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Editorial 2024

2023; Wiley; Volume: 33; Issue: 1 Linguagem: Inglês

10.1111/mec.17239

1365-294X

Loren H. Rieseberg, Emily Warschefsky, Jade Burton, Kaichi Huang, Benjamin Sibbett,

Microbial Community Ecology and Physiology

Molecular Ecology (MEC) continues to be one of the largest and most influential journals in the fields of ecology and evolution. In 2022, a total of 434 citable items were published in the journal, ranking third out of 53 journals in Clarivate's list of Evolutionary Biology journals and sixth of 171 Ecology journals. A similar pattern is seen for total citations, where MEC was cited 40,823 times (third in Evolutionary Biology and fourth in Ecology). Additional metrics include journal impact factor (4.9; eighth in Evolutionary Biology) and EigenFactor (0.030, fifth in Evolutionary Biology). The latter metric measures the number of times articles from the journal published in the past five years have been cited in the focal year. Google Scholar's h5-index, which is the h-index for articles published over the past five years, offers a longer term measure of journal influence. Molecular Ecology has an h5-index of 72, which ranks fourth among ecology journals. Lastly, journal downloads demonstrate wide interest in research published in MEC, reaching close to 1.9 million in 2021 and 2022. Molecular Ecology was among the first journals in ecology and evolution to require that data supporting the results of published papers be archived in an appropriate public archive (Rieseberg et al., 2010). Over the years, we expanded the policy to include code, programming scripts, and software, as well as detailed metadata. Earlier this year, members of the MEC and Molecular Ecology Resources (MER) Editorial Board (along with editors from other journals) contributed to an article in Ecology and Evolution that established minimum standards for data and code in ecology and evolution journals (Jenkins et al., 2023). While the recommendations largely reinforce what we are already doing, the article provides a description of best practices for archiving of data, metadata, programming scripts, and software, such that analyses published in a given study can be fully replicated. We will be linking the recommendation to our author guidelines. We also will be transitioning to requiring data and code be made available to editors and reviewers during peer review. In 2020, we published an editorial to indicate 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., 2020). We also established a journal policy that encourages authors to disclose benefits generated by their research under the Nagoya Protocol. This editorial was followed by an article that encouraged our authors to use Biocultural, Traditional Knowledge, and Cultural Institution Notices (Liggins et al., 2021). Such Notices are intended to raise the visibility of Indigenous communities within our research systems, encourage collaboration with Indigenous communities, and provide a platform for them to develop methodologies and permissions for biodiversity-related research on indigenous land. To continue the momentum, 'Indigenous perspectives/methodologies' has been added as an area of interest to our aims and scope, and 'Indigenous perspectives' and 'traditional ecological knowledge' have been added to keywords on the MEC/MER websites. Authors can now select 'Indigenous perspectives and methodologies' as a manuscript subject when submitting an article, and papers submitted using the new manuscript subject will be assigned to editors who have expertise and experience in this space. Like other publishers, Wiley has developed policies for the use of artificial intelligence (AI) tools such as ChatGPT and similar large language models (https://authorservices.wiley.com/ethics-guidelines/index.html). Because AIs lack legal standing and cannot be held accountable for published research or research design, Wiley does not permit them to be listed as authors of published articles. However, if AI tools are used in manuscript development, Wiley requires that such contributions be described in the Methods or Acknowledgements. Final decisions about whether AI usage is permissible in a given manuscript are made by the journal editorial board. In the case of the MEC Editorial Board, we believe that AI represents a potentially valuable editing tool that can improve the readability of manuscripts, potentially reducing barriers to publication for researchers, especially for those who speak English as a second language. While we encourage the use of AI editing tools for improving spelling, grammar, and clarity, we ask that authors acknowledge the use of AI tools in manuscript development as required by Wiley policy. In 