Evolutionary Applications

The Kirtland's warbler (Setophaga kirtlandii) is a rare migratory passerine species and habitat specialist of the North American Jack Pine Forests. Their near extinction in the 1970s classified them as endangered and protected under the Endangered Species Act of 1973. After decades of intense conservation management, their population size recovered, and they were delisted from federal protection in 2019. We explore the genomic consequences of this harsh bottleneck and recovery by comparing the genomic architecture of two closely related species whose population sizes have remained large and stable, Hooded Warblers (Setophaga citrina) and American Redstarts (Setophaga ruticilla). We used whole‐genome sequencing to characterize the distribution of runs of homozygosity and deleterious genetic variation. We find evidence that Kirtland's warblers exhibit genetic patterns consistent with recent inbreeding. Our results also show that Kirtland's warblers carry an excess proportion of deleterious variation, which could complicate management for this conservation‐reliant species. This analysis provides a genetically informed perspective that should be thoroughly considered when delisting other species from federal protections. Through the increasing accessibility of genome sequencing technology, it will be more feasible to monitor the genetic landscape of recovering populations to ensure their long‐term survival independent of conservation intervention.

In managed populations—whether for production or conservation—management practices can interfere with natural eco‐evolutionary processes, providing opportunities to mitigate immediate impacts of disturbances or enhance selection on tolerance traits. Here, we used a modelling approach to explore the interplay and feedback loops among drought regimes, natural selection and tree thinning in naturally regenerated monospecific forests. We conducted a simulation experiment spanning three nonoverlapping generations with the individual‐based demo‐genetic model Luberon2. Luberon2 integrates forest dynamics processes driving survival and mating success, including tree growth, competition, drought impacts and regeneration, with genetic variation in quantitative traits related to these processes. We focused on two variable traits: individual vigour, determining diameter growth potential without stress as the deviation from average stand growth, and individual sensitivity to drought stress as the slope of the relationship between diameter growth and drought stress level. We simulated simplified thinning scenarios, tailored to even‐aged stands. Considering plausible genetic variation and contrasting drought regimes, the predicted evolutionary rates for both traits aligned with documented rates in wild plant and animal populations. Thinning considerably reduced natural selective pressures caused by competition and drought compared to unthinned stands. However, the conventional thinning practice of retaining the larger trees resulted in indirect anthropogenic selection that enhanced genetic gain in vigour and lowered sensitivity by up to 30%. More intensive thinning aimed at reducing drought stress by reducing stand density hampered the selection against sensitivity to drought, potentially hindering long‐term adaptation. Conversely, avoiding the early, nonselective thinning step—thereby promoting both natural and anthropogenic selection—ultimately resulted in better stand performance while maintaining long‐term evolvability. This study emphasises the potential of evolution‐oriented forestry strategies to combine drought stress mitigation with genetic adaptation. It provides general insights into how population management, disturbance regimes and eco‐evolutionary responses interfere, aiding sustainable decision‐making amid environmental uncertainties.

Genetic mixing aims to increase the genetic diversity of small or isolated populations, by mitigating genetic drift and inbreeding depression, either by maximally increasing genetic diversity, or minimising the prevalence of recessive, deleterious alleles. However, few studies investigate this beyond a single generation of mixing. Here, we model genetic mixing using captive, low‐diversity recipient population of the threatened Southern brown bandicoot (Isoodon obesulus) over 50 generations and compare wild populations across south‐eastern Australia as candidate source populations. We first assess genetic differentiation between 12 populations, including the first genomic assessment of three mainland Australian and three Tasmanian populations. We assess genetic diversity in the 12 populations using an individualised autosomal heterozygosity pipeline, using these results to identify a candidate recipient population for genetic mixing simulations. We found that populations fell into four major groups of genetic similarity: Adelaide Hills, western Victoria, eastern Victoria, and Tasmania, but populations within these groups were also distinct, and additional substructure was observed in some populations. Our autosomal heterozygosity pipeline indicated significant variability in mean heterozygosity between populations, identifying one extremely genetically degraded population on Inner Sister Island, Tasmania. Genetic mixing simulations of a low heterozygosity captive population in Victoria suggested the greatest increase in heterozygosity would be reached by using highly differentiated populations as mixing sources. However, when removing populations that may represent taxonomically discrete lineages, neither metrics of differentiation nor heterozygosity was strongly correlated with modelled heterozygosity increase, indicating the value of simulation‐based approaches when selecting source populations for population mixing.

