Editorial 2022

Abstract

Molecular Ecology continues to be well cited, with an Impact Factor (IF) of 6.185 in 2020, ranking 7th out of 50 journals in evolutionary biology according to Clarivate's Journal Citation Reports. In terms of overall impact, Molecular Ecology ranks third among ecology journals and second 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 stems both from the large number of articles published in Molecular Ecology each year (386 in 2020), as well as the high median impact factor of our articles. Indeed, Molecular Ecology ranks second among ecology journals in Google Scholar's h5-median statistic and third among evolution journals by this measure. As discussed in last year's editorial we are now making open calls for Associate Editors. This approach has been successful, resulting in the recruitment of 10 new Associate Editors and helping to diversify the Editorial Board geographically. Molecular Ecology and Molecular Ecology Resources wished to consider implementing double-blind peer review in order to increase the diversity of published authors. The current single-blind model may cause biases against authors based on race, ethnicity, gender, institution, career stage, or other factors. To gain the molecular ecology community's views, we conducted a survey of authors’ and reviewers’ preferences for single-blind, double-blind, and transparent peer review. Out of 165 respondents, 43% preferred double-blind peer review, 33% preferred transparent review, and 24% preferred single-blind review. Definitions of each review model and the most common reasons given for preferring each model are shown in Table 1. Early career researchers were more in favour of double-blind review and less in favour of single-blind review compared to more established researchers (Figure 1). Career stage did not affect preferences for transparent peer review (Figure 1). Although double-blind was the most popular review model, a high number of survey respondents commented that anonymising manuscripts is impractical. Doing so is a significant burden for authors, and reviewers are often able to deduce authors’ identities from the manuscript content. Furthermore, many manuscripts are released as preprints before journal submission, and anonymity would conflict with benefit-sharing statements and with open data policies where manuscripts cite data or scripts attributed to the authors. Despite being the second most popular review model overall, several survey respondents strongly opposed transparent peer review. Concerns included the risk of critical reviewers receiving retaliation from authors, which is a particular threat for early career researchers. Reviewers may therefore feel pressured to comment favourably, or may decline to provide a review. Furthermore, the extra effort required to submit publishable reviews is not acknowledged, while published review documentation may rarely be viewed. In light of the concerns around double-blind and transparent peer review, Molecular Ecology and Molecular Ecology Resources will keep single-blind review but implement changes aimed at reducing potential biases. As preferences varied and were partly influenced by career stage, we also aim to introduce choice. Authors’ identities will be de-emphasised by removing their names from review invitation emails, and reviewers will be asked whether they wish to reveal their identity to the authors. Some Editors wish to be anonymous, and so Editors will be given the choice of whether to sign their decision letters. Editors’ names will be published on accepted articles to recognise their contributions to the review process. We also noted that a number of survey respondents commented that authors value Editors assessing reviews, ensuring that comments are constructive, and specifying which points should be responded to in order to improve the manuscript. These comments have been shared with the journal Editorial Boards, and we will provide Editors with training on standard practice for making decisions on manuscripts. Over the past two years, Molecular Ecology has built a healthy audience across social media. With over 5600 followers currently visiting @molecology and more than 40,000 in a month, the exposure of the work of molecular ecologists from all over the world has gained greater visibility (Figure 2). Members of the Junior Editorial Board (JEB) as well as authors and readers are sharing more than 350 tweets per month, which receive more than 1.5 million impressions (Figure 3). Future growth should ensure that members outside the scientific community will also be exposed to the work of molecular ecologists, thereby increasing their impact in society. The translation of complex work to a general audience is a challenging exercise, and