Patterns of pathogen prevalence are, at least partially, the result of coevolutionary host-pathogen interactions. Thus, exploring the distribution of host genetic variation in relation to infection by a pathogen within and across populations can provide important insights into mechanisms of host defence and adaptation. Here we use a landscape genomics approach (Bayenv) in conjunction with genome-wide data (ddRADseq) to test for associations between avian malaria (Plasmodium) prevalence and host genetic variation across 13 populations of the island endemic Berthelot’s pipit (Anthus berthelotii). Considerable and consistent spatial heterogeneity in malaria prevalence was observed among populations over a period of 15 years. The prevalence of malaria infection was also strongly positively correlated with pox (Avipoxvirus) prevalence. Multiple host loci showed significant associations with malaria prevalence after controlling for genome-wide neutral genetic structure. These sites were located near to or within genes linked to metabolism, stress response, transcriptional regulation, complement activity and the inflammatory response, many previously implicated in vertebrate responses to malarial infection. Our findings identify diverse genes - not just limited to the immune system - that may be involved in host protection against malaria and suggests that spatially variable pathogen pressure may be an important evolutionary driver of genetic divergence among wild animal populations, such as Berthelot’s pipit. Further, our data indicate that spatio-temporal variation in multiple different pathogens (e.g., malaria and pox in this case) may have to be studied together to develop a more holistic understanding of host pathogen-mediated evolution.

Natural hybridisation is now recognised as pervasive in its occurrence across the Tree of Life. Resurgent interest in natural hybridisation fuelled by developments in genomics has led to an improved understanding of the genetic factors that promote or prevent species cross-mating. Despite this body of work overturning many widely held assumptions about the genetic barriers to hybridisation, it is still widely thought that ploidy differences between species will be an absolute barrier to hybridisation and introgression. Here, we revisit this assumption, reviewing findings from surveys of polyploidy and natural hybrids in the wild. In a case study in the British flora, 203 hybrids representing 35% of hybrids with suitable data have formed via cross-ploidy matings, while a wider literature search revealed 48 studies (45 in plants and 3 in animals), where cross-ploidy hybridisation has been confirmed with genetic data. These results show cross-ploidy hybridisation is readily overlooked, and potentially common in some groups. General findings from these studies include strong directionality of hybridisation, with introgression usually towards the higher ploidy parent, and cross-ploidy hybridisation being more likely to involve allopolyploids than autopolyploids. Evidence for adaptive introgression across a ploidy barrier and cases of cross-ploidy hybrid speciation show the potential for important evolutionary outcomes.

Anthropogenic impact and loss of genetic diversity threaten more than 50% of raptors. These threats are particularly pronounced for island- endemic species, which occupy small areas, making them more vulnerable to rapid environmental changes. The Reunion harrier (Circus maillardi) is a typical example of the challenges encountered by island- endemic species. In this study, we characterize genetic variation at near-neutral and coding loci to test the historical impact of human activity on harrier populations, and evaluate their (mal)adaptive potential. We observed low but significant genetic differentiation between populations on the West and North-East sides of the island, echoing observations in other endemic species. Inbreeding was significant, with a substantial fraction of samples being first or second-degree relatives. Historical effective population sizes have declined from ~3000 to 300 individuals in the past 1000 years, with a more recent drop ~100 years ago consistent with human activity. Based on our simulations and comparisons with a close relative (Circus melanoleucos), this demographic history may have allowed purging of the most deleterious variants, but is unlikely to have allowed the purging of mildly deleterious variants. Our study provides an example of the massive impact that human activity may have on the genetic diversity and adaptive potential of island populations, and calls for urgent action to closely monitor the reproductive success of such endemic populations, in association with genetic studies.

