Understanding the structure and connectivity of coral populations is fundamental for developing marine conservation policies, especially in patchy environments such as archipelagos. The Nansei Islands, extending more than 1,000 km in southwestern Japan, are characterized by high levels of biodiversity and endemism, supported by coral reefs, although precise, detailed genetic attributes of corals are still largely unknown. In this study, we conducted population genomic analyses based on genome-wide, single-nucleotide polymorphisms (SNPs) of Acropora digitifera, a common species in the Nansei Islands, for which a complete genome is available. With ~24x sequencing coverage of entire genomes of 303 colonies collected at 21 locations, we identified more than four million genome-wide SNPs. While population structure analyses suggested weak genetic differentiation among sampled locations, the most southwestern location (the west end of the Yaeyama Islands) was genetically similar to the northernmost location (the Tanegashima Islands), separated by >1,000 km. Although examination of a migration network found a general tendency of northward migration along the Kuroshio Current, a substantial amount of southward migration was also detected, indicating important contributions of minor ocean currents to coral larval dispersal. Moreover, heterogeneity in the transition of effective population sizes among locations suggests different histories for individual subpopulations. The unexpected complexity of both past and present population dynamics in the Nansei Islands implies that heterogeneity of ocean currents and local environments, past and present, have influenced the population structure of this species, highlighting the importance of local scale assessments for effective coral restoration and management.

Toxoplasma infection in intermediate host species closely associates with inflammation. This association has led to suggestions that the behavioural changes associated with infection may be indirectly driven by the resulting sustained inflammation rather than a direct behavioural manipulation by the parasite. If this is correct, sustained inflammation in chronically infected rodents should present as widespread changes in the gastrointestinal microbiota due to the dependency between the composition of these microbiota and sustained inflammation. We conducted a randomized controlled experiment in rats that were assigned to a Toxoplasma-treatment, placebo-treatment or negative control group. We sacrificed rats during the chronic phase of infection, collected their cecal stool samples and sequenced the V3-V4 region of the 16S rRNA gene to characterise the bacterial community in these samples. Toxoplasma infection did not induce widespread changes in the bacterial community composition of the gastrointestinal tract of rats. Rather, we found sex differences in the bacterial community composition and only minor changes in Toxoplasma infected rats. We conclude that it is unlikely that sustained inflammation is the mechanism driving the highly specific behavioural changes observed in Toxoplasma-positive rats.

For many species, both local abundance and regional occupancy are highest near the center of their geographic distributions. One hypothesis for this pattern is that niche suitability declines with increasing distance from a species geographic center, such that populations near range margins are characterized by reduced density and increased patchiness. In these smaller edge populations, genetic drift is more powerful, leading to the loss of genetic diversity. This simple verbal model has been formalized as the central-marginal hypothesis, which predicts that core populations should have greater genetic diversity than edge populations. However, demographic shifts over time can generate a similar pattern. For example, in species with expanding ranges, populations at the range edge experience serial founder effects, creating a gradient of declining genetic diversity from the range core to edge. Testing the central-marginal hypothesis properly thus requires us to consider the confounding role of historical demography. Here, we account for the role of history in testing the central-marginal hypothesis using a genomic dataset of 25 species-level taxa of Australian skink lizards (genus: Ctenotus and Lerista). We found support for the central-marginal hypothesis in 16 of our 25 taxa, of which eight taxa recovered significant support. Unexpectedly, species with the strongest evidence for range expansion were the least likely to follow predictions of the central-marginal hypothesis. The majority of these species had range expansions that originated at the range edge, which led to lower genetic diversity at the range edge compared to the core, contrary to the central-marginal hypothesis.

Animal pollinators mediate gene flow among plant populations, but, in contrast to well-studied topographic and (Pleistocene) environmental isolating barriers, their impact on population genetic differentiation remains largely unexplored. Comparatively investigating how these multifarious factors drive microevolutionary histories is, however, crucial for better resolving macroevolutionary patterns of plant diversification. We here combined genomic analyses with landscape genetics and niche modelling across six related Neotropical plant species (424 individuals across 33 localities) differing in pollination strategy to test the hypothesis that highly mobile (vertebrate) pollinators more effectively link isolated localities than less mobile (bee) pollinators. We found consistently higher genetic differentiation (FST) among localities of bee- than vertebrate-pollinated species with increasing geographic distance, topographic barriers and historic climatic instability. High admixture among montane populations further suggested relative climatic stability of Neotropical montane forests during the Pleistocene. Overall, our results indicate that pollinators may differentially impact the potential for allopatric speciation, thereby critically influencing diversification histories at macroevolutionary scales.

