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1.
  • De Wit, Pierre, 1978, et al. (author)
  • Spatial genetic structure in a crustacean herbivore highlights the need for local considerations in Baltic Sea biodiversity management
  • 2020
  • In: Evolutionary Applications. - : Wiley. - 1752-4563 .- 1752-4571. ; 13:5, s. 974-990
  • Journal article (peer-reviewed)abstract
    • Incorporating species' eco-evolutionary responses to human-caused disturbances remains a challenge in marine management efforts. A prerequisite is knowledge of geographic structure and scale of genetic diversity and connectivity—the so-called seascape genetic patterns. The Baltic Sea is an excellent model system for studies linking seascape genetics with effects of anthropogenic stress. However, seascape genetic patterns in this area are only described for a few species and are completely unknown for invertebrate herbivores, which constitute a critical part of the ecosystem. This information is crucial for sustainable management, particularly under future scenarios of rapid environmental change. Here, we investigate the population genetic structure among 31 locations throughout the Baltic Sea, of which 45% were located in marine protected areas, in one of the most important herbivores of this region, the isopod crustacean Idotea balthica, using an array of 33,774 genome-wide SNP markers derived from 2b-RAD sequencing. In addition, we generate a biophysical connectivity matrix for I. balthica from a combination of oceanographic current models and estimated life history traits. We find population structure on scales of hundreds of kilometers across the Baltic Sea, where genomic patterns in most cases closely match biophysical connectivity, indicating passive transport with oceanographic currents as an important mean of dispersal in this species. We also find a reduced genetic diversity in terms of heterozygosity along the main salinity gradient of the Baltic Sea, suggesting periods of low population size. Our results provide crucial information for the management of a key ecosystem species under expected changes in temperature and salinity following global climate change in a marine coastal area. © 2019 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.
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2.
  • Ellegaard, Marianne, et al. (author)
  • Time capsules in natural sediment archives-Tracking phytoplankton population genetic diversity and adaptation over multidecadal timescales in the face of environmental change
  • 2018
  • In: Evolutionary Applications. - : Wiley. - 1752-4563 .- 1752-4571. ; 11:1, s. 11-16
  • Journal article (peer-reviewed)abstract
    • © 2017 John Wiley & Sons Ltd. Undisturbed records of resting stages produced in the past and stored in coastal sediments are very valuable to science, because they may provide unique insights into past evolutionary and ecological trajectories. Within marine phytoplankton, multidecadal time series of monoclonal strains germinated from resting stages have been established for diatoms (Skeletonema marinoi) and dinoflagellates (Pentapharsodinium dalei), spanning ca. a century. Phenotypic and genotypic analyses of these time series have revealed effects of past environmental changes on population genetic structure. Future perspectives include direct comparisons of phenotypes and genotypic data of populations, for example, by genomewide assays that can correlate phenotypic trends with genotypes and allele frequencies in temporally separated strains. Besides their usefulness as historical records, "seed" banks of phytoplankton resting stages also have the potential to provide an inoculum that influences present populations through "dispersal from the past" (the storage effect) and are important for adaptation to future environments through their standing genetic diversity.
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3.
  • Jahnke, Marlene, et al. (author)
  • Seascape genetics and biophysical connectivity modelling support conservation of the seagrass Zostera marina in the Skagerrak-Kattegat region of the eastern North Sea
  • 2018
  • In: Evolutionary Applications. - : Wiley. - 1752-4563 .- 1752-4571. ; 11:5, s. 645-661
  • Journal article (peer-reviewed)abstract
    • Maintaining and enabling evolutionary processes within meta-populations are critical to resistance, resilience and adaptive potential. Knowledge about which populations act as sources or sinks, and the direction of gene flow, can help to focus conservation efforts more effectively and forecast how populations might respond to future anthropogenic and environmental pressures. As a foundation species and habitat provider, Zostera marina (eelgrass) is of critical importance to ecosystem functions including fisheries. Here, we estimate connectivity of Z.marina in the Skagerrak-Kattegat region of the North Sea based on genetic and biophysical modelling. Genetic diversity, population structure and migration were analysed at 23 locations using 20 microsatellite loci and a suite of analytical approaches. Oceanographic connectivity was analysed using Lagrangian dispersal simulations based on contemporary and historical distribution data dating back to the late 19th century. Population clusters, barriers and networks of connectivity were found to be very similar based on either genetic or oceanographic analyses. A single-generation model of dispersal was not realistic, whereas multigeneration models that integrate stepping-stone dispersal and extant and historic distribution data were able to capture and model genetic connectivity patterns well. Passive rafting of flowering shoots along oceanographic currents is the main driver of gene flow at this spatial-temporal scale, and extant genetic connectivity strongly reflects the ghost of dispersal past sensu Benzie, . The identification of distinct clusters, connectivity hotspots and areas where connectivity has become limited over the last century is critical information for spatial management, conservation and restoration of eelgrass.
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4.
