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Molecular tools are an indispensable part of ecology and biodiversity sciences and implemented across all biomes. About a decade ago, the use and implementation of environmental DNA (eDNA) to detect biodiversity signals extracted from environmental samples opened new avenues of research. Initial eDNA research focused on understanding population dynamics of target species. Its scope thereafter broadened, uncovering previously unrecorded biodiversity via metabarcoding in both well‐studied and understudied ecosystems across all taxonomic groups. The application of eDNA rapidly became an established part of biodiversity research, and a research field by its own. Here, we revisit key expectations made in a land‐mark special issue on eDNA in Molecular Ecology in 2012 to frame the development in six key areas: (1) sample collection, (2) primer development, (3) biomonitoring, (4) quantification, (5) behaviour of DNA in the environment and (6) reference database development. We pinpoint the success of eDNA, yet also discuss shortfalls and expectations not met, highlighting areas of research priority and identify the unexpected developments. In parallel, our retrospective couples a screening of the peer‐reviewed literature with a survey of eDNA users including academics, end‐users and commercial providers, in which we address the priority areas to focus research efforts to advance the field of eDNA. With the rapid and ever‐increasing pace of new technical advances, the future of eDNA looks bright, yet successful applications and best practices must become more interdisciplinary to reach its full potential. Our retrospect gives the tools and expectations towards concretely moving the field forward. [ABSTRACT FROM AUTHOR]

Wildlife populations are becoming increasingly fragmented by anthropogenic development. Small and isolated populations often face an elevated risk of extinction, in part due to inbreeding depression. Here, we examine the genomic consequences of urbanization in a caracal (Caracal caracal) population that has become isolated in the Cape Peninsula region of the City of Cape Town, South Africa, and is thought to number ~50 individuals. We document low levels of migration into the population over the past ~75 years, with an estimated rate of 1.3 effective migrants per generation. As a consequence of this isolation and small population size, levels of inbreeding are elevated in the contemporary Cape Peninsula population (mean FROH = 0.20). Inbreeding primarily manifests as long runs of homozygosity >10 Mb, consistent with the effects of isolation due to the rapid recent growth of Cape Town. To explore how reduced migration and elevated inbreeding may impact future population dynamics, we parameterized an eco‐evolutionary simulation model. We find that if migration rates do not change in the future, the population is expected to decline, though with a low projected risk of extinction. However, if migration rates decline or anthropogenic mortality rates increase, the potential risk of extinction is greatly elevated. To avert a population decline, we suggest that translocating migrants into the Cape Peninsula to initiate a genetic rescue may be warranted in the near future. Our analysis highlights the utility of genomic datasets coupled with computational simulation models for investigating the influence of gene flow on population viability. [ABSTRACT FROM AUTHOR]

Populations of many bumblebee species are declining, with distributions shifting northwards to track suitable climates. Climate change is considered a major contributing factor. Arctic species are particularly vulnerable as they cannot shift further north, making assessment of their population viability important. Analysis of levels of whole‐genome variation is a powerful way to analyse population declines and fragmentation. Here, we use genome sequencing to analyse genetic variation in seven species of bumblebee from the Scandinavian mountains, including two classified as vulnerable. We sequenced 333 samples from across the ranges of these species in Sweden. Estimates of effective population size (NE) vary from ~55,000 for species with restricted high alpine distributions to 220,000 for more widespread species. Population fragmentation is generally very low or undetectable over large distances in the mountains, suggesting an absence of barriers to gene flow. The relatively high NE and low population structure indicate that none of the species are at immediate risk of negative genetic effects caused by high levels of genetic drift. However, reconstruction of historical fluctuations in NE indicates that the arctic specialist species Bombus hyperboreus has experienced population declines since the last ice age and we detected one highly inbred diploid male of this species close to the southern limit of its range, potentially indicating elevated genetic load. Although the levels of genetic variation in montane bumblebee populations are currently relatively high, their ranges are predicted to shrink drastically due to the effects of climate change and monitoring is essential to detect future population declines. [ABSTRACT FROM AUTHOR]