Rivers provide excellent models to understand how species diversity is generated and maintained across heterogeneous habitats. The lower Congo River (LCR) consists of a dynamic hydroscape exhibiting extraordinary aquatic biodiversity, endemicity, and ecological specialization. Previous studies have suggested that the numerous high-energy rapids throughout the LCR form physical barriers to gene flow, thus facilitating diversification and speciation, and generating ichthyofaunal diversity. However, this hypothesis has not been fully explored using genome-wide SNPs for fish species distributed across the LCR. In this study, we examined four species of lamprologine cichlids endemic to the LCR, of which three are sequentially distributed along the LCR without range overlap. Using genome-wide SNP data, we tested the hypotheses that high-energy rapids serve as physical barriers to gene flow that generate genetic divergence at inter- and intraspecific levels, and that gene flow occurs primarily in a downstream direction. Our results are consistent with the prediction that the rapids sometimes serve to reduce gene flow, but also suggest that at certain temporal and spatial scales, they may also act as promoters of gene flow. Furthermore, we detected both upstream and downstream gene flow between some populations of Lamprologus tigripictilis as well as hybridization between congeneric species. These results suggest that powerful high-energy rapids may therefore provide occasional multidirectional dispersal opportunities for riverine cichlid fishes, highlighting the complexity of factors driving evolutionary processes in the LCR.

DNA metabarcoding has been widely used to access and monitor species. However, several challenges remain open for its mainstream application in ecological studies, particularly when dealing with a quantitative approach. In a from the Cover article in this issue of Molecular Ecology, Cédric et al. (2021) report species-level ichthyoplankton dynamics for 97 fish species from two Amazon river basins using a clever quantitative metabarcoding approach employing a probe capture method. They clearly show that most species spawned during the rainy season when the floods started, but interestingly, species from the same genus reproduced in distinct periods (i.e., inverse phenology). Opportunistically, Cédric et al. (2021) reported that during an intense hydrological anomaly, several species had a sharp reduction in spawning activity, demonstrating a quick response to environmental cues. This is an interesting result since the speed at which fish species can react to environmental changes, during the spawning period, is largely unknown. Thus, this study brings remarkable insights into basic life history information that is imperative for proposing strategies that could lead to a realistic framework for sustainable fisheries management practices and conservation, fundamental for an under-studied and threatened realm, such as the Amazon River basin.

In 1859, Charles Darwin proposed that species are not fundamentally different from subspecies or the varieties from which they evolve. A century later, Dobzhansky (1958) suggested that many such lineages are ephemeral and are likely to revert differentiation through introgression (Fig. 1A); only a few evolve complete reproductive isolation and persist in sympatry. In this issue of Molecular Ecology, Bouzid et al. (2021) show how new analytical methods, when applied to genome data, allow us to more precisely determine whether or not species formation follows the paths outlined by Darwin and Dobzhansky (Fig. 1B). The authors study the diversification of the lizard Sceloporus occidentalis, finding a continuum of genetic interactions between the preservation of genetic identity to genetic merger, analogous to what is exemplified by ring species. In doing so, they teach us two tales on species formation: that lineages are fractal byproducts of evolutionary processes such as genetic drift and selection, and that lineages are often ephemeral and do not always progress into species. Studying ephemeral lineages like those in S. occidentalis allows us to capture divergence at its earliest stages, and potentially to determine the factors that allow lineages to remain distinct despite pervasive gene flow. These lineages thus serve as a natural laboratory to address long standing hypotheses on species formation.

Understanding how eco-evolutionary processes and environmental factors drive population differentiation and adaptation are key challenges in evolutionary biology of relevance for biodiversity protection. Differentiation requires at least partial reproductive separation, which may result from different modes of isolation such as geographic isolation (allopatry) or isolation by distance (IBD), resistance (IBR), and environment (IBE). Despite that multiple modes might jointly influence differentiation, studies that compare the relative contributions are scarce. Using RADseq, we analyse neutral and adaptive genetic diversity and structure in 11 pike (Esox lucius) populations along a latitudinal gradient (54.9 - 63.6°N), to investigate the relative effects of IBD, IBE and IBR, and to assess whether the effects differ between neutral and adaptive variation, or across structural levels. Patterns of neutral and adaptive variation differed, likely reflecting that they have been differently affected by stochastic and deterministic processes. The importance of the different modes of isolation differed between neutral and adaptive diversity, yet were consistent across structural levels. Neutral variation was influenced by interactions among all three modes of isolation, with IBR (seascape features) playing a central role, wheares adaptive variation was mainly influenced by IBE (environmental conditions). Taken together, this and previous studies suggest that it is common that multiple modes of isolation interactively shape patterns of genetic variation, and that their relative contributions differ among systems. To enable identification of general patterns and understand how various factors influence the relative contributions, it is important that several modes are simultaneously investigated in additional populations, species and environmental settings.