Across its Holarctic range, Arctic charr (Salvelinus alpinus) populations have diverged into distinct trophic specialists across independent replicate lakes. The major aspect of divergence between ecomorphs is in head shape and body shape, which are ecomorphological traits reflecting niche use. However, whether the genomic underpinnings of these parallel divergences are consistent across replicates was unknown but key for resolving the substrate of parallel evolution. We investigated the genomic basis of head shape and body shape morphology across four benthivore-planktivore ecomorph pairs of Arctic charr in Scotland. Through genome-wide association analyses, we found genomic regions associated with head shape (89 SNPs) or body shape (180 SNPs) separately and 50 of these SNPs were strongly associated with both body and head shape morphology. For each trait separately, only a small number of SNPs were shared across all ecomorph pairs (3 SNPs for head shape and 10 SNPs for body shape). Signs of selection on the associated genomic regions varied across pairs, consistent with evolutionary demography differing considerably across lakes. Using a comprehensive database of salmonid QTLs newly augmented and mapped to a charr genome, we found several of the head and body shape associated SNPs were within or near morphology QTLs from other salmonid species, reflecting a shared genetic basis for these phenotypes across species. Overall, our results demonstrate how parallel ecotype divergences can have both population-specific and deeply shared genomic underpinnings across replicates, influenced by differences in their environments and demographic histories.

The study of microbiomes across organisms and environments has become a prominent focus in molecular ecology. This perspective article explores methodological advancements, common challenges and future directions in the field. Key research areas include understanding the drivers of microbiome community assembly, linking microbiome composition to host genetics, exploring microbial functions, transience, and spatial partitioning, and disentangling non-bacterial components of the microbiome. Methodological advancements, such as quantifying absolute abundances, sequencing complete genomes, and utilizing novel statistical approaches, are also useful tools for understanding complex microbial diversity patterns. Our aims are to encourage robust practices in microbiome studies and inspire researchers to explore the next frontier of this rapidly changing field.

Introductions of invasive species to new environments often result in rapid rates of trait evolution. While in some cases these evolutionary transitions are adaptive and driven by natural selection, they can also result from patterns of genetic and phenotypic variation associated with the invasion history. Here, we examined the brown anole (Anolis sagrei), a widespread invasive lizard for which genetic data have helped trace the sources of non-native populations. We focused on the dewlap, a complex signaling trait known to be subject to multiple selective pressures. We measured dewlap reflectance, pattern, and size in 30 non-native populations across the southeastern United States. As well, we quantified environmental variables known to influence dewlap signal effectiveness, such as canopy openness. Further, we used genome-wide data to estimate genetic ancestry, perform association mapping, and test for signatures of selection. We found that among-population variation in dewlap characteristics was best explained by genetic ancestry. This result was supported by genome-wide association mapping, which identified several ancestry-specific loci associated with dewlap traits. Despite the strong imprint of this aspect of the invasion history on dewlap variation, we also detected significant relationships between dewlap traits and local environmental conditions. However, we found limited evidence that dewlap-associated genetic variants have been subject to selection. Our study emphasizes the importance of genetic ancestry and admixture in shaping phenotypes during biological invasion, while leaving the role of selection unresolved, likely due to the polygenic genetic architecture of dewlaps and selection acting on many genes of small effect.

Numerous mechanisms drive ecological speciation, including isolation by adaptation, barrier, distance, environment, hierarchy, and resistance. These promote genetic and phenotypic differentiation of local populations, formation of phylogeographic lineages, and ultimately, completed speciation via reinforcement. In contrast, it is possible that similar mechanisms might lead to lineage cohesion through stabilizing rather than diversifying ecomorphological selection and the long-term persistence of population structure within species. Processes that drive the formation and maintenance of geographic genetic diversity while facilitating high rates of migration and limiting phenotypic divergence may thereby result in population structure that is not accompanied by divergence towards reproductive isolation. We suggest that this framework can be applied more broadly to address the classic dilemma of “structure versus speciation” when evaluating phylogeographic diversity, unifying population genetics, species delimitation, and the underlying study of speciation. We demonstrate one such instance in the Seepage Salamander (Desmognathus aeneus) from the southeastern United States. Recent studies estimated up to 6.3% mitochondrial divergence and 4 phylogenomic lineages with broad admixture across geographic hybrid zones, which could potentially represent distinct species. However, while limited dispersal promotes substantial isolation by distance, extreme microhabitat specificity appears to yield stabilizing selection on ecologically mediated phenotypes. As a result, climatic cycles promote recurrent contact between lineages that are not adaptively differentiated and therefore experience repeated bouts of high migration and introgression through time. This leads to a unified, single species with deeply divergent phylogeographic lineages that nonetheless do not appear to represent incipient species.