Understanding the evolutionary history of a species is essential for effective conservation management. Malus sieversii, a relict broad‐leaf forest tree found in arid Central Asian mountains, has a narrow and fragmented distribution and is classified as an endangered species in China. This species is considered one of the ancestors of the domesticated apple trees. In the present study, we sampled five populations of M. sieversii and its wide‐ranging congener M. baccata from China. Through deep whole‐genome resequencing, we analyzed the population's genetic diversity, genetic structure, demographic history, fixation of deleterious mutations, and genomic divergence. Our results revealed that M. baccata exhibits a higher level of genetic diversity than M. sieversii. The effective population size of M. sieversii decreased, whereas that of M. baccata recovered after the bottleneck effect. In M. sieversii, the genetic structure of the Yili region was distinct from that of the Tacheng region. Populations at the rear edge of the Tacheng region showed a stronger fixation of deleterious mutations than those in the Yili region. Genomic divergence indicated that the positively selected genes were associated with physiological processes within the genomic islands between the Yili and Tacheng regions. Based on these findings, we recommend the establishment of two separate conservation units for the Yili and Tacheng lineages to preserve their genetic resources. Given the limited distribution range and high fixation rate of deleterious mutations, urgent protective measures are recommended for the Tacheng lineage.

Connectivity is integral to the dynamics of metapopulations through dispersal and gene flow, and understanding these processes is essential for guiding conservation efforts. Abalone, broadcast‐spawning marine snails associated with shallow rocky habitats, have experienced widespread declines, and all seven North American species are threatened. We investigated the connectivity and population genomics of pinto/northern abalone (Haliotis kamtschatkana), the widest‐ranging of abalone species. We employed reduced representation sequencing (RADseq) to generate single nucleotide polymorphism (SNP) data, assessing population connectivity and potential adaptive variation at 12 locations across the full range from Alaska to Mexico. Despite depleted populations, our analysis of over 6000 SNPs across nearly 300 individuals revealed that pinto abalone maintains a high genetic diversity with no evidence of a genetic bottleneck. Neutral population structure and isolation by distance were extremely weak, indicating panmixia across the species' range (global FST = 0.0021). Phylogenetic analysis, principal components analysis, and unsupervised clustering methods all supported a single genetic population. However, slight population differentiation was noted in the Salish Sea and Inside Passage regions, with evidence for higher barriers to dispersal relative to outer coastal areas. This north‐central region may also represent the species' ancestral range based on relatively low population‐specific FST values; the northern and southern extremes of the range likely represent range expansions. Outlier analysis did not identify consensus loci implicated in adaptive variation, suggesting limited adaptive differentiation. Our study sheds light on the evolutionary history and contemporary gene flow of this threatened species, providing key insights for conservation strategies, particularly in sourcing broodstock for ongoing restoration efforts.

Maize (Zea mays ssp. mays L.) landraces are traditional American crops with high genetic variability that conform a source of original alleles for conventional maize breeding. Northern Argentina, one the southernmost regions of traditional maize cultivation in the Americas, harbours around 57 races traditionally grown in two regions with contrasting environmental conditions, namely, the Andean mountains in the Northwest and the tropical grasslands and Atlantic Forest in the Northeast. These races encounter diverse threats to their genetic diversity and persistence in their regions of origin, with climate change standing out as one of the major challenges. In this work, we use genome‐wide SNPs derived from ddRADseq to study the genetic diversity of individuals representing the five groups previously described for this area. This allowed us to distinguish two clearly differentiated gene pools, the highland northwestern maize (HNWA) and the floury northeastern maize (FNEA). Subsequently, we employed essential biodiversity variables at the genetic level, as proposed by the Group on Earth Observations Biodiversity Observation Network (GEO BON), to evaluate the conservation status of these two groups. This assessment encompassed genetic diversity (Pi), inbreeding coefficient (F) and effective population size (Ne). FNEA showed low Ne values and high F values, while HNWA showed low Ne values and low Pi values, indicating that further genetic erosion is imminent for these landraces. Outlier detection methods allowed identification of putative adaptive genomic regions, consistent with previously reported flowering‐time loci and chromosomal regions displaying introgression from the teosinte Zea mays ssp. mexicana. Finally, species distribution models were obtained for two future climate scenarios, showing a notable reduction in the potential planting area of HNWA and a shift in the cultivation areas of FNEA. These results suggest that maize landraces from Northern Argentina may be unable to cope with climate change. Therefore, active conservation policies are advisable.

