Domestication has profoundly influenced the development of human agriculture, and is characterized by intense artificial selection. Feralization occurs when domestic animals return to the wild. Although feralization does not fully reverse domestication traits, the selective pressures and evolutionary mechanisms driving it remain poorly understood. In northern Europe and Asia, wild, semi-domesticated and feral reindeer (Rangifer tarandus) populations coexist, offering a unique opportunity to study feralization. We studied genomic signatures of selection in semi-domesticated, feral and wild reindeer populations in Norway. Analysis of population structure confirmed historical records indicating the feral population formed a monophyletic clade that originated from neighbouring semi-domesticated reindeer. However, we also found evidence for excess allele-sharing between wild and feral reindeer, indicating hybridization between these lineages. Signatures of selection were identified using a top-down approach (orthologues of domestication candidate genes) and a bottom-up approach (FST and extended haplotypes). We found that candidate regions under selection have higher rates of excess allele-sharing between wild and feral populations. This provides the first evidence of reversed selection pressures during feralization in reindeer and reveals a link between selection and hybridization. Together, our findings suggest that hybridization likely promoted adaptive introgression during feralization. We discuss the implications of our findings for conserving the genetic integrity of endangered wild reindeer populations.

Abstract Twenty-five years ago, the book The Ecology of Adaptive Radiation by Dolph Schluter presented a testable framework that integrated ecology, genetics, and natural history to explain the mechanisms driving adaptive radiation, the rapid diversification of a single lineage into multiple species occupying distinct ecological niches. One important contribution was to re-orientate the study of adaptive radiation from macro- to microevolution, emphasizing processes and mechanisms rather than patterns, thereby reshaping how adaptive radiation is conceptualized and studied. In this review, we revisit questions raised in Schluter’s foundational work to evaluate progress over the past quarter-century, focusing on eight key questions, grouped under four main themes, that remain unresolved. We first discuss the role of opportunity and diversification in radiations: whether there are consistent stages of adaptive radiation, whether they undergo early bursts, and how can we measure and identify ecological opportunity that may initiate radiation. Turning to traits, we first discuss the genetic basis of adaptation, the role of evolvability in adaptive radiation, the stability of adaptive landscapes and how lineages cross adaptive valleys. Finally, we focus on the role of speciation in the context of adaptive radiation. In our suggestions for future directions in the field over the next 25 years, we highlight the need to deepen the taxonomic scope of adaptive radiation and to improve our knowledge of the molecular basis of adaptive radiation. We argue that we are only at the beginning of our understanding of the role of gene flow in generating novel genetic combinations and driving the formation of new species. We suggest that there is a need to shift from a retrospective focus to a predictive eco-evolutionary dynamics framework. Finally, we appeal for the need to further develop our understanding of the role of plasticity in adaptive radiation and the role that subtle differences in organismal traits might play in improving our comparative analyses.

Background Islands harbour exceptional concentrations of endemic biodiversity, yet their biotas have been profoundly reshaped by human colonisation. In the Azores, deforestation and the introduction of invasive mammals drove major ecological transformations, and the fossil record reveals that the archipelago once supported avian communities far more diverse than those of today. During palaeontological expeditions conducted between 2011 and 2018, we recovered cranial and postcranial remains from several islands that were unambiguously assigned to the genus Fringilla , but exhibited substantially enlarged cranial morphology relative to the extant Azorean common chaffinch ( F. moreletti ). Remarkably, skull and beak proportions closely resembled those of the Canary Islands blue chaffinches ( F. teydea and F. polatzeki ), raising the possibility of a shared evolutionary origin. Results Using endogenous DNA extracted from fossil remains, we reconstructed complete or near-complete mitochondrial genomes from seven individuals. Combined with dense taxonomic sampling and whole-genome resequencing across Fringilla , these data enabled reconstruction of the evolutionary history of the Azorean forms. Contrary to expectations based on morphology, phylogenetic analyses unequivocally placed the extinct giant morphotypes within the clade of extant Azorean common chaffinches. Conclusions These findings reveal an extraordinary degree of ecological plasticity in passerines and demonstrate that pronounced morphological divergence can evolve without substantial genome-wide divergence. More broadly, our results highlight the importance of integrating genomic and morphological evidence when reconstructing the evolutionary history of extinct island taxa.

