Abstract Hybridization between widespread species and narrow endemics poses a serious conservation threat, often leading to extinction via genetic swamping. In this study, we applied an integrated approach—combining genetics, morphometrics, and functional ecology—to investigate the implications of hybridization between the widespread species Limonium cossonianum and the Critically Endangered L. estevei . We combined molecular markers (AFLPs, ITS, and chloroplast markers), morphometric analyses, and elemental profiling of leaves and soils. Elemental profiles provided a novel proxy for biogeochemical niche differentiation, while genetic markers resolved phylogenetic relationships and the direction and extent of gene flow. Crucially, our results revealed extensive and asymmetric introgression occurring exclusively from the hybrid into L. cossonianum , with no evidence of genetic swamping affecting the genetic integrity of L. estevei . Elementome analyses showed that L. cossonianum occupies a significantly distinct biogeochemical niche, whereas L. estevei and the hybrid share similar elemental composition. Furthermore, the hybrid’s elementome exhibited a mosaic inheritance pattern, suggesting a novel functional strategy that may contribute to its local persistence. We conclude that the mechanisms of niche differentiation, coupled with reproductive asymmetry, have acted as an evolutionary shield for L. estevei , protecting this species from extinction through genetic swamping. Our findings indicate that, although hybridization does not currently threaten the genetic integrity of L. estevei , its long-term persistence will depend on the conservation of the highly specific edaphic conditions on which the species relies. Given the marked soil specialization documented here, strategies focusing on the preservation of its functional and edaphic niche are likely to be essential.

Scientists use reintroductions to restore native species to their historical ranges but sometimes overlook effects of dispersal on genetic structure of restored populations. Unidirectional or biased gene flow can result in genetic swamping, where unique variation in a recipient population is replaced by genotypes from the source population. In theory, this can result in loss of advantageous alleles and adaptive capacity. In Great Smoky Mountains National Park native Brook Trout (Salvelinus fontinalis) are being restored to streams from which they had been extirpated. Multiple source lineages are mixed in restoration sites to maximize genetic diversity. However, in our study system, translocated fish were released unevenly along a rugged mountain stream, resulting in an upstream population coming from only one source stock and a downstream population that was a mixture of three source stocks. A natural cascade allows downstream dispersal but prevents or constrains upstream movement. Theory predicts that such biased movement will lead to genetic swamping, i.e., reduction or loss of representation of ancestral lineages released only in the downstream population. However, the rate of gene flow and degree of asymmetry were unknown. Here, we used genetic and population density data to confirm the directionality of dispersal, estimate the rate of genetic swamping, and assess alternative mitigation strategies. Our results indicate that the downstream population has already become dominated by ancestry from the upstream source and translocation from within the restored stream will not achieve the intended genetic diversity. Instead, introducing additional fish from the original source stocks above the natural barrier would be necessary to equalize the contribution of all three source populations. Our results emphasize the importance of understanding the interplay between dispersal and genetic structure for conservation planning.

SummaryHybrid zones provide excellent opportunities to study evolutionary processes linked to interspecific gene flow, including introgression, genetic erosion, polyploid establishment, and speciation. The genus Cardamine (Brassicaceae) serves as an excellent model for polyploid evolution, including one of the few well‐documented neo‐allopolyploid species that have evolved in the last 300 yr.Using a combination of flow cytometric screening of nuclear DNA content, next‐generation restriction site‐associated DNA sequencing, and genomic in situ hybridization, we uncovered an unprecedented case of extensive interspecific hybridization in Cardamine, involving four parental species and their predominantly triploid offspring.We demonstrate the recurrent and polytopic origins of both autotriploids and allotriploids, the latter integrating different parental genomes. Our findings highlight Cardamine rivularis as a central player in this system, likely producing unreduced female gametes at a high rate, which drives the formation of diverse triploids. However, this species may also face the risk of genetic swamping and ecological displacement. The substantial genetic variation of the hybrids, their high frequency, partial fertility, and efficient clonal spread suggest significant evolutionary potential.Overall, we propose that these hybrid zones provide a rare and valuable natural laboratory for studying the emergence of neo‐allopolyploids and the mechanisms shaping polyploid evolution.