Identifying genetic conservation units (CUs) in threatened species is critical for the preservation of adaptive capacity and evolutionary potential in the face of climate change. However, delineating CUs in highly mobile species remains a challenge due to high rates of gene flow and genetic signatures of isolation by distance. Even when CUs are delineated in highly mobile species, the CUs often lack key biological information about what populations have the most conservation need to guide management decisions. Here we implement a framework for rigorous CU identification in the Canada Warbler (Cardellina canadensis), a highly mobile migratory bird species of conservation concern, and then integrate demographic modeling and genomic offset within a CU framework to guide conservation decisions. We find that whole-genome structure in this highly mobile species is primarily driven by putative adaptive variation. Identification of CUs across the breeding range revealed that Canada Warblers fall into two Evolutionarily Significant Units (ESU), and three putative Adaptive Units (AUs) in the South, East and Northwest. Quantification of genomic offset within each AU reveals significant spatial variation in climate vulnerability, with the Northwestern AU being identified as the most vulnerable to future climate change based on genomic offset predictions. Alternatively, quantification of past population trends within each AU revealed the steepest population declines have occurred within the Eastern AU. Overall, we illustrate that genomics-informed CUs provide a strong foundation for identifying current and potential future regional threats that can be used to manage highly mobile species in a rapidly changing world.

Rodents are key reservoirs of zoonotic pathogens and play an important role in disease transmission to humans. Importantly, anthropogenic land-use change has been found to increase the abundance of synanthropic rodents, particularly rodent reservoirs of zoonotic disease. Anthropogenic environments also affect the microbiome of synanthropic wildlife, influencing wildlife health and potentially introducing novel pathogens. Our objective was to characterize the microbiome and investigate the prevalence of zoonotic bacterial pathogens in synanthropic rodents in native and anthropogenic environments to better understand their role in pathogen maintenance and transmission. We sampled wild Peromyscus mice in agricultural and undeveloped landscapes and forest and synanthropic habitat in Minnesota, USA and conducted 16S amplicon sequencing using long-read Nanopore sequencing technology on fecal samples to characterize the rodent microbiome. We compared community composition and diversity between habitats and screened for the presence of putative pathogenic bacteria species. Microbiome community composition differed significantly between agricultural and undeveloped landscapes and forest and synanthropic habitat while microbiome richness, diversity, and evenness were lower in undeveloped-forest habitat compared to all other habitats. We detected overall low abundance and diversity of putative pathogenic bacteria, though the greatest number of pathogenic bacteria were detected in the agricultural-forest habitat. Our findings show that rodent microbiome community composition differs across landscapes and habitat types but suggest that landscape-level anthropogenic factors may be most important to predict zoonotic pathogen abundance. Ultimately, understanding how anthropogenic land-use change and synanthropy affect rodent microbiomes and pathogen prevalence is important to managing transmission of rodent-borne zoonotic diseases to humans.