2023, MEC maintained a robust social media presence, building upon the success of previous years. The molecology X account (formerly Twitter) boasted a following of over 7400 followers, with an average of more than 49 tweets posted per month. Monthly impressions reached about 28,500, which is slightly less than in previous years, likely due to changes in the social media landscape this year and concerns among academics about these changes. To enhance our outreach, we collaborated with the Wiley social media team (WileyEcolEvol) to strategically broaden our audience. We will continue to monitor community trends and to explore new possibilities to better serve the molecular ecology community, providing a crucial direct source of information about the scientific work published in MEC and MER. In conjunction with X, we continued our commitment to providing an in-house information source through the Spotlight blog in 2023. With a total of 142 posts since 2019, Molecular Ecology Spotlight featured interviews with authors and highlighted influential papers, amassing over 23,000 visitors and 37,000 views. We adopted a new way of interviewing this year with more tailored questions to enhance the dynamism of interviews and promote deeper engagement with authors. This should help the lay community, as well as the broader scientific community, understand the research conducted by molecular ecologists and its implications. It continues to be a fundamental mission of MEC and MER to provide hands-on training on editorial duties to outstanding early career researchers. PhD and postdoctoral researchers, who are recognized by the Harry Smith prize, are invited to join our Junior Editorial Board (JEB). To ensure the JEB provides useful experiences to our members, we are in the process of implementing a new three-year stepped programme which is designed to offer exposure to a range of editorial tasks. Our members will continue to work together to execute the running of our social media platforms (Twitter and Blog) creating content and increasing the journal's visibility. In addition, second-year JEB members will gain experience in editing manuscripts with the guidance of an assigned mentor. In the final year of the JEB tenure, members will support the journals by attracting the best research, through organizing special issues and review articles. Together, with their experience and enthusiasm, the JEB forms an invaluable asset to the journals. 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 2023, the Molecular Ecology Prize was awarded to Dr. Uma Ramakrishnan, a Professor of Ecology and Evolution at the National Centre for Biological Sciences, Bangalore, India. Dr. Ramakrishnan is best known for her studies on the tiger and other large mammals, which are the 'poster children' for India's natural resources. Her studies have included census estimates from combined camera traps and genetic surveys, historical inferences from genetic data and museum specimens, and demonstrations of gene flow impacting genomic variation and inbreeding depression. Dr. Ramakrishnan's research has led to valuable conservation applications, for example by providing evidence used in a Supreme Court ruling that wildlife corridors must be included in certain highway expansions. Dr. Ramakrishnan's work on science communication and community service is exemplary, and she is an important role model to scientists around the world. 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 5 years of postdoctoral or fellowship experience. 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. The 2023 Harry Smith Prize was awarded to Antonino Malacrinò for his paper 'Host species identity shapes the diversity and structure of insect microbiota' (Malacrinò, 2022). His work, published as an 'Invited Reviews and Syntheses' article, presents an example for leveraging the powerful open data and provides new insights into the field of microbiome research. The award committee, which is made up of JEB members, also recognized an excellent paper by Alexander Blumenfeld and colleagues titled, 'Consistent signatures of urban adaptation in a native, urban invader ant Tapinoma sessile paper', as the runner-up for the Harry Smith Prize. Blumenfeld et al. (2022) conducted genetic, behavioural, and chemical analyses of natural and urban populations of Tapinoma sessile. They documented multiple independent transitions in social organization in response to urbanization, as well as restricted gene flow between urban and natural populations, adding to growing evidence that human-altered habitats profoundly influence the ecology and evolution of species. The past year saw the loss of two of our most distinguished and longest-serving editors, Robert (Bob) Wayne and Louis