Molecular Ecology

Abiotic conditions deteriorate predictably at the edges of plant distribution ranges. Any adverse environmental settings could interfere with the functioning of nutritional mutualisms, such as arbuscular mycorrhiza. Documenting how transitioning from the kernel of a plant distribution towards the edges changes how mycorrhiza functions remains nonetheless underexplored. We questioned here whether arbuscular mycorrhizal fungal (AMF) richness and AMF community turnover decline towards the edges of the distribution of three AMF‐associating tree species, Artocarpus hypargyreus, Machilus breviflora and Xanthophyllum hainanense. We assayed roots from 62 tree individuals over a representative fraction of their distribution range and used molecular tools to assay AMF. Contrary to our expectations, we observed increases in AMF richness across marginal populations of those tree species and minimal differences in community turnover. We observed many AMF indicator species of marginal populations of the three hosts, which nonetheless all represented rare AMF taxa. Remarkably, the distance from the kernel of the distribution explained an independent fraction of AMF community variance compared to abiotic parameters and host selectivity. We uncover a novel axis of AMF community variation, the relative distance between the kernel and the edges of the distribution for the plant host. Exploring the significance of this new axis could bring new insights into the functioning of arbuscular mycorrhizal fungi by addressing questions related to how mycorrhizal plants handle stress and what drives host selectivity in the arbuscular mycorrhiza.

Wildlife populations globally have experienced widespread historical declines due to anthropogenic and environmental impacts, yet for some species, contemporary management and conservation programmes have enabled recent recovery. The impacts of decline and recovery on genomic diversity and, vice versa, the genetic factors that contribute to conservation success or failure are rich areas for inquiry, with implications for shaping how we manage species into the future. To comprehensively characterise these processes in natural systems requires range‐wide sampling and international collaboration, particularly for species with wide dispersal capabilities, broad geographic distributions, and complex regional metapopulation dynamics. Here, we present the first range‐ and genome‐wide population genomic analysis of grey seals based on 3812 nuclear SNPs genotyped in 188 samples from 17 localities. Our analyses support the existence of three main grey seal populations centred in the NW Atlantic, NE Atlantic and Baltic Sea, and point to the existence of previously unrecognised substructure within the NE Atlantic. We detected remarkably low levels of genetic diversity in the NW Atlantic population, and demographic analyses revealed a turbulent history of NE Atlantic and Baltic Sea grey seals, with bottlenecks in the Middle Ages and the 20th century due to hunting and habitat alterations. We found some localities deviated from isolation by distance patterns, likely reflecting wide‐scale metapopulation dynamics associated with recolonisation and recovery in regions where they were historically extirpated. We identify at least six grey seal genetic populations and reveal marked genetic effects of past declines and recent recovery across the species' range.

Wild congeners of cultivated fruit trees are vital sources of genetic diversity for crop improvement and key targets for conservation. However, cultivating crops within the range of rare wild congeners increases the risk of interspecific hybridization, threatening the genomic integrity of wild species. This is a concern for Pyrus in Central Asia, where a critically endangered wild species, P. korshinskyi, coexists with cultivated Pyrus communis and another widespread species, P. regelii, forming a species complex in which species boundaries are unclear, complicating conservation efforts. Here, we sought to assess: (1) the distinctiveness of species, (2) the extent to which interspecific hybridization and introgression may reduce the genetic integrity of P. korshinskyi, and (3) genetic diversity and structure within P. korshinskyi. Using RAD sequencing to genotype 185 individuals from 13 presumed wild and ex situ populations in Kyrgyzstan, we found that P. korshinskyi is genetically distinct, highly morphologically variable, but occasionally hybridises with both P. regelii and P. communis. Morphometric analyses indicate that the parental species and hybrids can be differentiated based on leaf characters. Unexpectedly, several reportedly wild populations of P. korshinskyi were found to be clonally propagated; unfortunately, because Pyrus exhibits gametophytic self‐incompatibility and all of the trees are the same genotype, these propagated populations are mate limited, limiting their conservation value. While P. korshinskyi populations are genetically diverse, further efforts are needed to preserve wild genetic diversity ex situ. These findings guide conservation strategies to maintain genetic integrity and diversity of P. korshinskyi both in situ and ex situ, underscoring the importance of genetic analyses for conserving crop wild relatives, especially in complex cultivated‐wild mosaics.