ABSTRACT Introgression is an important biological process that has a major impact on the evolutionary potential of species. Admixed offspring from parental individuals of different species, or in other word evolutionarily distinct gene‐pools, may enable the exchange of genomic information between these two species without leading to genetic swamping. Here, we argue that conservation biologists must take into account both the adaptive and maladaptive consequences resulting from introgression by evaluating the biological and environmental context: past, present and future. Our argument is based on recent insights confirming species boundaries to be permeable, with scenarios suggesting increased permeability in the future. As a consequence, closely related species may form syngameons that enhance the evolutionary potential and resilience to environmental change by exchanging genetic information. Here, we focus on three aspects of introgression in applied conservation. Firstly, introgression between species in their native habitats may be considered as a natural strategy of these species to enhance their resilience to environmental change. Secondly, introgression between species, particularly native and nonnative, may rarely lead to genetic swamping but need to be monitored carefully to avoid the loss of the species identity of native threatened species. Thirdly, introgression between threatened and non‐threatened species need to be considered as unique opportunities to recover alleles that are already lost in the gene pool of highly threatened species experiencing the attraction of the extinction vortex, especially where admixed individuals already exist naturally. In summary, we are calling for the replacement of a static Linnean species concept by a species concept that considers species a dynamic gene pools with permeable boundaries enabling the exchange of genetic information, enhancing adaptive capacity without losing species integrity.

Pumas (Puma concolor) occupy a vast geographical range spanning from Canada to Argentina. Due to urbanization and unregulated hunting, pumas in Florida, known as panthers, are the only breeding population east of the Mississippi River. In the 1990s, Florida panthers numbered <30 individuals suffering from inbreeding depression. In 1995, eight pumas from Texas were translocated into southern Florida to mitigate the effects of isolation. This translocation reduced inbreeding depression and increased population size. While genetic rescue is often suggested as a means of ameliorating the effects of small population size, the underlying genetic mechanism and its long-term efficacy remain understudied. We sequenced the genomes of posttranslocation Florida panthers (PTFPs) to elucidate the genomic consequences of genetic rescue. We inferred local ancestry across the genomes of PTFPs and found that no regions have been entirely replaced by Texas ancestry, discarding the possibility of genetic swamping. Furthermore, the beneficial effects of the translocation were likely caused by a reduction in homozygosity, alleviating recessive deleterious load, rather than by a reduction in the number of deleterious variants. We did not find evidence that selection has favored replacement of original Florida DNA with Texas DNA in any systematic fashion. Using simulations, we found that heterozygosity increased in the long-term compared to a no translocation scenario; however, the effects on fitness are more transient. Our findings hold significant implications not only for the management of Florida's panther population, but also for informing strategies for genetic rescue in other wild, inbred populations encompassing broader conservation efforts.

As distant hybridization has profound implications for evolutionary biology, aquaculture, and biodiversity conservation, this study aims to elucidate patterns of maternal inheritance, genetic divergence, and phylogenetic relationships by synthesizing mitochondrial genome (mitogenome) data from 74 distant hybrid fish species. These hybrids span diverse taxa, including 48 freshwater and 26 marine species, with a focus on Cyprinidae (n = 35) and Epinephelus (n = 14), representing the most frequently hybridized groups in freshwater and marine systems, respectively. Mitogenome lengths were highly conserved (15,973 to 17,114 bp); however, the genetic distances between hybrids and maternal species varied from 0.001 to 0.17, with 19 hybrids (25.7%) showing distances &gt;0.02. Variable sites in these hybrids were randomly distributed but enriched in hypervariable regions, such as the D-loop and NADH dehydrogenase subunits 1, 3 and 6 (ND2, ND3, and ND6) genes, likely reflecting maternal inheritance (reported in Cyprinus carpio × Carassius auratus). Moreover, these genes were under purifying selection pressure, revealing their conserved nature. Phylogenetic reconstruction using complete mitogenomes revealed three distinct clades in hybrids: (1) Acipenseriformes, (2) a freshwater cluster dominated by Cypriniformes and Siluriformes, and (3) a marine cluster comprising Centrarchiformes, Pleuronectiformes, Scombriformes, Cichliformes, Anabantiformes, Tetraodontiformes, Perciformes, and Salmoniformes. The prevalence of Cyprinidae hybrids underscores their importance in aquaculture for hybridization, where traits such as rapid growth and disease resistance are enhanced. In contrast, marine hybrids are valued for their market value and adaptability. While mitogenome data robustly support maternal inheritance in most cases, exceptions suggest complex mechanisms, such as doubly uniparental inheritance (DUI), in distantly related crosses. Moreover, AT-skew of genes in hybrids revealed a paternal leakage of traits in mitogenomes. This study also highlights ecological risks, such as genetic swamping in native populations, emphasizing the need for responsible hybridization practices. These findings advance our understanding of the role of hybridization in fish evolution and aquaculture, providing a genomic framework and policy recommendations for optimizing breeding programs, hybrid introduction, and mitigating conservation challenges.

