Editorial 2023

Abstract

Molecular Ecology (MEC) is committed to The Declaration on Research Assessment (DORA), which recognizes the need to improve the ways in which researchers and the outputs of scholarly research are evaluated (https://sfdora.org/). For this reason, we will no longer be promoting the impact factor of MEC as a standalone metric, but instead will highlight several different metrics that demonstrates it quality and influence in the community. These include the total number of citable items in the journal in 2021 (468, ranking third out of 52 journals in Clarivate's list of Evolutionary Biology journals), total citations (45,664, third of 52), journal impact factor (6.62; seventh of 52), and EigenFactor – which measures the number of times articles from the journal published in the past five years have been cited in the focal year (0.033, fourth of 52). The latter arguably offers a more accurate measure of journal quality than the journal impact factor. Molecular Ecology also ranks fifth among ecology journals and fourth among evolution journals as measured by Google Scholar's h5-index, which is the h-index for articles published over the past five years. This can be viewed as a comprehensive measure of journal influence. Lastly, the journal continues to see large increases in annual article downloads, which reached close to 1.9 million in 2021. Open access (OA) has been a growing talking point across the scientific community for a number of years, and our recent annual meeting for Molecular Ecology and its sister journal, Molecular Ecology Resources (MER), discussed this topic in depth. OA has been gathering pace in ecology and evolutionary biology related subjects and the proportion of OA articles is growing each year in both journals; with 40% of the total content published in MEC in 2021 being Gold OA funded. The driving force behind the growth in OA is the increasing number of mandates introduced by funders and institutions, which require that the research they fund is open and unrestrictive upon publication. This has led to fundamental changes to publishing business models and has required scholarly journals to rethink their processes and strategies in order to adapt to – and thrive – in this new OA environment. The concept of making the transition from a hybrid subscription title to a fully OA journal is not new, and we anticipate that the vast majority of journals will move toward a gold OA model eventually. Our publisher, Wiley, has been supporting the transition to OA in numerous ways, mainly through offering flexible models to libraries and institutions in the form of Transformational Agreements that help to migrate existing subscription spend to fund OA publishing. These are going a long way in supporting institutional requirements and complying with policy and funder mandates so that we can all transition to OA in a sustainable way. The benefits for publishing open access are clear. OA makes research findings available to everyone; driving forward the pace and strength of global innovation and invention, and authors retain copyright of their work. Although there is no one consensus on the best way to achieve and maintain OA yet, it is clear that it is the direction of travel for journals and it is here to stay. At the editorial office for MEC and MER, we have therefore reached a point in which we need to acknowledge that the future almost certainly involves a transition to fully OA and follow the trajectory of a growing number of journals that have transitioned to OA already. It is important to highlight that our criteria for manuscript evaluation, the peer review process and our publication ethics will remain unchanged when this happens, and we will continue to publish rigorous research and uphold our community's standards. We recognize that the costs of OA may create barriers to publication for some authors and this has been a key talking point with our publisher. There is still much to be done to address areas of inequality with OA and we must look at new ways to support authors without access to funding. Wiley offers automatic APC waivers and discounts to authors from countries listed under Research4Life, and it is also worth checking with your institution if they have special open access arrangements with Wiley, such as a Wiley Open Access Account or Transformational Agreement. We look forward to the continued support of our authors, reviewers and readers when the time comes for the journals to adopt this new phase of publishing. The Nagoya Protocol is an international agreement to ensure that the benefits arising from the utilization of genetic resources are shared equitably (https://www.cbd.int/abs/). In 2020, we published a joint editorial to express our support for the Nagoya Protocol and the principle of benefit sharing, as well as to educate our authors and readers about their responsibilities under the Protocol (Marden et al., 2022). Concomitantly, we