Early‐life experiences can predict the environments experienced later in life, giving individuals an opportunity to develop adaptive behaviour appropriate to a likely future environment. Epigenetic mechanisms such as DNA methylation (DNAm) have been implicated in developmental behavioural plasticity; however, studies investigating this possibility are limited in taxonomic breadth and ecological relevance. We investigated the impact of early‐life exposure to predation stress on behaviour and DNAm in the brains of Trinidadian guppies (Poecilia reticulata). We exposed guppies throughout development to either an alarm cue (conspecific skin extract), inducing predation stress, or a control cue (water) for 8 weeks and then raised them to adulthood under identical conditions. Then, we conducted two behavioural assays, an open‐field and a grouping test, before performing whole‐genome bisulfite sequencing on whole brains. Guppies exposed to the alarm cue during development exhibited increased grouping (shoaling) in adulthood compared to those exposed to the control treatment, but there were no detectable impacts on activity, boldness, or exploratory behaviour. We also identified stable shifts in brain DNAm in response to developmental alarm cue exposure in genes involved in behavioural regulation. Some differentially methylated sites were significantly associated with shoaling propensity in both males and females. Additionally, males and females differed in the magnitude of DNAm responses and the genes impacted, suggesting distinct roles for DNAm between the sexes. This study shows how early‐life predation stress can induce behavioural changes in adulthood and that shifts in neural DNAm could be an underlying mechanism responsible for these changes.

The spruce budworm (Choristoneura fumiferana; SBW) is a periodically outbreaking forest insect pest that affects the boreal forests of North America through extensive defoliation and tree mortality. Causes of widespread spatial synchrony of SBW outbreaks remain a key question in the ecology and management of this species. While the Moran effect (correlated favourable environmental conditions) and density‐dependent dispersal (from epicentres of demographic explosions) have been proposed and supported as drivers of synchronised outbreaks, the relative contribution of long‐distance dispersal is still poorly understood. In this study, we use a novel approach to distinguish resident from migrant moths and to assign migrants to likely source clusters with the goal of better characterising regional dispersal. First, we characterise the genetic diversity and structure of resident SBW larvae and three phenologically separated groups of moths over one flight season using Genotyping‐by‐Sequencing. Then, using a novel machine learning approach, we assign putative migrants to their likely source populations. We hypothesised that migrant moths and resident larvae would be genetically distinct and could be assigned to source populations. Our findings revealed complex patterns of moth dispersal and population differentiation within a single season, including two spatially overlapping genetic clusters. We observed subtle but significant genetic differences between resident larvae and migrant moths, supporting the hypothesis that long‐distance dispersal contributes to outbreak dynamics and synchrony. These insights enhance our understanding of SBW population dynamics and suggest that effective management strategies, such as the Early Intervention Strategy (EIS), must account for the role of dispersal in mitigating the detrimental effects of major outbreaks.

Stingless bees in the genus Tetragonula are social insects with a fully sterile worker caste, and are therefore well‐placed to provide insights into the genomic changes associated with ‘superorganismal’ life histories. Here we assemble the genome of Tetragonula carbonaria and characterise the population structure and divergence of both T. carbonaria and its cryptic congener T. hockingsi in eastern Australia, revealing three distinct populations for T. carbonaria and two partially differentiated subpopulations for T. hockingsi. We then combine our genomic results with RNA‐seq data from different T. carbonaria castes (queens, males, workers) to test two hypotheses about genomic adaptations in social insects: the ‘Relaxed Constraint’ hypothesis, which predicts indirect, and therefore relaxed, selection on worker‐biased genes; and the ‘Adapted Worker’ hypothesis, which predicts intensified positive selection on worker genes due to their evolutionarily novel functions. Although we do not find a direct signal of either weaker purifying selection or elevated positive selection in worker‐biased genes based on deviations from neutral expectations of nucleotide change between the two species, other evidence does support a model of relaxed selection on worker‐biased genes: such genes show higher nucleotide diversity and greater interspecies divergence than queen‐biased genes. We also find that differentially caste‐biased genes exhibit distinct patterns of length, GC content and evolutionary origin. These findings, which converge with patterns found in other social insects, support the hypothesis that social evolution produces distinct signatures in the genome. Overall, Tetragonula bees emerge as a valuable model for studying the genomic basis of social complexity in insects.

