Forest trees face threats from many insect pest species, underscoring the importance of understanding their defense mechanisms for survival. In a North American conifer species Picea glauca, white spruce, a defense-related gene, βglu1, is responsible for releasing phenolic compounds (acetophenones) to defend against its insect defoliator, Choristoneura fumiferana, the eastern spruce budworm. βglu1 is also expressed in a Eurasian conifer species Picea abies, Norway spruce, although no major insect defoliator is present within the species’ natural range. We compared range-wide variation of βglu1 transcript levels from foliage samples of P. glauca in North America and P. abies in Europe using RT-qPCR and targeted transcriptome sequencing. βglu1 transcript levels were highly correlated between the two methods, with wide ranges of variation being detected within and between populations in both species. We found a significant longitudinal gradient in βglu1 transcript levels in P. glauca, with one βglu1 gene form being differentially expressed across populations, but not in P. abies. The expression level differences in P. glauca are consistent with the historically higher C. fumiferana outbreak frequency and severity in eastern compared to western populations, with C. fumiferana defoliation severity being a significant explanatory variable for βglu1 transcript levels. Climate per se was not a significant explanatory factor in either species. Overall, these results enhance our understanding of potential adaptive variation in acetophenone defenses in P. glauca, while the factors influencing βglu1 transcript variation in P. abies require further investigation.

Haploblocks are regions of the genome that coalesce to an ancestor as a single unit. Differentiated haplotypes in these regions can result from the accumulation of mutational differences in low-recombination chromosomal regions, especially when selective sweeps occur within geographically structured populations. We introduce a method to identify large well-differentiated haploblock regions (LHBRs), based on the variance in standardized heterozygosity (ViSHet) of single nucleotide polymorphism (SNP) genotypes among individuals, calculated across a genomic region (500 SNPs in our case). We apply this method to the greenish warbler (Phylloscopus trochiloides) ring species, using a newly assembled reference genome and genotypes at more than 1 million SNPs among 257 individuals. Most chromosomes carry a single distinctive LHBR, containing 4-6 distinct haplotypes that are associated with geography, enabling detection of hybridization events and transition zones between taxa. LHBRs have exceptionally low within-haplotype nucleotide variation and moderately low between-haplotype nucleotide distance, suggesting their establishment through recurrent selective sweeps at varying geographic scales. Meiotic drive is potentially a powerful mechanism of producing such selective sweeps, and the LHBRs are likely to often represent centromeric regions where recombination is restricted. Links between populations enable introgression of favored haplotypes and we identify one haploblock showing a highly discordant distribution compared to the rest of the genome, being present in two distantly separated geographic regions that are at similar latitudes in both east and west Asia. Our results set the stage for detailed studies of haploblocks, including their genomic location, gene content, and contribution to reproductive isolation.

Ongoing climate change mandates improved understanding of how temperature fluctuations influence organismal evolution and behavior. Detritus-based nest-retreats in spiders have originated multiple times in parallel—hypothesized to be an adaptive response to climatic fluctuations. We investigated the potential role of climate change in shaping the evolution of nest-retreats over geological timescales, and the short-term effect of temperature on the morphology and energy investment of nest-retreat in Campanicola campanulata. Phylogenetic analyses reconstruct twelve origins of nest-retreats, first appearing in the Eocene, and diversifying during the Late Cenozoic Icehouse period. Spiders respond to experimentally lowered temperatures by making larger nest-retreats, indicating a direct impact of temperature on retreat architecture. Our results for the first time affirm the thermoregulatory function of spider nests and suggest that temperature impacts nest-retreats across both evolutionary and ecological timescales. Nest-retreat spiders can serve as a model to study the origins of thermoregulatory nest-building in animals and how it may be impacted by ongoing climate change.

Long homozygous chromosome segments are known as runs of homozygosity (ROH); these reflect patterns of identity by descent and can be used to measure individual inbreeding, map recessive traits, and reconstruct demographic histories. Here we review some key considerations with ROH detection and the inferences pertaining to inbreeding and demographic analyses in wild populations.