ABSTRACTOf the many threats to species' survival, genetic threats such as hybridisation and introgression are often overlooked. Threatened or range‐restricted species that hybridise with more abundant and widespread relatives can be particularly vulnerable to declines or extinction via demographic or genetic swamping. Conservation of these species requires detection of hybridisation, but this can be difficult when hybrids are morphologically indistinguishable from parental species (i.e., cryptic). We used single nucleotide polymorphism data to examine hybridisation and introgression between the endangered Booroolong frog (Litoria booroolongensis) and the more abundant eastern stony creek frog (Litoria wilcoxii), two Australian stream frog species not previously reported to hybridise. To assess whether hybrids and parental individuals could be identified by phenotype, we compared morphological and genotypic classifications of individuals. Genotyping revealed relatively high rates of hybridisation and introgression (19% (24/126) were F1 or F2 hybrids, or backcrosses) in the New South Wales Central Tablelands. Hybrids were present in all sites where the species were syntopic (five of seven sites), suggesting that hybridisation is constrained primarily by a lack of opportunity. Within these sites, the median rate of hybridisation was 31.8% (range: 5.3–100%). Based on the likely extent of syntopy, hybridisation is plausible across more than 70% of the geographic range of L. booroolongensis, with potentially negative consequences for the species' persistence. Concerningly, only 42% of hybrids were correctly identified by morphology. Our results emphasise the need for genetic data to accurately distinguish hybrids and suggest that hybridisation could be occurring undetected between many related species, representing a potentially insidious threat to threatened and range‐restricted species. Conservation policies will need to consider the possibility of hybridisation and evaluate its consequences to appropriately manage and prevent further declines of threatened species.

ABSTRACTThe tropical Andes face unprecedented warming and shifting precipitation patterns due to climate change and land‐use alteration, challenging the future of Andean forests. During the Quaternary, many Andean trees responded to climate change through upslope migrations but, while there is evidence of such ongoing migrations in many species, they are at rates far below what is needed to remain in equilibrium with the current climate. Similarly, given the number of generations required for adaptation and the long lifespans of many tropical trees, it is unlikely that most species will be able to adapt fast enough. This synthesis explores the role of migration‐induced secondary contact and hybridisation as potential mechanisms for accelerating the adaptive response of Andean forests. Hybridisation, historically underappreciated in tropical trees, is increasingly recognised as an important driver of speciation and ecological diversity. It may facilitate gene flow and introgression, providing novel genetic combinations that enhance species resilience to climate change. This process can generate new allelic diversity, allowing species to adapt more rapidly than through mutation or selection on standing variation alone. However, hybridisation can also lead to negative outcomes like genetic swamping and outbreeding depression. Conservation strategies should consider the potential benefits and risks of hybridisation in maintaining biodiversity under changing environmental conditions. As habitat fragmentation and deforestation exacerbate the challenges faced by these forests, preserving habitat connectivity will be crucial to facilitate migration and gene flow, potentially aiding the survival of many Andean tree species in the Anthropocene.