Bernatchez. Both joined the Editorial Board of MEC in 1997 and became senior editors in 1999. Bob helped develop the journal's Aims and Scope and authored the sentence, 'Molecular Ecology publishes papers that utilize molecular genetic techniques to address consequential questions in ecology, evolution, behaviour, and conservation', which continues to be the primary guide for editorial decisions. When Bob passed away in December 2022, he was the journal's longest-serving editor (26 years!). In addition to editing regular manuscripts, Louis served as a review editor for MEC and MER for 15 years (2004–2018), recruiting more than a dozen reviews annually on topics that covered the full disciplinary range of molecular ecology, from microbes to plants to animals and from population and conservation genetics to ecological interactions to environmental genomics. Louis also published more papers (119!) in MEC than any other author. In recognition of his many contributions to the journal, as well as the field of molecular ecology, Louis was awarded the 2016 Molecular Ecology Prize. 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 perspectives, special issues, reviews, opinion papers, 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. Please let us know if you would like to contribute a perspective, review, or opinion, or organize a special issue. We also use our annual editorial to highlight scientific advances published over the past year in the journal (below). Every year, impactful papers are chosen by the editorial board to be highlighted by News and Views perspectives. Among these, a few standout articles are distinguished as From the Cover pieces. The nine From the Cover pieces from 2023 showcase how the applications of new analytical methodologies and tools have advanced our understanding of molecular ecology in both novel and established study systems, across organizational scales, and through time. Three From the Cover manuscripts published by Gaertner et al. (2023), Shi et al. (2023), and Bucholz et al. (2023), examine adaptation, gene flow, and speciation across biological scales—from the cellular to the species and community levels. Understanding how evolutionary forces shape the genomic architecture underpinning adaptive variation is crucial for elucidating how species evolve in response to their changing environments. To explore this concept, Shi et al. (2023) analyse genome-wide data from broadcast-spawning and nest-spawning riverine fish species, which are expected to differ in their levels of gene flow. The authors find that, in general, higher levels of gene flow are associated with tighter clustering of adaptive alleles, which protects them from recombination. In their perspective piece, Schaal and Smith (2023) explain that this work 'provides robust empirical support of foundational theoretical and simulation studies' and helps reveal the complex nature of how adaptation evolves in different organisms. How different are species at the cellular level? Gaertner et al. (2023) address this question by investigating differentiation in cellular 'housekeeping functions' in two closely related species of hares. The authors use fibroblasts obtained from wild hares to examine genetic and gene regulation differences between closely related mountain and brown hares, which are interfertile but ecologically distinct. Gaertner et al. show differences in gene expression patterns between the two hare species, which affect fundamental cellular processes including cell growth, respiration, and metabolism, providing clear evidence that speciation can have significant impacts on cellular-level functions. Moreover, as Palsson and Steele (2023) note in their accompanying perspective, 'This study suggests immortalized fibroblasts have utility for ecological and evolutionary research, to explore divergence in cellular and metabolic traits and the cellular basis of organismal physiology'. Several hypotheses have been proposed to explain the relationships between genomic diversity and species abundance and diversity. Bucholz et al. test three such hypotheses, conducting extensive field surveys and genomic sequencing of freshwater mussel species across the southeastern USA. The authors find support for the more-individuals hypothesis, which posits that areas with higher organismal abundance also exhibit greater species richness, as well as for a relationship between genomic diversity and measures of community and species abundance. However, they do not find positive correlations between species diversity and within-species genomic diversity. Petersen and Wares (2023) conclude that 'their analyses highlight the among-species variability in relationships among these different levels of organization … pushing