  • Pienta, Kenneth J., et al. (author)
  • Poly-aneuploid cancer cells promote evolvability, generating lethal cancer
  • 2020
  • In: Evolutionary Applications. - : Wiley. - 1752-4563 .- 1752-4571. ; 13:7, s. 1626-1634
  • Journal article (peer-reviewed)abstract
    • Cancer cells utilize the forces of natural selection to evolve evolvability allowing a constant supply of heritable variation that permits a cancer species to evolutionary track changing hazards and opportunities. Over time, the dynamic tumor ecosystem is exposed to extreme, catastrophic changes in the conditions of the tumor—natural (e.g., loss of blood supply) or imposed (therapeutic). While the nature of these catastrophes may be varied or unique, their common property may be to doom the current cancer phenotype unless it evolves rapidly. Poly-aneuploid cancer cells (PACCs) may serve as efficient sources of heritable variation that allows cancer cells to evolve rapidly, speciate, evolutionarily track their environment, and most critically for patient outcome and survival, permit evolutionary rescue, therapy resistance, and metastasis. As a conditional evolutionary strategy, they permit the cancer cells to accelerate evolution under stress and slow down the generation of heritable variation when conditions are more favorable or when the cancer cells are closer to an evolutionary optimum. We hypothesize that they play a critical and outsized role in lethality by their increased capacity for invasion and motility, for enduring novel and stressful environments, and for generating heritable variation that can be dispensed to their 2N+ aneuploid progeny that make up the bulk of cancer cells within a tumor, providing population rescue in response to therapeutic stress. Targeting PACCs is essential to cancer therapy and patient cure—without the eradication of the resilient PACCs, cancer will recur in treated patients.
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5.
  • Watson, Hannah, et al. (author)
  • Urbanization is associated with modifications in DNA methylation in a small passerine bird
  • 2021
  • In: Evolutionary Applications. - : Wiley. - 1752-4563 .- 1752-4571. ; 14:1, s. 85-98
  • Journal article (peer-reviewed)abstract
    • Urbanization represents a fierce driver of phenotypic change, yet the molecular mechanisms underlying observed phenotypic patterns are poorly understood. Epigenetic changes are expected to facilitate more rapid adaption to changing or novel environments, such as our towns and cities, compared with slow changes in gene sequence. A comparison of liver and blood tissue from great tits Parus major originating from an urban and a forest site demonstrated that urbanization is associated with variation in genome-wide patterns of DNA methylation. Combining reduced representation bisulphite sequencing with transcriptome data, we revealed habitat differences in DNA methylation patterns that suggest a regulated and coordinated response to the urban environment. In the liver, genomic sites that were differentially methylated between urban- and forest-dwelling birds were over-represented in regulatory regions of the genome and more likely to occur in expressed genes. DNA methylation levels were also inversely correlated with gene expression at transcription start sites. Furthermore, differentially methylated CpG sites, in liver, were over-represented in pathways involved in (i) steroid biosynthesis, (ii) superoxide metabolism, (iii) secondary alcohol metabolism, (iv) chylomicron remodelling, (v) cholesterol transport, (vi) reactive oxygen species (ROS) metabolic process and (vii) epithelial cell proliferation. This corresponds with earlier studies identifying diet and exposure to ROS as two of the main drivers of divergence between organisms in urban and nonurban environments. Conversely, in blood, sites that were differentially methylated between urban- and forest-dwelling birds were under-represented in regulatory regions, more likely to occur in nonexpressed genes and not over-represented in specific biological pathways. It remains to be determined whether diverging patterns of DNA methylation represent adaptive evolutionary responses and whether the conclusions can be more widely attributed to urbanization.
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6.
  • Wollein Waldetoft, Kristofer, et al. (author)
  • Proliferation and benevolence—A framework for dissecting the mechanisms of microbial virulence and health promotion
  • 2020
  • In: Evolutionary Applications. - : Wiley. - 1752-4563 .- 1752-4571. ; 13:5, s. 879-888
  • Journal article (peer-reviewed)abstract
    • Key topics in the study of host–microbe interactions—such as the prevention of drug resistance and the exploitation of beneficial effects of bacteria—would benefit from concerted efforts with both mechanistic and evolutionary approaches. But due to differences in intellectual traditions, insights gained in one field rarely benefit the other. Here, we develop a conceptual and analytical framework for the integrated study of host–microbe interactions. This framework partitions the health effects of microbes and the effector molecules they produce into components with different evolutionary implications. It thereby facilitates the prediction of evolutionary responses to inhibition and exploitation of specific molecular mechanisms.
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7.
  • Dalin, Peter (author)
  • Evolution of critical day length for diapause induction enables range expansion of Diorhabda carinulata, a biological control agent against tamarisk (Tamarix spp.)