Surviving the extinction vortex? Discovering remnant stands of Senecio hercynicus (Compositae, Senecioneae) evading genetic swamping by its congener S. ovatus in the Bavarian and Bohemian Forest region

Abstract The accumulation of genetic differences through time can lead to reproductive isolation between populations and the origin of new species. However, hybridization between emerging species can occur at any point before isolation is complete. The evolutionary consequences of this hybridization may vary depending on when it occurred. If hybridization occurred later during the process, when ecological and genetic differences have accumulated between diverging lineages, low hybrid fitness can result in selection against gene flow. If hybridization occurred earlier, when barriers present were too weak to limit introgression, then hybridization can lead to genetic swamping. Alternatively, adaptive introgression can occur at any point during speciation. Thus, by understanding the history and genomic consequences of hybridization at different points along the speciation continuum, we can begin to understand how variation present within populations translates to divergence between species. Here, we identified the genomic signals of introgressive hybridization at different points during the divergence of two monkeyflower taxa endemic to the Channel Islands of California. We found that both ancient and recent introgression have shaped their genomes, but the impacts of selection on this foreign material varied. There was no signal of selection against ancient introgression, but we did find strong evidence for selection against recent introgression, potentially because there are more reproductive barriers in place now, reducing fitness in recent hybrids. Thus, this study reveals that hybridization can occur at multiple points throughout the divergence history of a radiation, but the processes shaping genome wide levels of introgression can change over time.

The red-legged partridge (Alectoris rufa) is a popular game bird species that is in decline in several regions of southwestern Europe. The introduction of farm-reared individuals of a distinct genetic make-up in hunting reserves can result in genetic swamping of wild populations. Here we present a de novo genome assembly for the red-legged partridge based on long-read sequencing technology. The assembled genome size is 1.14 Gb, with scaffold N50 of 37.6 Mb and contig N50 of 29.5 Mb. Our genome is highly contiguous and contains 97.06% of complete avian core genes. Overall, the quality of this genome assembly is equivalent to those available for other close relatives such as the Japanese quail or the chicken. This genome assembly will contribute to the understanding of genetic dynamics of wild populations of red-legged partridges with releases of farm-reared reinforcements and to appropriate management decisions of such populations.

Strong gene flow from outcrossing relatives tends to blur species boundaries, while divergent ecological selection can counteract gene flow. To better understand how these two forces affect the maintenance of species boundaries, we focused on a species complex including a rare species, maple-leaf oak (Quercus acerifolia), which is found in only four disjunct ridges in Arkansas. Its limited range and geographic proximity to co-occurring close relatives create the possibility for genetic swamping. In this study, we gathered genome-wide single nucleotide polymorphisms (SNPs) using restriction-site-associated DNA sequencing (RADseq) from 190 samples of Q. acerifolia and three of its close relatives, Q. shumardii, Q. buckleyi, and Q. rubra. We found that Q. shumardii and Q. acerifolia are reciprocally monophyletic with low support, suggesting incomplete lineage sorting, introgression between Q. shumardii and Q. acerifolia, or both. Analyses that model allele distributions demonstrate that admixture contributes strongly to this pattern. Populations of Q. acerifolia experience gene flow from Q. shumardii and Q. rubra, but we found evidence that divergent selection is likely maintaining species boundaries: 1) ex situ collections of Q. acerifolia have a higher proportion of hybrids compared to the mature trees of the wild populations, suggesting ecological selection against hybrids at the seed/seedling stage; 2) ecological traits co-vary with genomic composition; and 3) Q. acerifolia shows genetic differentiation at loci hypothesized to influence tolerance of radiation, drought, and high temperature. Our findings strongly suggest that in maple-leaf oak, selection results in higher divergence at regions of the genome despite gene flow from close relatives.

Abstract Understanding the genomic composition of endangered species across its populations is important for conservation and management. Betula microphylla, an endangered species in Northwest China, grows in close proximity to B. tianshanica and B. pendula. However, whether populations of B. microphylla are genetically distinct or introgressed from B. tianshanica and B. pendula remains less clear. Here, we included restriction-site associated DNA (RAD) data for 135 individuals of B. microphylla, B. tianshanica, and B. pendula with RAD data of 87 individuals generated in this study. PCA results identify three genetic clusters, corresponding to B. pendula, B. tianshanica, and B. microphylla. ADMIXTURE analyses show two admixed populations of B. microphylla from B. tianshanica and one admixed population from B. pendula. ABBA-BABA test indicates that the genetic admixture in B. microphylla reflects significant signals of introgression from B. tianshanica and B. pendula. Furthermore, we identified 378 functional genes within the introgressed regions with eight genes related to environmental stress. Conservation strategies to protect genetically distinct populations of B. microphylla from genetic swamping by B. pendula need to be implemented. In addition, ex situ conservation of B. microphylla and conservation efforts towards B. tianshanica should be taken into consideration as the two may represent sister taxa or different subspecies.