The malaria vector Anopheles coluzzii is widespread across West Africa and is the sole vector species on the islands of São Tomé and Príncipe. Our interest in the population genetics of this species on these islands is part of an assessment of their suitability for a field trial involving the release of genetically engineered A. coluzzii. The engineered construct includes two genes that encode anti‐Plasmodium peptides, along with a Cas9‐based gene drive. We investigated gene flow among A. coluzzii subpopulations on each island to estimate dispersal rates between sites. Sampling covered the known range of A. coluzzii on both islands. Spatial autocorrelation suggests 7 km to be the likely extent of dispersal of this species, whereas estimates based on a convolutional neural network were roughly 3 km. This difference highlights the complexity of dispersal dynamics and the value of using multiple approaches. Our analysis also revealed weak heterogeneity among populations within each island but did identify areas weakly resistant or permissive of gene flow. Overall, A. coluzzii on each of the two islands exist as single Mendelian populations. We expect that a gene construct that includes a low‐threshold gene drive and has minimal fitness impact should, once introduced, spread relatively unimpeded across each island.

Biological invasions pose significant threats to ecological and economic stability, with invasive pests like the Asian longhorned beetle (Anoplophora glabripennis Motschulsky, ALB) causing substantial damage to forest ecosystems. Effective pest management relies on comprehensive knowledge of the insect's biology and invasion history. This study uses genomics to address these knowledge gaps and inform existing biosurveillance frameworks. We used 2768 genome‐wide single nucleotide polymorphisms to compare invasive A. glabripennis populations in North America, using genomic variation to trace their sources of invasion and spread patterns, thereby refining our understanding of this species' invasion history. We found that most North American A. glabripennis infestations were distinct, resulting from multiple independent introductions from the native range. Following their introduction, all invasive populations experienced a genetic bottleneck which was followed by a population expansion, with a few also showing secondary spread to satellite infestations. Our study provides a foundation for a genome‐based biosurveillance tool that can be used to clarify the origin of intercepted individuals, allowing regulatory agencies to strengthen biosecurity measures against this invasive beetle.

Estimates of current genetic diversity and population connectivity are especially important for endangered species that are subject to illegal harvesting and trafficking. Genetic monitoring can also ensure that management units are sustaining viable populations, while estimating genetic structure and population dynamics can influence genetic rescue efforts and reintroduction from captive breeding and confiscated animals. The Hyacinth Macaw (Anodorhynchus hyacinthinus) is a charismatic endangered species with a fragmented (allopatric) distribution. Using low coverage genomes, we aimed to investigate the dynamics across the remaining three large disjunct populations of Hyacinth Macaws in Brazil to inform conservation strategies. We obtained low coverage DNA data for 54 individuals from seven sampling sites. Our results showed that Hyacinth Macaws have four genetically structured clusters with relatively high levels of diversity. The Pantanal biome had two genetically distinct populations, with no obvious physical barriers that might explain this differentiation. We detected signs of gene flow between populations, with some geographical regions being more connected than others. Estimates of effective population size in the past million years of the species' evolutionary history showed a decline trend with the lowest Ne in all populations reached within the last few thousand years. Our findings suggest that populations from the Pantanal biome are key to connecting sites across its distribution, and maintaining the integrity of this habitat is important for protecting the species. Given the genetic structure found, we also highlight the need of conserving all wild populations to ensure the protection of the species' evolutionary potential.

Scots pine is a crucial component of ecosystems in Europe and Asia and a major utility species that comprises more than 60% of total forest production in Poland. Despite its importance, the genetic relationships between key conservation and the commercial value of Scots pine ecotypes in Poland remain unclear. To address this problem, we analyzed 27 populations (841 trees) of the most valuable Polish Scots pine ecotypes, including the oldest natural stands in all 24 regions of provenance established for the species in the country. By examining maternally inherited mitochondrial markers, nuclear microsatellite loci, and thousands of SNP markers from a genotyping array, we evaluated the genetic structure between and within them. These multilevel genomic data revealed high genetic similarity and a homogeneous structure in most populations, suggesting a common historical origin and admixture of populations after the postglacial recolonization of Central Europe. This research presents novel data on existing genomic resources among local ecotypes defined within strictly managed Polish regions of provenance, challenging their validity. Formal tests of the progeny of seed stands are needed to check whether the diversity in adaptation and quantitative traits still supports the delineation of provenance regions. In parallel, the health status of selected populations and the viability of seeds from these regions should be monitored to detect early‐stage symptoms of their environmental stress. It seems reasonable that periodic shortages of forest reproductive material (FRM) in a given region of provenance could be supplemented with the one from other regions that match their climatic envelope. Together, our results have important implications for the management of native Scots pine stands, particularly elite breeding populations, as they contribute to the discussion of the boundaries of provenance regions and the transfers of FRM that face increasing climate change.