The intensification of land use over past millennia has accelerated habitat loss and fragmentation. This is hypothesized to lead to reductions in population sizes and restrictions in gene flow, processes that amplify genetic drift with profound negative impacts on species and populations. However, empirical data on the population genetic impacts of habitat fragmentation remain limited, particularly for presumed abundant species such as insects. Reports of dramatic insect and arthropod declines are increasing, and their short generation times and limited dispersal capacities make them especially vulnerable to habitat fragmentation. To substantiate the hypothesis that habitat fragmentation negatively impacts genetic composition and demography, we combined historical agricultural land use data from Denmark with whole‐genome resequencing of 25 populations of the collembolan Entomobrya nicoleti from natural grasslands. Abundance data indicate that agricultural expansion reduces habitat suitability and fragments populations. Demographic modelling shows that intensification of agricultural land use coincides with severe declines in effective population sizes. It is likely that these declines have yet to reach their full effect on current levels of genetic diversity because of the ‘drift debt,’ where the genetic diversity of recently declined populations will erode over future generations. Gene flow estimates revealed sharp recent declines that coincide with agricultural intensification. Our results underscore that even seemingly abundant species in fragmented landscapes can experience severe reductions in effective population size and gene flow. These demographic shifts predict future genetic erosion, highlighting the delayed yet inevitable consequences of habitat fragmentation for population persistence.

Geographic isolation plays a pivotal role in speciation by restricting gene flow between populations through distance or physical barriers. However, the speciation process is complex, influenced by the interplay between dispersal ability and geographic isolation, as seen in “great speciators” – bird species that simultaneously have broad island distributions but high levels of subspecific diversity. Comparing genomic population differentiation in species that occupy both continental and island settings can reveal the effects of different forms of geographic isolation and validate if the primary mechanism proposed to catalyse a great speciator pattern, that is, dispersal reduction following island colonisation, has occurred. The highly diverse white‐eye family Zosteropidae includes several great speciators, including the silvereye (Zosterops lateralis), with 16 subspecies (11 occurring on islands), distributed on the Australian continent and numerous southwest Pacific islands. We compared continental and island patterns of divergence using whole genome and morphological data. Australian mainland populations showed a low genetic population structure, lack of isolation by distance patterns and low morphological diagnosability, suggesting that the species' dispersal propensity in a continental setting is sufficient to overcome multiple forms of geographic barriers and large geographic distances. In contrast, except for island populations less than 200 years old, most island populations were highly genomically structured with clearer morphological diagnosability even if separated by relatively short geographic distances. The inferred reduction of dispersal propensity in island situations is consistent with the proposed model of great speciator formation on islands. Our phylogenomic analyses also allowed resolution of the silvereyes' evolutionary position, showing their relatively early emergence (~1.5 Mya) within the rapidly radiating Zosteropidae, while population‐level analyses demonstrated where morphological subspecies and genomic data align and disagree. However, the silvereye example also shows how uncertainties about relationships remain when reconstructing evolutionary history in rapidly radiating groups, even when whole genome data is available. Altogether, our results show how within‐species genomic and morphological patterns measured over broad spatial scales and with varying geographic contexts can help reveal when particular stages of speciation such as great speciators are likely to emerge.

As a part of epigenetic modifications, DNA methylation involves the addition of a methyl group to cytosine. In plants, this process occurs in three sequence contexts (CG, CHG and CHH) through two pathways: de novo DNA methylation and DNA methylation maintenance. DNA methylation is highly conserved between ecotypes due to its heritability and role in genomic stability. However, numerous naturally occurring differentially methylated regions (NMRs) exist between ecotypes, which are also heritable and contribute to differential gene expression and phenotypic variation. Decreased DNA methylation observed in mutants of RdDM or DNA methylation maintenance pathways highlights the potential roles of these pathways in NMR formation and inheritance. Nevertheless, the complexity of plant DNA methylation across different contexts and pathways has made the contributions of these two pathways in NMR formation and inheritance remain unclear. To address this, we chose two Arabidopsis thaliana ecotypes, Col‐0 (Col) and C24, and utilised mutants of pol4/5 and ddm1 in both ecotypes. By examining the changes in NMRs within these mutants, we aimed to elucidate the roles of DNA methylation pathways in NMR formation and inheritance. Our results revealed (1) NMRs can be categorised into three types, but classification is not solely based on methylation contexts; (2) compared to RdDM, the DNA methylation maintenance pathway plays a more dominant role in NMR formation and is less influenced by SNPs; (3) DNA methylation maintenance, rather than RdDM, controls NMR inheritance. Our findings highlight the role of the DNA methylation maintenance pathway in NMR formation and inheritance.