forward into the important frontier of community-wide genomic assessment for theoretical and conservation applications'. While the field of evolutionary biology has long been captivated by the dynamics of coevolutionary relationships, From the Cover articles by Epstein et al. (2023), Hague et al. (2023), and Leclaire et al. (2023) show that new research continues to provide us with a more nuanced and comprehensive understanding of coevolutionary processes. Epstein et al. examine the well-studied legume-rhizobia symbiosis, using GWAS and population genomic approaches to evaluate signatures of selection in both the plant and microbial genomes. While previous work has suggested that such symbiotic relationships may involve fitness conflicts between the two partners characterized by positive or balancing selection on symbiosis genes, the authors find little evidence to support this hypothesis. Instead, the results of Epstein et al. show, for both the legume and rhizobial partners, traits involved in symbiosis are primarily under stabilizing selection. As Carlson and Frederickson (2023) write in their perspective, this work indicates 'that there is little ongoing fitness conflict between legumes and rhizobia that shapes host and symbiont genomes'. Antagonistic relationships can also lead to coevolution, often characterized by an arms race between the two organisms involved. Hague et al. examine how such cases of coevolution can have cascading effects across trophic levels. The authors use the fascinating system of toxic Pacific newts and their predators, garter snakes, which show a geographic mosaic of arms race escalation, with an increase in newt toxicity matched by increased toxin resistance and retention in garter snakes. Using a combination of experimental and observational data, Hague et al. identify clines of coevolution across the species range and find that two populations of snakes within coevolutionary hotspots have also developed bright coloration, likely serving as an aposematic signal to their own predators. Thompson (2023) notes in his paired perspective that 'the effects of coevolution may ripple throughout networks of interacting species'. Whether host-microbiome relationships should be classified as coevolution remains a topic of some debate. Nevertheless, recent studies are revealing the far-reaching impacts of the microbiome, which extend beyond host health to include host behaviour, development, and reproductive outcomes. Leclaire et al. (2023) explore the microbiome's effects on reproductive success in the black-legged kittiwake, a wild seabird species. The authors show that specific microbiome compositions across different portions of a female bird's body (neck and flank feathers, choanae, outer bill, and cloaca) are associated with multiple measures of reproductive success, but do not find the same result in male birds. As Turjeman (2023) notes in the accompanying perspective, this work provides correlative evidence for an important role of the microbiome in host reproductive fitness—a topic which deserves additional study. Research documenting how the Anthropocene is shaping biodiversity is increasingly focusing on understanding the implications for the future of affected species and the broader ecosystems they inhabit. The From the Cover manuscripts by Beichman et al. (2023), Crossley et al. (2023), and Kocher et al. (2023) approach this topic in vastly different systems and from different angles, demonstrating that the impacts of anthropogenic activity are often complex and context-specific. Beichman et al. examine the implications of historical declines in California sea otter populations, which were nearly hunted to extinction in the 18th–19th centuries. As Kreiner and Booker (2023) write in their accompanying perspective, the authors 'combine a population genomic spatiotemporal data set and theoretical simulations not only to quantify past demographic change in response to sea otter exploitation, but also to understand the consequences of population collapse on species persistence'. Beichman et al. identify genomic signatures of population decline which their forward-in-time modelling suggests could have negative impacts on the recovery of sea otter populations. However, the authors also find that these impacts may be buffered by historically low effective populations prior to the fur trade. While some human activities, like the fur trade, have had obvious impacts on species diversity, others have been less apparent. Crossley et al. examine some of the ways in which land use change, specifically agriculture, has affected aquatic insect biodiversity over time. Utilizing existing genetic data from over 700 aquatic insect species, the authors demonstrate that croplands have