The spotted‐wing drosophila, Drosophila suzukii and the cosmopolitan vinegar fly D. melanogaster feed on soft fruit and berries and widely overlap in geographic range. The presence of D. melanogaster reduces egg‐laying in D. suzukii, possibly because D. melanogaster outcompetes D. suzukii larvae feeding in the same fruit substrate. Flies use pheromones to communicate for mating, but pheromones also serve a role in reproductive isolation between related species. We asked whether a D. melanogaster pheromone also modulates oviposition behaviour in D. suzukii. A dual‐choice oviposition assay confirms that D. suzukii lays fewer eggs on blueberries exposed to D. melanogaster flies and further shows that female flies have a stronger effect than male flies. This was corroborated by treating berries with synthetic pheromones. Avoidance of D. suzukii oviposition is mediated by the female D. melanogaster pheromone (Z)‐4‐undecenal (Z4‐11Al). Significantly fewer eggs were laid on berries treated with synthetic Z4‐11Al. In comparison, the male pheromone (Z)‐11‐octadecenyl acetate (cVA) had no effect on D. suzukii oviposition. Z4‐11Al is a highly volatile compound that is perceived via olfaction and it is accordingly behaviourally active at a distance from the source. D. suzukii is known to engage in mutual niche construction with the yeast Hanseniaspora uvarum, which strongly attracts flies. Adding Z4‐11Al to fermenting H. uvarum significantly decreased D. suzukii flight attraction in a laboratory wind tunnel and a field trapping assay. That a D. melanogaster pheromone regulates oviposition in D. suzukii demonstrates that heterospecific pheromone communication contributes to reproductive isolation and resource partitioning in cognate species. Stimulo‐deterrent diversion or push‐pull methods, building on combined use of attractant and deterrent compounds, have shown promise for control of D. suzukii. A pheromone that specifically reduces D. suzukii attraction and oviposition adds to the toolbox for D. suzukii integrated management.

Habitat fragmentation and the acceleration of environmental change threaten the survival of many plant species. The problem is especially pronounced for plant species with self‐incompatibility mating systems, which are obligate outcrossers, thus requiring high mate availability to persist. In such situations, plant populations suffering decreased fitness could be rescued by: (a) improving local habitat conditions (habitat rescue), (b) increasing the number of individuals (demographic rescue), or (c) introducing new genetic variation (genetic rescue). In this study, we used a spatially and genetically explicit individual‐based model to approximate the demography of a small (N = 250) isolated self‐incompatible population using a timescale of 500 years. Using this model, we quantified the effectiveness of the different types of rescues described above, singly and in combination. Our results show that individual genetic rescue is the most effective type of rescue with respect to improving fitness and population viability. However, we found that introducing a high number of individuals (N > 30) to a small population (N = 50) at the brink of extinction through demographic rescue can also have a positive effect on viability, improving average fitness by 55% compared to introducing a low number of individuals (N = 10) over a long timescale (> 500 years). By itself, habitat rescue showed the lowest effects on viability. However, combining genetic and habitat rescue provided the best results overall, increasing both persistence (> 30%) and mate availability (> 50%). Interestingly, we found that the addition of even a small number of new S alleles (20%) can be highly beneficial to increase mate availability and persistence. We conclude that genetic rescue through the introduction of new S alleles and an increase in habitat suitability is the best management strategy to improve mate availability and population viability of small isolated SI plant populations to overcome the effects of demographic stochasticity and positive density dependence.