Phenotypic plasticity is a major mechanism whereby organisms adjust their traits within-generations to changes in environmental conditions. In the context of range expansions, plasticity is thought to be especially important, as plastic changes in traits can lead to rapid adaptation. One epigenetic process in particular, DNA methylation, enables organisms to adjust gene expression contingent on the environment, which suggests it may play a role in range expansions. At present, we know little about how methylation is regulated in wildlife, especially expression of the enzymes responsible for altering methyl marks on the genome. In this study, we compared expression of three epigenetic regulator genes (DNA methyltransferase 1, DNMT1; DNA methyltransferase 3, DNMT3; and one ten-eleven translocation methylcytosine dioxygenase, TET2) in three tissues (gut, liver, and spleen) of house sparrows Passer domesticus from nine countries. Some countries are in the native range of the species (Israel, the Netherlands, Norway, Spain, and Vietnam) whereas others are sites the species has colonized in the last 150 years (i.e. Australia, Canada, New Zealand, and Senegal). In this exploratory study, we asked whether non-native birds and/or birds from sites with comparatively unpredictable climates would express different levels of these genes. We found that all three genes were expressed more in sparrows from the native range and from areas with more stable temperatures. Expression of all three genes was also strongly correlated among-locations and within-individuals, but mean expression was quite different among tissues. Many factors (e.g. urbanization of the capture site, sex of the bird) did not significantly affect gene expression, but others surprisingly did (e.g. latitude). Our results suggest that these enzymes could be important in range expansions or geographic distribution generally, but more detailed investigations will be insightful.

Whole-genome sequencing efforts, have during the past decade, unveiled the central role of genomic rearrangements—such as chromosomal inversions—in evolutionary processes, including local adaptation in a wide range of taxa. However, employment of reference genomes from distantly or even closely related species for mapping and the subsequent variant calling can lead to errors and/or biases in the datasets generated for downstream analyses. Here, we capitalize on the recently generated chromosome-anchored genome assemblies for Arctic cod (Arctogadus glacialis), polar cod (Boreogadus saida), and Atlantic cod (Gadus morhua) to evaluate the extent and consequences of reference bias on population sequencing datasets (approx. 15–20 × coverage) for both Arctic cod and polar cod. Our findings demonstrate that the choice of reference genome impacts the mapping statistics, including mapping depth and mapping quality, as well as core population genetic estimates, such as heterozygosity levels, nucleotide diversity (π), and cross-species genetic divergence (DXY). Furthermore, using a more distantly related reference genome can lead to inaccurate detection and characterization of chromosomal inversions, i.e., in terms of size (length) and location (position), due to inter-chromosomal reorganizations between species. Additionally, we observe that some of the verified species-specific inversions are split across multiple genomic regions when mapped against a heterospecific reference. Inaccurate identification of chromosomal rearrangements as well as biased population genetic measures could potentially lead to erroneous interpretation of species-specific genomic diversity, impede the resolution of local adaptation, and thus, impact predictions of their genomic potential to respond to climatic and other environmental perturbations.

Gut microbiomes are central to host ecology and evolution, yet the mechanisms driv-ing their diversification remain elusive, partly because host evolution and biogeography are often confounded. The recent radiation of chaffinches in Macaronesia, coupled with their broadly similar ecologies across islands, makes them an ideal replicated natural experiment to separate spatial from host-driven effects on microbiome structure. Us-ing long-read 16S rRNA gene sequencing, diet metabarcoding, and whole-genome host data, we show that gut microbiome diversity aligns with predictions of island biogeog-raphy theory rather than host colonization history, revealing that microbial dispersal limitation independent of the host is a dominant mechanism of community assembly. Geography and diet primarily explain bacterial presence–absence patterns, whereas host genetic differentiation and heterozygosity influence abundant, potentially resident taxa. Challenging previous assumptions about birds, we detect clear signals of phylosymbiosis (i.e. similar microbiome composition among closely related hosts), however phylogenetic reconciliation reveals these associations result from convergent host filtering of environ-mentally acquired bacteria, likely via shared diets or physiological traits, rather than de-tectable co-diversification. Our study reframes our understanding of avian host-microbe relationships, revealing that birds maintain host-specific microbiome associations within biogeographic constraints, but these arise from ecological filtering processes rather than co-evolutionary partnerships. ### Competing Interest Statement The authors have declared no competing interest. Consejo Superior de Investigaciones Científicas, https://ror.org/02gfc7t72, PGC2018-097575-B-I00