Cichlid fishes have the highest rates of evolutionary turnover of sex chromosomes among vertebrates. Many large structural polymorphisms in the radiation of cichlids in Lake Malawi are associated with sex chromosomes and may also carry adaptive variation. Here, we investigate the structure and evolutionary history of an inversion polymorphism that includes both a ZW sex locus and an orange‐blotch colour polymorphism in the rock‐dwelling cichlid fishes of Lake Malawi. We use long‐read sequencing to characterise the sequence and breakpoints of the inversion. We quantify allele frequency differences across the inversion in population samples of the genera Metriaclima and Labeotropheus. We also examine expression differences of genes in the inversion. The simple inversion spans 7 Mb and is flanked by CACTA transposons that may have catalysed the rearrangement. The region includes ~600 genes, several of which show large differences in expression. Some of these genes are candidates for the sex and colour phenotypes. This inversion is an accessible model system for studying the role of structural polymorphisms and sex chromosome turnover in the adaptive radiation of cichlids in the lakes of East Africa.

Marine phytoplankton play essential roles in global primary production and biogeochemical cycles. Yet, the evolutionary genetic underpinnings of phytoplankton adaptation to complex marine and coastal environments, where many environmental variables fluctuate and interact, remain unclear. We combined population genomics with experimental transcriptomics to investigate the genomic basis underlying a natural evolutionary experiment that has played out over the past 8000 years in one of the world's largest brackish water bodies: the colonisation of the Baltic Sea by the ancestrally marine diatom Skeletonema marinoi. To this end, we combined target capture of the entire nuclear genome with pooled shotgun sequencing, and showed that the method performs well on both cultures and single cells. Genotype–environment association analyses identified > 1000 genes with signals of selection in response to major environmental gradients in the Baltic Sea, which apart from salinity, include marked differences in temperature and nutrient supply. Locally adapted genes were related to diverse metabolic processes, including signal transduction, cell cycle, DNA methylation and maintenance of homeostasis. The locally adapted genes showed significant overlap with salinity‐responsive genes identified in a laboratory common garden experiment, suggesting the Baltic salinity gradient contributes to local adaptation of S. marinoi. Taken together, our data show that local adaptation of phytoplankton to complex coastal environments, which are characterised by a multitude of environmental gradients, is driven by widespread changes in diverse metabolic pathways and functions.

Comparative studies of whole genomes have increasingly shown that genetic introgression between closely related species is surprisingly common across the tree of life, making the description of biodiversity and understanding the process of speciation complex and challenging. The adaptive radiation of cichlid fishes in Lake Malawi, that is characterised by hybrid origins and cases of recent introgression, provides a valuable model system to study the evolutionary implications of introgression. However, many potential sources of introgression into the radiation have not yet been investigated. Here we use whole genome data from 239 species from Lake Malawi and 76 species from surrounding African river and lake systems to identify previously unknown introgression events involving the Malawi radiation. Computing genome‐wide excess allele sharing (ABBA‐BABA statistics) and window‐based statistics, we find that three independent riverine cichlid lineages show significantly higher allele sharing with the Malawi radiation than expected, suggesting historical genetic exchange. Introgressed haplotypes are distributed relatively uniformly across the Malawi radiation, indicating that most hybrid‐derived polymorphism was acquired and sorted before the formation of the contemporary Malawi radiation. Our results point towards several previously unknown contributors to the Malawi cichlid hybrid swarm and show that the history of one of the largest vertebrate radiations is more complex than previously thought.