Reliable estimates of population abundance and demographics are essential for managing harvested species. Ice‐associated phocids, “ice seals,” are a vital resource for subsistence‐dependent coastal Native communities in western and northern Alaska, USA. In 2012, the Beringia distinct population segment of the bearded seal, Erignathus barbatus nauticus, was listed as “threatened” under the US Endangered Species Act requiring greater scrutiny for management assessments. We sought to estimate requisite population parameters from harvested seals by using close‐kin mark‐recapture (CKMR) methods, the first such application for marine mammals. Samples from 1758 bearded seals harvested by Bering, Chukchi, and Beaufort Sea communities during 1998–2020 were genotyped, genetically sexed, and aged by tooth annuli. After rigorous quality control, kin relationships were established for 1484 seals including two parent–offspring pairs (POPs) and 25 potential second‐order kin pairs. Most of the second‐order kin were half‐sibling pairs (HSPs), but four were potential grandparent‐grandchild pairs (GGPs). There were no full sibling pairs, suggesting a lack of mate fidelity. Mitochondrial DNA analysis identified 17 potential HSPs as paternally related, providing substantial evidence of persistent heterogeneity in reproductive success among adult males. The statistical CKMR model incorporates probabilities associated with POPs, HSPs, and GGPs and assumes known ages and a stable population. Our top model accommodates heterogeneity in adult male breeding success and yields an abundance estimate of ~409,000 with a coefficient of variation (CV) = 0.35, which is substantially greater than the “non‐heterogeneity” model estimate of ~232,000 (CV = 0.21), an important difference for managing a harvested species. Using CKMR methods with harvested species provides estimates of abundance with the added opportunity to acquire information about adult survival, fecundity, and breeding success that could be applied to other species of concern, marine and terrestrial.

The mesopelagic zone represents one of the few habitats that remains relatively untouched from anthropogenic activities. Among the many species inhabiting the north Atlantic mesopelagic zone, glacier lanternfish (Benthosema glaciale) is the most abundant and widely distributed. This species has been regarded as a potential target for a dedicated fishery despite the scarce knowledge of its population genetic structure. Here, we investigated its genetic structure across the North Atlantic and into the Mediterranean Sea using 121 SNPs, which revealed strong differentiation among three main groups: the Mediterranean Sea, oceanic samples, and Norwegian fjords. The Mediterranean samples displayed less than half the genetic variation of the remaining ones. Very weak or nearly absent genetic structure was detected among geographically distinct oceanic samples across the North Atlantic, which contrasts with the low motility of the species. In contrast, a longitudinal gradient of differentiation was observed in the Mediterranean Sea, where genetic connectivity is known to be strongly shaped by oceanographic processes such as current patterns and oceanographic discontinuities. In addition, 12 of the SNPs, in linkage disequilibrium, drove a three clusters' pattern detectable through Principal Component Analysis biplot matching the genetic signatures generally associated with large chromosomal rearrangements, such as inversions. The arrangement of this putative inversion showed frequency differences between open‐ocean and more confined water bodies such as the fjords and the Mediterranean, as it was fixed in the latter for the second most common arrangement of the fjord's samples. However, whether genetic differentiation was driven by local adaptation, secondary contact, or a combination of both factors remains undetermined. The major finding of this study is that B. glaciale in the North Atlantic‐Mediterranean is divided into three major genetic units, information that should be combined with demographic properties to outline the management of this species prior to any eventual fishery attempt.

The subtropical forests of East Asia are renowned for their high plant diversity, particularly the abundance of ancient relict species. However, both the evolutionary history of these relict species and their capacity for resilience in the face of impending climatic changes remain unclear. Using whole‐genome resequencing data, we investigated the lineage differentiation and demographic history of the relict and endangered tree, Bretschneidera sinensis (Akaniaceae). We employed a combination of population genomic and landscape genomic approaches to evaluate variation in mutation load and genomic offset, aiming to predict how different populations may respond to climate change. Our analysis revealed a profound genomic divergence between the East and West lineages, likely as the result of recurrent bottlenecks due to climatic fluctuations during the glacial period. Furthermore, we identified several genes potentially linked to growth characteristics and hypoxia response that had been subjected to positive selection during the lineage differentiation. Our assessment of genomic vulnerability uncovered a significantly higher mutation load and genomic offset in the edge populations of B. sinensis compared to their core counterparts. This implies that the edge populations are likely to experience the most significant impact from the predicted climate conditions. Overall, our research sheds light on the historical lineage differentiation and contemporary genomic vulnerability of B. sinensis. Broadening our understanding of the speciation history and future resilience of relict and endangered species such as B. sinensis, is crucial in developing effective conservation strategies in anticipation of future climatic changes.

