecology Symposium on 6th July 2012 in Ottawa, the day before Evolution 2012 gets underway. The structure of the meeting will follow the basic format of Molecular Ecology, with plenary talks in each of the journal subject areas, followed by panel discussions that will focus on future advances. To broaden participation, the symposium will include an online component, which will involve live streaming of the talks and discussions involving both in-the-room delegates and those participating online. The current speaker line-up is available at http://www.molecularecologist.com/ottawa-2012/. With the widespread implementation of the Joint Data Archiving Policy, large numbers of ecological and evolutionary data sets are becoming available. Data archiving, combined with the enormous rate at which new data are being generated, will allow us to address many questions in ecology and evolution with a degree of rigour and decisiveness that was not possible even several years ago. Thus, we strongly encourage the submission of meta-analysis studies to Molecular Ecology. Meta-analysis studies will typically be published as part of our ‘Invited Reviews’ section, which will be renamed ‘Invited Reviews and Meta-analyses’. Louis Bernatchez edits this section, and if you have a review or meta-analysis study that you would like to develop for Molecular Ecology please contact him (louis.bernatchez@bio.ulaval.ca) to ensure that it is an appropriate topic for the journal. We have been delighted by the positive response to the implementation of our Joint Data Archiving Policy at the beginning of 2011. Following discussions with our editors and authors, it is clear that the utility of archived data is greatly enhanced when the scripts used in the analyses are also made available. Given that these scripts may be a mix of proprietary and freely available code, we have decided against making their deposition compulsory, but we nonetheless strongly encourage authors to make these scripts available whenever possible. We wish to express our gratitude to our many referees for the donation of their time to the journal and to the discipline of molecular ecology; people who reviewed for us between 1 November 2010 and 15 October 2011 are listed at the end of this editorial. One of the most challenging aspects of editing a large journal like Molecular Ecology is maintaining consistency in our editorial decisions across the wide range of topics covered by the journal and among our highly respected but diverse subject editors. This is exacerbated by the rapidly changing norms in the field in terms of molecular tools and analytical approaches. An especially contentious issue concerns the publication of phylogeographic studies based on the analyses of a single locus. We sometimes choose not to review such studies because conclusions drawn from such limited data may not be reliable. However, we do not have a blanket policy to reject them without review because there are questions for which analysis of a single locus is appropriate. Authors, referees and editors have on occasion suggested that we establish guidelines regarding the minimum number of loci, populations and individuals for a study to be considered for publication in Molecular Ecology. However, we have been reluctant to formulate such guidelines because they would depend on the question being addressed, the kind of molecular markers employed, the geographic range of the focal taxa and so forth. Likewise, such guidelines would have to be modified on a yearly basis as standards of the field continue to ratchet upwards. Nonetheless, we feel that knowledge of current norms in Molecular Ecology with respect to these parameters would be useful to our authors and editors. Here we present information on the numbers of loci, populations and individuals employed by studies published in the journal from January to September 2011 (1-6; Tables 1–4). Average number of microsatellite loci employed by studies published in Molecular Ecology from January to September 2011. Error bars indicate one standard deviation of uncertainty. Average number of single nucleotide polymorphisms (SNPs) employed by studies published in Molecular Ecology from January to September 2011. Error bars indicate one standard deviation of uncertainty. Average number of nuclear genes employed by studies published in Molecular Ecology from January to September 2011. Error bars indicate one standard deviation of uncertainty. Average number of amplified fragment length polymorphisms (AFLPs) employed by studies published in Molecular Ecology from January to September 2011. Error bars indicate one standard deviation of uncertainty. Average number of populations analysed by studies published in Molecular Ecology from January to September 2011. Error bars indicate one standard deviation of uncertainty. Average number of individuals analysed by studies published in Molecular Ecology from January to September 2011. Error bars indicate one standard deviation of uncertainty. There are no real surprises. For example, an average of 17.4 microsatellite loci are employed in studies published in the journal in 2011 (Fig. 1; Table 1). The largest numbers