Crop-to-wild gene flow and its fitness consequences for a wild fruit tree: Towards a comprehensive conservation strategy of the wild apple in Europe

Lessons from Ethiopian coffee landscapes for global conservation in a post-wild world

The reality for conservation of biodiversity across our planet is that all ecosystems are modified by humans in some way or another. Thus, biodiversity conservation needs to be implemented in multifunctional landscapes. In this paper we use a fascinating coffee-dominated landscape in southwest Ethiopia as our lens to derive general lessons for biodiversity conservation in a post-wild world. Considering a hierarchy of scales from genes to multi-species interactions and social-ecological system contexts, we focus on (i) threats to the genetic diversity of crop wild relatives, (ii) the mechanisms behind trade-offs between biodiversity and agricultural yields, (iii) underexplored species interactions suppressing pest and disease levels, (iv) how the interactions of climate change and land-use change sometimes provide opportunities for restoration, and finally, (v) how to work closely with stakeholders to identify scenarios for sustainable development. The story on how the ecology and evolution of coffee within its indigenous distribution shape biodiversity conservation from genes to social-ecological systems can inspire us to view other landscapes with fresh eyes. The ubiquitous presence of human-nature interactions demands proactive, creative solutions to foster biodiversity conservation not only in remote protected areas but across entire landscapes inhabited by people.

Genomic evidence of genuine wild versus admixed olive populations evolving in the same natural environments in western Mediterranean Basin

Crop-to-wild gene flow is a mechanism process widely documented, both in plants and animals. This can have positive or negative impacts on the evolution of admixed populations in natural environments, yet the phenomenon is still misunderstood in long-lived woody species, contrary to short-lived crops. Wild olive Olea europaea L. occurs in the same eco-geographical range as domesticated olive, i.e. the Mediterranean Basin (MB). Moreover, it is an allogamous and anemophilous species whose seeds are disseminated by birds, i.e. factors that drive gene flow between crops and their wild relatives. Here we investigated the genetic structure of western MB wild olive populations in natural environments assuming a homogenous gene pool with limited impact of cultivated alleles, as previously suggested. We used a target sequencing method based on annotated genes from the Farga reference genome to analyze 27 western MB olive tree populations sampled in natural environments in France, Spain and Morocco. We also target sequenced cultivated olive tree accessions from the Worldwide Olive Germplasm Bank of Marrakech and Porquerolles and from an eastern MB wild olive tree population. We combined PCA, sNMF, pairwise FST and TreeMix and clearly identified genuine wild olive trees throughout their natural distribution range along a north-south gradient including, for the first time, in southern France. However, contrary to our assumption, we highlighted more admixed than genuine wild olive trees. Our results raise questions regarding the admixed population evolution pattern in this environment, which might be facilitated by crop-to-wild gene flow.

The East Asian wild apples, Malus baccata (L.) Borkh and Malus hupehensis (Pamp.) Rehder., are additional contributors to the genomes of cultivated European and Chinese varieties

The domestication process in long-lived plant perennials differs dramatically from that of annuals, with a huge amount of genetic exchange between crop and wild populations. Though apple is a major fruit crop grown worldwide, the contribution of wild apple species to the genetic makeup of the cultivated apple genome remains a topic of intense study. We used population genomics approaches to investigate the contributions of several wild apple species to European and Chinese rootstock and dessert genomes, with a focus on the extent of wild-crop gene flow. Population genetic structure inferences revealed that the East Asian wild apples, Malus baccata (L.) Borkh and M. hupehensis (Pamp.), form a single panmictic group, and that the European dessert and rootstock apples form a specific gene pool whereas the Chinese dessert and rootstock apples were a mixture of three wild gene pools, suggesting different evolutionary histories of European and Chinese apple varieties. Coalescent-based inferences and gene flow estimates indicated that M. baccata - M. hupehensis contributed to the genome of both European and Chinese cultivated apples through wild-to-crop introgressions, and not as an initial contributor as previously supposed. We also confirmed the contribution through wild-to-crop introgressions of Malus sylvestris Mill. to the cultivated apple genome. Apple tree domestication is therefore one example in woody perennials that involved gene flow from several wild species from multiple geographical areas. This study provides an example of a complex protracted process of domestication in long-lived plant perennials, and is a starting point for apple breeding programmes.