introduced a requirement that research published in the journals be compliant with the Convention on Biological Diversity (CBD) and Nagoya Protocol agreements. We also revised our Data Accessibility Statement (now Data Accessibility and Benefit-Sharing Statement) to encourage authors to disclose benefits generated by their research under the Nagoya Protocol. Our hope was that identification of the benefits generated from biodiversity research would help the general public, policymakers, and influencers better understand current practices in the research community, as well as the value of such research for biodiversity conservation and capacity building. We also suspected that asking researchers to report on benefit sharing would encourage them to evaluate their own research practices to ensure that they are fully aligned with the CBD and Nagoya Protocol agreements. We were recently contacted by the Secretariat of CBD, which is supportive of our efforts and had questions about uptake in Molecular Ecology and Molecular Ecology Resources. Therefore, we queried Manuscript Central about responses to our question regarding compliance with the Nagoya Protocol. About two thirds of our papers claim to be compliant and one third claim that the Protocol is not applicable to their research (Table 1). We also surveyed manuscripts published in MEC in 2022 to estimate the proportion of papers reporting on benefit sharing, which is low (circa 20%). We are hoping that as awareness of the Nagoya Protocol and benefit-sharing requirements increases, more authors will report on the benefits from their research. Lastly, we have copied the most common reported benefits below to provide insights about benefit sharing in the MEC community: Most frequent: Benefits from this research accrue from the sharing of our data and results on public databases (all statements, although the wording varied). Also common: Research will inform conservation efforts. A research collaboration was developed with scientists from the countries providing genetic samples, and all collaborators were included as coauthors. Results shared with provider community. So far, >90% of papers reporting on benefit sharing included coauthors from the country or countries providing the samples. Molecular Ecology continued to have a strong presence in social media during 2022. As Figure 1 shows, contributions from the social media team to Twitter increased similarly to previous years, and these tweets were visited frequently. The number of followers has grown to more than 6300, making the MEC and MER Twitter feed (@molecol) a highly diverse and attractive platform for scientists and the public. Although the future of social media platforms can be uncertain, they will continue to be one of the most direct sources of information about the science published in MEC and MER. Our efforts to provide access to an in-house information source about molecular ecology research, Spotlight, continued during 2022. The 132 posts published since 2019 showcase interviews with authors and highlight many impactful papers published in MEC and MER. So far, Spotlight has had more than 19 k visitors and has been viewed over 30 k times. This platform is a powerful hedge against the vicissitudes of public and private services for international discourse and rapid dissemination of information. The molecular ecology community benefits from an open and welcoming conversation, so social media platforms like @molecol and Spotlight are invaluable mediators of the community's zeitgeist. A fundamental mission of MEC and MER, is to provide hands-on training on editorial duties to outstanding early career researchers (ECRs). PhD and postdoctoral researchers who have published excellent papers in the two journals continue to join our Junior Editorial Board (JEB). With their expertise and enthusiasm, they contribute to multiple aspects of the running of the journal and mentor each other on the learning and execution of social media, selection of reviews and special issues, and how to remain alert to the best research in the preprint world and that needs a home like MEC or MER. This diverse group of young researchers has infused novelty and charisma into the journal and will continue to do so in years to come. Stay tuned for how the JEB evolves in 2023 and continue to access the excellent resources they contribute to the community. The Molecular Ecology Prize is awarded annually to “an outstanding scientist who has made significant contributions to molecular ecology,” as selected by an independent award committee. In 2022, the Prize was awarded to Dr Kerstin Johannesson, Professor of Marine Ecology, University of Gothenburg, Sweden. Trained as a marine ecologist, her research over the past 40 years has focussed on understanding how marine organisms become adapted to their environment. Toward this goal, she performed pioneering molecular ecology work that fully integrated