Disentangling the effects of ecological disruptions operating at different spatial and temporal scales in shaping past species' demography is particularly important in the current context of rapid environmental changes driven by both local and regional factors. We argue that volcanic oceanic islands provide useful settings to study the influence of past ecological disruptions operating at local and regional scales on population demographic histories. We investigate potential drivers of past population dynamics for three closely related species of passerine birds from two volcanic oceanic islands, Reunion and Mauritius (Mascarene archipelago), with distinct volcanic history. Using ABC and PSMC inferences from complete genomes, we reconstructed the demographic history of the Reunion Grey White‐eye (Zosterops borbonicus (Pennant, 1781)), the Reunion Olive White‐eye (Z. olivaceus (Linnaeus, 1766)) and the Mauritius Grey White‐eye (Z. mauritianus (Gmelin, 1789)) and searched for possible causes underlying similarities or differences between species living on the same or different islands. Both demographic inferences strongly support ancient and long‐term expansions in all species. They also reveal different trajectories between species inhabiting different islands, but consistent demographic trajectories in species or populations from the same island. Species from Reunion appear to have experienced synchronous reductions in population size during the Last Glacial Maximum, a trend not seen in the Mauritian species. Overall, this study suggests that local events may have played a role in shaping population trajectories of these island species. It also highlights the potential of our conceptual framework to disentangle the effects of local and regional drivers on past species' demography and long‐term population processes. [ABSTRACT FROM AUTHOR]

With their ability to rapidly increase in frequency, gene drives can be used to modify or suppress target populations after an initial release of drive individuals. Recent advances have revealed many possibilities for different types of drives, and several of these have been realized in experiments. These drives have advantages and disadvantages related to their ease of construction, confinement and capacity to be used for modification or suppression. Though characteristics of these drives have been explored in modelling studies, assessment in continuous space environments has been limited, often focusing on outcomes rather than fundamental properties. Here, we conduct a comparative analysis of many different gene drive types that have the capacity to form a wave of advance in continuous space using individual‐based simulations in continuous space. We evaluate the drive wave speed as a function of drive performance and ecological parameters, which reveals substantial differences between drive performance in panmictic versus spatial environments. In particular, we find that suppression drive waves are uniquely vulnerable to fitness costs and undesired CRISPR cleavage activity in embryos by maternal deposition. Some drives, however, retain robust performance even with widely varying efficiency parameters. To gain a better understanding of drive waves, we compare their panmictic performance and find that the rate of wild‐type allele removal is correlated with drive wave speed, though this is also affected by other factors. Overall, our results provide a useful resource for understanding the performance of drives in spatially continuous environments, which may be most representative of potential drive deployment in many relevant scenarios. [ABSTRACT FROM AUTHOR]

Across the animal kingdom, newly independent juveniles form social associations that influence later fitness, mate choice and gene flow, but little is known about the ontogeny of social environments, particularly in wild populations. Here we test whether associations among young animals form randomly or are influenced by environmental or genetic conditions established by parents. Parents' decisions determine natal birth sites, which could affect who independent young initially encounter; secondly, mate choice determines genetic condition (e.g. inbreeding) of young and the parental care they receive, which can affect sociability. However, genetic and environmental factors are confounded unless related offspring experience different natal environments. Therefore, we used a long‐term genetic pedigree, breeding records and social network data from three cohorts of a songbird with high extra‐pair paternity (hihi, Notiomystis cincta) to disentangle (1) how nest location and relatedness contribute to association structure once juveniles disperse away from birth sites, and (2) if juvenile and/or parental inbreeding predicts individual sociability. We detected positive spatial autocorrelation: hihi that fledged closer by were more likely to associate even after dispersing, irrespective of genetic relatedness. Juvenile inbreeding did not predict sociability, but those raised by more inbred fathers formed more, stronger, associations, which did not depend on whether that male was the genetic parent or not. These results suggest that the natal environment created by parents, rather than focal genetic condition, establishes the foundation for social associations. Overall, we highlight how social inheritance may play an important role in population dynamics and evolutionary potential in wild animals. [ABSTRACT FROM AUTHOR]

