Editorial and retrospective 2010

The year 2009 has been another excellent period for Molecular Ecology. The impact of the journal increased from 5.17 in 2007 to 5.33 in 2008; it currently ranks sixth in impact among 124 journals listed in ISI's Ecology category, and fifth out of 39 journals listed in ISI's Evolutionary Biology journal category. Molecular Ecology also increased in size, with 403 articles published in 2008, making it the largest Evolutionary Biology journal and second largest Ecology journal. We also have increased the speed with which papers are published. For original and resubmitted manuscripts, we take an average of 30.4 days to make a decision (including those returned without review). For papers that are peer reviewed, we return a decision within an average of 40.6 days. Accepted manuscripts are moved to Online Early publication in 41 days (on average), with the print version appearing c. 23 days later. Thus, the time from submission to print publication of a typical paper averages 105 days or c. 3½ months. We thank our academic editors, reviewers, as well as our editorial and production staff, for their efficient processing of manuscripts. Several important policy decisions were made at our editorial board meeting this summer. These are reported below: Due to concerns about the availability and preservation of data from ecological and evolutionary studies, most of the leading journals in ecology and evolution will soon be introducing a new data archiving policy (Whitlock et al. 2010). Our current archiving policy applies only to DNA sequence data, which must be made available on GenBank or another public archive. However, the new policy will be applicable to all data-supporting results in papers published in Molecular Ecology. A more lengthy rationale for the policy can be found in Whitlock et al. (2010). Molecular Ecology's policy will read as follows: Molecular Ecology expects, as a condition for publication, that data supporting the results in the paper should be archived in an appropriate public archive, such as GenBank, Gene Expression Omnibus, TreeBASE, Dryad, or the Knowledge Network for Biocomplexity. Data are important products of the scientific enterprise, and they should be preserved and usable for decades in the future. Authors may elect to have the data publicly available at time of publication, or, if the technology of the archive allows, may opt to embargo access to the data for a period up to a year after publication. Exceptions may be granted at the discretion of the editor, especially for sensitive information such as human subject data or the location of endangered species. Our policy will not go into force until January 2011, but in the meantime, we encourage authors to submit their data to the relevant repositories. DNA sequence data from either Sanger or next generation sequencing should continue to be archived in GenBank or another public database. Expression data should be submitted to the Gene Expression Omnibus or an equivalent database, whereas phylogenetic trees should be submitted to TreeBASE. More idiosyncratic data, such as microsatellite allele frequency data, can be archived in a more flexible digital data library such as the US National Science Foundation-sponsored Dryad archive at http://datadryad.org. Once the policy is in force in 2011, authors will be expected to archive the data supporting their results and conclusions, along with sufficient details so that a third party can interpret them correctly. As discussed by Whitlock et al. (2010), this will likely 'require a short additional text document, with details specifying the meaning of each column in the data set. The preparation of such shareable data sets will be easiest if these files are prepared as part of the data analysis phase of the preparation of the paper, rather than after acceptance of a manuscript'. In spring 2008, we moved from an e-mail-based manuscript management system to a web-based system. An unexpected consequence of this transition has been a substantial increase in the speed of the review and publication process for all papers submitted to Molecular Ecology, essentially rendering our separate 'Fast Track' editorial process obsolete. Nonetheless, we feel that there is a need to accommodate high impact, short format research papers. Thus, we have replaced the Fast Track category with a new 'From the Cover' section. As with Fast Track, the 'From the Cover' section contains papers of exceptional interest to a wide audience and that address significant questions in ecology, evolution, behaviour or conservation. We will consider papers previously reviewed by other high-impact journals, with the added innovation that we will utilize all documents associated with the previous review process. The use of these review materials does not guarantee acceptance or that the manuscript will not receive external review. However, papers with largely positive reviews from leading general science journals will receive immediate consideration for publication and may not require additional review. If the authors hope to avoid additional review, they need to revise the manuscript according to reviewers' comments and submit a cover letter that describes these changes and explains why their paper would be appropriate for publication as a Cover article in Molecular Ecology. Upon receipt, Senior Editor Bob Wayne will immediately review submissions for content and impact. Submissions that do not meet stringent standards will be returned at that stage without review, or they will be invited for