ecological and molecular approaches to study the sea snail, Littorina saxatilis, which she developed into a model species. Her work has inspired numerous researchers across Europe to also use Littorina as an ideal model to study the “tug of war” between evolutionary forces that have driven ecotypic divergence across different habitats of littoral zones. A biography of Dr Johannesson and her contributions to the field of molecular ecology can be found on pages 26–29 of this issue. The Harry Smith Prize recognizes the best paper published in Molecular Ecology or Molecular Ecology Resources in the previous year by graduate students or early career scholars with no more than five years of postdoctoral or fellowship experience. The winner of the 2022 Harry Smith Prize was Arne Jacobs from the University of Glasgow who has been awarded the Harry Smith Prize for his “From the Cover” article in MEC, “Alternative splicing and gene expression play contrasting roles in the parallel phenotypic evolution of a salmonid fish” (Jacobs & Elmer, 2021). Jacobs specializes in the study of the genomic and gene regulatory basis of evolution and development in fish and lampreys. The award committee, which is made up of JEB members, also recognized two outstanding nominees as second and third runners-up: Angel G. Rivera-Colón and Jana Wold, respectively. Rivera-Colón led a “From the Cover” article in MER, presenting a software package to simulate RADseq data for protocol optimization (Rivera-Colón et al., 2021); and Wold led a synthetic review of the potential value in considering structural genomic variants in conservation genomics (Wold et al., 2021). The prize is named after Professor Harry Smith FRS, who founded the journal and served as both its Chief and Managing Editor during the journal's critical early years. He continued as the journal's Managing Editor until 2008, and went out of his way to encourage early career scholars. In lieu of a scientific society for molecular ecologists, Molecular Ecology offers an intellectual home for the molecular ecology community. This includes our social platform (see above), which focuses on research published in Molecular Ecology and Molecular Ecology Resources, our News and Views section, special issues, reviews, and so forth. We also support the Molecular Ecologist blog (http://www.molecularecologist.com/), which covers research and news reported in venues beyond Molecular Ecology, and with an eye to the interests of people who are not necessarily experts in the field. Lastly, we use our annual editorial to highlight scientific advances published over the past year in the journal (below). Each year, a select number of noteworthy articles are nominated by members of the editorial board to receive News and Views Perspectives. Among these, a few exceptional pieces are highlighted as From the Cover manuscripts. The From the Cover pieces published in 2022 demonstrate how combinations of innovative perspectives, methods, and molecular tools continue to advance the breadth and depth of our knowledge of molecular ecology. At the heart of evolutionary biology is the question of how biodiversity arises and is maintained over time and through space. Three of this year's From the Cover manuscripts directly explore this theme, examining the forces underlying biogeographic patterns (Salis et al., 2022), recent species diversification (Jaynes et al., 2022), and local adaptation (Wright et al., 2022). In their From the Cover manuscript, Salis et al. (2022) examine the dispersal of two groups of megafaunal carnivores, brown bears and lions, from Eurasia into North America amidst Pleistocene cycles of glaciation and sea level change. The authors sequenced near-complete mitochondrial genomes from an impressive number of subfossil samples (103 bears, 39 lions) from across Beringia, analysing these data sets using a novel phylogeographic framework. Their results reveal remarkably similar patterns of population dynamics among the two groups, characterized by multiple distinct waves of migration, synchronous local extinctions, and population turnover. As Gaughran and vonHoldt (2022) note in their paired perspective, the authors' rigorous methodology allows them to show that these demographic changes are linked to periods of climatic change, and enables them to paint an unprecedented portrait of the dispersal of these two groups of carnivores from 20,000–100,000 years ago. Overall, the work of Salis et al. (2022) provides important context for understanding the role of landscape change in the complex ecological and evolutionary history of megafaunal biogeography, and sets the stage for work on other historically impacted regions (e.g., Japan, Mesoamerica), as well as work exploring how contemporary climatic change will impact extant biodiversity. A From the Cover article by Jaynes et al. (2022) explores diversification of a charismatic lineage of giant tree frogs from Central and West