Binturong (Arctictis binturong) is a threatened carnivore that inhabits the forests of South and Southeast Asia. Despite its wide range, binturong is relatively scarce across its habitat distribution and is currently under the threat of poaching and illegal trade. Captive breeding has unfortunately been conducted rather haphazardly with a lack of origin record maintained, implicating potential risks to the management such as inbreeding or genetic swamping. This study thus aims to characterise the phylogenetic relationship of Indonesian binturong within the context of Southeast Asian binturong and further probe the distinctness of lineages originating from Java, Sumatra, Indonesian Borneo, and Bangka using Cytochrome B (CytB) and Cytochrome C Oxidase Subunit 1 (CO1). Genetic distance, phylogram topology, and haplotype analysis of both encoding genes further corroborate the distinctness of Java, Borneo, and Bangka binturong from other binturong from Indochinese regions such as India, Laos, and Myanmar. Search for prospective single nucleotide polymorphism markers to discriminate island lineages consistently found that each Java, Bangka, and Bornean binturong be distinct from each other and other lineages, especially when assessed using haplotype-based clustering. Assigning binturong originated from Sumatra is nonetheless more complicated, suggesting the possibility. Our findings substantiated the much-needed systematic research of Southeast Asian binturong as ex-situ insurance population management grows in Indonesia and other parts of the world to protect the diversity of binturong lineages and their corresponding unique evolutionary history.

Australian blue mussels (Mytilus spp.) are an increasingly important sustainable product of the Australian aquaculture industry. Although important for commercial fisheries, aquaculture may have adverse environmental and ecological impacts. This study assessed the impact of standard hatchery-imposed selection practices on the genetic diversity of farmed blue mussels. Using microsatellite markers, relatedness and genetic structure analyses showed that hatchery-reared larvae have high levels of genetic diversity without a significant decline as they move through the hatchery rearing process. Selection and/or genetic drift does appear to be operating during the hatchery rearing process, however, evidenced by an increase in relatedness among larvae over time. Significant shifts in allele frequency as well as genetic clusters provides further evidence that selection is acting on larvae due to the selection practice applied at the hatchery. Comparison of the level of genetic diversity and genetic differentiation of adults from wild and farmed populations provided no evidence that farmed mussels have lower diversity, or that they are genetically swamping local natural populations. The data suggest that careful design and implementation of mussel breeding programs can maintain high genetic diversity among larvae that does not lead to genetic swamping of natural mussel populations in the surrounding area.

Abstract Rice paddies are wetland ecosystems recognized as important habitats for many organisms; however, the hybridization‐related extinction risk of native plant species has not been investigated in this system so far. Eclipta L. (Compositae) is a common paddy weed in Japan; however, its genetic composition might be altered due to the hybridization between the native E. thermalis and the closely related exotic E. alba. We examined Eclipta's genetic composition using 12 microsatellite markers (612 samples collected from 109 populations) and found (i) widespread geographical distribution of E. alba in Japan, (ii) hybridization with E. thermalis, and a large number of later‐generation hybrids, and (iii) widely varying situations among regions and populations. Eclipta alba appears to have invaded an open niche in northern Japan but has not yet reached southern Japan. Both E. alba and E. thermalis were found in central Japan; however, the latter had become rare due to hybridization‐mediated processes such as competition, and demographic and genetic swamping. Notably, endogenous and exogenous selection plays an important role in the invasion of E. alba, but to varying degrees among different areas. In summary, considering the genetic variability in E. thermalis, the genetic cluster of mainland Japan is in a highly critical situation due to the invasion of E. alba.