resubmission as regular full papers. From the Cover manuscripts must be brief and focused, in 4000 words or less, with up to five display items (tables and figures). Accepted articles will be highlighted in the journal on the cover and in the table of contents and will frequently be featured in commentaries and press alerts. Although only a handful of papers published in Molecular Ecology involve experiments with animals, it is important these experiments be conducted properly, minimize suffering and comply with relevant regulations. Thus, we have developed the following policy: We expect that papers submitted to Molecular Ecology comply with the laws on animal experimentation in the countries where the work was conducted. All experimental procedures must be properly described and should be designed to minimize the suffering of animals. We are pleased to announce that after a brief hiatus in 2009, Molecular Ecology has two excellent special issues lined up for 2010. The first, due in February and edited by Diethard Tautz, Hans Ellegren and Detlef Weigel, is entitled 'Next generation Molecular Ecology'. The papers in this issue offer a glimpse of the enormous potential that next-generation sequencing technology offers researchers in ecology and evolution: the chance to tackle existing problems with tremendous statistical power, and the ability to test new hypotheses unimaginable a few short years ago. The second special issue of 2010 will focus on 'Landscape Genetics', another rapidly developing and increasingly important field. The organizers, Lisette Waits and Victoria Sork, have brought together empirical and methodological contributions from leading workers in this area, with the aim of establishing the benchmark for research in this nascent field. We would like to extend our gratitude to the guest editors of both issues for their hard work so far, and we are delighted that they chose Molecular Ecology to showcase these cutting edge studies. A recent article in Oikos (Johnson et al. 2009c) asks the provocative question: where is the ecology in molecular ecology? The article reports on a survey of research published in Ecology, Evolution, and Molecular Ecology. Evolutionary studies are shown to be considerably more likely to employ molecular tools than are ecological studies. Also, papers published in Molecular Ecology are more likely to have an evolutionary than ecological focus, a trend we have commented on previously (Rieseberg & Smith 2002). So why do ecologists less frequently employ molecular techniques than evolutionary biologists? Johnson et al. (2009c) put forward two possible explanations. One possibility is that, for cultural reasons, the ecological sciences have been more resistant to the use of molecular tools than evolutionary biology. A second possible explanation, which we find more satisfying, is that many ecological questions can be answered without the aid of molecular techniques, whereas most evolutionary questions clearly benefit from molecular data. Nonetheless, as editors of Molecular Ecology, we have been pleasantly surprised at the many creative ways in which molecular tools are being used to address ecological questions. We also believe that the molecular biology techniques have infiltrated ecology to a greater extent than is generally recognized. Some of the ecological topics that have been addressed with molecular tools over the past year include: ecological speciation (Galindo et al. 2009; Sadedin et al. 2009), population demography (Curtis et al. 2009; Jackson et al. 2009; Liu & Ely 2009; Lundemo et al. 2009), population dynamics (Bayon et al. 2009), evolutionary ecology (Aubin-Horth & Renn 2009; Cartwright 2009; Latta 2009), behavioural ecology (Beekman et al. 2009; Berg et al. 2009; Du & Lu 2009; Johnson et al. 2009a), disease ecology (Abrego et al. 2009a; Almeida et al. 2009; Jaatinen et al. 2009; Rudge et al. 2009), macroecology (Elias et al. 2009; Parnell et al. 2009; Thomas 2009; Wilson 2009), community ecology (Abrego et al. 2009b; Carletto et al. 2009; Clare et al. 2009; Haselkorn et al. 2009), invasion ecology (Chun et al. 2009; Henry et al. 2009a; Mikheyev et al. 2009; Rollins et al. 2009), population interactions (Reisser et al. 2009), transgene escape (Pineyro-Nelson et al. 2009b; Snow 2009) and so forth. Thus, we feel that the content of Molecular Ecology is becoming more relevant to ecologists, a trend we hope will accelerate in the future. The 2009 Molecular Ecology Prize was awarded to Professor Terry Burke, of the University of Sheffield. Terry was the first chief editor of Molecular Ecology, and he pioneered the use of DNA fingerprinting methods for parentage analyses in birds. He also has made significant general contributions to our understanding of the molecular and quantitative genetics of natural populations. A biography of Terry and his contributions to molecular ecology can be found on page 23 of this issue. We regret to report that several of our longest serving and/or most distinguished editors have stepped down this year: Roger Butlin, John Dallas, Franco Widmer and John Wakeley. We thank them for their many contributions to the journal. Fortunately, several distinguished scientists have agreed to join our editorial board to serve both as replacements for our departing editors and to help handle the ever-increasing number of submissions (we expect to receive >1400 submissions this year). The new editors include Sean Rogers (University of Calgary), Rosemary Gillespie (University of California, Berkeley), Aurelie Bonin (Indiana University), Roger