Africa. The large sampling effort (230 individuals across 109 localities) and integration of behavioural, genetic, ecological and geographical data allows the authors to gain a nuanced understanding of the phylogeography of these three species at both the inter- and intraspecific levels. Their results show that the group of frogs diversified across a historically fragmented landscape and that species boundaries are now maintained in secondary sympatry through differential mating behaviour (male advertisement calls). As Carstens and Moshier (2022) note in their accompanying perspective piece, the work of Jaynes et al. (2022) exemplifies how using multiple data types increases the power of phylogeographic studies. Scientists have long been curious about the mechanisms driving local adaptation within a species. What elements of the environment (abiotic, biotic) are organisms adapting to? What traits are involved in adaptation? What is the genetic basis for these traits, and do they come with trade-offs? A From the Cover manuscript by Wright et al. (2022) examines these questions by measuring individual fitness traits in F2 mapping populations of Trifolium repens planted across three reciprocal common gardens. This creative experimental design enables the authors to both identify phenotypic traits associated with adaptation and uncover the genetic architecture underlying those traits. While previous work in T. repens had suggested herbivory defence chemistry could be driving local adaptation, Wright et al. (2022) instead found life history strategies to be the critical factor, indicating abiotic selective pressures may be driving differentiation. Further, the authors' genetic analysis reveals that some of the regions associated with adaptation exhibit allelic trade-offs (antagonistic pleiotropy). As Anderson (2022) points out in the paired perspective, such work elucidating the environmental factors and genetic mechanisms involved in local adaptation is crucial for making informed predictions about the impacts of global climate change. Three other From the Cover manuscripts published in 2022 specifically examine the role that species interactions (e.g., predator–prey [Yong et al., 2022], plant-insect [Kahilainen et al., 2022], host–parasite-microbiome [Lutz et al., 2022]) play in evolution. Parallel evolution has been studied across a few well-known “natural experiments” to explore the repeatability and predictability of evolution. One such textbook case is that of the Trinidadian guppy, which has repeatedly colonized multiple drainages that have regions of high and low predation. In a From the Cover manuscript, Yong et al. (2022) re-examine male guppy “conspicuousness” across these habitat types in 16 guppy populations from seven drainage systems. The authors measure the magnitude and direction of changes in male conspicuousness using an innovative framework, quantitative colour pattern analysis, which incorporates knowledge about the visual perception of potential mates and predators (cichlids). The authors fail to find consistent changes in male conspicuousness across drainage systems, putting this study at odds with prior work suggesting conspicuousness, which is preferred by females, has evolved in parallel in response to the release of predatory selection pressures. In a perspective on this piece, Fuller (2022) discusses how this work provides important new insights, but does not entirely close the case of guppy coloration trade-offs – future studies must be done to reconcile the increasing body of work that supports and disputes the role of predation in male coloration in this classical study system. Species within a given trophic network may have different independent responses to altered environmental variables, but the ultimate outcome depends on the combined responses of these organisms. Plant-insect interactions are considered to be especially vulnerable to the impacts of climate change, as many of these species have coevolved specialized relationships. A From the Cover manuscript by Kahilainen et al. (2022) explores this topic in a classical insect study system, the fritillary butterflies in a Finnish archipelago. The authors gain insight into the natural variation present in insect stress response mechanisms, using a three-pronged approach that examines the response of larval host plants to water stress and the subsequent impacts on larval development and transcriptomic profiles. By examining family-level larval responses, Kahilainen et al. (2022) provide evidence of heritable, intrapopulation variability in ecologically-relevant plasticity within this species of butterfly species. Lehmann and Wheat (2022) note in their perspective on this work that the authors found larger than expected variability in larval performance across a small spatial scale, suggesting some insect populations may be more resilient to environmental change than anticipated. In recent years, our understanding