The European wildcat population in Scotland is considered critically endangered as a result of hybridization with introduced domestic cats,1,2 though the time frame over which this gene flow has taken place is unknown. Here, using genome data from modern, museum, and ancient samples, we reconstructed the trajectory and dated the decline of the local wildcat population from viable to severely hybridized. We demonstrate that although domestic cats have been present in Britain for over 2,000 years,3 the onset of hybridization was only within the last 70 years. Our analyses reveal that the domestic ancestry present in modern wildcats is markedly over-represented in many parts of the genome, including the major histocompatibility complex (MHC). We hypothesize that introgression provides wildcats with protection against diseases harbored and introduced by domestic cats, and that this selection contributes to maladaptive genetic swamping through linkage drag. Using the case of the Scottish wildcat, we demonstrate the importance of local ancestry estimates to both understand the impacts of hybridization in wild populations and support conservation efforts to mitigate the consequences of anthropogenic and environmental change.

Abstract The Argentinian Ministry of Environment has approved the translocation of 45 guanacos from Southern Patagonia to the Pampas region, a distance of 1500 km, as the initial phase toward future translocations into a National Park located in the Chaco region, another 1600 km further North. This decision raises concerns about the technical and ethical aspects of the translocation. Firstly, there is a lack of proper evaluation and scientific evidence to support the need, opportunity, and feasibility of this translocation. The guanaco population is currently over one million and is increasing, and genetic differences exist among local populations. The translocation could produce anthropogenic‐driven admixed populations, leading to genetic swamping and disrupting evolutionary processes. Second, there are ethical conflicts around managing wild species populations that prioritize private objectives and disregard local, publicly funded science. Rewilding projects require a deep understanding of interacting ecosystem processes, and of the socio‐economic context. This management decision violates guiding principles for rewilding and should have followed proper scientific evaluation and transparent local consultation.

Preserving natural genetic diversity and ecological function of wild species is a central goal in conservation biology. As such, anthropogenic hybridization is considered a threat to wild populations, as it can lead to changes in the genetic makeup of wild species and even to the extinction of wild genomes. In European wildcats, the genetic and ecological impacts of gene flow from domestic cats are mostly unknown at the species scale. However, in small and isolated populations, it is known to include genetic swamping of wild genomes. In this context, it is crucial to better understand the dynamics of hybridization across the species range, to inform and implement management measures that maintain the genetic diversity and integrity of the European wildcat. In the present paper, we aim to provide an overview of the current scientific understanding of anthropogenic hybridization in European wildcats, to clarify important aspects regarding the evaluation of hybridization given the available methodologies, and to propose guidelines for management and research priorities.

Societal Impact StatementHybridisation is an important evolutionary force in plants, but it can potentially lead to genetic swamping and extinction of one or both parental species. The threat of extinction is of particular concern if hybridisation occurs between native and introduced species, especially when the native is of national importance. The widespread occurrence of non‐native bluebells in the United Kingdom has raised concerns that the iconic native bluebell could be at risk due to extinction by hybridisation from introduced non‐native bluebells. This study determines the taxonomic identity of non‐natives and investigates the amount of hybridisation occurring in natural and semi‐natural UK bluebell populations.Summary The widespread occurrence of a non‐native bluebell taxon in the UK has raised concerns that the iconic native bluebell H. non‐scripta (Asparagaceae) could be at risk due to extinction by hybridisation from introduced non‐native congeners. Understanding the nature of this threat requires quantification of the extent of hybridisation between the native and non‐native taxa. An additional complication is taxonomic uncertainty regarding the identity of the non‐native bluebells in the United Kingdom that are colloquially referred to as the ‘Spanish’ bluebell (H. hispanica). We collected 501 bluebell samples from 56 populations in the United Kingdom (H. non‐scripta and non‐natives) and the Iberian Peninsula (H. hispanica). The samples were assayed for variation at 1871 nuclear and 17 plastid single nucleotide polymorphisms. Our genetic analyses demonstrated that non‐native bluebells in the United Kingdom are not H. hispanica but the hybrid between H. hispanica and H. non‐scripta. Moreover, they supported the hypothesis that Portugal is the country of origin of the first H. hispanica introductions to the United Kingdom. The frequency of hybrids was about 16%. Backcrosses between the (hybrid) non‐native bluebell and the native H. non‐scripta were primarily found in public parks. Of the sampled individuals for H. non‐scripta from natural habitats, only 2% showed evidence of introgression. Although hybridisation might be frequent in locations where non‐native bluebells have been introduced, we found no evidence of large‐scale introgression in natural H. non‐scripta populations. Therefore, our results do not support concerns of an ‘extinction by hybridisation’ scenario.