Spotlight, the journal blog, aims to mediate such dialogue. Members of the JEB continue to post summaries of highlighted papers, and “interviews with the author,” particularly those of early career researchers (ECR), which help the broad audience to understand the inception of ideas, implementation of experiments, and interpretation of results. The audience to Spotlight is growing (Figure 4), with visits to both old and new posts, suggesting that the personal experiences of researchers represent a legacy for new members of the scientific community. We expect to slowly grow the output of Spotlight and diversify its portfolio. A major focus of Molecular Ecology is to act as a catalyst of researcher development, particularly those starting their careers. In its third year, the JEB has become an important asset for the journal and is continuing to extend its reach as new cohorts of young researchers join its ranks. We saw the first cohort depart in 2021. Dr. Megan Smith, Dr. Nick Fountain-Jones, and Dr. Luke Brown started their tenure three years ago and we are grateful for their creativity and hard work in helping establish many of the protocols currently employed across the journal. Besides contributing to the Social Media presence of Molecular Ecology and Molecular Ecology Resources, the JEB plays a role in preprint invitations, adjudicating the Harry Smith Prize, and spearheading Special Issues. More recently, the JEB has taken leadership over Reviews and Synthesis under the guidance of several members of the senior editorial board of Molecular Ecology and Molecular Ecology Resources. The JEB’s involvement in this new role is expected to increase the diversity of reviews we publish in 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 2021, the prize was awarded to Dr. Fuwen Wei, Professor of Animal Ecology and Conservation Biology in the Institute of Zoology, Chinese Academy of Sciences. Dr. Wei is a pioneer in conservation genomics and metagenomics of endangered animals, focusing mainly on giant and red pandas. He has applied genetic and genomic techniques to assess the past, present and future of giant panda populations, infer their evolutionary and demographic processes, and reveal their adaptive mechanisms for feeding on their specialized bamboo diet. He also has proposed and elaborated targeted strategies for the long-term survival of pandas, which were featured in Science as “Hope for Wild Pandas”. With 5 books and over 270 peer-reviewed journal articles, he is a global leader in molecular ecology and conservation genomics. He has trained numerous students and postdocs, and fostered international cooperation among zoologists and conservation biologists. His impressive accomplishments have earned him numerous awards and recognition, for instance, the Lifetime Achievement Award for Giant Panda Research and Conservation and the Outstanding Science and Technology Achievement Prize of Chinese Academy of Sciences. A biography of Dr. Wei and his contributions to the field of molecular ecology can be found on pages 31–36 of this issue. The Harry Smith Prize recognizes the best paper published in Molecular Ecology 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 2021 Harry Smith Prize was Yann Dorant at the Université Laval in Québec for his paper titled ‘Copy number variants outperform SNPs to reveal genotype-environment association in a marine species’ (Dorant et al., 2020). The paper shows how reduced-representation sequencing can cost effectively detect both copy number and SNP variation, in this case applied to the analysis of local adaptation in the American lobster. In a similar vein, runner-up Kaichi Huang at the University of British Columbia demonstrated how reduced-representation sequencing can be use to identify inversions segregating in natural populations – in this case between dune and non-dune sunflower ecotypes – and assess their role in ecotype formation (Huang et al., 2020). Second runner-up Tom Booker, also at the University of British Columbia, employed a combination of computer simulations and empirical data to demonstrate that recombination cold spots have a longer-tailed distribution of FST values than regions with higher recombination rates, leading to an excess of false positives in the former and a deficit in the latter (Booker et al., 2020). Dorant, Huang, and Booker have joined our JEB as part of the prize. 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. As in past years, we are grateful to our many referees, who are listed at the end of this editorial, for the contribution of their time to the journal and to the discipline. 