Invasive species are predicted to adjust their morphological, physiological, and life-history traits to adapt to their non-native environments. Although a loss of genetic variation during invasion may restrict local adaptation, introduced species often thrive in novel environments. Despite being founded by just a few individuals, the bumblebee Bombus terrestris (Hymenoptera: Apidae) has successfully spread across the island of Tasmania (Australia) in less than 30 years, becoming abundant and competitive with native pollinators. We use RADseq to investigate the neutral and adaptive genetic processes associated with environmental and morphological variation following the invasion of B. terrestris in Tasmania. Across 15 sites, we found high gene flow with low genetic diversity, significant isolation-by-distance, and spatial variation in effective migration rates. A longitudinal band of restricted migration was evident across the mid-central region of Tasmania, corresponding to sites with high elevation, pastural land, low wind speeds and low precipitation seasonality. Tajima’s D indicated a recent population expansion for central sites extending from the south to the north of the island. Significant selection signatures were found for loci in relation to precipitation, wind speed, and wing loading. Candidate loci were annotated to genes with functions related to cuticle water retention, and insect flight muscle stability. Understanding how a genetically impoverished invasive bumblebee has rapidly adapted to a novel island environment provides further understanding about the evolutionary processes that determine successful insect invasions, and the potential for invasive hymenopteran pollinators to spread globally.

While the role of selection in divergence along the speciation continuum is theoretically well understood, defining specific signatures of selection in the genomic landscape of divergence is empirically challenging. Modelling approaches can provide insight into the potential role of selection on the emergence of a heterogenous genomic landscape of divergence. Here, we extend and apply an individual-based approach that simulates the phenotypic and genotypic distributions of two populations under a variety of selection regimes, genotype-phenotype maps, modes of migration, and genotype-environment interactions. We show that genomic islands of high differentiation and genomic valleys of similarity may respectively form under divergent and parallel selection between populations. For both types of between-population selection, negative and positive frequency-dependent selection within populations generated genomic islands of higher magnitude and genomic valleys of similarity respectively. Divergence rates decreased under strong dominance with divergent selection, as well as in models including genotype-environment interactions under parallel selection. For both divergent and parallel selection models, divergence rate was higher under an intermittent migration regime between populations, in contrast to a constant level of migration across generations, despite an equal number of total migrants. We highlight that interpreting a particular evolutionary history from an observed genomic pattern must be done cautiously, as similar patterns may be obtained from different combinations of evolutionary processes. Modelling approaches such as ours provide an opportunity to narrow the potential routes that generate the genomic patterns of specific evolutionary histories.

The Astyanax mexicanus complex include two different morphs, a surface and a cave adapted ecotype, found at three mountain ranges in Northeastern Mexico: Sierra de El Abra, Sierra de Guatemala, and Sierra de la Colmena (Micos). Since their discovery, multiple studies have attempted to characterize the timing and the number of events that gave rise to the evolution of these cave-adapted ecotypes. Here, using RAD-seq and genome-wide sequencing, we assessed the phylogenetic relationships, genetic structure, and gene flow events between the cave and surface Astyanax mexicanus populations, to estimate the time and mode of evolution of the cave-adapted ecotypes. We also evaluated the body shape evolution across different cave lineages using geometric morphometrics to examine the role of phylogenetic signal vs. environmental pressures. We found strong evidence of parallel evolution of cave-adapted ecotypes derived from two separate lineages of surface fish and hypothesize that there may be up to four independent invasions of caves from surface fish. Moreover, a strong congruence between the genetic structure and geographic distribution was observed across the cave populations, with the Sierra de Guatemala the region exhibiting most genetic drift among the cave populations analyzed. Interestingly, we found no evidence of phylogenetic signal in body shape evolution, but we found support for parallel evolution in body shape across independent cave lineages, with cavefish from the Sierra de El Abra reflected the most divergent morphology relative to surface and other cavefish populations.