The development of high-throughput sequencing (HTS) technologies has greatly improved our capacity to identify fungi and unveil their ecological roles across a variety of ecosystems. Here we provide an overview about current best practices in metabarcoding analysis of fungal communities, from experimental design through molecular and computational analyses. By re-analysing published datasets, we find that operational taxonomic units (OTUs) outperform amplified sequence variants (ASVs) in recovering fungal diversity, which is particularly evident for long markers. Additionally, analysis of the full-length ITS region allows more accurate taxonomic placement of fungi and other eukaryotes compared with the ITS2 subregion. We conclude that metabarcoding analyses of fungi are especially promising for co-analyses with the functional metagenomic or transcriptomic data, integrating fungi in the entire microbiome, recovery of novel fungal lineages and ancient organisms as well as barcoding of old specimens including type material.

While adaptation is commonly thought to result from selection on DNA sequence-based variation, recent studies have highlighted an analogous epigenetic component as well. However, the extent to which these adaptive mechanisms to adaptation to environmental heterogeneity are redundant or complementary remains unclear. To address the underlying genetic and epigenetic mechanisms and their relationship underlying environmental adaptation, we screened the genomes and epigenomes of nine global populations of a predominately sessile marine invasive tunicate, Botryllus schlosseri. We detected clear population genetic and epigenetic differentiation, which were both significantly influenced by local environments, and the minimum annual sea surface temperature (T_min) was simultaneously identified as the top explanatory variable for both types of variation. However, there remain some degree of difference in population structure patterns between two levels, suggesting a certain level of autonomy in epigenetic variation. From the functional perspective, a set of functional genes and biological pathways were shared between two levels, indicating a conjoint contribution of genetic and epigenetic variation to environmental adaptation. Moreover, we also detected genetic- or epigenetic-specific genes/pathways in relation to a wide variety of core processes potentially underlying adaptation to local environmental factors, suggesting the partly independent relationship between two mechanisms. We infer that complementary genetic and epigenetic routes to adaptation are available in this system. Collectively, these mechanisms may facilitate population persistence under environmental changes and sustain successful invasions in novel but contrasting environments.

Intense research efforts on phylogeography over the last two decades uncovered major biogeographical trends and renewed our understandings of plant domestication in the Mediterranean. We aim to investigate the evolutionary history and the origin of domestication of the carob tree that has been cultivated for millennia for food and fodder. We used >1000 microsatellite genotypes to identify carob evolutionary units (CEUs) based on genetic diversity structure and geography. We investigated genome-wide diversity and evolutionary patterns of the CEUs with 3557 SNPs generated by restriction-site associated DNA sequencing (RADseq). The 56 populations sampled across the Mediterranean basin, classified as natural, semi-natural or cultivated, were examined. Although, RADseq data are consistent with previous studies identifying a strong West-to-East genetic structure and considerable admixture in some geographic parts, we reconstructed a new phylogeographic scenario with two migration routes occurring from a single refugium likely located in South-Western Morocco. Our results do not favour the regionally bound or single origin of domestication. Indeed, our findings support a cultivation model of locally selected wild genotypes, albeit punctuated by long-distance westward dispersals of domesticated varieties by humans, concomitant with major cultural waves by Romans and Arabs in the regions of dispersal. Ex-situ efforts to preserve carob genetic resources should prioritize accessions from both western and eastern populations, with emphasis on the most differentiated CEUs situated in South-Western Morocco, South Spain and Eastern Mediterranean. Our study underscores the relevance of natural and seminatural habitats of Mediterranean forests and their refugia in the conservation efforts of tree crops.