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). The News and Views section of Molecular Ecology highlights some of the year's most noteworthy papers as From the Cover manuscripts. In 2021, these 10 articles showcase the innovative approaches being taken to advance the field of molecular ecology. From the Cover pieces in 2021 all share the common theme of examining drivers of biological diversity, adaptation, and selection processes, using creative and innovative methodological approaches to tackle important outstanding questions in the field. Metabarcoding has revolutionized our ability to survey biological diversity in a number of previously intractable habitats. Taking advantage of this tool, a From the Cover manuscript by Arribas et al. (2021) used haplotype-level community metabarcoding to examine soil arthropod diversity in three regions of the Iberian mountains, gleaning data from >1000 species and 3000 haplotypes. The authors used this rich dataset to explore turnover of community assembly across and within habitats, finding strong differentiation at both spatial scales. These results indicate that dispersal limitations are an important driver of soil arthropod diversity and suggest we may be underestimating global diversity of this taxonomic group. When considering how symbiosis drives diversity, examples of co-speciation between symbiotic lineages are often cited, yet a From the Cover paper by Dal Forno et al. (2021) provides a fascinating example of how rapid radiation of one symbiotic partner can occur without complementary diversification of the other. The authors used genetic sequence data to examine the diversity of fungal (mycobiont) and cyanobacterial (photobiont) partners that form Dictyonema lichens. While recent work has shown Dictyonema mycobiont diversity to be extremely high, with more than 200 species described so far, Dal Forno et al. find cyanobacterial diversity to be far lower, identifying just three main lineages. Consequently, the same Dictyonema photobionts are shared across long-diverged fungal lineages, supporting the analogy of lichens as fungal “farmers” that circulate amenable photobiont “crops” amongst themselves. Major environmental shifts can drive – or devastate – biodiversity. In a From the Cover article, Stiller et al. (2021) explored how historical changes in sea level shaped modern population dynamics of charismatic leafy sea dragons, which inhabit shallow seas along the southern continental shelf of Australia. The authors first reconstructed the species’ historical habitat availability during and since the last glacial maximum. They then sampled individuals across the modern day range, sequencing 857 ultraconserved elements (UCEs) to analyze population structure and diversity. The combination of approaches allowed Stiller et al. to provide a detailed picture of how sea level change and habitat availability interacted with demographic expansions and contractions in leafy sea dragons, resulting in the complex patterns of diversity we see today. For generations, biologists have debated how and why the tropics contain such vast diversity. A From the Cover article by Brousseau et al. (2021) helps to shed light on the processes that drive this diversity, using the hyperdominant Amazonian species Eperua falcata. Following a reciprocal transplant study over the course of three years, the authors found strong maternal effects and phenotypic plasticity, but also uncovered genetic and phenotypic divergence between individuals from different micro and regional habitats. The authors then used genome wide scans to key in on loci under differential selection between microhabitats, many of which involve physiological processes such as stress response and biotic interactions. As Dick (2021) writes in the accompanying perspective, the work of Brousseau et al. “signals an exciting direction in molecular ecology and especially in its applications to the origins and maintenance of tropical tree diversity.” Understanding the links between diversity, selection, and adaptation is increasingly important in the face of changing and erratic climatic conditions. However, this can be especially difficult for forest trees, which are long-lived and often have large, complex genomes. In a From the Cover article, Depardieu et al. (2021) use a clever combination of dendrochronological, environmental, and genomic data to characterize drought tolerance in 43 populations of white spruce (Picea glauca) in a common garden plot established in 1979. Coupling environmental data on temperature, precipitation, and aridity along with dendrometric (tree-ring) data on anatomical, growth response, and climate sensitivity traits, the authors performed genotype-environment and genotype-phenotype associations as well as transcriptomic analysis, ultimately identifying candidate genes involved in drought tolerance and response. As Opgenoorth and Rellstab (2021) suggest in the paired perspective, the work of Depardieu et al. exemplifies how combining complementary lines of evidence can circumvent some of the challenges associated with studying forest trees. While standing genetic variation within a species can provide a basis for adaptation, how does limited gene flow between populations impact this process? A From the Cover article by Kemppainen et al. (2021) sought to answer this question using nine-spined stickleback, a species with relatively reduced gene flow compared to its more well-known, three-spined relative. Like three-spined stickleback, multiple populations of the nine-spined species colonized freshwater habitats, independently evolving reduced pelvic structures in the process. Kemppainen et al. used three QTL mapping populations to show that the genetic mechanisms underlying this phenotype are more diverse in nine-spined stickleback than in the three-spined species. This work demonstrates how population dynamics shapes adaptation, even in seemingly similar systems. Recent years have brought an appreciation for the complex suite of molecular mechanisms responsible for phenotypic variation and adaptation, including gene expression, methylation, and alternative splicing. This year, a set of four From the Cover manuscripts by Ahmad et al. (2021), Jacobs and Elmer (2021), Hsu et al. (2021), and Lindner et al. (2021) provided important advancements in this regard. Examining wild salmon populations, Ahmad et al. not only provide a clear example that selection acts at the level of transcripts, but also quantify the strength and form of this selection. The authors use a clever genetic mark-recapture experimental design coupled with repeated sampling for RNAseq to examine gene expression in salmon with parasitic infections. Their results show widespread disruptional, rather than directional, selection across transcripts linked to survival. As Josephson and Bull (2021) write in the accompanying perspective, such within-generational studies are critical to understanding how selection acts at different temporal scales. Much like differential gene expression, alternative splicing of pre-mRNA can contribute to trait divergence, yet little is known about its role in adaptive differentiation in wild populations. A From the Cover article by Jacobs and Elmer (2021) examines both gene expression and alternative splicing in the parallel adaptation of Arctic charr ecotypes. Across three pairs of benthic-pelagic population pairs, the authors find remarkably little overlap in differentially expressed and differentially spliced genes. In another surprising finding, Jacobs and Elmer show differentially spliced genes are more likely to play a central (“hub”) role in regulatory networks. This work highlights the important and distinct role alternative splicing is likely playing in adaptive evolution and signals a need for more research focused on this topic. While laboratory experiments offer a way to examine how populations adapt to changes in isolated environmental variables, it is unclear how often these results reflect the responses that would in natural settings. In a perspective on the From the Cover manuscript of Hsu et al. (2021), Phillips and Burke (2021) ask “Can laboratory evolution experiments teach us about natural populations?” To explore this question, Hsu et al. examined changes in gene expression profiles of laboratory-reared Drosophila under two temperature conditions over the course of 80 generations. The authors identified over 200 genes that evolved changes in expression in response to the temperature regimes, carefully distinguishing these from genes that were altered as a result of general lab conditions (e.g., space constraints). Hsu et al. then compared the suite of temperature-responsive genes identified in the lab to those identified from Drosophila found in natural temperature clines, finding significant overlap between the two. This work demonstrates that, at least in some cases, carefully designed lab experiments can predict how natural populations will respond to changing environments. Organisms adapt to environmental changes at the physiological and morphological level, but how do more complex phenotypes, like behavior, respond? A From the Cover article by Lindner et al. (2021) shows how rapid changes in DNA methylation can modulate reproductive timing in a small songbird. By sampling females throughout the breeding season, the authors were able to examine temporal changes in DNA methylation. Lindner et al. find rapid, directional shifts in the methylation of the promoter region of 10 genes, including one known to be involved in the reproductive cycle of chickens. Heckwolf and Meyer (2021) note that, as we strive to predict how and whether