Annuality and perenniality represent two different life‐history strategies in plants, and an analysis of genomic differentiation between closely related species of different life histories bears the potential to identify the underlying targets of selection. Additionally, understanding the interactions between patterns of recombination and signatures of natural selection is a central aim in evolutionary biology, because patterns of recombination shape the evolution of genomes by affecting the efficacy of selection. Here, our aim was to characterise the landscape of genomic differentiation between weedy annual rye (Secale cereale L.) and wild perennial rye (Secale strictum C. Presl), and explore the extent to which signatures of selection are influenced by recombination rate variation. We used population‐level sequence data of annual and perennial rye to analyse population structure and their demographic history. Based on our analyses, annual and perennial rye diverged approximately 26,500 years ago (ya) from an ancestral population size of ~85,000 individuals. We analysed patterns of genetic diversity and genetic differentiation, and found highly differentiated regions located in low‐recombination regions, indicative of linked selection. Although all highly differentiated regions, as revealed by FST‐outlier scans, were located in low‐recombining regions, not all chromosomes showed this tendency. We therefore performed a gene ontology enrichment analysis, which showed that highly differentiated regions comprise genes involved in photosynthesis. This enrichment was confirmed when FST outlier scans were performed separately in low‐ and intermediate‐recombining regions, but not in high‐recombining regions, suggesting that local recombination rate variation in rye affects outlier scans. Cultivated rye is an annual crop, but the introduction of perenniality may be advantageous in regions with poor soil quality or under low‐input farming. Although the resolution of our analysis is limited to a broad‐scale, knowledge about the evolutionary divergence between annual and perennial rye might support breeding efforts towards perennial rye cultivation.

Sustainable fisheries management is important for the continued harvest of the world's marine resources, especially as they are increasingly challenged by a range of climatic and anthropogenic factors. One of the pillars of sustainable fisheries management is the accurate identification of the biological units, i.e., populations. Here, we developed and implemented a genetic baseline for Atlantic herring harvested in the Norwegian offshore fisheries to investigate the validity of the current management boundaries. This was achieved by genotyping > 15,000 herring from the northern European seas, including samples of all the known populations in the region, with a panel of population‐informative SNPs mined from existing genomic resources. The final genetic baseline consisted of ~1000 herring from 12 genetically distinct populations. We thereafter used the baseline to investigate mixed catches from the North and Norwegian Seas, revealing that each management area consisted of multiple populations, as previously suspected. However, substantial numbers (up to 50% or more within a sample) of herring were found outside of their expected management areas, e.g., North Sea autumn‐spawning herring north of 62° N (average = 19.2%), Norwegian spring‐spawning herring south of 62° N (average = 13.5%), and western Baltic spring‐spawning herring outside their assumed distribution area in the North Sea (average = 20.0%). Based upon these extensive observations, we conclude that the assessment and management areas currently in place for herring in this region need adjustments to reflect the populations present. Furthermore, we suggest that for migratory species, such as herring, a paradigm shift from using static geographic stock boundaries towards spatial dynamic boundaries is needed to meet the requirements of future sustainable management regimes.

Molecular methods are routinely used to estimate the effective size of populations (Ne). However, underlying model assumptions are frequently violated to an unknown extent. Although simulations can detect sources of bias and help to adjust sampling strategies and analyses methods, additional information from empirical data can also be used to calibrate methods and improve molecular Ne estimation methods. Here, we take advantage of long‐term genetic and ecological monitoring data of the grey wolf (Canis lupus) in Germany, and detailed population genetic studies in Poland, Spain and Portugal to improve Ne estimation strategies in this species, and species with similar life history traits. We first calculated Ne from average lifetime reproductive success and detailed census data from the German population, which served as a baseline to compare to molecular estimates based on linkage disequilibrium and sibship frequency. This yielded a robust Ne/Nc estimation that we used to calibrate molecular estimates of German, Polish and Iberian wolf populations. The linkage disequilibrium method was strongly influenced by spatial genetic structure, much more than the sibship frequency method. When Ne was estimated in local neighbourhoods, both methods yielded comparable results. Estimates of the metapopulation effective size seemed to correspond generally well with the sum of the estimates of local neighbourhoods. Overall, we found that the number of packs is a good proxy of the effective population size. Using this as a rule of thumb, we evaluated for all European wolf populations the Ne 500 indicator and concluded that half of the European wolf populations do not yet fulfil this criterion.

In population genetics idealized Wright‐Fisher (WF) populations are generally considered equivalent to real populations with regard to the major evolutionary processes that influence genotype and allele frequencies. As a result we often model the response of populations by focusing on the effective size Ne. The Diversity Partitioning Theorem (DPT) shows that you cannot model the behavior of a system solely on the basis of a diversity (accounting for unevenness among items) without taking richness into account. I show that the census population size (the number of adults, Nc) is equivalent to a richness, and that the effective size Ne is equivalent to a true diversity. It follows logically from the DPT that we require both Ne and Nc to understand how drift, selection, mutation, and gene flow interact to shape the course of evolution of populations. Here I review evidence that both Nc and Ne affect evolutionary trajectories of populations for neutral and adaptive processes. This also influences how we should consider evolutionary potential and genetic criteria for conservation of populations. The effective size of a population is of huge importance in evolutionary biology, but it should not be the sole focus when population size is concerned. Applied evolutionary studies need to integrate Nc in the equation more consistently when modeling the response to selection, mutation, migration, and drift.