degraded aquatic insect genetic diversity, with the sharpest declines observed in areas where croplands have expanded since the 1950s. In contrast, the authors show that genetic diversity in these species rebounds after croplands are converted to other land uses, even including urbanization. As Atmore and Buss (2023) write in their perspective, 'This study highlights the power of using publicly available data to answer crucial questions regarding the current biospheric emergency'. Theories about how biodiversity loss impacts disease prevalence are of critical importance in the Anthropocene, but are often difficult to test because of the complex life histories of many pathogens. Kocher et al. test the 'dilution effect' theory, wherein pathogens are controlled by the presence of inefficient disease vectors in the ecosystem. The authors combine DNA metabarcoding with innovative modelling approaches to examine the dynamics between the tropical parasite Leishmania, its mammalian reservoirs, and sand fly vectors. While the authors do find a decrease of infection prevalence in sand flies when mammal diversity is high, supporting the dilution effect, they also observed an increased density of sandflies, leading to little overall effect of mammal diversity on the density of infected vectors, which, as Levi and Massey (2023) point out in their accompanying perspective, is 'the most important indicator of Leishmania transmission risk'. Opinion papers present ideas and viewpoints that are relevant to molecular ecology. These opinions may be speculative or controversial and are intended to encourage discussion and debate about important issues in our discipline. In 2023, six Opinion articles were published in the journals. Pegg et al. (2023) describe ongoing efforts to forecast the risk of cross-species disease transmission, an area of research that has received increased attention due to the COVID-19 pandemic. They make the case that analyses of the sugars, or glycans, that coat host cell surface macromolecules will be critical for increasing the accuracy of risk assessment. In another broadly important Opinion paper, Čapková Frydrychová (2023) argues that key assumptions about telomere biology and aging do not hold up when considered across a wide range of taxa, but suggests that discrepancies can be resolved when considered in the context of organismal reproductive strategies. Two of the Opinion pieces focused on how genomic data can be best utilized to enhance our understanding of organismal evolution. In a reversal from the early days of phylogeography and genomics, many population studies report on variation in the nuclear genome only. As noted by Blair (2023), this is an unfortunate oversight since organellar information can be useful for species identification, as well as for addressing important questions such dispersal mechanisms and the evolution of species limits. Blanchet et al. (2023) put forward a framework—based on analyses of phylogenetically conserved candidate genes and associated functional traits—for investigating eco-evolutionary processes across biological scales. The final two Opinion articles address longstanding evolutionary questions. One of these concerns the maintenance of genetic variation at life history genes, since variation at such loci should be degraded by natural selection. Arnqvist and Rowe (2023) hypothesize that negative frequency-dependent selection is often responsible for polymorphism at major life history genes, with potentially cascading effects on variation at other life history genes through epistatic selection. The other Opinion piece tackles the longstanding confusion and inconsistent usage of the terms parallel and convergent evolution. Cerca (2023) argues that they are best distinguished in relation to the ancestral condition, with parallel evolution taking place from the same ancestral condition and convergent evolution arising from different ancestral conditions. In 2023, we published three special issues that showcase the research being done in emerging areas of molecular ecology. The first of these was entitled 'Ecological and Evolutionary Inferences from Long-Read Sequencing'. As Dan Bock, Jianquan Liu, Polina Novikova, and Loren Rieseberg write in their editorial, this compilation of 19 manuscripts 'highlights ways in which molecular ecologists are utilizing long-read information to explore the ecological and evolutionary roles of repetitive or otherwise complex loci' (Bock et al., 2023). The articles in this special issue make use of diverse study systems, including plants, animals, bacteria, and viruses, but share common themes: profiling complex epigenetic modifications (Nielsen et al., 2023), linking complex genetic loci to genomic novelty (Burley et al., 