Host density, genetic diversity and social structure are key factors influencing disease transmission in wildlife populations, but their interactions remain poorly understood in insects. We assessed how populations of two common bumble bee species, Bombus pascuorum and B. terrestris are structured across island and mainland sites in the British Isles and France. B. pascuorum formed distinct genetic clusters on islands, with varying levels of heterozygosity with only the Isle of Arran in Scotland clustering with mainland populations. B. terrestris populations were less structured, indicating a higher dispersal ability; however, populations on the Isle of Man and the Scilly Isles showed low heterozygosity, and the Isle of Man was genetically separated from other islands and mainland populations. Nest density was similar between species. To assess how population structure affects pathogen prevalence, we tested bees for five micro-parasitic and four viral pathogens, expecting higher pathogen transmission within nests and in dense, genetically homogenous populations. B. pascuorum from the same nest showed more similar infection profiles than bees from different nests, indicating increased intra-colony transmission. Contrary to expectations, islands with high heterozygosity showed high viral prevalence and no reduction in micro-parasite infections. Bumble bee nest density was linked to a higher prevalence of Apicystis bombi, while other pathogens showed inconsistent patterns. These results suggest that while social structure affects pathogen transmission, genetic diversity does not consistently reduce prevalence. Instead, generalist bumble bee pathogens could be more affected by host species diversity and density. Island populations with limited gene flow and low genetic diversity may be more vulnerable to pathogen pressure, particularly under changing environmental conditions.

Caloric restriction (CR) studies have traditionally focused on species with conventional reproductive roles, emphasizing female’s greater investment in costly gametes and parental care. The divergent impact of CR on males and females is evident across species, the factors driving this variation, i.e., resource allocation in reproductive elements vs. distinct life histories remain unclear. To address this, we investigated the effects of CR on growth, gene expression, and intestinal microbiota in the lined seahorse Hippocampus erectus, a species with male pregnancy and unique life history. Juvenile seahorses were subjected to ad libitum (AL) or CR for 5 months. CR stunted male (but not female) growth and brood pouch development, reflecting the energy demands associated with pouch development and parental care. Transcriptome analysis demonstrated organ- and sex-specific responses to CR with distinct lipid and energy-related pathways activated in male and female livers, indicative of survival enhancement strategies. Fasting had minimal impact on spermatogenesis, but downregulated lipid metabolic and inflammatory genes in ovaries, emphasizing the importance of pre-copulatory resource allocation in female gametes. While microbial diversity increased with fasting, no discernible sex-specific effect on hind-gut microbiota was identified. Our research indicates that nutrient limitation´s impact on males and females is influenced by their allocation of resources to reproduction and parental investment, rather than being solely determined by biological sex. We underscore the significance of studying species with diverse reproductive strategies, sex roles, mating systems, and life-history strategies to understand the sex-specific effects of caloric restriction.

Community composition is determined largely by drift, selection, dispersal, and speciation. The crucial issue is disentangling the relative importance of different processes in community assembly. However, this issue has not been adequately discussed in benthic foraminiferal communities. Here, we studied the community composition, co-occurrence network, and community assembly of benthic foraminifera (protozoa) on the Xisha carbonate platform and their coupled relationships. The community composition was determined via the environmental DNA (eDNA) technique. Heavy metals, grain sizes, loss on ignition (LOI), organic carbon, and pH were measured for environmental assessment. The results showed that spatial variations in foraminiferal community composition were mainly controlled by organic carbon, whereas the effects of other variables were minimal. Similarly, spatial variations in the co-occurrence network were determined by organic carbon and pH. Despite the impacts of environmental variables on community composition, null and neutral models demonstrated that foraminiferal community assembly is driven by ecological drift instead of selection. This study is the first to couple community composition and co-occurrence networks with community assembly processes. A hypothesis was proposed that selection increases community heterogeneity and network heterogeneity, whereas stochastic processes eliminate such heterogeneities. This mechanism would bridge the gap between processes and community patterns. A comparison with our previous study revealed that foraminiferal community assembly may depend on specific systems (habitats). This insight could inform new strategies for the conservation of marine biodiversity.