of loci were assayed in studies of ‘Ecological Genomics’ and ‘Molecular Adaptation’ and the fewest in studies of ‘Kinship, Parentage and Behaviour’ (Fig. 1). This difference is reasonable given that many questions in the latter category can be answered with 6–10 loci, whereas there is almost no limit to the number of loci that can be useful in genome-wide scans for evidence of selection. Approximately half of microsatellite studies in the subject categories ‘Phylogeography’ and ‘Speciation and Hybridization’ also include information on organellar variation. However, the inclusion of organellar data was less frequent in other subject areas and absent in studies of ‘Kinship, Parentage and Behaviour’ (Table 1). The number of studies that employ single nucleotide polymorphisms (SNPs) for inference about pattern and process in molecular ecology is too small to make meaningful comparisons between subject areas (Fig. 2; Table 2). Nonetheless, it is clear that the number of SNPs employed is typically more than 10 times that of microsatellites. This is not surprising given that SNPs are more amenable to high throughput genotyping than microsatellites. Because the information content of SNPs, which are bi-allelic, is much less than that of microsatellites, it is reassuring that the reduced information content per SNP is more than made up for by the greater number SNPs that are assayed in an average study when compared to microsatellites. Interestingly, unlike microsatellite studies, articles that reported on SNP variation rarely included organellar data. Studies that employ nuclear genes for inference assay fewer loci than do comparable studies with microsatellite or SNP markers, although there are outlier studies (Fig. 3; Table 3). This is especially true for ‘Phylogeography’ studies or studies of ‘Ecological Interactions’ (Fig. 3). The relatively few nuclear genes assayed in many studies presumably reflect the time and expense associated with gathering sequence data for low-copy nuclear genes. Similar to the microsatellite studies, about half of the nuclear gene studies also assay variation in organellar DNA. Amplified fragment length polymorphism (AFLP) studies are rapidly being replaced in Molecular Ecology by sequence-based markers such as SNPs and restriction site–associated DNA (RAD) sequencing. Nonetheless, a substantial number of AFLP studies were published in Molecular Ecology in 2011 (Fig. 4; Table 4). The information content of an AFLP fragment is very low because AFLPs are bi-allelic and dominant. Thus, it is reassuring that all AFLP studies published in Molecular Ecology employed >100 loci and most studies assayed between 200 and 600 loci. In addition to the 155 studies listed in Tables 1–4, ten studies were published in Molecular Ecology during this period that were based solely on one or more organellar genes. Also, two of the studies that employed nuclear gene sequence data were based on a single gene. In total, 12 of 165 studies (7%) included in our survey are based on data from a single locus. Thus, while single locus studies are uncommon in the journal, they are not yet extinct. However, going forward we recommend that authors base their inferences on multiple loci if at all possible to ensure that their articles are sent out for review and are reviewed favourably by referees. We also examined current standards with respect to the number of populations and individuals typically assayed in the different subject categories included in Molecular Ecology (5, 6). Most studies analyse between 10 and 20 populations and between 200 and 500 individuals. There are two outlier subject categories: ‘Ecological Genomics’ studies typically analyse about half as many populations as studies from other subject areas (Fig. 5), whereas ‘Kinship, Parentage and Behaviour’ studies assay approximately three times more individuals than studies published in the other subject categories (Fig. 6). The latter observation is satisfying because studies in ‘Kinship, Parentage and Behaviour’ typically employ fewer loci than do studies in other categories, but make up for this by studying much larger numbers of individuals. The data presented above are intended to provide guidance regarding the numbers of populations, individuals and loci that were perceived by editors and reviewers as acceptable for publication in Molecular Ecology. However, we anticipate that these standards will continue to evolve, with increasingly large data sets made feasible by improved technology and methodologies. Moreover, sampling strategies and marker choices should be designed to best address the question motivating the study. As we stress in our guide to authors, our main criterion is that studies utilize molecular genetic techniques to address consequential questions in ecology, evolution, behaviour and conservation. If your sampling scheme, molecular genetic approaches and data analyses strategies are well designed for investigating an important question in ecology or evolutionary biology, then your study stands a very good chance of being published in Molecular Ecology. We handle a large volume of articles and sometimes make decisions that are unpopular