Demographic and reproductive impacts of hybridization unrelated to hybrid viability in a native plant

PREMISE

Introduced species can influence native congeners through production of hybrids and introgression, but impacts not involving viable hybrids, such as reduced conspecific offspring and increased asexual seed production, are rarely examined. Here we tested for these demographic and reproductive consequences of hybridization between introduced, domesticated apple (Malus domestica) and native crabapple (M. coronaria) in southern Canada.

METHODS

We applied four pollination treatments (open, M. coronaria, M. domestica, open + M. coronaria) to focal M. coronaria trees across multiple years and assessed the number and reproductive origins of resulting seeds (hybrid or conspecific endosperm and, for each, sexual or asexual embryo) using flow cytometry.

RESULTS

In open-pollinated fruit, 27% of seeds had hybrid endosperm; 52% of embryos were asexual. The number of conspecific embryos (sexual or asexual) per fruit did not decline significantly with increasing hybridization, indicating no seed discounting, but hand pollinations using only domestic apple or crabapple pollen reduced the number of conspecific embryos significantly. Hybridization was not associated with a change in percentage asexual embryos, overall, but there was an increase in asexual embryos in tetraploid seeds, the maternal and most common offspring ploidy.

CONCLUSIONS

We conclude that hybridization can influence native Malus in ways beyond the production of viable hybrids, with significant implications for population dynamics and genetic structure.

Ecological and evolutionary drivers of phenotypic and genetic variation in the European crabapple [Malus sylvestris (L.) Mill.], a wild relative of the cultivated apple

BACKGROUND AND AIMS

Studying the relationship between phenotypic and genetic variation in populations distributed across environmental gradients can help us to understand the ecological and evolutionary processes involved in population divergence. We investigated the patterns of genetic and phenotypic diversity in the European crabapple, Malus sylvestris, a wild relative of the cultivated apple (Malus domestica) that occurs naturally across Europe in areas subjected to different climatic conditions, to test for divergence among populations.

METHODS

Growth rates and traits related to carbon uptake in seedlings collected across Europe were measured in controlled conditions and associated with the genetic status of the seedlings, which was assessed using 13 microsatellite loci and the Bayesian clustering method. Isolation-by-distance, isolation-by-climate and isolation-by-adaptation patterns, which can explain genetic and phenotypic differentiation among M. sylvestris populations, were also tested.

KEY RESULTS

A total of 11.6 % of seedlings were introgressed by M. domestica, indicating that crop-wild gene flow is ongoing in Europe. The remaining seedlings (88.4 %) belonged to seven M. sylvestris populations. Significant phenotypic trait variation among M. sylvestris populations was observed. We did not observe significant isolation by adaptation; however, the significant association between genetic variation and the climate during the Last Glacial Maximum suggests that there has been local adaptation of M. sylvestris to past climates.

CONCLUSIONS

This study provides insight into the phenotypic and genetic differentiation among populations of a wild relative of the cultivated apple. This might help us to make better use of its diversity and provide options for mitigating the impact of climate change on the cultivated apple through breeding.

The genome sequence of the European crab apple, Malus sylvestris (L.) Mill., 1768

We present a genome assembly from an individual Malus sylvestris (the European or 'wild' crab apple; Streptophyta; Magnoliopsida; Rosales; Rosaceae). The genome sequence is 642 megabases in span. Most of the assembly (99.98%) is scaffolded into 17 chromosomal pseudomolecules. The mitochondrial and chloroplast genomes were also assembled, with respective lengths of 396.9 kilobases and 160.0 kilobases.

Evidence of an additional centre of apple domestication in Iran, with contributions from the Caucasian crab apple Malus orientalis Uglitzk. to the cultivated apple gene pool

Divergence processes in crop-wild fruit tree complexes in pivotal regions for plant domestication such as the Caucasus and Iran remain little studied. We investigated anthropogenic and natural divergence processes in apples in these regions using 26 microsatellite markers amplified in 550 wild and cultivated samples. We found two genetically distinct cultivated populations in Iran that are differentiated from Malus domestica, the standard cultivated apple worldwide. Coalescent-based inferences showed that these two cultivated populations originated from specific domestication events of Malus orientalis in Iran. We found evidence of substantial wild-crop and crop-crop gene flow in the Caucasus and Iran, as has been described in apple in Europe. In addition, we identified seven genetically differentiated populations of wild apple (M. orientalis), not introgressed by the cultivated apple. Niche modelling combined with genetic diversity estimates indicated that these wild populations likely resulted from range changes during past glaciations. This study identifies Iran as a key region in the domestication of apple and M. orientalis as an additional contributor to the cultivated apple gene pool. Domestication of the apple tree therefore involved multiple origins of domestication in different geographic locations and substantial crop-wild hybridization, as found in other fruit trees. This study also highlights the impact of climate change on the natural divergence of a wild fruit tree and provides a starting point for apple conservation and breeding programmes in the Caucasus and Iran.