Genome sharing in gonochorous species is expected to result in intraspecific conflicts due to intersexual competition. The emergence of sexual dimorphism is thus connected to the evolution of mechanisms that, starting from a similar genomic background, produce sufficiently disparate phenotypes to attenuate sexually antagonistic selection. From a molecular perspective it can be briefly summarised by sex-specific differences in gene expression, splicing, non-coding regulation or epigenetic marks. The tawny owl (Strix aluco) is a reverse sexually dimorphic species where females and males evolved distinct body sizes (smaller males), which results in sex-specific roles and therefore are a robust example of resolved sexual conflict. Here we explore, transcriptional variation among 27 juvenile tawny owls with the objective of investigating molecular signatures of resolved sexual conflict. Tawny owls also exhibit melanin-based colour polymorphism, which, given the body size differences between sexes, suggest a sex-specific onset of pigmentation. Our results show substantial sex-specific variation in terms of differentially expressed genes, single nucleotide polymorphisms and alternative exon usage in genes involved in life history traits (ZGRF1, VLDLR), behaviour (GSK3B, SLC12A) and aspects of growth (GHR, EGF, EPS8L2). Exploring sex-specific DEG revealed enrichment for biological functions associated with melanogenesis and pigment granulation in males, which together with the identification of a single up-regulated gene involved in melanogenesis (RAB38) in brown males strongly suggests different timings for the onset of pigmentation between sexes. Overall, our results reveal some of the sex-specific molecular signatures expected to be observed in the context of a resolved sexual conflict.

Microevolutionary processes shape adaptive responses to heterogeneous environments, where these effects vary both among and within species. However, it remains largely unknown to which degree signatures of adaptation to environmental drivers can be detected based on the choice of spatial scale and genomic marker. We studied signatures of local adaptation across two levels of spatial extents, investigating complementary types of genomic variants–single nucleotide polymorphisms (SNPs) and polymorphic transposable elements (TEs)–in populations of the alpine model plant species Arabis alpina. We coupled environmental factors, derived from remote sensing digital elevation models at very high resolution (0.5m), with whole-genome sequencing data of 304 individuals across four populations. By comparing putatively adaptive loci detected between each local population versus a regional assessment including all populations simultaneously, we demonstrate that responses of A. alpina to similar amounts of abiotic variation are largely governed by local evolutionary processes. Furthermore, we find minimally overlapping signatures of local adaptation between SNPs and polymorphic TEs. Notably, functional annotations of candidate genes for adaptation revealed several symbiosis-related genes associated with the abiotic factors studied, which could represent selective pressures from biotic agents. Our results highlight the importance of considering different spatial extents and types of genomic polymorphisms when searching for signatures of adaptation to environmental variation. Such insights provide key information on microevolutionary processes and could guide management decisions to mitigate negative impacts of climate change on alpine plant populations.

Genomic studies have shown that introgressive hybridization is a common phenomenon across the tree of life, particularly among young radiations. As incipient speciation tends to be induced by vicariance events, it is assumed that introgressive hybridization is more frequent in young species radiations in which allopatrically distributed species have a high probability of comming into secondary contact. In this study we draw on whole genomic data to investigate spatio-temporal introgression patterns in a songbird radiation that has colonized a highly dynamic island region in the Indo-Pacific. Some taxa within this radiation have colonized remote oceanic islands whereas others occur on landmasses and islands in the Sahul region that were at times connected during Pleistocene periods of low sea level. Our results show that introgressive hybridization has been pervasive within this young radiation, despite prominent plumage differences between taxa. Geographical proximity has been an important factor for hybridization and we further find that species occupying islands in the environmentally unstable Sahul region exhibit particularly high signatures of introgressive hybridization. Yet, one species appears to have been shielded against hybridization, perhaps due to specific ecological specializations. Finally, we identify a hybrid species on an island where two oceanic radiations meet. Collectively, our results support a growing body of literature that suggests that reticulate speciation is much more common than previously thought. This has implications for our understanding of how species form and how species are maintained through time.

The North American boreal forest is a massive ecosystem, and its keystone herbivore is the snowshoe hare (Lepus americanus). Hares are exposed to considerable environmental extremes in diet and weather, food availability, and predation risk. Gut microbiomes have been suggested to facilitate adaptive animal responses to environmental change, but severe environmental challenges to homeostasis can also disrupt host-microbiome relationships. To better understand gut microbiome contributions to animal acclimation, we studied the fecal bacterial microbiome of wild hares across two types of extreme environmental change that are integral to their natural history: (1) seasonal transitions between summer and winter, and (2) changes over the ~10 year “boom-bust” population cycles that are characterized by shifting food resource availability and predation pressure. When compared to summer, hares in winter had lower bacterial richness and were depleted in twenty families (including Oxalobacteraceae and Christensenellaceae) but enriched for Ruminococcaceae (a family which contains plant fibre degrading microbiota) alongside nine other bacterial groups. Marked bacterial microbiome differences also occurred across phases of the population cycle. Bacterial microbiomes were lower in richness and compositionally distinct in the peak compared to the increase or decline phases of the population cycle. Direct measures of host physiology and diet quality (fecal fibre contents) most strongly supported food resource availability as a mechanism underlying phase-based differences in bacterial communities, but fecal fibre contents could not fully account for bacterial microbiome variation across phases.