South American savannas are a disjunct biome with an unclear evolutionary history. We tested hypotheses about their Quaternary history and the evolution of savanna cores through fragmentation or dispersal from the Cerrado. We used genomic data (genotyping‐by‐sequencing) and ecological niche models of the Burnished‐buff Tanager (Stilpnia cayana Linnaeus 1766) to evaluate intraspecific differentiation, gene flow, past range shifts and landscape genomics association. We found clear genomic differences between populations on each side of the Amazon basin and high admixture in Marajó Island and Bolivia. Landscape genomics analysis indicated that the Amazon River, isolation by distance and temperature predict genomic differentiation in this bird. Taken together, the results suggest that a combination of dispersal from the Cerrado, isolation due to geographic distance, and the Amazon River basin, and local adaptation shaped species diversification.

Most studies of sex‐biased genes explore their evolution in familiar chromosomal sex determination systems, leaving the evolution of sex differences under alternative reproductive systems unknown. Here we explore the system of paternal genome elimination employed by mealybugs (Hemiptera: Pseudococcidae) which have no sex chromosomes. Instead, all chromosomes are autosomal and inherited in two copies, but sex is determined by the ploidy of expression. Females express both parental alleles, but males reliably silence their paternally inherited chromosomes, creating genome‐wide haploid expression in males and diploid expression in females. Additionally, sons do not express alleles directly inherited from their fathers, potentially disrupting the evolution of male‐benefiting traits. To understand how these dynamics impact molecular evolution, we generated sex‐specific RNAseq, a new gene annotation, and whole‐genome population sequencing of the citrus mealybug, Planococcus citri. We found that genes expressed primarily in females hold more variation and evolve more quickly than those expressed in males or both sexes. Conversely, we found more apparent adaptation in genes expressed mainly in males than in those expressed in females. Put together, in this paternal genome elimination system there is slower change on the male side but, by increasing selective scrutiny, an increase in the degree of adaptation in these genes. These results expand our understanding of evolution in a non‐Mendelian genetic system and the data we generated should prove useful for future research on this pest insect.

Hybridization and interspecific gene flow play a substantial role in the evolution of plant taxa. The eastern North American white oak syngameon, a group of approximately 15 ecologically, morphologically and genomically distinguishable species, has long been recognised as a model system for studying introgressive hybridization in temperate trees. However, the prevalence, genomic context and environmental correlates of introgression in this system remain largely unknown. To assess introgression in the eastern North American white oak syngameon and population structure within the widespread Quercus macrocarpa, we conducted a rangewide survey of Q. macrocarpa and four sympatric eastern North American white oak species. Using a Hyb‐Seq approach, we assembled a dataset of 3412 thinned single‐nucleotide polymorphisms (SNPs) in 445 enriched target loci including 62 genes putatively associated with various ecological functions, as well as associated intronic regions and some off‐target intergenic regions (not associated with the exons). Admixture analysis and hybrid class inference demonstrated species coherence despite hybridization and introgressive gene flow (due to backcrossing of F1s to one or both parents). Additionally, we recovered a genetic structure within Q. macrocarpa associated with latitude. Generalised linear mixed models (GLMMs) indicate that proximity to range edge predicts interspecific admixture, but rates of genetic differentiation do not appear to vary between putative functional gene classes. Our study suggests that gene flow between eastern North American white oak species may not be as rampant as previously assumed and that hybridization is most strongly predicted by proximity to a species' range margin.

Adaptation to environmental heterogeneity is a key driver of between‐population genomic differentiation, yet we know very little about how genomic divergence is affected by adaptation to multiple ecological factors. Using an experimental evolution approach, we whole‐genome re‐sequenced ‘fast‐cycling’ Brassica rapa plants which had evolved during eight generations of selection from different combinations of soil type, aphid herbivore presence or absence, and either bee‐ or hand pollination. Our results show that bumblebee pollination was the strongest driver of genomic divergence and that the degree of genomic divergence was strongly associated with the number of SNP markers identified in genomic selection scans. Furthermore, we found that the number of SNPs under selection was affected by herbivory in a soil‐dependent way. More specifically, aphid herbivory was associated with an increased number of selected SNPs for bee‐pollinated plants that evolved in tuff soil but was associated with a decreased number of selected SNPs for bee‐pollinated plants that evolved in the more resource‐limiting limestone soil. We also found that a higher number of selected SNPs was associated with higher rates of phenotypic evolution for 27 phenotypic traits including morphology and scent. Finally, we found that variation in pleiotropy between treatments was related to both the degree of genomic divergence and the number of SNPs under selection. Our results demonstrate that different soil types promote unique adaptive genomic architectures in response to biotic interactions, thus increasing genomic divergence between plant populations.