Fitness and Ecological Risk of Hybrid Progenies of Wild and Herbicide-Tolerant Soybeans With EPSPS Gene

Exogenous genes of transgenic crops are usually transferred to their wild-type relatives through pollen-mediated gene flow, which may change the ecological fitness and ability to invade wild populations, resulting in the weeding of wild plants and other unpredictable environmental impacts. In this study, the F₁ generation of herbicide-resistant soybeans and wild soybeans was obtained by artificial pollination, F₂ generation seeds were obtained by self-crossing, and the fitness of the parents and their F₁ and F₂ generations were tested. The foreign protein EPSPS was expressed normally in the hybrid between transgenic and wild soybeans; however, the protein expression was significantly lower than that in transgenic soybeans. The fitness of the F₁ hybrid between transgenic and wild soybeans was significantly lower than that of its parent. Compared with those of the wild soybeans, the F₂ generation soybeans improved in some fitness indices, while the emergence rate, pollen germination rate, and number of full seeds per pod, pods per plant, and full seeds per plant did not significantly differ. The aboveground biomass and 100-seed weight of the F₂ generation were higher than those of wild soybeans. Fitness among the F₂-negative plants, homozygous, and heterozygous positive plants did not significantly vary. Improved fitness and presence of foreign genes in the F₂ soybean were not significantly correlated. As the F₂ generation of transgenic and wild soybeans had no fitness cost and the flowering stage were overlapped, the foreign gene might still spread in the wild soybean population.

Loquat (Eriobotrya japonica (Thunb.) Lindl) population genomics suggests a two-staged domestication and identifies genes showing convergence/parallel selective sweeps with apple or peach

Crop domestication and evolution represent key fields of plant and genetics research. Here, we re-sequenced and analyzed whole genome data from 51 wild accessions and 53 representative cultivars of Eriobotrya japonica, an important semi-subtropical fruit crop. Population genomics analysis suggested that modern cultivated E. japonica experienced a two-staged domestication fitting the "marginality model," being initially domesticated in west-northern Hubei province from a mono-phylogenetic wild progenitor, then refined mainly in Jiangsu, Zhejiang and Fujian provinces of China. Cultivated E. japonica has experienced little reduction in genome-wide nucleotide polymorphism compared with wild forms. Genes responsible for sugar biosynthesis were enriched in regions harboring putative selective sweeps. An approach based on co-clustering into gene families and evaluating chromosome colinearity of orthologous and paralogous genes was used to identify convergent/parallel selective sweeps among different crops. Specifically, more than one hundred of orthologs and paralogs undergoing selective sweeps were identified between loquat, apple and peach, among which 14 encoded "UDP glycosyltransferase 1." In sum, the study not only provided valuable information for breeding of E. japonica, but also enriched knowledge of crop domestication.

Genetic structure of Malus sylvestris and potential link with preference/performance by the rosy apple aphid pest Dysaphis plantaginea

The European crabapple Malus sylvestris, a crop wild relative of Malus domestica, is a major contributor to the cultivated apple genome and represents a potential source of interesting alleles or genes, particularly pest resistance traits. An original approach was used to explore the trophic interaction between M. sylvestris populations and its pest, the rosy apple aphid (Dysaphis plantaginea). Using 13 microsatellite markers, population genetic structure and level of crop-to-wild introgressions were inferred between M. sylvestris seedlings from three sites in Europe (Denmark, France, Romania), and M. domestica seedlings. Genetically characterized plants were also used to analyze aphid feeding behavior and fitness parameters. First, aphids submitted to two genetically close M. sylvestris populations (the Danish and French) exhibited similar behavioral parameters, suggesting similar patterns of resistance in these host plants. Second, the Romanian M. sylvestris population was most closely genetically related to M. domestica. Although the two plant genetic backgrounds were significantly differentiated, they showed comparable levels of sensitivity to D. plantaginea infestation. Third, aphid fitness parameters were not significantly impacted by the host plant's genetic background. Finally, crop-to-wild introgression seemed to significantly drive resistance to D. plantaginea independent of host plant population genetic structure, with hybrids being less suitable hosts.