species can cope with changing climates, the work of Lindner et al. provides insight into how gene-environment interactions modulate critical stages of life history. In 2021 we published two Special Issues and one Special Feature. The first, a Special Issue titled “Environmental DNA for biomonitoring” edited by Jan Pawlowski, Aurélie Bonin, Frédéric Boyer, Tristan Cordier, and Pierre Taberlet, was a follow up to the pioneering 2012 special issue “Environmental DNA” (Taberlet et al., 2012). In the past decade, technological advances and rapidly decreasing costs of sequencing have increased the size and taxonomic breadth of eDNA datasets and reference databases. The first group of papers in the special issue focuses on novel analytical tools (e.g. machine learning, Apothéloz-Perret-Gentil et al., 2021; Frühe et al., 2021; Mauffrey et al., 2021), types of sequence data (e.g. shotgun sequencing of eRNA, Broman et al., 2021; paleo-metabarcoding, Ibrahim et al., 2021), and bioindicators (e.g. microbes, Frühe et al., 2021; Lanzén et al., 2021; Mauffrey et al., 2021) and how best to apply these to assess ecological status (Cordier et al., 2021). The second group of manuscripts within the special issue focuses on the use of eDNA for monitoring fish biodiversity. As Pawlowski, Bonin, et al. (2021) point out in their introduction to the special issue, fish are among the most important bioindicators, and the use of eDNA to monitor fish diversity is well-established. Papers in this section go beyond baseline biodiversity monitoring to propose methods for estimating fish abundance from eDNA (Fukaya et al., 2021; Pont et al. 2021; Yates, Glaser, et al., 2021) and using eDNA to determine how abiotic and biotic factors shape temporal and spatial distributions of fish species (Aglieri et al., 2021; Brys et al., 2021; Littlefair et al., 2021; McColl-Gausden et al., 2021). An important step in implementing new molecular tools is validation of the data, which is the focus of the second group of papers within the special issue. In the case of eDNA, validation involves comparing eDNA approaches to traditional methods of biodiversity monitoring, including bulk DNA metabarcoding (Antich et al., 2021; Gleason et al., 2021; Harper et al., 2021; van de Loos & Nijland, 2021; Suter et al., 2021) and macrofauna surveys (Drinkwater et al., 2021; He et al., 2021; Lopes et al., 2020). Additional papers within this section examine the impacts of marker selection (Ficetola et al., 2021; Martins et al., 2021; Meyer et al., 2021), methods of soil preservation (Guerrieri et al., 2021), and optimization of data analysis (Mächler et al., 2021). The final three papers within the special issue highlight innovative approaches to eDNA analysis that allow for inference into metapopulation dynamics and demographic trends (Martel et al., 2021; Shum & Palumbi, 2021) and the creative use of cow dung to assess insect diversity (Sigsgaard et al., 2021). As Pawlowski, Bonin, et al. (2021) write at the end of their introduction, “…these papers attest to major efforts that have been done to improve eDNA methodology at every step of the workflow from sampling to data analysis” yet the editors emphasize that “it is now high time to move on and to transform the eDNA field into a truly applied science.” The Special Feature published this year “Resistance evolution, from genetic mechanism to ecological context” was edited by Regina Baucom, Ana Caicedo, Daniel Croll, Kenneth Olsen and Sarah Yakimowski. As pointed out in the introduction to the special issue (Baucom et al., 2021), this suite of papers builds on a long history of understanding adaptation through the lens of resistance to pesticides, herbicides, and fungicides. The first section of the special feature focuses on the genetic and genomic insights garnered by studies of resistance evolution. The papers in this section advance the field through examining resistance genes in the context of genome-scale dynamics such as intragenic variation (Clarkson et al., 2021), pleiotropic constraints (Kreiner et al., 2021), and copy number variation at both the local (Yakimowski et al., 2021) and landscape scales (Gaines et al., 2021; Ravet et al., 2021). A few of these manuscripts provide novel insight into the evolution of fungal plant pathogens, examining the parallel evolution of particular mutations conferring resistance among species (Hawkins & Fraaije, 2021) and comparing the genomic architecture of resistance across continents (Hartmann et al., 2021). The second half of the special feature focuses on the ecological context of resistance evolution, providing an overview of how herbicides impact the ecoevolutionary dynamics of agriculturally-adjacent communities of plants and their associated biota (Iriart et al., 