of the central and complex role microbiomes play in organismal biology has begun to take shape. In a From the Cover manuscript, Lutz et al. (2022) explore the fascinating tripartite relationship between Afrotropical bats, their microbial associates, and ectoparasitic flies which serve as malarial vectors. The authors sampled the skin, oral, and gut microbiomes of 283 bats from eight species across 14 field sites in Kenya and Uganda – notably, these individuals were being vouchered for independent biodiversity inventories, highlighting how such collections can and should be multipurpose. The authors found a significant association between skin and oral (but not gut) microbial communities and the presence of ectoparasitic flies and malarial parasites, respectively, suggesting microbiomes may serve as an important mediator in the host–parasite relationship. Though these results do not indicate the directionality of this association, they are in congruence with other work that indicates microbial communities may produce or influence the production of volatile organic compounds, an olfactory cue many parasites use to locate their hosts. As Speer (2022) points out in the accompanying perspective, the work of Lutz et al. (2022) serves as a reminder that different host microbial communities may play distinct roles, and that we still have a long way to go toward incorporating the microbiome into our understanding of species interactions and evolutionary processes. Finally, a From the Cover manuscript by Mariac et al. (2022) demonstrates how new quantitative barcoding methodologies can be used to gain insight into otherwise intractable systems. Aiming to characterize the basic reproductive biology of hyperdiverse Amazonian freshwater fishes, the authors performed monthly sampling of ichthyoplankton from two Peruvian tributaries across two consecutive years. The results of this work provide a fundamental understanding of the diversity, reproductive timing, and relative abundance of fishes spawning across these two river systems and represents an important resource for management of a critical Amazonian food source. Serendipitously, the authors also captured data from before and after an unusual and rapid fluctuation in river water levels which led to the cessation or drastic reduction of spawning across nearly all species, demonstrating the level of sensitivity and rapid response of species to environmental cues. As Cardoso Carvalho (2022) points out in the accompanying perspective, the continued refinement of methods should be expected to rapidly shift metabarcoding toward being a mainstream practice for biodiversity monitoring and will inform the development of sustainable management practices for numerous taxa. Volume 31 showcased reviews and syntheses on fish environmental DNA (Yao et al., 2022), metabarcoding in fungi (Tedersoo et al., 2022), in situ conservation of crop relatives' diversity (Wambugu & Henry, 2022), marine phylogeography (Martins et al., 2022), the role of species identity on insect microbiota (Malacrinò, 2022), and how humans affect rates of phenotypic change (Sanderson et al., 2022). These reviews signalled sentiments for a need to discover diversity across diverse taxa and that the conservation of diversity remains a fundamental concern of molecular ecologists. Moreover, the role of our species in driving population change, mainly through harvesting, was consolidated (Sanderson et al., 2022) as one of the significant factors associated with contemporary trait evolution. It will be interesting to read the mood and thinking of the molecular ecology community in the following years as we face further challenges from climate change and enter a new technological phase where sequencing and assembly of large whole genomes becomes a reality. As with previous marker revolutions (e.g., microsatellites, RNA chips, and RAD sequencing), we will see the rapid accumulation of data. However, how scientists use it to answer questions about organisms' biology will remain an essential standard of scientific inquiry. In 2022 we published a special issue entitled “Telomeres in Ecology and Evolution”, edited by David Richardson, Pat Monaghan, Mats Olsson, Simon Verhulst, and Sean Rogers. This compilation of 33 manuscripts applies our knowledge of telomeres, much of which has come from the biomedical realm, to the ecology and evolution of natural populations. As the editors write in the opening piece, the manuscripts within this issue “illustrate the breadth of taxa now being investigated and ways in which emerging hypotheses, formed from the perspective of ecology, evolution, and conservation, are being tested” (Monaghan et al., 2022). The first few manuscripts in this issue provide essential background information, examining the different telomere dynamics among species and across life stages (Brown et al., 2022; Remot et al., 2022) and providing a framework for ecological and evolutionary