Application of genome-wide insertion/deletion markers on genetic structure analysis and identity signature of Malus accessions

BACKGROUND

Apple (Malus ssp.), one of the most important temperate fruit crops, has a long cultivation history and is economically important. To identify the genetic relationships among the apple germplasm accessions, whole-genome structural variants identified between M. domestica cultivars 'Jonathan' and 'Golden Delicious' were used.

RESULTS

A total of 25,924 insertions and deletions (InDels) were obtained, from which 102 InDel markers were developed. Using the InDel markers, we found that 942 (75.3%) of the 1251 Malus accessions from 35 species exhibited a unique identity signature due to their distinct genotype combinations. The 102 InDel markers could distinguish 16.7-71.4% of the 331 bud sports derived from 'Fuji', 'Red Delicious', 'Gala', 'Golden Delicious', and other cultivars. Five distinct genetic patterns were found in 1002 diploid accessions based on 78 bi-allele InDel markers. Genetic structure analysis indicated that M. domestica showed higher genetic diversity than the other species. Malus underwent a relatively high level of wild-to-crop or crop-to-wild gene flow. M. sieversii was closely related to both M. domestica and cultivated Chinese cultivars.

CONCLUSIONS

The identity signatures of Malus accessions can be used to determine distinctness, uniformity, and stability. The results of this study may also provide better insight into the genetic relationships among Malus species.

Threat to Asian wild apple trees posed by gene flow from domesticated apple trees and their "pestified" pathogens

Secondary contact between crops and their wild relatives poses a threat to wild species, not only through gene flow between plants, but also through the dispersal of crop pathogens and genetic exchanges involving these pathogens, particularly those that have become more virulent by indirect selection on resistant crops, a phenomenon known as "pestification." Joint analyses of wild and domesticated hosts and their pathogens are essential to address this issue, but such analyses remain rare. We used population genetics approaches, demographic inference and pathogenicity tests on host-pathogen pairs of wild or domesticated apple trees from Central Asia and their main fungal pathogen, Venturia inaequalis, which itself has differentiated agricultural and wild-type populations. We confirmed the occurrence of gene flow from cultivated (Malus domestica) to wild (Malus sieversii) apple trees in Asian forests, potentially threatening the persistence of Asian wild apple trees. Pathogenicity tests demonstrated the pestification of V. inaequalis, the agricultural-type population being more virulent on both wild and domesticated trees. Single nucleotide polymorphism (SNP) markers and the demographic modelling of pathogen populations revealed hybridization following secondary contact between agricultural and wild-type fungal populations, and dispersal of the agricultural-type pathogen population in wild forests, increasing the threat of disease in the wild apple species. We detected an SNP potentially involved in pathogen pestification, generating an early stop codon in a gene encoding a small secreted protein in the agricultural-type fungal population. Our findings, based on joint analyses of paired host and pathogen data sets, highlight the threat posed by cultivating a crop near its centre of origin, in terms of pestified pathogen invasions in wild plant populations and introgression in the wild-type pathogen population.

Genetic integrity is still maintained in natural populations of the indigenous wild apple species Malus sylvestris (Mill.) in Saxony as demonstrated with nuclear SSR and chloroplast DNA markers