Growing genetically resistant plants allows pathogen populations to be controlled and reduces the use of pesticides. However, pathogens can quickly overcome such resistance. In this context, how can we achieve sustainable crop protection? This crucial question has remained largely unanswered despite decades of intense debate and research effort. In this study, we used a bibliographic analysis to show that the research field of resistance durability has evolved into three subfields: (1) "plant breeding" (generating new genetic material), (2) "molecular interactions" (exploring the molecular dialogue governing plant–pathogen interactions) and (3) "epidemiology and evolution" (explaining and forecasting of pathogen population dynamics resulting from selection pressure[s] exerted by resistant plants). We argue that this triple split of the field impedes integrated research progress and ultimately compromises the sustainable management of genetic resistance. After identifying a gap among the three subfields, we argue that the theoretical framework of population genetics could bridge this gap. Indeed, population genetics formally explains the evolution of all heritable traits, and allows genetic changes to be tracked along with variation in population dynamics. This provides an integrated view of pathogen adaptation, in particular via evolutionary–epidemiological feedbacks. In this Opinion Note, we detail examples illustrating how such a framework can better inform best practices for developing and managing genetically resistant cultivars. [ABSTRACT FROM AUTHOR]

Rarity, range restriction, and narrow endemism tend to carry dire and urgent conservation implications for imperilled species. What is also clear is that human‐associated extinction risk factors such as urbanization and deforestation pose overwhelming threats to range‐restricted species. In this issue of Molecular Ecology, Antunes et al. (2022) demonstrate that these threats can also impact widespread species. By comparing newts in the genus Lissotriton that co‐occur in the same geographical region, they expose the distinctness of risks facing species with different habitat preferences. Their study emphasizes the importance of local‐scale landscape genetics to reveal the nuances of population connectivity that might otherwise be missed by studying a broader spatial scale. [ABSTRACT FROM AUTHOR]

Migration is typically associated with risk and uncertainty at the population level, but little is known about its cost–benefit trade‐offs at the species level. Migratory insects in particular often exhibit strong demographic fluctuations due to local bottlenecks and outbreaks. Here, we use genomic data to investigate levels of heterozygosity and long‐term population size dynamics in migratory insects, as an alternative to classical local and short‐term approaches such as regional field monitoring. We analyse whole‐genome sequences from 97 Lepidoptera species and show that individuals of migratory species have significantly higher levels of genome‐wide heterozygosity, a proxy for effective population size, than do nonmigratory species. Also, we contribute whole‐genome data for one of the most emblematic insect migratory species, the painted lady butterfly (Vanessa cardui), sampled across its worldwide distributional range. This species exhibits one of the highest levels of genomic heterozygosity described in Lepidoptera (2.95 ± 0.15%). Coalescent modelling (PSMC) shows historical demographic stability in V. cardui, and high effective population size estimates of 2–20 million individuals 10,000 years ago. The study reveals that the high risks associated with migration and local environmental fluctuations do not seem to decrease overall genetic diversity and demographic stability in migratory Lepidoptera. We propose a "compensatory" demographic model for migratory r‐strategist organisms in which local bottlenecks are counterbalanced by reproductive success elsewhere within their typically large distributional ranges. Our findings highlight that the boundaries of populations are substantially different for sedentary and migratory insects, and that, in the latter, local and even regional field monitoring results may not reflect whole population dynamics. Genomic diversity patterns may elucidate key aspects of an insect's migratory nature and population dynamics at large spatiotemporal scales. [ABSTRACT FROM AUTHOR]