2021), examining differences in the enteric microbiome of insecticide-susceptible and -resistant populations of corn rootworm (Paddock et al., 2021), and disentangling the relationship between glyphosate resistance, self-fertilization, and inbreeding and outbreeding depression in morning glory (Van Etten et al., 2021). As the editors write in the conclusion of their editorial piece, these works go beyond the surface level knowledge of biochemical and genetic targets of pesticides to increase our understanding of the genomic and ecological dynamics involved in resistance evolution. The final special issue of 2021, “Whole genome sequencing in molecular ecology”, was edited by Rebecca Taylor, Evelyn Jensen, David Coltman, Andrew Foote, and Sangeet Lamichhaney. This timely special issue showcases “an array of studies that leverage the resolution of whole genome sequencing (WGS) to provide new insights into the molecular ecology of a range of species and ecosystems” (Taylor, Jensen, et al., 2021). One theme among the papers within the special issue centers on methodological approaches and advances in whole genome sequencing (WGS) and includes manuscripts highlighting the role of WGS in producing improved genome assemblies that allow a clearer picture of diversity at intra- and infra-organismal levels (Blom, 2021; Wold et al., 2021; Yamaguchi et al., 2021). Additional articles that compare WGS to the in-vogue methods of reduced representation libraries (RRL), genotyping by sequencing (GBS) and restriction site associated DNA sequencing (RADseq) provide convincing evidence for the superiority of WGS in many regards (Duntsch et al., 2021; Lou et al., 2021; Szarmach et al., 2021), while others use WGS to address previously insurmountable challenges (Vekemans et al., 2021; Yoder & Tiley, 2021). Many of the manuscripts in this special issue provide methodological resources that will undoubtedly serve our community for years to come, including bioinformatics pipelines (Lou et al., 2021; Ribeiro et al., 2021) and a compendium of tools for WGS data analysis (Bourgeois & Warren, 2021). A second theme within the special issue is that of empirical studies using WGS to infer demographic dynamics across evolutionary timescales. These papers demonstrate that, even with samples from just a few individuals, WGS can be used to detect shifts in historical effective population size along with signatures of gene flow and isolation (Foote et al., 2021; Sarabia et al., 2021; Taylor, Manseau, et al., 2021; Torres Vilaça et al., 2021; Vershinina et al., 2021). At shallower timescales, WGS data can also be used to disentangle complex evolutionary processes such as the adaptive roles of introgression (Comeault et al., 2021; Errbii et al., 2021), hybridization (Santos et al., 2021), horizontal gene transfer (Wolfe et al. 2021), and low recombining regions (Purcell et al., 2021) such as inversions (Owens et al., 2021). A final manuscript on this topic provides a comprehensive review of how the particular advantages of WGS compared to RRL allow for a fine-scale picture of the evolutionary history of invasive species (North et al., 2021). As noted in the editorial, “WGS is assisting conservation by providing conclusive assessments of population structure, which when coupled with analyses of demographic history is providing deeper understanding into how populations arrived at their present states” (Taylor, Jensen, et al., 2021). A collection of papers in this special issue demonstrate the implications of such advances across charismatic study systems including Southern White Rhinos (Sánchez-Barreiro et al., 2021), Komodo dragons (Iannucci et al., 2021), Galapagos tortoises (Jensen et al., 2021), Mexican wolves (Taron et al., 2021), and New Zealand's alpine parrots (Martini et al., 2021). The special issue also includes a suite of papers work that use WGS to uncover the genetic basis of adaptive traits including immune response (Batley et al. 2021; Moreno Santillán et al., 2021) and environmental heterogeneity (Nunez et al., 2021). Multiple studies take advantage of the comprehensive genomic data to examine polygenic adaptations (Montejo-Kovacevich et al., 2021; Pereira et al., 2021), while others use WGS to conduct genotype environment association (GEA) analysis, revealing a fine-scale look at genomic regions involved in adaptation to particular environmental variables (Colicchio et al., 2021; DeRaad et al., 2021). As the editors write in their conclusion, “the contributions presented in this special issue herald a new era in molecular ecology, as we anticipate that a burgeoning and widespread application of WGS will provide unprecedented insights into consequential questions in ecology and evolution,” (Taylor, Jensen, et al., 2021). Important discussion