Natal dispersal is a key life history trait determining fitness and driving population dynamics, genetic structure, and species distributions. Despite existing evidence that not all phenotypes are equally likely to successfully establish in new areas, the mechanistic underpinnings of natal dispersal remain poorly understood. The propensity to disperse into a new environment can be favoured by a high degree of phenotypic plasticity, which facilitates local adaptation and may be achieved via epigenetic mechanisms, which modify gene expression and enable rapid phenotypic changes. Epigenetic processes occur in particular genomic regions—DNA methylation on CpG sites in vertebrates—and thus individual genomes may differ in their capacity to be modified epigenetically. This ‘Epigenetic potential’ (EP) may represent the range of phenotypic plasticity attainable by an individual and be a key determinant of successful settlement in novel areas. We investigated the association between EP—quantified as the number of genome-wide CpG variants—and natal dispersal propensity in a long-term study population of Pied flycatchers ( Ficedula hypoleuca) monitored since colonisation of a new habitat 35 years ago. We tested this association at three levels, comparing EP between: (i) individuals dispersing between and within habitat patches; (ii) immigrants to the population and locally born individuals; and (iii) individuals from first (comprising colonisers or their direct descendants) and later generations of the population (consisting of locally born individuals, which did not show natal dispersal between habitat patches). Results show a significant, positive association between EP and dispersal propensity in comparisons (i)—only in females—and (iii), but not (ii). Furthermore, CpG variants were non-randomly distributed across the genome, suggesting species- and/or population-specific CpGs being more frequent in promoters and exons. Our findings point to EP playing a role in dispersal propensity at spatial and temporal scales, supporting the idea that epigenetically driven phenotypic plasticity facilitates dispersal and environmental coping in free-living birds.

DNA methylation, which can change within-individuals over time and regulate gene expression, is important to many aspects of avian biology. It is particularly important in avian responses to various stressors associated with introductions, such as infection and environmental changes. However, it remains unclear whether native and introduced bird populations differ in their epigenetic responses to stressors, and how DNA methylation may contribute to the success of non-native populations because of the limited availability of epigenetic studies. To address this knowledge gap, we used epiRADseq to investigate changes in DNA methylation within-individual house sparrows Passer domesticus prior to and eight hours after a simulated bacterial infection. We compare wild-caught house sparrows from introduced populations with those from native populations, assessing the number of genomic locations that exhibit changes in methylation, the magnitude of those changes, and the variance among individuals. Our results show that individuals from introduced populations experience more widespread changes in DNA methylation, with greater magnitude and higher variance, compared to their counterparts from native populations. These findings suggest that DNA methylation plays a significant role in an individual's response to infection. They also indicate that individuals from introduced populations may exhibit distinct epigenetic responses compared to their native counterparts, consistent with the concept of epigenetic buffering.

Human-commensalism has been intuitively characterised as an interspecific interaction whereby non-human individuals benefit from tight associations with anthropogenic environments. However, a clear definition of human-commensalism, rooted within an ecological and evolutionary framework, has yet to be proposed. Here, we define human-commensalism as a population-level dependence on anthropogenic resources, associated with genetic differentiation from the ancestral, non-commensal form. Such a definition helps us to understand the origins of human-commensalism and the pace and form of adaptation to anthropogenic niches, and may enable the prediction of future evolution in an increasingly human-modified world. Our discussion encourages greater consideration of the spatial and temporal complexity in anthropogenic niches, promoting a nuanced consideration of human-commensal populations when formulating research questions.