Identifying and understanding patterns of biological diversity is crucial at a time when even the most remote and pristine marine ecosystems are threatened by resource exploitation such as deep-seabed mining. Metabarcoding provides the means through which to perform comprehensive investigations of diversity by examining entire assemblages simultaneously. Nematodes commonly represent the most abundant infaunal metazoan group in marine soft sediments. In this meta-analysis, we compiled all publicly available metabarcoding datasets targeting the 18S rRNA v1-v2 region from sediment samples to conduct a global-scale examination of nematode Amplicon Sequence Variant (ASV) alpha diversity patterns, evolutionary distinctiveness (ED) and phylogenetic community structure at different depths and environments. We found that nematode ASV richness followed a parabolic trend, increasing from the intertidal to the shelf, reaching a maximum in the bathyal and decreasing in the abyssal zone. No depth- or environment-specific assemblages were identified as a large fraction of genera were shared. Contrastingly, the vast majority of ASVs were unique to each environment and/or depth zone; genetic diversity was thus highly localised. The abyssal samples had the highest ED values, indicating that a relatively stable yet very old environment can produce highly diversified assemblages. Overwhelmingly, nematode ASVs in all environments exhibited phylogenetic clustering, pointing to environmental filtering as the primary force defining community assembly rather than competitive interactions. This finding stresses the importance of habitat preservation for the maintenance of marine nematode diversity.

The origin of new genes has long been a central interest of evolutionary biologists. However, their novelty evades reconstruction by the classical tools of evolutionary modeling. This evasion of insight from deep ancestral investigation necessitates intensive study of model species within well-sampled, recently diversified, clades. One such clade is the model genus Neurospora, members of which lack recent gene duplications, yet harbor clusters of lineage-specific genes (LSGs) adjacent to the telomeres. Several Neurospora species are comprehensively characterized organisms apt for studying the evolution of LSGs. Using gene synteny, we documented that 78% of Neurospora LSGs clusters are located in chromosomal regions featuring extensive tracts of non-coding DNA and duplicated genes. Here we report several instances of LSGs that are likely from regional rearrangements and potentially from gene rebirth. To broadly investigate functions of LSGs, we assembled transcriptomics data from 68 experimental data points and identified co-regulatory modules using Weighted Gene Correlation Network Analysis, revealing that LSGs are widely but peripherally involved in known regulatory machinery for diverse functions. The ancestral status of mas-1 and its neighbors was investigated in detail, suggesting that it arose from an ancient lysophospholipase precursor that is ubiquitous in lineages of the Sordariomycetes; mas-1 plays a role in cell-wall integrity and cellular sensitivity to antifungal toxins. Our discoveries illuminate a “rummage region” in the N. crassa genome that enables formation of new genes and functions to arise via gene duplication and relocation, followed by fast mutation and recombination facilitated by tandem repeats and deconstrained non-coding sequences.

Untangling the responses of protistan communities associated with soil and plant compartments and their associations with bacterial and fungal communities to pathogen invasion are critical for understanding the ecological processes governing plant microbiome assembly. Here we examined the protistan communities across the soil–plant continuum of healthy chili peppers and those with Fusarium wilt disease (FWD) and integrated the bacterial and fungal microbiome data from our previous investigation in China. We found that FWD was associated with a significant enrichment of phagotrophic protists in roots and an increase in the proportion and connectivity of these phagotrophic protists in intra- and interkingdom networks. Specifically, FWD increased the negative correlations between phagotrophic protists (especially Cercozoa and Ciliophora) and several members of Actinobacteria, Alphaproteobacteria, and Gammaproteobacteria in the interkingdom networks. Furthermore, the microbiomes of diseased plants not only exhibit a higher relative abundance of functional genes related to bacterial anti-predator responses compared to healthy plants, but also contained a greater abundance of metagenome-assembled genomes possessing functional traits involved in this response. The increased microbial interkingdom correlations among bacteria, fungi, and protists, coupled with the enhanced effects of protists on bacteria and fungi, as well as the notable bacterial anti-predator feedback in the diseased plant microbiome, all suggest that FWD catalyzes the associations between different groups of microbiomes. These findings highlight the role of predatory protists in shaping microbial assembly and functionality through top-down forces during pathogenic stress, potentially contributing to co-evolution within these soil and plant microbiomes.