Malus sylvestris (Mill.) is the only indigenous wild apple species in Central Europe. Agriculture, forestry, and urbanization increasingly endanger Malus sylvestris natural habitats. In addition, the risks of cross-hybridization associated with increase in the cultivation of the domesticated apple Malus × domestica (Borkh.) threaten the genetic integrity of M. sylvestris. The present study investigated the number of hybrids, genetic diversity, and genetic structure of 292 putative M. sylvestris that originate from five different natural M. sylvestris populations in Saxony, Germany. All samples were genetically analyzed using nine nuclear microsatellite markers (ncSSR) and four maternally inherited chloroplast markers (cpDNA) along with 56 apple cultivars commonly cultivated in Saxony. Eighty-seven percent of the wild apple accessions were identified as pure M. sylvestris. The cpDNA analysis showed six private haplotypes for M. sylvestris, whereas three haplotypes were present in M. sylvestris and M. × domestica. The analysis of molecular variance (AMOVA) resulted in a moderate (ncSSR) and great (cpDNA) variation among pure M. sylvestris and M. × domestica individuals indicating a low gene flow between both species. The genetic diversity within the pure M. sylvestris populations was high with a weak genetic structure between the M. sylvestris populations indicating an unrestricted genetic exchange between these M. sylvestris populations. The clear distinguishing of M. sylvestris and M. ×domestica confirms our expectation of the existence of pure M. sylvestris accessions in this area and supports the argument for the implementation of preservation measures to protect the M. sylvestris populations in Saxony.

Drought tolerance of wild versus cultivated tree species of almond and plum in the field

Trees of the genus Prunus produce some of the most widely consumed fruits globally. The combination of climate change-related warming and increased drought stress, scarcity of freshwater resources for irrigation, and increasing demands due to population growth creates a need for increased drought tolerance in these tree species. Recently, we have shown in the field that a native wild pear species performs better under drought than two cultivated pear species. Here, a comparative field study was conducted in Israel to investigate traits associated with drought tolerance in almond (cultivated Prunus dulcis (Mill.) D. A. Webb vs wild Prunus ramonensis Danin) and plum (cultivated Prunus domestica L. vs wild Prunus ursina Kotschy). Measurements of xylem embolism and shoot and root carbon reserves were done along a year, including seasonal drought in the wild and a 35-day drought experiment in the orchards. Synchronous measurements of native xylem embolism and shoot water potential showed that cultivated and wild almond trees lost ~50% of hydraulic conductivity at -2.3 and -3.2 MPa, respectively. Micro-CT images confirmed the higher embolism ratio in cultivated versus wild almond, whereas the two plum species were similar. Dynamics of tissue concentrations of nonstructural carbohydrates were mostly similar across species, with higher levels in cultivated versus wild plum. Our results indicate an advantage for the wild almond over its cultivated relative in terms of xylem resistance to embolism, a major risk factor for trees under drought stress. This result is in line with our previous experiment on pear species. However, the opposite trends observed among the studied plum species mean that these trends cannot be generalized. It is possible that the potential for superior drought tolerance in wild tree species, relative to their cultivated relatives, is limited to wild species from dry and hot habitats.

Intercrops can mitigate pollen-mediated gene flow from transgenic cotton while simultaneously reducing pest densities

Genetically modified (GM) cotton, engineered to express Bt toxins that protect it from insect damage, has become the most successfully commercialized GM crop in China since its authorization in 1997. In light of the potential ecological consequences of pollen-mediated gene flow (PGF) from GM plants, a two year field trial was conducted to test the effects on PGF of sunflower, Helianthus annuus, buckwheat, Fagopyrum esculentum, and soybean, Glycine max, as intercrops in non-GM cotton fields during 2017 and 2018. DNA tests for hybridized seed were used to estimate rates of PGF in intercrop treatments. PGF was the lowest in cotton intercropped with either buckwheat or sunflower, likely due to the trapping of pollen in these flowers, and/or the diversion of pollinators away from cotton flowers. PGF declined as an exponential function of distance from the GM cotton; Y = -lnx was the model of best fit for estimating pollen dispersal potential. A sunflower intercrop reduced the peak abundance of Aphis gossypii, (Hemiptera: Aphididae), Bemisia tabaci (Hemiptera: Aleyrodidae), and Nysius ericae (Hemiptera: Lygaeidae) on cotton plants, although densities of Tetranychus cinnabarinus (Acari: Tetranychidae), were increased. A buckwheat intercrop had very similar effects on these pests, likely due to attraction of their natural enemies. We conclude that sunflower and buckwheat are suitable intercrops for reducing PGF from GM cotton, and may be useful for reducing PGF from other insect-pollinated GM crops in the agricultural landscape, while simultaneously contributing to control of specific pests. This is the first demonstration, to our knowledge, that intercrops can be used to reduce PGF from transgenic plants.