Triploid oysters are commonly used as the basis for production in the aquaculture of eastern oysters along the USA East and Gulf of Mexico coasts. While they are valued for their rapid growth, incidents of triploid mortality during summer months have been well documented in eastern oysters, especially at low salinity sites. We compared global transcriptomic responses of diploid and triploid oysters bred from the same three maternal source populations at two different hatcheries and outplanted to a high (annual mean salinity = 19.4 ± 6.7) and low (annual mean salinity = 9.3 ± 5.0) salinity site. Oysters were sampled for gene expression at the onset of a mortality event in the summer of 2021 to identify triploid‐specific gene expression patterns associated with low salinity sites, which ultimately experienced greater triploid mortality. We also examined chromosome‐specific gene expression to test for instances of aneuploidy in experimental triploid oyster lines, another possible contributor to elevated mortality in triploids. We observed a strong effect of hatchery conditions (cohort) on triploid‐specific mortality (field data) and a strong interactive effect of hatchery, ploidy, and outplant site on gene expression. At the low salinity site where triploid oysters experienced high mortality, we observed downregulation of transcripts related to calcium signaling, ciliary activity, and cell cycle checkpoints in triploids relative to diploids. These transcripts suggest dampening of the salinity stress response and problems during cell division as key cellular processes associated with elevated mortality risk in triploid oysters. No instances of aneuploidy were detected in our triploid oyster lines. Our results suggest that triploid oysters may be fundamentally less tolerant of rapid decreases in salinity, indicating that oyster farmers may need to limit the use of triploid oysters to sites with more stable salinity conditions.

While it is recognised that most, if not all, multicellular organisms harbour neoplastic processes within their bodies, the timing of when these undesirable cell proliferations are most likely to occur and progress throughout the organism's lifetime remains only partially documented. Due to the different mechanisms implicated in tumourigenesis, it is highly unlikely that this probability remains constant at all times and stages of life. In this article, we summarise what is known about this variation, considering the roles of age, season and circadian rhythm. While most studies requiring that level of detail be done on humans, we also review available evidence in other animal species. For each of these timescales, we identify mechanisms or biological functions shaping the variation. When possible, we show that evolutionary processes likely played a role, either directly to regulate the cancer risk or indirectly through trade‐offs. We find that neoplastic risk varies with age in a more complex way than predicted by early epidemiological models: rather than resulting from mutations alone, tumour development is dictated by tissue‐ and age‐specific processes. Similarly, the seasonal cycle can be associated with risk variation in some species with life‐history events such as sexual competition or mating being timed according to the season. Lastly, we show that the circadian cycle influences tumourigenesis in physiological, pathological and therapeutic contexts. We also highlight two biological functions at the core of these variations across our three timescales: immunity and metabolism. Finally, we show that our understanding of the entanglement between tumourigenic processes and biological cycles is constrained by the limited number of species for which we have extensive data. Improving our knowledge of the periods of vulnerability to the onset and/or progression of (malignant) tumours is a key issue that deserves further investigation, as it is key to successful cancer prevention strategies.

Identification of the geographic origin of invasive species can be critical to effective management and amelioration of negative impacts in the introduced range. Liriomyza huidobrensis is a polyphagous leafmining fly that is a devastating pest of many vegetable and floriculture crops around the world. Considered native to South and possibly Central America, L. huidobrensis became invasive in the 1980s and has since spread to at least 30 countries on five continents. We used phylogeographic analysis of over 2 kb of mitochondrial cytochrome oxidase I and II sequence data from 403 field‐collected specimens from both native and introduced populations to investigate the geographic origins of invasive L. huidobrensis worldwide. Within South America, there was substantial genetic variation, as well as the strong phylogeographic structure typical of a native range. In contrast, leafminers from the introduced range and Central America all contained little genetic variation and shared the same small set of haplotypes. These haplotypes trace to Peru as the ultimate geographic origin of invasive populations. Central America is rejected as part of the original geographic range of L. huidobrensis. Within Peru, the primary export region of Lima shared an extremely similar pattern of reduced haplotype variation to the invasive populations. An additional 18 specimens collected at US ports of entry did not share the same haplotype profile as contemporary invasive populations, raising perplexing questions on global pathways and establishment success in this species.