How organisms that are part of the same trophic network respond to environmental variability over small spatial scales has been studied in a multitude of systems. Prevailing theory suggests a large role for plasticity in key traits among interacting species that allows matching of life cycles or life‐history traits across environmental gradients, for instance insects tracking host‐plant phenology across variable environments (Posledovich et al. 2018). A key aspect that remains understudied is the extent of intrapopulation variability in plasticity and whether stressful conditions canalize plasticity to an optimal level, or alternatively if variation in plasticity indeed could increase fitness in itself via alternative strategies. In a From the Cover article in this issue of Molecular Ecology, Kahilainen et al. (2022) investigate this issue in a classical insect study system, the metapopulation of the Glanville fritillary butterfly (Melitea cinxia) in the Åland archipelago of Finland. The authors first establish how a key host plant responds to water limitation, then quantify among‐family variation in larval growth and development across control and water‐limited host plants. Finally, they use RNA sequencing to gain mechanistic insights into some of these among‐family differences in larval performance in response to host‐plant variation, finding results suggesting the existence of heritable, intrapopulation variability in ecologically relevant plasticity. This final step represents a critically important and often overlooked component of efforts to predict sensitivity of biological systems to changing environmental conditions, since it provides a key metric of adaptive resilience present in the system. [ABSTRACT FROM AUTHOR]

The demographic history of a population is important for conservation and evolution, but this history is unknown for many populations. Methods that use genomic data have been developed to infer demography, but they can be challenging to implement and interpret, particularly for large populations. Thus, understanding if and when genetic estimates of demography correspond to true population history is important for assessing the performance of these genetic methods. Here, we used double‐digest restriction‐site associated DNA (ddRAD) sequencing data from archived collections of larval summer flounder (Paralichthys dentatus, n = 279) from three cohorts (1994–1995, 1997–1998 and 2008–2009) along the U.S. East coast to examine how contemporary effective population size and genetic diversity responded to changes in abundance in a natural population. Despite little to no detectable change in genetic diversity, coalescent‐based demographic modelling from site frequency spectra revealed that summer flounder effective population size declined dramatically in the early 1980s. The timing and direction of change corresponded well with the observed decline in spawning stock census abundance in the late 1980s from independent fish surveys. Census abundance subsequently recovered and achieved the prebottleneck size. Effective population size also grew following the bottleneck. Our results for summer flounder demonstrate that genetic sampling and site frequency spectra can be useful for detecting population dynamics, even in species with large effective sizes. [ABSTRACT FROM AUTHOR]

Symbiotic interactions can determine the evolutionary trajectories of host species, influencing genetic variation through selection and changes in demography. In the context of strong selective pressures such as those imposed by infectious diseases, symbionts providing defences could contribute to increase host fitness upon pathogen emergence. Here, we generated genome‐wide data of an amphibian species to find evidence of evolutionary pressures driven by two skin symbionts: a batrachochytrid fungal pathogen and an antifungal bacterium. Using demographic modelling, we found evidence of decreased effective population size, probably due to pathogen infections. Additionally, we investigated host genetic associations with infection status, antifungal bacterium abundance and overall microbiome diversity using structural equation models. We uncovered relatively lower nucleotide diversity in infected frogs and potential heterozygote advantage to recruit the candidate beneficial symbiont and fight infections. Our models indicate that environmental conditions have indirect effects on symbiont abundance through both host body traits and microbiome diversity. Likewise, we uncovered a potential offsetting effect among host heterozygosity–fitness correlations, plausibly pointing to different ecological and evolutionary processes among the three species due to dynamic interactions. Our findings revealed that evolutionary pressures not only arise from the pathogen but also from the candidate beneficial symbiont, and both interactions shape the genetics of the host. Our results advance knowledge about multipartite symbiotic relationships and provide a framework to model ecological and evolutionary dynamics in wild populations. Finally, our study approach can be applied to inform conservation actions such as bioaugmentation strategies for other imperilled amphibians affected by infectious diseases. [ABSTRACT FROM AUTHOR]