Horizontal gene transfer via plasmids is important for the dissemination of antibiotic resistance genes among medically relevant pathogens. Specifically, the transfer of IncHI1A plasmids is believed to facilitate the spread of antibiotic resistance genes, such as carbapenemases, within the clinically important family Enterobacteriaceae. The microbial community of urban wastewater treatment plants has been shown to be highly permissive towards conjugal transfer of IncP1 plasmids. Here, we tracked the transfer of the P1 plasmid pB10 and the clinically relevant HI1A plasmid R27 in the microbial communities present in urban residential sewage entering full-scale wastewater treatment plants. We found that both plasmids readily transferred to these communities and that strains in the sewage were able to further disseminate them. Furthermore, that R27 has a broad potential host range, but a low host divergence. Interestingly, although the majority of R27 transfer events were to members of Enterobacteriaceae, we found a subset of transfer to other families, even other phyla. Indicating, that HI1A plasmids facilitate horizontal gene transfer both within Enterobacteriaceae, but also across families of especially Gammaproteobacteria, such as Moraxellaceae, Pseudomonadaceae and Shewanellaceae. pB10 displayed a similar potential host range as R27. In contrast to R27, pB10 had a high host divergence. By culture enrichment of the transconjugant communities, we show that sewage strains of Enterobacteriaceae and Aeromonadaceae can stably maintain R27 and pB10, respectively. Our results suggest that dissemination in the urban residual water system of HI1A plasmids may result in an accelerated acquisition of antibiotic resistance genes among pathogens.

Hybridization plays an important and underappreciated role in shaping the evolutionary trajectories of species. Following the introduction of a non-native organism to a novel habitat, hybridization with a native congener may affect the probability of establishment of the introduced species. In most documented cases of hybridization between a native and a non-native species, a mosaic hybrid zone is formed, with hybridization occurring heterogeneously across the landscape. In contrast, most naturally occurring hybrid zones are clinal in structure. Here we report on a long-term microsatellite dataset that monitored hybridization between the invasive winter moth, Operophtera brumata (Lepidoptera: Geometridae), and the native Bruce spanworm, O. bruceata, over a 12-year period. Our results document one of the first examples of the real-time formation and geographic settling of a clinal hybrid zone. In addition, by comparing one transect in Massachusetts where extreme winter cold temperatures have been hypothesized to restrict the distribution of winter moth, and one in coastal Connecticut, where winter temperatures are moderated by Long Island Sound, we find that the location of the hybrid zone appears to be independent of environmental variables and maintained under a tension model wherein the stability of the hybrid zone is constrained by population density, reduced hybrid fitness, and low dispersal rates. Documenting the formation of a contemporary clinal hybrid zone may provide important insights into the factors that shaped other well-established hybrid zones.

Invertebrates are important for restoration processes as they are key drivers of many landscape-scale ecosystem functions, including pollination, nutrient cycling and soil formation. However, invertebrates are often overlooked in restoration monitoring because they are highly diverse, poorly described, and time-consuming to survey, and require increasingly scarce taxonomic expertise to enable identification. DNA metabarcoding is a relatively new tool for rapid survey that is able to address some of these concerns, and provide information about the taxa with which invertebrates are interacting via food webs and habitat. Here we evaluate how invertebrate communities may be used to determine ecosystem trajectories during restoration. We collected ground-dwelling and airborne invertebrates across chronosequences of mine-site restoration in three ecologically disparate locations in Western Australia and identified invertebrate and plant communities using DNA metabarcoding. Ground-dwelling invertebrates showed the clearest restoration signals, with communities becoming more similar to reference communities over time. These patterns were weaker in airborne invertebrates, which have higher dispersal abilities and therefore less local fidelity to environmental conditions. Although we detected directional changes in community composition indicative of invertebrate recovery, patterns observed were inconsistent between study locations. The inclusion of plant assays allowed identification of plant species, as well as potential food sources and habitat. We demonstrate that DNA metabarcoding of invertebrate communities can be used to evaluate restoration trajectories. Testing and incorporating new monitoring techniques such as DNA metabarcoding is critical to improving restoration outcomes.

Temperature and precipitation regimes are rapidly changing, resulting in forest dieback and local extinction events, particularly in Mediterranean-type climates. Strategic forest management approaches that enhance forests’ resilience to future climates are urgently required, however adaptation to climates in heterogeneous landscapes with multiple selection pressures may be complex. For widespread trees in Mediterranean-type climates we hypothesized that patterns of local adaptation are associated with climate; precipitation is a stronger factor of adaptation than temperature; functionally related genes show similar signatures of adaptation; and adaptive variants are independently sorting across the landscape. To test our hypotheses, we sampled 28 populations across the geographic and climatic distribution of Eucalyptus marginata (jarrah), in south-west Western Australia, and obtained 13,534 independent single nucleotide polymorphic (SNP) markers across the genome. While overall levels of population differentiation were low (FST=0.04), environmental association analyses found a total of 2,336 unique SNPs potentially associated with five climate variables of temperature and precipitation. Allelic turnover was identified for SNPs associated with temperate seasonality and mean precipitation of the warmest quarter (39.2% and 36.9% deviance explained, respectively), suggesting that both temperature and precipitation are important factors in adaptation. SNPs within similarly function genes, according to gene ontology enrichment analysis, had analogous allelic turnover along climate gradients, while SNPs among temperature and precipitation variables had orthogonal patterns of adaptation. These contrasting patterns of adaptation provide evidence that there may be standing genomic variation adapted to changing climates, providing the substrate needed to promote adaptive management strategies to bolster forest resilience in the future.