with authors. While the majority of authors accept an unfavourable decision and make use of the feedback before submitting elsewhere, there are cases where it is worth contacting us to discuss the decision further. As there is sometimes confusion on what constitutes a valid reason for revisiting a decision, we have provided some guidance below regarding when a complaint is likely to be successful (an earlier version of this piece can be found at http://www.molecularecologist.com/). To begin, here are some general suggestions that will make it more likely that a challenge will be successful. First, we recommend not contacting the journal immediately after receiving a decision you disagree with, as the tone of these complaint letters is seldom constructive. Second, avoid using ‘Reply All’ when passing decision letters to co-authors, particularly if you include some invective, as these messages sometimes come back to the journal. Third, before you launch a challenge, please check with your co-authors, as they may prefer to submit elsewhere instead. It is worth noting that complaint letters that attempt to identify negative reviewers and dismiss their concerns on the grounds that they are prejudiced against your work are seldom successful. Guesses on reviewer identity are often wrong, and they also constitute an ad hominem attack on that person’s integrity. Furthermore, even if your nemesis did give a signed negative review, this is not grounds to overturn the decision. The editor was almost certainly aware of this issue when they decided to reject your article, and the rejection implies that the editor either agrees with their criticisms of your work or else based the rejection on comments of another referee. Once you have had a few days to read through the decision, and you are still convinced that it is unfair, then compose a carefully worded letter that explains why the decision needs to be revisited. Be warned that challenging a decision along the following lines almost never works out: – ‘You gave my paper a ‘reject, encourage resubmission’ decision, but it should have been an ‘acceptance with minor revisions’. For Molecular Ecology, a reject-encourage typically indicates that the article needs extensive changes (potentially including additional data) and that the editor wants to send it through the review process again. It is also generally best to respond to individual reviewer and editor comments as part of the resubmission rather than to challenge the decision itself. – ‘Two of the reviewers loved it and only suggested minor edits, but Referee 3 was much more negative and made you reject it’. A decision is not based on an average of the review recommendations, and if the comments of Referee 3 convinced the editor that the article is flawed, no amount of adulation from reviewers who missed these problems is going to change that. – ‘I accidentally included the wrong dataset/analyses/conclusions, and this is why the paper was rejected’. We can only review the materials that have been sent to us, so please check your manuscript files carefully before submitting. – ‘You published a very similar paper back in 2006, so it is inconsistent to reject our manuscript now’. The field is constantly changing and the standards for publication are always moving higher. If your data and methods were cutting-edge five years ago, it saves everyone time if you submit to a more specialized journal. Furthermore, even if a manuscript similar to your own has appeared in the most recent issue, that accepted manuscript could have other merits that led to its acceptance. Please also bear in mind that we have likely already rejected numerous other similar articles this year, and those decisions are not made public. – ‘We resubmitted our paper, but while the original reviewers liked the new version, the comments you received from the new referees made you reject it’. Molecular Ecology has a policy of only allowing one ‘reject, encourage resubmission’ per article, which prevents interminable rounds of ‘reject-encourage/resubmission/finding new reviewers/they find new problems/yet another reject-encourage’. Resubmitted articles do get accepted about 70% of the time, so clearly it is possible to prepare a new version that convinces both the original and the new reviewers that the manuscript is worth publishing. Lastly, if none of the original reviewers were able to look at the resubmission, our only option is to use new referees. So when should you challenge a rejection? The reason that most often leads us to revisit a decision is evidence that the peer review process was flawed in some way that unfairly biased the evaluation of your article. For example, a reviewer might claim that a particular analysis is vital to your study. However, if the analysis is actually in the article and somehow neither the editor nor the reviewer noticed it, then certainly the decision would be revisited. Similarly, if a reviewer convinces the editor that some aspect of the methods is fundamentally flawed, but the criticism can be shown to be incorrect, then it would be worth appealing the decision. It should be noted that while instances such as the two