Phenotypic plasticity, the ability of a given genotype to produce alternative phenotypes in response to its environment of development, is an important mechanism for coping with variable environments. While the mechanisms underlying phenotypic plasticity are diverse, their relative contributions need to be investigated quantitatively to better understand the evolvability of plasticity across biological levels. This requires relating plastic responses of the epigenome, transcriptome, and organismal phenotype, and investigating how they vary with the genotype. Here we carried out this approach for responses to osmotic stress in Dunaliella salina, a green microalga that is a model organism for salinity tolerance. We compared two strains that show markedly different demographic responses to osmotic stress, and showed that these phenotypic responses involve strain‐ and environment‐specific variation in gene expression levels, but a relative low—albeit significant—effect of strain × environment interaction. We also found an important genotype effect on the genome‐wide methylation pattern, but little contribution from environmental conditions to the latter. However, we did detect a significant marginal effect of epigenetic variation on gene expression, beyond the influence of genetic differences on epigenetic state, and we showed that hypomethylated regions are correlated with higher gene expression. Our results indicate that epigenetic mechanisms are either not involved in the rapid plastic response to environmental change in this species, or involve only few changes in trans that are sufficient to trigger concerted changes in the expression of many genes, and phenotypic responses by multiple traits. [ABSTRACT FROM AUTHOR]

Many mammalian species use photoperiod as a predictive cue to time seasonal reproduction. In addition, metabolic effects on the reproductive axis may also influence seasonal timing, especially in female small, short‐lived mammals. To get a better understanding of how annual cycling environmental cues impact reproductive function and plasticity in small, short‐lived herbivores with different geographic origins, we investigated the mechanisms underlying integration of temperature in the photoperiodic‐axis regulating female reproduction in a Northern vole species (tundra vole, Microtus oeconomus) and in a Southern vole species (common vole, Microtus arvalis). We show that photoperiod and temperature interact to determine appropriate physiological responses; there is species‐dependent annual variation in the sensitivity to temperature for reproductive organ development. In common voles, temperature can overrule photoperiodical spring‐programmed responses, with reproductive organ mass being higher at 10°C than at 21°C, whereas in autumn they are less sensitive to temperature. These findings are in line with our census data, showing an earlier onset of spring reproduction in cold springs, while reproductive offset in autumn is synchronized to photoperiod. The reproductive organs of tundra voles were relatively insensitive to temperature, whereas hypothalamic gene expression was generally upregulated at 10°C. Thus, both vole species use photoperiod, whereas only common voles use temperature as a cue to control spring reproduction, which indicates species‐specific reproductive strategies. Due to global warming, spring reproduction in common voles will be delayed, perhaps resulting in shorter breeding seasons and thus declining populations, as observed throughout Europe. [ABSTRACT FROM AUTHOR]

Larval exchange among marine populations is a vital driver of population dynamics and has the potential to inform conservation actions, but accurately measuring dispersal remains challenging. Consequently, empirical dispersal kernels have been measured for only a few marine species. Here, we obtained indirect dispersal estimates using an isolation‐by‐distance (IBD) model in the coral reef fish Elacatinus lori and assessed the accuracy of these estimates by comparing them to direct measurements of dispersal from genetic parentage analysis. Specifically, drawing on the IBD slope and effective population density, we indirectly estimated sigma (σ), the spread of a dispersal distribution. While the spread of the directly measured distribution was σ = 3.93 km (95% CI: 3.29–4.71 km), the spread of the IBD distribution was σ = 4.10 km (95% CI: 3.23–5.03) and σ = 2.90 km (95% CI: 2.26–3.59), assuming a random or monogamous mating system, respectively. Parameterizing Laplace dispersal kernels with these values of σ yielded patterns that were remarkably similar to a kernel fit to the direct parentage data. We also found that, like many marine fishes, E. lori has a large effective population size. However, uncertainty in effective size did not ultimately have a strong effect on the IBD‐based dispersal estimates. Taken together, these findings illustrate that accurate dispersal estimates can be produced by indirect IBD methods and suggest that this more feasible approach to estimating dispersal may be broadly applicable to the study of marine larval dispersal. [ABSTRACT FROM AUTHOR]