Evaluating the factors that promote invasive ant abundance is critical to assess their ecological impact and inform their management. Many invasive ant species show reduced nestmate recognition and an absence of boundaries between unrelated nests, which allow populations to achieve greater densities due to reduced intraspecific competition. We examined nestmate discrimination and colony boundaries in introduced populations of the red imported fire ant (Solenopsis invicta; hereafter, fire ant). Fire ants occur in two social forms: monogyne (colonies with a single egg-laying queen) and polygyne (colonies with multiple egg-laying queens). In contrast with monogyne nests, polygyne nests are thought to be interconnected due to the reduced antagonism between non-nestmate polygyne workers, perhaps because polygyne workers habituate the colony to an odor unique to Gp-9b-carrying adults. However, colony boundaries and nestmate discrimination are poorly documented, particularly for worker-brood interactions. To delimit boundaries between field colonies, we correlated the exchange of a 15N-glycine tracer dissolved in a sucrose solution with social form. We also evaluated nestmate discrimination between polygyne workers and larvae in the laboratory. Counter to our expectations, polygyne colonies behaved identically to monogyne colonies, suggesting both social forms maintain strict colony boundaries. Polygyne workers also preferentially fed larval nestmates and may have selectively cannibalized non-nestmates. The levels of relatedness among workers in polygyne colonies was higher than those previously reported in North America (mean ±SE: 0.269 ± 0.037). Our study highlights the importance of combining genetic analyses with direct quantification of resource exchange to better understand the factors influencing ant invasions.

Structural variations (SVs) have been associated with genetic diversity and adaptation in diverse taxa. Despite these observations, it is not yet clear what their relative importance is for microevolution, especially with respect to known drivers of diversity, e.g., nucleotide substitutions, in rapidly adapting species. Here we examine the significance of SVs in pesticide resistance evolution of the agricultural super-pest, the Colorado potato beetle, Leptinotarsa decemlineata. By employing a trio-binning procedure, we develop near chromosomal reference genomes to characterize structural variation within this species. These updated assemblies represent >100-fold improvement of contiguity and include derived pest and ancestral non-pest individuals. We identify >200,000 SVs, which appear to be non-randomly distributed across the genome as they co-occur with transposable elements. SVs intersect exons for genes associated with insecticide resistance, development, and transcription, most notably cytochrome P450 (CYP) genes. To understand the role that SVs might play in adaptation, we incorporate an additional 66 genomes among pest and non-pest populations of North America into the SV graph. Single nucleotide polymorphisms (SNPs) and SVs have a similar proportion in coding and non-coding regions of the genome, but there is a deficit of SNPs in SVs, suggesting SVs may be under selection. Using multiple lines of evidence, we identify 28 positively selected genes that include 337 SVs and 442 outlier SNPs. Among these, there are four associated with insecticide resistance. Two of these genes (CYP4g15 and glycosyltransferase-13) are physically linked by a structural variant and have previously been shown to be co-induced during insecticide exposure.

Host switching allows parasites to expand their niches. However, successful switching may require suites of adaptations and also may decrease performance on the old host. As a result, reductions in gene flow accompany many host switches, driving speciation. Because host switches tend to be rapid, it is difficult to study their demographic parameters in real-time. Fundamental factors that control subsequent parasite evolution, such as the size of the switching population or the extent of immigration from the original host, remain largely unknown. To shed light on the host switching process, we explored the history of independent switches by two ectoparasitic honey bee mites (Varroa destructor and V. jacobsoni). Both switched to the western honey bee (Apis mellifera) after it was brought into contact with their ancestral host (Apis cerana), ~70 and ~12 years ago, respectively. Varroa destructor subsequently caused worldwide collapses of honey bee populations. Using whole-genome sequencing on 63 mites collected in their native ranges from both the ancestral and novel hosts, we were able to reconstruct the known temporal dynamics of the switch. We further found multiple previously undiscovered mitochondrial lineages on the novel host, along with the genetic equivalent of tens of individuals that were involved in the initial host switch. Despite being greatly reduced, some gene flow remains between mites adapted to different hosts. Our findings suggest that while reproductive isolation may facilitate the fixation of traits beneficial for exploitation of the new host, ongoing genetic exchange may allow genetic amelioration of inbreeding effects.