Thorpe (University of Bangor), Tatiana Giraud (Université Paris-Sud XI), Daniel Falush (University of Oxford), Madeleine van Oppen (Australian Institute of Marine Science) and Dany Garant (University of Sherbrooke). In addition, we will also welcome Arianne Albert as a second News and Views Editor; she will be assisting Nolan Kane with our increasingly popular Perspectives section. Welcome to all of you!! Lastly, we wish to express our gratitude to our many referees (listed below) for the donation of their time to the journal and to the discipline of molecular ecology. In recent years, we have begun publishing a retrospective (below) to discuss and highlight significant advances in molecular ecology in the previous year. This is part of a broader effort to showcase the science published in Molecular Ecology, which includes our News and Views section, cover banners, press releases and so forth. For most of the 20th century, speciation in the absence of geographic isolation (i.e. sympatric speciation) was considered to be unlikely because of the homogenizing effects of gene flow. However, recent theoretical work indicates sympatric speciation is feasible in the presence of strong disruptive natural selection and/or genetic architectures that minimize the antagonism between selection and recombination. The problem has been finding convincing empirical examples (Coyne & Orr 2004). A number of studies published in Molecular Ecology in 2009 tackled this problem. Although allopatric divergence is considered most likely in some instances (Guzik et al. 2009; McBride et al. 2009; Virgilio et al. 2009), several apparent examples of sympatric speciation are discussed, including Schizothoracine fish (Zhao et al. 2009), coral barnacles (Tsang et al. 2009), marine snails (Galindo et al. 2009; Sadedin et al. 2009) and cichlid fishes (reviewed in (Salzburger 2009). Also, early stages of sympatric divergence were characterized in Capsella (Hameister et al. 2009) and cotton–melon aphids (Carletto et al. 2009). The journal also saw a follow-up study of one of the most famous cases of sympatric speciation involving two sister species of the palm genus Howea from Lord Howe Island. Because the two palms are restricted to this very small island and are wind-pollinated, it seems likely that they diverged in sympatry (Savolainen et al. 2006). Nonetheless, this scenario has been questioned because Lord Howe Island was larger in the past, possibly affording opportunities for partial geographic isolation (Stuessy 2006). The present study showed that genetic structuring in both species is low, implying that spatial separation played a minor role, if any, in the development of reproductive isolation (Babik et al. 2009a). Likewise, little admixture was observed between the two species, indicating that the reproductive barriers are strong. These results confirm that the Howea palms likely do represent a legitimate example of speciation in the absence of significant geographic barriers to gene flow. The widespread application of molecular marker approaches to the analysis of natural populations has made it feasible to estimate the frequency and direction of hybridization involving numerous species of animals and plants. However, very few studies have attempted to explain variation in hybridization rates. A potentially important factor, first posited by the ichthyologist Carl Hubbs, is the relative abundance of the hybridizing species. Hubbs reasoned that hybridization would be most frequent when species abundances were unbalanced because a locally rare species would encounter mostly heterospecific gametes. Lepais et al. (2009) tested this conjecture by analyzing more than 2000 European oak trees with 10 microsatellite markers. Hybrids were surprisingly common, conservatively representing between 11% and 31% of genotypes within sampled populations. As predicted by Hubbs, locally dominant species were under-represented among the hybrids. Hybridization can have both negative and positive consequences for biodiversity. On the negative size, hybridization can lead to the breakdown of reproductive barriers and merger of species (so-called de-speciation). It can also lead to the extinction of rare populations through outbreeding depression or through genetic assimilation by a more widespread congener. Positive outcomes include increased rates of adaptive evolution, the formation of new races and species, and the reinforcement of reproductive barriers. Unfortunately, little is known about the relative importance of these different outcomes. However, a significant literature on the topic is being developed in Molecular Ecology and other journals, and ordering the importance of the various consequences or outcomes of hybridization is now becoming feasible. A surprise has been the very high number of instances in which hybridization appears to be contributing to adaptive evolution. For example, this year in Molecular Ecology we were able to identify six examples where hybridization was thought to be contributing to adaptation (Gagnaire et al. 2009; Gaskin et al. 2009; Hird & Sullivan 2009; Nolte et al. 2009; Pillon et al. 2009; Zidana et al. 2009), but only one case where it was a serious extinction threat (McDevitt et al. 2009). One of the most gratifying outcomes of phylogeographic studies has been the frequent discovery of cryptic species––species that are similar in morphology, but appear to represent reproductively independent lineages. Reproductive independence is usually inferred from the discovery of significant divergence in molecular