Globalization and intensified volume of trade and transport around the world are accelerating the rate of biological invasions. It is therefore increasingly important to understand the processes through which invasive species colonize new habitats, often to the detriment of native flora. The initial steps of an invasion are particularly critical, as the introduced species relies on limited genetic diversity to adapt to a new environment. However, our understanding of this critical stage of the invasion is currently limited. We used a citizen science approach and social media to survey the distribution of invasive sunflower in Israel. We then sampled and sequenced a representative collection and compared it with available genomic data sets of North American wild sunflower, landraces and cultivars. We show that invasive wild sunflower is rapidly establishing throughout Israel, probably from a single, recent introduction from Texas, while maintaining high genetic diversity through ongoing gene flow. Since its introduction, invasive sunflower has spread quickly to most regions, and differentiation was detected despite extensive gene flow between clusters. Our findings suggest that rapid spread followed by continuous gene flow between diverging populations can serve as an efficient mechanism for maintaining sufficient genetic diversity at the early stages of invasion, promoting rapid adaptation and establishment in the new territory. [ABSTRACT FROM AUTHOR]

Fungal species have numerous important environmental functions. Where these functions occur will depend on how fungi are spatially distributed, but the spatial structures of fungal communities are largely unknown, especially in understudied hyperdiverse tropical tree canopy systems. Here we explore fungal communities in a Costa Rican tropical rainforest canopy, with a focus on local‐scale spatial structure and substrate specificity of fungi. Samples of ~1 cm3 were collected from 135 points along five adjacent tree branches, with intersample distances from 1 to 800 cm, and dissected into four substrates: outer host tree bark, inner bark, dead bryophytes and living bryophytes. We sequenced the ITS2 region to characterize total fungal communities. Fungal community composition and diversity varied among substrate types, even when multiple substrates were in direct contact. Fungi were most diverse in living bryophytes, with 39% of all operational taxonomic units (OTUs) found exclusively in this substrate, and the least diverse in inner bark. Fungal communities had significant positive spatial autocorrelation and distance decay of similarity only at distances less than 1 m. Similarity among samples declined by half in less than 10 cm, and even at these short distances, similarities were low with few OTUs shared among samples. These results indicate that community turnover is high and occurs at very small spatial scales, with any two locations sharing very few fungi in common. High heterogeneity of fungal communities in space and among substrates may have implications for the distributions, population dynamics and diversity of other tree canopy organisms, including epiphytic plants. [ABSTRACT FROM AUTHOR]

Pleistocene glacial cycles influenced the diversification of high‐latitude wildlife species through recurrent periods of range contraction, isolation, divergence, and expansion from refugia and subsequent admixture of refugial populations. We investigate population size changes and the introgressive history of caribou (Rangifer tarandus) in western Canada using 33 whole genome sequences coupled with larger‐scale mitochondrial data. We found that a major population expansion of caribou occurred starting around 110,000 years ago (kya), the start of the last glacial period. Additionally, we found effective population sizes of some caribou reaching ~700,000 to 1,000,000 individuals, one of the highest recorded historical effective population sizes for any mammal species thus far. Mitochondrial analyses dated introgression events prior to the LGM dating to 20–30 kya and even more ancient at 60 kya, coinciding with colder periods with extensive ice coverage, further demonstrating the importance of glacial cycles and events prior to the LGM in shaping demographic history. Reconstructing the origins and differential introgressive history has implications for predictions on species responses under climate change. Our results have implications for other whole genome analyses using pairwise sequentially Markovian coalescent (PSMC) analyses, as well as highlighting the need to investigate pre‐LGM demographic patterns to fully reconstruct the origin of species diversity, especially for high‐latitude species. [ABSTRACT FROM AUTHOR]