Effective population size (Ne) is a quantity of central importance in evolutionary biology and population genetics, but often notoriously challenging to estimate. Analyses of Ne are further complicated by the many interpretations of the concept and the alternative approaches to quantify Ne utilising different properties of the data. Each method is also informative over different time scales, suggesting that a combination of approaches should allow piecing together the entire continuum of Ne, spanning from the recent to more distant past. To test this in practice, we inferred the Ne continuum for 45 populations of nine‐spined sticklebacks (Pungitius pungitius) using whole‐genome data with both LD‐ and coalescent‐based methods. Our results show that marine populations exhibit the highest Ne values in contemporary, recent, and historical times, followed by coastal and freshwater populations. The results also demonstrate the impact of both recent and historical gene flow on Ne estimates and show that simple summary statistics are informative in comprehending the events in the very recent past and aid in more accurate estimation of NeC${N}_e^C$, the contemporary Ne, as well as in reconstruction and interpretation of recent demographic histories. Although our sample size for each large population is limited, we found that GONE can provide reasonable Ne estimates. However, due to challenges in detecting subtle genetic drift in large populations, these estimates may represent the lower bound of Ne. Finally, we show that combining GONE and CurrentNe2, both sensitive to population structure, with MSMC2 provides a meaningful interpretation of Ne dynamics over time.

Migratory birds are inherently vagile, a strategy that may reduce the impacts of habitat loss and fragmentation on genetic diversity. However, specialist resource requirements and range‐edge distribution can counteract these benefits. The European nightjar (Caprimulgus europaeus) is a long‐distance migratory bird and resource specialist. Like other long‐distance migrants, nightjar populations have declined across the British Isles and Northwestern Europe over the past century. With this decline well documented in the British Isles, there is a need to quantify its genetic impacts. We applied full genome resequencing to 60 historic (1841–1980) and 36 contemporary British nightjars. Nightjars exhibited a statistically significant 34.8% loss in heterozygosity and an increase in inbreeding over the last ~180 years, showing a departure from panmixia towards weak spatial structure in the modern population. Such fine‐scale structuring in migratory birds is rare. Our results provide a case study of fragmentation's impact on a species with specialist resource requirements at its range limit. Similar demographic declines in nightjars and other long‐distance migrants across Northern and Western Europe suggest that genetic patterns seen in the British population may reflect those in other nightjar populations and European avifauna. Whilst our results indicate no immediate conservation concern, they depict a trajectory of declining genetic diversity, increasing inbreeding and genetic structure, potentially shared with other migratory species. Our study highlights the value of applying spatiotemporal population genetics analysis to migratory birds, despite their inherent vagility.

The spatial distribution of the European anchovy has expanded in the northern part of its range in the Northeast Atlantic in recent decades. However, whether this results from a northward range shift of southern conspecifics or the expansion of a local northern population is unknown. Using for the first time whole‐genome sequencing, we explore current patterns of genetic diversity and population sub‐structuring of European anchovy in the Northeast Atlantic, with special focus on recently expanded North Sea areas. Genomic data suggested three distinct groups: Northern (North Sea and Kattegat), Southern (Ireland and Central Portugal) and Cadis (South Portugal). Despite most of the genome being homogenised by high levels of gene flow characteristic of small pelagic fish, several large regions of high genetic differentiation were observed. This suggests that genomic population boundaries might be maintained by local adaptation within chromosome structural variants (inversions). Admixture analysis indicates that the ongoing northern range shift involves both migrants of southern origin and expansion of the local North Sea population. Historical demographic inference suggests that anchovies survived the last glacial period with small population sizes, followed by a split into the current Northern and Southern groups at the end of the last glacial maximum. The Southern group then expanded into the North Sea as the ice sheets retreated, in an expansion involving a large number of individuals, which is consistent with the retention of most of the genetic diversity. In comparison with other small pelagic fish, the genetic patterns found in anchovies (deeply divergent groups, no loss of genetic diversity during expansion, mixing between groups) align well with those found in European sprat, while sardines fit the pattern of expansion of a leading‐edge population, with reduced genetic diversity and much shallower divergence between populations. This study contributes to a better understanding of population structure, range shifts and local adaptation in small pelagic fish under climate change, informing conservation and management efforts.