A Multifaceted Overview of Apple Tree Domestication

The apple is an iconic tree and a major fruit crop worldwide. It is also a model species for the study of the evolutionary processes and genomic basis underlying the domestication of clonally propagated perennial crops. Multidisciplinary approaches from across Eurasia have documented the pace and process of cultivation of this remarkable crop. While population genetics and genomics have revealed the overall domestication history of apple across Eurasia, untangling the evolutionary processes involved, archeobotany has helped to document the transition from gathering and using apples to the practice of cultivation. Further studies integrating archeogenetic and archeogenomic approaches will bring new insights about key traits involved in apple domestication. Such knowledge has potential to boost innovation in present-day apple breeding.

Origins of the Apple: The Role of Megafaunal Mutualism in the Domestication of Malus and Rosaceous Trees

The apple (Malus domestica [Suckow] Borkh.) is one of the most economically and culturally significant fruits in the world today, and it is grown in all temperate zones. With over a thousand landraces recognized, the modern apple provides a unique case study for understanding plant evolution under human cultivation. Recent genomic and archaeobotanical studies have illuminated parts of the process of domestication in the Rosaceae family. Interestingly, these data seem to suggest that rosaceous arboreal crops did not follow the same pathway toward domestication as other domesticated, especially annual, plants. Unlike in cereal crops, tree domestication appears to have been rapid and driven by hybridization. Apple domestication also calls into question the concept of centers of domestication and human intentionality. Studies of arboreal domestication also illustrate the importance of fully understanding the seed dispersal processes in the wild progenitors when studying crop origins. Large fruits in Rosaceae evolved as a seed-dispersal adaptation recruiting megafaunal mammals of the late Miocene. Genetic studies illustrate that the increase in fruit size and changes in morphology during evolution in the wild resulted from hybridization events and were selected for by large seed dispersers. Humans over the past three millennia have fixed larger-fruiting hybrids through grafting and cloning. Ultimately, the process of evolution under human cultivation parallels the natural evolution of larger fruits in the clade as an adaptive strategy, which resulted in mutualism with large mammalian seed dispersers (disperser recruitment).

Apple whole genome sequences: recent advances and new prospects

In 2010, a major scientific milestone was achieved for tree fruit crops: publication of the first draft whole genome sequence (WGS) for apple (Malus domestica). This WGS, v1.0, was valuable as the initial reference for sequence information, fine mapping, gene discovery, variant discovery, and tool development. A new, high quality apple WGS, GDDH13 v1.1, was released in 2017 and now serves as the reference genome for apple. Over the past decade, these apple WGSs have had an enormous impact on our understanding of apple biological functioning, trait physiology and inheritance, leading to practical applications for improving this highly valued crop. Causal gene identities for phenotypes of fundamental and practical interest can today be discovered much more rapidly. Genome-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and pedigrees. High-density genetic maps are constructed efficiently and quantitative trait loci for valuable traits are readily associated with positional candidate genes and/or converted into diagnostic tests for breeders. We understand the species, geographical, and genomic origins of domesticated apple more precisely, as well as its relationship to wild relatives. The WGS has turbo-charged application of these classical research steps to crop improvement and drives innovative methods to achieve more durable, environmentally sound, productive, and consumer-desirable apple production. This review includes examples of basic and practical breakthroughs and challenges in using the apple WGSs. Recommendations for "what's next" focus on necessary upgrades to the genome sequence data pool, as well as for use of the data, to reach new frontiers in genomics-based scientific understanding of apple.

Extensive hybridization following a large escape of domesticated Atlantic salmon in the Northwest Atlantic

Domestication is rife with episodes of interbreeding between cultured and wild populations, potentially challenging adaptive variation in the wild. In Atlantic salmon, Salmo salar, the number of domesticated individuals far exceeds wild individuals, and escape events occur regularly, yet evidence of the magnitude and geographic scale of interbreeding resulting from individual escape events is lacking. We screened juvenile Atlantic salmon using 95 single nucleotide polymorphisms following a single, large aquaculture escape in the Northwest Atlantic and report the landscape-scale detection of hybrid and feral salmon (27.1%, 17/18 rivers). Hybrids were reproductively viable, and observed at higher frequency in smaller wild populations. Repeated annual sampling of this cohort revealed decreases in the presence of hybrid and feral offspring over time. These results link previous observations of escaped salmon in rivers with reports of population genetic change, and demonstrate the potential negative consequences of escapes from net-pen aquaculture on wild populations.