Overexploitation of large and highly connected marine fish populations may impact their future evolutionary potential and recovery, but understanding the underlying changes to genetic diversity can be challenging. The collapse of Northern Cod (Gadus morhua), historically the largest population of Atlantic Cod in the northwest Atlantic, raised questions regarding the potential biological consequences for the populations’ genetic diversity. Using low-coverage whole genome sequencing (lcWGS) on collections from the 1990s and 2010s, we detected a decline in genetic diversity of Atlantic Cod along the Canadian Atlantic coast. Most recent collections exhibited lower genetic diversity (i.e., Watterson’s θ) and fewer genetically distinguishable groups than 1990s collections. Runs of homozygosity were also longer and more numerous in the 2010s collections. Our results demonstrate a loss in genetic diversity at the population and individual level following the fishery collapse and indicate that genetic diversity can be lost even in numerically large populations. The loss of genetic diversity may have important implications for fisheries conservation.

Microbiota are increasingly recognized as key players in regulating host biological functions, influencing both the ecology and evolution of organisms. However, the factors shaping microbiota diversity and structure in natural environments remain underexplored, especially the relative importance of host genetics versus environmental factors. In this study, we address this gap using the freshwater snail Bulinus truncatus, an intermediate host for some human and animal Schistosoma parasites, as a model species. We developed 31 new microsatellite markers to assess the population structure of B. truncatus across 9 sites in Senegal. We then applied metabarcoding to characterize the diversity and structure of individual snail bacterial microbiota and environmental communities associated with each sampling site using environmental DNA. We also used molecular diagnostics to determine trematode infection status of B. truncatus individuals. By integrating these data through multiple regression on distance matrices (MRM) analyses, we quantified the influence of B. truncatus population genetics, spatial distribution, environmental bacterial communities, and infection status on the snail’s microbiota structure. Our results show that the genetic structure of B. truncatus populations, and to a lower extent geographic distribution, are the main factors explaining the snail’s microbiota compositions. Neither the environmental bacterial communities nor trematode infection status significantly contributed to microbiota structure. A portion of the variance in microbiota composition remains unexplained, suggesting that additional ecological or intrinsic factors might be involved. These findings provide new insights into the drivers of microbiota structure in natural populations and highlight the complexity of host-microbiota-environment interactions.

jabbrv-ltwa-all.ldf jabbrv-ltwa-en.ldf Understanding the processes that drive spatial genetic differentiation is essential for understanding how populations adapt to environmental change. By evaluating the relative influence of these drivers, we can gain insights into evolutionary dynamics and the potential for species to respond to shifting landscapes. Three well-accepted drivers of spatial patterns in genetic variation are isolation-by-distance (IBD), where individuals are more genetically similar the closer they are geographically; isolation-by-environment (IBE), where gene flow is reduced due to selection against migrants in unsuitable ecological conditions; and isolation-by-resistance (IBR), where landscape features limit dispersal. We employed a macrogenetic approach, conducting a multi-species, multi-driver, meta-analysis of published genomic SNP data to identify general patterns driving spatial genetic differentiation of mammals globally. Three species distribution models were built per species to test different aspects of IBR, using combinations of landscape and bioclimatic variables. Using two model selection techniques, we find that landscape resistance models better explain genetic differentiation than bioclimatic resistance models. Among the three drivers, IBR was most frequently selected as the best model of genetic differentiation in mammals across both model selection tests, with IBD a close second and IBE the worst performing model. However, the importance of IBE increased with increasing spatial scale, with populations spread over larger distances more likely to be diverging due to IBE than IBR or IBD. Our findings suggest that anthropogenic habitat fragmentation significantly shapes genetic variation in mammals worldwide, underscoring the importance of mitigating the impacts of habitat fragmentation to prevent isolation and extinction of mammalian species.