markers and/or reciprocal monophyly in phylogenetic trees. Examples published in Molecular Ecology in 2009 are listed in Table 1. A major focus of Molecular Ecology since its inception has been the description and explanation of patterns of genetic variation within species. In particular, there have numerous attempts to identify and order the factors that account for spatial genetic structure. Three factors have emerged as most explanatory: habitat adaptation, geographic distance, and physical features of the environment. However, molecular ecology is a science of case studies, and conclusions require integration of information from numerous studies. In 2009, the majority of papers addressing this question in Molecular Ecology found evidence that geographic distance and physical barriers were most likely to influence patterns of gene flow and population genetic structure (Table 2), whereas habitat adaptation had a much lesser role. However, there are a number of reasons why the importance of habitat adaptation might be under-estimated. First, habitat adaptation is more difficult to quantify and its effects on spatial genetic structure are less frequently tested than geographic distance or physical barriers. Second, habitat adaptation is expected to have chromosomally local effects, whereas geographic distance and physical barriers are anticipated to have genome-wide effects. Because most studies published in Molecular Ecology sample only a small fraction of the genome, they are unlikely to detect changes in genetic variation due to local selection. In future, as more genome scans are published in the journal, we expect to evidence of a for habitat adaptation in the spatial genetic structure of populations. The effects of habitat are not Although several studies et al. 2009; Liu et al. 2009) found that habitat lead to spatial genetic structure and variation within this was not found to be the et al. et al. (2009) and et al. (2009) found little in genetic variation in and high and A more general survey of genetic variation in rare and endangered populations found very genetic variation in some rare species et al. 2009; et al. 2009; et al. 2009; Johnson et al. but surprisingly high variation in et al. 2009; et al. 2009; Henry et al. 2009b; et al. 2009; & 2009). In more common, species, high variation and little spatial genetic structure are this is found to be the case et al. 2009; et al. 2009; et al. 2009) due to high and/or other species high spatial genetic with little gene flow between populations et al. 2009; & 2009; et al. 2009). The importance of including markers in of is becoming increasingly of such studies published in 2009 in Molecular Ecology (Table only & 2009; et al. 2009; et al. 2009; & Johnson 2009) full between and markers. a marker may not be to the full of an one study with five different markers et al. 2009) important in the of the with evidence of hybridization and among lineages. for of between and markers include hybridization and et al. 2009; et al. 2009), of but not et al. 2009), between and rates & 2009; & 2009), and in the of evolution of and markers et al. 2009). studies on species have been published over the past with a between the number of of the invasion and the of genetic variation present in the species (Table Several species thought to have have high of genetic variation & 2009; et al. 2009; et al. 2009), in one case than in populations et al. 2009). a few species with have variation et al. 2009a; et al. 2009), as those with few et al. 2009; et al. 2009). 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(2009) found a in a population of with a with had the is between genome-wide and the of and a research effort has been at and For example, et al. (2009) found that the of that with were both less and less likely to in their first year. One problem with these studies is that of may not et al. 2009), and there are also in the microsatellite data to both parentage and the frequency of between 2009; & 2009). One possible is to use very of these studies into the This was by et al. used to the effects of and selection on the found apparent of on but to detect both and selection in several of the on have increasingly in Molecular Ecology over the past few years, a effort at understanding the ecology, evolution and population structure of (Table This is for as these can rapidly et al. 2009; et al. 2009), on et al. 2009; et al. 2009) or within a geographic in by et al. 2009; et al. 2009). on and are as more can and without et al. 2009). the and of these new is clearly in the absence of information on the existing population structure. An major on the escape of has to in the of Molecular Ecology. As highlighted by Snow researchers have found evidence of of locally of by gene flow from in et al. 2009) and (Pineyro-Nelson et al. 2009a), the cases involving the escape of A by & 2009) that the evidence for transgene escape was not and that the evidence of in populations were to et al. that the by and are to and out that their results are by sequence and data. has on the of genetic between populations. a new which he is to for in allele & (2009) a on previously published studies, and was with genetic a potential out by that and can be by either or were shown to be with each other in this data so may be largely & (2009) used to that is on that it be in of gene flow. In his (2009) out the of each that is for because of its to as well as but that is as a of We a of gratitude to the number of have to the discipline of molecular

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