Hybridisation and admixture are common in nature and can serve as important sources of adaptive potential by generating novel genotype combinations and phenotypes. However, hybrid incompatibilities can also reduce hybrid fitness. Given the pervasiveness of admixture and its potential role in facilitating adaptation, understanding how admixture influences the rate and repeatability of evolution is critical for advancing our understanding of evolutionary dynamics. Yet, few studies have examined how patterns of evolutionary repeatability in admixed lineages are shaped by strong ecological pressures. In this experiment, we evaluated patterns of evolution and repeatability in admixed and non‐admixed cowpea seed beetles (Callosobruchus maculatus) adapting to a novel, stressful host: lentil. Specifically, we asked (1) whether admixture facilitates adaptation to lentil, (2) whether repeatability is greater in admixed or non‐admixed lineages, and (3) to what extent repeatability in admixed lineages is driven by selection on globally adaptive alleles versus epistatic effects and hybrid incompatibilities. We found that admixture facilitated adaptation to lentil, and evolutionary rescue–defined as adaptation that prevents population extinction–occurred in all lineages. Evolutionary repeatability was highest in two admixed lineages, though evident across all lineages. Adaptation to lentil appeared largely driven by selection on globally adaptive alleles. Nevertheless, even under conditions of evolutionary rescue in a marginal environment, the purging of hybrid incompatibilities contributed substantially to repeated evolution in admixed lineages.

Coalescent modelling of hybrid zones can provide novel insights into the historical demography of populations, including divergence times, population sizes, introgression proportions, migration rates and the timing of hybrid zone formation. We used coalescent analysis to determine whether the hybrid zone between phylogeographic lineages of the Plateau Fence Lizard (Sceloporus tristichus) in Arizona formed recently due to human‐induced landscape changes, or if it originated during Pleistocene climatic shifts. Given the presence of mitochondrial DNA from another species in the hybrid zone (Southwestern Fence Lizard, S. cowlesi), we tested for the presence of S. cowlesi nuclear DNA in the hybrid zone as well as reassessed the species boundary between S. tristichus and S. cowlesi. No evidence of S. cowlesi nuclear DNA is found in the hybrid zone, and the paraphyly of both species raises concerns about their taxonomic validity. Introgression analysis placed the divergence time between the parental hybrid zone populations at approximately 140 kya and their secondary contact and hybridization at approximately 11 kya at the end of the Pleistocene. Introgression proportions estimated for hybrid populations are correlated with their geographic distance from parental populations. The multispecies coalescent with migration provided significant support for unidirectional migration moving from south to north, which is consistent with spatial cline analyses that suggest a slow but steady northward shift of the centre of the hybrid zone over the last two decades. When analysing hybrid populations sampled along a linear transect, coalescent methods can provide novel insights into hybrid zone dynamics.

Anthropogenic climate change has caused widespread loss of species biodiversity and ecosystem productivity worldwide, with amphibians being particularly affected. Predicting the future of amphibians, a critical group for maintaining biodiversity and for balancing ecosystem structure and function, is essential for effective conservation planning in the Anthropocene. In this study, we used Amolops species as a model to assess their vulnerabilities under future climate change. Through genotype–environment association (GEA) analyses, we identified climate‐associated SNPs, revealing that temperature and precipitation were key drivers for local adaptation in these species. Genetic offset analysis showed that the marginal and high‐latitude populations of the Amolops mantzorum and Amolops monticola groups were at greater risk of local extinction as a result of a mismatch of genetic‐environmental associations under future climate conditions. Ecological niche models predicted that, from 2011 to 2100, approximately 67% of Amolops species would experience significant habitat loss. We introduced the life strategy index (LSI) to assess species vulnerability, considering the interplays of evolution, ecology, and colonisation. Our LSI analysis showed that Amolops deng and Amolops tuberodepressus face a high extinction risk, in contrast with A. mantzorum, features strong adaptability and a low extinction risk. The LSI framework not only enables the systematic assessment of species vulnerability but also identifies key contributing factors through comprehensive evaluation across ecological, evolutionary, and colonisation dimensions, thereby facilitating the development of targeted conservation strategies.