Visual communication in fish is often shaped by the light environment they inhabit, which influences both sensory (e.g., eye size, opsin gene expression) and signaling traits (e.g., body reflectance). This study explores the phenotypic variation in the visual communication traits of six species of centrarchids (Centrarchidae) inhabiting two contrasting light environments. We measured morphological, molecular, and signaling traits to determine their variation across photic conditions. Our findings reveal significant interspecific variation in sensory traits but no consistent phenotypic variation between light environments. Centrarchids showed robust visual systems with red-green dichromatic vision, which was largely unaffected by different light habitats. We also found significant molecular evolution in the visual opsin genes, although these changes were not associated with environmental conditions. However, body reflectance displayed species-specific responses to environmental conditions, suggesting that signaling traits may be more flexible than sensory traits. Overall, our results challenge the generality of the current paradigm in visual ecology, which portrays visual systems in fish as highly tunable owing to photic conditions. Our study highlights the potential evolutionary or developmental constraints on centrarchid visual systems and their implications for adaptability to various habitats and novel environmental threats.

The growing nutritional demand of the world population poses great challenges to sustainable and productive agriculture. Entomopathogenic nematodes (EPNs) are an economically interesting alternative to traditional methods of pest control, despite poorly understood aspects of their biology and genomics. This study provides a comprehensive characterization of the genome of Heterorhabditis bacteriophora and its capacity to resist benzoxazinoids that are sequestered as defense compounds by an important insect pest. We performed a de novo chromosome-scale assembly of the H. bacteriophora genome and compared it with the genomes of other nematodes, highlighting syntenic orthologs and genome organization in EPNs. Co-phylogenetic analyses and genetic structure data of several H. bacteriophora isolates and their Photorhabdus symbionts suggest divergent evolutionary scenarios of these two species groups. Population genomics analyses within H. bacteriophora identified genetic variation distinguishing between strains susceptible and resistant to benzoxazinoids. Genome-wide differentiation (FST) pointed to genomic regions related to deoxyribonucleotide biosynthetic processes, polypeptide N-acetylgalactosaminyltransferase activity and single-stranded DNA endodeoxyribonuclease activity that were shaped by strong selective pressures. Having identified candidate genes associated with insect pathogenicity and benzoxazinoid resistance, our findings provide a foundation for future work on the efficacy and infectivity of EPNs in pest management.

The repeated evolution of herbicide resistance in agriculture provides an unprecedented opportunity to understand how organisms rapidly respond to strong anthropogenic-driven selection pressure. In populations of the grass species Bromus tectorum L., resistance to multiple herbicides has been recently identified. To understand the evolutionary origins and spread of resistance, we investigated the resistance mechanisms in 49 B. tectorum populations to acetolactate synthase (ALS) inhibitors and photosystem II inhibitors, two widely used herbicide modes of action. We assessed the genetic diversity, structure, and relatedness in a subset of 21 populations. Resistance to ALS inhibitors was associated with multiple types of non-synonymous mutations in ALS, the target site gene. Mechanisms not related to the target site evolved and were common in the populations studied. Resistance to photosystem II inhibitors was confirmed in two populations and was conferred by non-synonymous mutations in the plastid gene psbA. Population genetics analyses showed low levels of genetic diversity, suggesting that local selection pressure processes have shaped the populations. We also found evidence of long-distance gene flow among distinct growing regions and cropping systems. The results suggest that both gene flow via pollen and/or seed dispersal, and multiple local and independent evolutionary events were involved in the spread of herbicide-resistant B. tectorum. Our results provide an empirical example of the rapid repeated evolution of a trait under strong anthropogenic selection and elucidate the evolutionary origins of herbicide resistance in a plant species of agricultural importance.

In eusocial insects, social parasitism - the exploitation of the host’s brood care behaviour for survival and reproduction – can occur either within or between species. Parasite queens invade host nests and aggressively replace the resident queen. While the adoption of conspecific queens is a common feature of species with multi-queen colonies (polygyny), the origin of parasitic founding is not fully understood. Functionally monogynous ants, in which nestmate queens establish social and reproductive hierarchies by biting and antennal boxing, might provide a link between peaceful adoption and social parasitism. In this study we aimed to evaluate whether alien queens might usurp colonies of the functionally monogynous ant Leptothorax gredleri. Ovary dissection of queens from 33 nests showed that multiple queens with developed ovaries can occasionally cooccur in the same nest. Genetic analysis highlighted frequent exchanges of the dominant queens. We evidenced that alien queens may take over reproduction, suggesting possible occurrences of intraspecific social parasitism in L. gredleri.