described above would be grounds for appeal, there is no guarantee that the decision will be overturned. It might be, for example, that there were other major flaws in the article that were largely responsible for its rejection rather than any mistakes made by the referees or editors. We do occasionally overturn decisions, and if we are convinced by the authors that a mistake was made in the review process resulting in a faulty decision, we will either alter the decision or invite a new version of the article. This is infrequent, about one in every 50 rejections, but it does happen! All data for this manuscript are given in Tables 1–4. We are very grateful to the large number of individuals who have contributed to the field of molecular ecology by reviewing manuscripts for the journal. The following list contains people who reviewed articles for Molecular Ecology between 1 November 2010 and 15 October 2011. Marco Abbiati Patrick Abbot Cathryn L. Abbott Yoshihisa Abe Maria Ana Aboim Karina Acevedo-Whitehouse Guillauve Achaz Silvia Gonzalez Acinas Jennifer R. Adams Mark Adams Sina Adl Peter H. Adler Aneil Agrawal Andres Aguilar O. Mario Aguilar Ramiro Aguilar Gabriela Aguileta Robert Ahern Dirk Ahrens Sally N. Aitken Mikael Akesson Joshua Akey Ihsan A. Al-Shehbaz Cedric Alaux Dirk Albach Rafael G. Albaladejo Filipe Alberto Miguel Alcaide Alexandre Aleixo Jussi S. Alho Sajid Ali Robin Allaby Dominique Allaine François Allal Geraldine A. Allen Fred W. Allendorf Dilara Ally S. Elizabeth Alter David Althoff Diego F. Alvarado-S. Nadir Alvarez Paulo C. Alves Anthony S. Amend William Amos Liselotte W. Andersen Corey D. Anderson Frank Anderson Joseph H. Anderson Kirk E. Anderson Leif Andersson Malte Andersson Peter Andolfatto Carl André Nikos Andreakis Marco Andrello Rose L. Andrew Cecile Ane Lisa Angeloni Bernard Angers Stephen Ansell Tiago Antao Agostinho Antunes José M. Aparicio Joseph J. Apodaca Julien April Smita Apte Hitoshi Araki Frederick I. Archer Elizabeth Archie William R. Ardren Paul Arens Dave Armitage Jean-Francois Arnaud Sophie Arnaud-Haond Matt Arnegard Michael L. Arnold J. W. (Pim) Arntzen Rosa Arroyo-Garcia Wolfgang Arthofer Tom Artois Rebekka Artz Nadia Aubin-Horth Ralf Aurahs Didier Aurelle Frederic Austerlitz Jeremy Austin Brian J. Avery John Avise Diego Ayala David Ayre Debra Ayres Abdu F. Azad Eric Baack Wieslaw Babik Roberto Bacilieri Niclas Backstrom Cecile Bacles C. F. Baer A.-G. Bagnères-Urbany Wei-Ning Bai Donovan Bailey John Bailey John Baines Andrew Baird Allan J. Baker Robert Baker Christopher Balakrishnan Jose Luis Balcazar David Balding Laura Baldo N. Balkenhol Sam C. Banks Anna A. Bannikova Anne-Laure Bañuls Paul H. Barber Martin J. Barbetti Britany Barker Daniel Barker Marta Barluenga Apurba K. Barman Ian Barnes Ross Barnett Craig Barrett Rowan Barrett Nicholas V. Bartell Nick Barton Detlef Bartsch Patrick Basset Arnaud Bataille P. Bauda Alex Baumel Iliana B. Baums Line K. Bay Eric Bazin Gemma Beatty Jean Beaulieu Nicolas Bech Ronan Becheler Trevor Bedford Trevor Beebee Peter Beerli Dominik Begerow Adi Behar Luciano B. Beheregaray Rayna C. Bell Thomas Bell Eva Bellemain Gilles Bena Keith Bennett Stephen J. Bent Paul Bentzen E. C. Berg Sara Bergek Sarah Bergemann Patrick Bergeron Stewart Berlocher Giacomo Bernardi Daniel Berner Theresa M. Bert Domonique Berteaux Karine Berthier Cécile Berthouly Stefan Bertilsson Giorgio Bertorelle Martine Berube Nora Besansky Guillaume Besnard Ricardo Betancur-R. Martin Beye Etienne Bezault Debashish Bhattacharya Ryan Bickel Martin Bidartondo Roman Biek Sarah Arnao Billeter Christopher Bird C. W. Birky Andrew Bissett Annie Frank Michael S. Peter H. Andrew J. Jennifer L. Daniel H. J. L. J. Didier Elizabeth G. Andrew Nicholas Jean Brian C. K. Sarah R. Ian Daniel G. L. Sara Daniel A. C. M. Jennifer A. Michael John Christopher P. Thomas Andrew V. Joseph Joshua E. Patrick C. Thomas J. A. Michael Frank Jeremy Theresa Julien Ana Ryan J. J. M. Michael David B. Ana A. Maria C. Michael Stephen Martin Frank D. R. Mark Robert W. David G. Deborah Charlesworth A. H. Stephen E. Patrick I. Mark R. M. Alberto Elizabeth L. Keith Andrew Anthony Fred Robert I. John A. Robin David G. Marco M. J. B. W. Alex Sarah Craig D. Allan J. Bernard J. D. E. A. Tom Robert H. I. Thomas D. M. S. C. John A. S. David William S. S. Michael Marta H. Guillaume Sophie L. E. Eric F. Stefan Nicolas David Michael K. Andrew Jennifer Joseph Carl Christopher Ian A. E. Jose Alexandre F. F. S. Stephen David E. A. Tom V. Thomas Alex J. Peter J. J. Eric David Andrew L. V. P. Keith Luis B. Robert A. A. Mark Ryan R. J. Laura S. J. Guillaume G. I. Anna Cecile J. C. J. Paul J. A. Brian F. Marco F. David L. C. Debra Martin C. Matt David J. Ian Alex D. M. G. Diego Brian L. William Alexandre R. O. Elizabeth L. C. L. Daniel J. W. Patrick R. E. Peter Michael G. Ryan C. J. John John O. J. M. Roberto C. A. J. H. Robert Thomas Luis D. J. Thomas John Stephen R. S. Frederick S. J. Gonzalez Gonzalez Ana M. Sara Michael R. David Anna Dave Jennifer Andrew John William S. Anthony L. Martin E. Paul F. Frederic Guillaume Thomas Gilles R. Ryan J. Frank Dominik David C. L.

Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.