2023; Ferguson et al., 2023; Peona et al., 2023; Wierzbicki et al., 2023), conservation genomics (Li, Yang, et al., 2023; Yan et al., 2023), adaptation genomics (Cohen et al., 2023; Hotaling et al., 2023; Li, Wang, et al., 2023; Nacif et al., 2023; Shipilina et al., 2023; Xie et al., 2023; Zhu et al., 2023), genomics of speciation and hybridization (Mérot et al., 2023; Wersebe et al., 2023; Zhang et al., 2023), and genomics of species interactions (Handy et al., 2023; van Steenbrugge et al., 2023). The editors conclude that the works in this special issue demonstrate 'that complex genetic and epigenetic variation, while traditionally more difficult to study, can make a substantial contribution to processes such as adaptation and speciation' (Bock et al., 2023). The second Special Issue, Evolutionary Ecology of Human-Associated Microbes, was edited by Tatiana Giraud, Jeanne Ropars, Eva Stukenbrock, Katherine Ryan Amato, and Ricardo Rodriguez de la Vega. These 21 papers focus on various types of microbial diversity, including domesticates, pathogens, and host-associated microbiota, using a range of methodologies including population and evolutionary genomics, metagenomics, and field and laboratory experiments. As a whole, the papers address a few main subjects: domesticated microorganisms and microorganisms thriving in anthropogenic environments (Harrouard et al., 2023; Silva et al., 2023; von Gastrow et al., 2023), fungal pathogens (Ali et al., 2023; Louet et al., 2023; Rogério et al., 2023; Saubin et al., 2023; Stalder et al., 2023; Wang et al., 2023; Zewdie et al., 2023), metagenomics and microbiomes of animals and human (Bischofberger & Hall, 2023; Corsi et al., 2023; Mac Alpine et al., 2023; Moeller, 2023; Pedro et al., 2023; Peimbert & Alcaraz, 2023; Tessandier et al., 2023; Yuan et al., 2023), and metagenomics and microbiomes of crops (Gao et al., 2023; Richard et al., 2023). Collectively the articles in this Special Issue 'underline the huge impact of the anthropogenic environment in microbial evolution, including the emergence and spread of pathogens as well as the benefits provided by domesticated or mutualistic fungi and bacteria' (Giraud et al., 2023). Finally, our third Special Issue, Insights into Ecological & Evolutionary Processes via Community Metabarcoding includes 'papers that highlight the power of high-throughput sequencing (HTS) data to address classic questions in ecology and evolution, particularly focused on metabarcoding (amplicon) datasets in conjunction with complementary -omics data types and/or models/theory to infer overall ecosystem processes' (Gillespie et al., 2023). The impressive collection of 44 manuscripts covers a wide range of topics: community assembly processes (Andujar et al., 2022; Arjona et al., 2022; Emerson et al., 2022; Govender et al., 2022; Guerrieri et al., 2022; Ip, Chang, Oh, et al., 2022; Kiemel et al., 2022; Li et al., 2022; Macheriotou et al., 2023; Menéndez-Serra et al., 2023; Nappi et al., 2022; Noguerales et al., 2023; Overcast et al., 2023; Pino et al., 2023; Van der Loos et al., 2022; Wang et al., 2022), interaction networks (Ando et al., 2022; Bell et al., 2022; Dürrbaum et al., 2022; Encinas-Viso et al., 2022; Ficetola & Taberlet, 2023; Graham et al., 2022; Ip, Chang, Tun, et al., 2022; Lowe et al., 2022; Lu et al., 2022; Lue et al., 2022; Pitteloud et al., 2022; Srivathsan et al., 2022; Tommasi et al., 2022), cross-scale interactions and microbiomes (Brinker et al., 2022; Câmara dos Reis et al., 2022; Hu et al., 2022; Kivistik et al., 2022; Manthey et al., 2022; Merges et al., 2022; Michel et al., 2022; Molina et al., 2022; Navine et al., 2022; Pereira et al., 2022; Perez-Lamarque & Morlon, 2022; Rolshausen et al., 2022), and invasive species/homogenization (Andrés et al., 2023; Graham et al., 2022; Hampel et al., 2022; Kennedy et al., 2022; Overcast et al., 2023). The editorial team of Rosemary Gillespie, Holly Bik, Michael Hickerson, Henrik Krehenwinkel, Isaac Overcast, and Andrew Rominger writes that, taken together, this body of work 'highlights the critical insights that can be gained using high-throughput approaches, particularly in relation to biodiversity dynamics' (Gillespie et al., 2023). We hope this editorial provided useful 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 2022 and 30 September 2023. Aanen, Duur Abad-Recio, Ion Abbott, Jessica Abreu, Clare Adams, Nicole Adams, Rachelle Affenzeller, Matthias Afiq-Rosli, Lutfi Aguilar, Andres Aguillon, Stepfanie Aguirre, Windsor Ahi, Ehsan Pashay Ahrens, Collin Aivelo, Tuomas Akita, Tetsuya Albach, Dirk Alberoni, Daniele Aldred, Nick Allen, Michael Allen, Natalie Allio, Rémi Almer, Jasmin Alonso, Conchita Alverson, Andrew Amos, William Amsler, Charles An, Shiheng Anastasiad