Genetic repositories are invaluable resources foundational to various biological disciplines. While their data and metadata reliability are essential for robust research outcomes, numerous studies have highlighted data quality and consistency issues. Here, we detect and quantify errors at the most fundamental level by analysing the congruence of sequences derived from the same genetic marker and specimen voucher across tetrapods. Our analysis reveals that 32% of re‐sequenced vouchers (with identical field or museum numbers) yield unequal sequences, ranging from a few mutations to significant divergences (0.06%–33.95%). These divergences may result from sample misidentification, labelling errors, fidelity disparities between sequencing methods, or contamination at various stages of the research process. Our findings demonstrate errors within GenBank at its most basal level and suggest that, although undetectable, a similar error rate likely exists in non‐re‐sequenced data. These previously overlooked errors are concerning because they arise from replicated experiments, which are uncommon, and raise serious questions about the reliability of non‐re‐sequenced specimens. Such errors can compromise the accuracy of biodiversity assessments (e.g., taxonomic assessment, eDNA and barcoding), phylogenetic analyses and conservation planning by artificially inflating the intraspecific divergence or misidentifying (to‐be‐described) species. Additionally, the accuracy of large‐scale biological studies that rely on such data can be compromised. Our concerning results call for protocols ensuring sample traceability to the specimens or tissues during the whole process of data generation, analysis and deposition in a database. We propose a third‐party annotation system for individual GenBank records that would allow flagging common errors and alert both the original submitter and all users to potential problems without modifying the original records.

Fish exhibit a diverse array of reproductive strategies adapted to various ecological niches. Parental egg‐care, including live‐bearing, mouth‐brooding, and male egg protection by brood pouches, represents an effective strategy for ensuring larval survival and has emerged independently in multiple lineages. Despite the recognised evolutionary bias that favours a strategy transition from non‐carer to egg‐carer, the genetic mechanisms underlying this bias and the commonalities among parental egg‐care species remain elusive. This study explores the relationship between egg‐care and the chorion hardening system crucial for protecting eggs in non‐care species. By analysing whole genome sequences of 240 species of Acanthopterygii across 25 orders, we discovered that multiple genes associated with chorion hardening have become pseudogenes in various egg‐care species, indicating a collapse of the chorion hardening system in these fish. These findings suggest that the evolutionary bias in fish reproductive strategies not only aims to enhance survival efficiency but also imposes a constraint on egg‐care species, preventing them from reverting to a reproductive strategy relying on a hardened chorion. In particular, alveolin, previously characterised as a single mutant resulting in significantly fragile chorion in medaka, suggests a strong correlation between egg‐care strategy and gene loss. Our results suggest an evolutionary dead‐end because gene loss may impose an evolutionary constraint at the behavioural level. The observed association between gene loss and reproductive strategies provides insights into suitable reproductive environments for each species and may facilitate non‐invasive estimation of reproductive strategies in species with unknown breeding strategies.

Cameroon Blackbelly sheep are a domestic breed of hair sheep from West/Central Africa. They are popular with small‐holder farmers in Cameroon as they are highly resilient to local environmental challenges and are prolific a‐seasonal breeders. The aim of this study was to characterise the genetics of Cameroon Blackbelly sheep in relation to global sheep populations and to investigate their relationship to Caribbean hair sheep. We first examined the genetic diversity of the Cameroon Blackbelly breed relative to global sheep populations using 50K SNP data. We also used whole genome sequence data to further investigate relationships between Cameroon Blackbelly and breeds from Africa and Europe, as well as the Barbados Blackbelly breed from the Caribbean, which is phenotypically similar to Cameroon Blackbelly. ADMIXTURE results based on 50K and WGS data demonstrated both West/Central African and European ancestries for the Barbados Blackbelly sheep. Results from f4‐statistics‐based qpAdm analyses supported these findings. Local ancestry inference identified several genomic regions in Barbados Blackbelly with high proportions of West/Central African ancestry. One of these, on OAR3, includes various keratin genes, suggesting that these genes may play a role in the shared coat phenotypes of the Barbados Blackbelly and Cameroon Blackbelly. This result is consistent with previous reports of adaptive introgression of coat characteristics in both wild and domesticated species. The findings of our study support the view that sheep were transported from West/Central Africa to the Caribbean as part of the transatlantic slave trade and European colonisation, similar to introductions proposed for cattle and goats.