Host-associated microbiota can be affected by factors related to environmental change, such as urbanization and invasive species. For example, urban areas often affect food availability for animals, which can change their gut microbiota. Invasive parasites can also influence microbiota through either competition or indirectly through a change in the host immune response. These interacting factors can have complex effects on host fitness, but few studies have disentangled the relationship between urbanization and parasitism on an organism’s gut microbial composition. To address this gap in knowledge, we investigated the effects of urbanization and parasitism by the invasive avian vampire fly (Philornis downsi) on the gut microbiota of nestling small ground finches (Geospiza fuliginosa) on San Cristóbal Island, Galápagos. We conducted a factorial study in which we experimentally manipulated parasite presence in an urban and non-urban area. Feces were then collected when nestlings to characterize the gut microbiota (i.e., alpha and beta diversity, community composition). Although we did not find an interactive effect of urbanization and parasitism on the microbiota, we did find main effects of each variable. Urban and parasitized nestlings had lower bacterial diversity and differences in relative abundance of bacterial phyla and genera compared to non-urban non-parasitized nestlings, respectively. Overall, this study advances our understanding of the complex effects of anthropogenic stressors on the gut microbiota of birds.

The commercially important Atlantic bluefin tuna (Thunnus thynnus), a large migratory fish, has experienced notable recovery aided by accurate resource assessment and effective fisheries management efforts. Traditionally, this species has been perceived as consisting of eastern and western populations, spawning respectively in the Mediterranean Sea and the Gulf of Mexico, with mixing occurring throughout the Atlantic. However, recent studies have emerged challenging this assumption by revealing weak genetic differentiation and identifying a previously unknown spawning ground in the Slope Sea used by Atlantic bluefin tuna of uncertain origin. To further understand the current and past population structure and connectivity of Atlantic bluefin tuna, we have assembled a unique dataset including thousands of genome-wide Single Nucleotide Polymorphisms (SNPs) from five hundred larvae, young of the year and spawning adult samples covering the three spawning grounds and including individuals of other Thunnus species. Our analyses support two weakly differentiated but demographically connected ancestral populations that interbreed in the Slope Sea. Moreover, we also identified signatures of introgression from albacore into the Atlantic bluefin tuna genome, exhibiting varied frequencies across spawning areas, indicating strong gene flow from the Mediterranean Sea towards the Slope Sea. We hypothesize that the observed genetic differentiation may be attributed to increased gene flow caused by a recent intensification of westward migration by the eastern population, which could have implications for the genetic diversity and conservation of western populations. Future conservation efforts should consider these findings to address potential genetic homogenization in the species.

Epigenetic mechanisms, such as DNA methylation, can influence gene regulation and affect phenotypic variation, raising the possibility that they contribute to ecological adaptation. To being to address this issue requires high-resolution sequencing studies of natural populations to pinpoint epigenetic regions of potential ecological and evolutionary significance. However, such studies are still relatively uncommon, especially in insects, and are mainly restricted to a few model organisms. Here, we characterize patterns of DNA methylation for natural populations of Timema cristinae adapted to two host plant species (i.e., ecotypes). By integrating results from sequencing of whole transcriptomes, genomes, and methylomes, we investigate whether environmental, host, and genetic differences of these stick insects are associated with methylation levels of cytosine nucleotides in CpG context. We report an overall genome-wide methylation level for T. cristinae of ~14%, being enriched in gene bodies and impoverished in repetitive elements. Genome-wide DNA methylation variation was strongly positively correlated with genetic distance (relatedness), but also exhibited significant host-plant effects. Using methylome-environment association analysis, we pinpointed specific genomic regions that are differentially methylated between ecotypes, with these regions being enriched for genes with functions in membrane processes. The observed association between methylation variation with genetic relatedness and the ecologically-important variable of host plant suggest a potential role for epigenetic modification in T. cristinae adaptation. To substantiate such adaptive significance, future studies could test if methylation has a heritable component and the extent to which it responds to experimental manipulation in field and laboratory studies.