hypotheses around telomeres (Tobler et al., 2022). The second set of manuscripts explores the effects of ecological and environmental stressors on telomere dynamics, suggesting that telomeres, serving as a proxy for fitness consequences, might be used for conservation monitoring (Salmón & Burraco, 2022). These studies show the critical impacts of stress during early-life stages (Sheldon, Eastwood, et al., 2022; van Lieshout et al., 2022) and the presence of among-individual variation in telomeric response to stress (Brown et al., 2022; Kärkkäinen, Laaksonen, et al., 2022; Reichard et al., 2022). Additional studies also emphasize that what qualifies as a stressor depends greatly on the biology of the organism (Friesen et al., 2022; Wood et al., 2022), and demonstrate there is much to be gained by examining telomere dynamics across diverse forms of life (Bae et al., 2022; Boonekamp et al., 2022; McLennan et al., 2022; Power et al., 2022; Rouan et al., 2022). The third suite of articles in this special issue addresses the idea that telomeres may mediate life history trade-offs, examining correlations between telomere length and reproductive fitness (Heidinger et al., 2022; Kauzálová et al., 2022; Ravindran et al., 2022; Sepp et al., 2022) physical state (e.g., body mass, size: Atema et al., 2022; Le Pepke, Kvalnes, Rønning, et al., 2022), and cancer prevalence (Le Pepke & Eisenberg, 2022; Ujvari et al., 2022) in natural and experimental systems. A final group of manuscripts explores the intriguing nature of heritability of telomere length and rate of shortening (Bauch et al., 2022; Kärkkäinen, Briga, et al. 2022; Le Pepke, Kvalnes, Lundregan, et al., 2022; Sparks et al., 2022; Vedder et al., 2022). Throughout the special issue, a number of articles also delve into the putative mechanisms underlying telomere dynamics (Metcalfe & Olsson, 2022; Wolf et al., 2022) including telomerase activity, which is crucial to telomere maintenance (Noguera et al., 2022; Sheldon, Ton, et al., 2022; Smith et al., 2022). Collectively, the body of work in this special issue demonstrates the powerful and complex role telomeres play in the ecology and evolution of natural populations and highlights the need for continued research in this area (Monaghan et al., 2022). As always, this journal encourages submission of Opinions and Comments to foster ongoing discussions in print on key topics in the field. Notable debates in the pages of MEC included discussions on dietary metabarcoding (Littleford-Colquhoun, Freeman, Sackett, et al., 2022, Littleford-Colquhoun, Sackett, Tulloss, et al., 2022; Tercel & Cuff, 2022) and interpreting the genome-wide effects of hitchhiking (Charlesworth & Jensen, 2022; Gompert et al., 2022). Other opinions discussed diverse topics, including the potential for chromosomal inversions to constrain adaptation to new environments (Roesti et al., 2022), the evolutionary importance of alternative splicing (Singh & Ahi, 2022), ways to optimize genome sequencing depth for studying autopolypoids (Jighly, 2022), a probabilistic approach to understanding species (Kollár et al., 2022), and the value of pedigrees for conservation genomics (Galla et al., 2022). We hope this editorial has provided insights into journal activities, editorial issues under discussion, and the exceptional science being published in the journal. We also wish to thank our readers, authors, reviewers, and editors for your continued support, and we welcome suggestions on how to improve the journal. We thank 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 October 2021 and 30 September 2022. Abbott, Jessica Abreu, Clare Adair, Karen Adyasari, Dini Agnarsson, Ingi Aguillon, Stepfanie Aguirre-Liguori, Jonas Ahmadi, Mohsen Ahmed-Braimah, Yasir Ahrens, Collin Aivelo, Tuomas Akman, Melis Albaina, Aitor Albertson, Renee Alcantara, Suzana Aleixo, Alexandre Allen, Geraldine Allio, Rémi Alseth, Ellinor Amaral, C.R.L. Amos, William An, Shiheng Anastasiadi, Dafni Anderson, Kirk Andersson, Leif Andrade, Sonia Andrei, Adrian-Stefan Andreina Pacheco, Maria Andrello, Marco Andres, Aida Andrew, Carrie Andujar, Carmelo Angers, Bernard Arbogast, Brian Archambeau, Juliette Arct, Aneta Arenas, Miguel Arif, Saad Armenta, Tiffany Arstingstall, Katherine Atmore, Lane Attenborough, Robert Aubin-Horth, Nadia Aurelle, Didier Autenrieth, Marijke Avila-Magaña, Viridiana Babayan, Simon Babik, Wieslaw Backstrom, Niclas Baetscher, Diana Bagatini, Inessa Bagdonaite, Leva Bain, Anthony Baird, Stuart Baiz, Marcella Bakker, Matthew Balard, Alice Balbuena, Juan-Antonio Bálint, Miklós Ballare, Kimberly Ballinger, Matthew Banerjee, Shreya Barah, Pankaj Barbosa, Soraia Barbour, Alan Barker, Brittany Barnard-Kubow, Karen Barratt, Christopher Barreiro, Aldo Barrett, Craig Barrett, Rowan Barth, Julia Barts, Nick Basiita, Rose Bass, Chris Bates, Kieran Bath, Eleanor Bauch, Christina Baud, Amelie Bay, Rachel Bayer, Till Bazzicalupo, Anna Becheler, Arnaud Becke