In long‐distance dispersal events, colonising species typically begin with a small number of founding individuals. A growing body of research suggests that establishment success of small founding populations can be determined by the context of the colonisation event and the new environment. Here, we illuminate the importance of these sources of context dependence. Using a spatially explicit, temporally dynamic, mechanistic, individual‐based simulator of a model amphibian species, the cane toad (Rhinella marina), we simulated colonisation scenarios to investigate how (1) the number of founding individuals, (2) the number of dispersal events, (3) landscape's spatial composition and configuration of habitats (‘spatially heterogeneous landscapes’) and (4) the timing of arrival with regards to dynamic environmental conditions (‘dynamic environmental conditions’) influence the establishment success of small founding populations. We analysed the dynamic effects of these predictors on establishment success using running‐window logistic regression models. We showed establishment success increases with the number of founding individuals, whereas the number of dispersal events had a weak effect. At ≥ 20 founding individuals, propagule size swamps the effects of other factors, to whereby establishment success is near‐certain (≥ 90%). But below this level, confidence in establishment success dramatically decreases as number of founding individuals decreases. At low numbers of founding individuals, the prominent predictors are landscape spatial heterogeneity and dynamic environmental conditions. For instance, compared to the annual mean, founding populations with ≤ 5 individuals have up to 18% higher establishment success when they arrive in ‘packed’ landscapes with relatively limited and clustered essential habitats and right before the breeding season. Accounting for landscape spatial heterogeneity and dynamic environmental conditions is integral in understanding and predicting population establishment and species colonisation. This additional complexity is necessary for advancing biogeographical theory and its application, such as in guiding species reintroduction efforts and invasive alien species management.

Biological invasions have caused the loss of freshwater biodiversity worldwide. The interplay between adaptive responses and demographic characteristics of populations impacted by invasions is expected to be important for their resilience, but the interaction between these factors is poorly understood. The freshwater gastropod Amnicola limosus is native to the Upper St. Lawrence River and distributed along a water calcium concentration gradient within which high‐calcium habitats are impacted by an invasive predator fish (Neogobius melanostomus, round goby), whereas low‐calcium habitats provide refuges for the gastropods from the invasive predator. Our objectives were to (1) test for adaptation of A. limosus to the invasive predator and the low‐calcium habitats, and (2) investigate if migrant gastropods could move from refuge populations to declining invaded populations (i.e., demographic rescue), which could also help maintain genetic diversity through gene flow (i.e., genetic rescue). We conducted a laboratory reciprocal transplant of wild F0 A. limosus sourced from the two habitat types (high calcium/invaded and low calcium/refuge) to measure adult survival and fecundity in home and transplant treatments of water calcium concentration (low/high) and round goby cue (present/absent). We then applied pooled whole‐genome sequencing of 12 gastropod populations from across the calcium/invasion gradient. We identified patterns of life‐history traits and genetic differentiation across the habitats that are consistent with local adaptation to low‐calcium concentrations in refuge populations and to round goby predation in invaded populations. We also detected restricted gene flow from the low‐calcium refugia towards high‐calcium invaded populations, implying that the potential for demographic and genetic rescue is limited by natural dispersal. Our study highlights the importance of considering the potentially conflicting effects of local adaptation and gene flow for the resilience of populations coping with invasive predators.

Fast‐paced selective pressures imposed by climate change and anthropogenic activities call for adaptive evolutionary responses to emerge at ecological timescales. However, the evolution and heritability of genomic variation underlie mechanistic constraints, which dictate a slower pace of adaptation exclusively relying on standing genetic variation and novel mutations. Environmentally responsive epigenetic mechanisms can allow acclimatisation and adaptive phenotypes to arise faster than DNA sequence‐based mechanisms alone. Nevertheless, the knowledge gap between identifying epigenetic marks and effectively deeming them functional is still wide in a natural context and often outside the scope of model organisms. With this Special Issue, we aimed to narrow this gap by presenting a compilation of original research articles, reviews and opinions on the topic of epigenetics in wild populations. We contextualised this collection within the overarching topic of conservation biology, as we firmly propose that epigenetic research can significantly enhance the effectiveness of conservation measures. Contributions highlighted the putative role of epigenetic variation in the acclimatisation and adaptive potential of species and populations directly and indirectly affected by climatic shifts and anthropogenic actions. They further exemplified how epigenetic variation can be used as biomarkers for monitoring variations in physiology, phenology and behaviour. Lastly, reviews and perspective articles illustrated the past and present of epigenetic research in wild populations while suggesting future research avenues.