  • 2012
  • In: Evolutionary applications. - : Wiley. - 1752-4571. ; 5, s. 511-523
  • Journal article (peer-reviewed)abstract
    • In classical weed biological control, small collections of arthropods are made from one or a few sites in the native range of the target plant and are introduced to suppress the plant where it has become invasive, often across a wide geographic range. Ecological mismatches in the new range are likely, and success using the biocontrol agent may depend on postrelease evolution of beneficial life history traits. In this study, we measure the evolution of critical day length for diapause induction (day length at which 50% of the population enters dormancy), in a beetle (Diorhabda carinulata) introduced into North America from China to control an exotic shrub, Tamarix spp. Beetle populations were sampled from four sites in North America 7 years after introduction, and critical day length was shown to have declined, forming a cline over a latitudinal gradient At one field site, decreased critical day length was correlated with 16 additional days of reproductive activity, resulting in a closer match between beetle life history and the phenology of Tamarix. These findings indicate an enhanced efficacy and an increasingly wider range for D. carinulata in Tamarix control.
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8.
  • Weeks, Andrew R., et al. (author)
  • Assessing the benefits and risks of translocations in changing environments : a genetic perspective
  • 2011
  • In: Evolutionary Applications. - : Wiley. - 1752-4571. ; 4:6, s. 709-725
  • Journal article (peer-reviewed)abstract
    • Translocations are being increasingly proposed as a way of conserving biodiversity, particularly in the management of threatened and keystone species, with the aims of maintaining biodiversity and ecosystem function under the combined pressures of habitat fragmentation and climate change. Evolutionary genetic considerations should be an important part of translocation strategies, but there is often confusion about concepts and goals. Here, we provide a classification of translocations based on specific genetic goals for both threatened species and ecological restoration, separating targets based on ‘genetic rescue’ of current population fitness from those focused on maintaining adaptive potential. We then provide a framework for assessing the genetic benefits and risks associated with translocations and provide guidelines for managers focused on conserving biodiversity and evolutionary processes. Case studies are developed to illustrate the framework.
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9.
  • Andersson, Björn, et al. (author)
  • Evaluating the contribution of historical and contemporary temperature to the oospore production of self-fertile Phytophthora infestans
  • 2024
  • In: Evolutionary applications. - 1752-4571. ; 17
  • Journal article (peer-reviewed)abstract
    • Reproductive systems play an important role in the ecological function of species, but little is known about how climate change, such as global warming, may affect the reproductive systems of microbes. In this study, 116 Phytophthora infestans isolates sampled from five different altitudes along a mountain were evaluated under five temperature regimes to determine the effects of historical and experimental temperature on the reproductive system of the pathogen. Both altitude, a proxy for historical pathogen adaptation to temperature, and temperature used in the experiment affected the sexual reproduction of the pathogen, with experimental temperature, that is, contemporary temperature, playing a role several times more important than historical temperature. Furthermore, the potential of sexual reproduction, measured by the number of oospores quantified, increased with the temperature breadth (i.e., difference between the highest and lowest temperature at which sexual reproduction takes place) of the pathogen and reached the maximum at the experimental temperature of 21(degrees)C, which is higher than the annual average temperature in many potato-producing areas. The results suggest that rising air temperature associated with global warming may increase the potential of sexual reproduction in P. infestans. Given the importance of sexuality in pathogenicity and ecological adaptation of pathogens, these results suggest that global warming may increase the threat of P. infestans to agricultural production and other ecological services and highlight that new epidemiological strategies may need to be implemented for future food security and ecological resilience.
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10.
  • Bekkevold, D., et al. (author)
  • Northern European Salmo trutta (L.) populations are genetically divergent across geographical regions and environmental gradients
  • 2020
  • In: Evolutionary Applications. - : Wiley. - 1752-4571. ; 13:2, s. 400-416
  • Journal article (peer-reviewed)abstract
    • The salmonid fish Brown trout is iconic as a model for the application of conservation genetics to understand and manage local interspecific variation. However, there is still scant information about relationships between local and large-scale population structure, and to what extent geographical and environmental variables are associated with barriers to gene flow. We used information from 3,782 mapped SNPs developed for the present study and conducted outlier tests and gene-environment association (GEA) analyses in order to examine drivers of population structure. Analyses comprised >2,600 fish from 72 riverine populations spanning a central part of the species' distribution in northern Europe. We report hitherto unidentified genetic breaks in population structure, indicating strong barriers to gene flow. GEA loci were widely spread across genomic regions and showed correlations with climatic, abiotic and geographical parameters. In some cases, individual loci showed consistent GEA across the geographical regions Britain, Europe and Scandinavia. In other cases, correlations were observed only within a sub-set of regions, suggesting that locus-specific variation was associated with local processes. A paired-population sampling design allowed us to evaluate sampling effects on detection of outlier loci and GEA. Two widely applied methods for outlier detection (pcadapt and bayescan) showed low overlap in loci identified as statistical outliers across sub-sets of data. Two GEA analytical approaches (LFMM and RDA) showed good correspondence concerning loci associated with specific variables, but LFMM identified five times more statistically significant associations than RDA. Our results emphasize the importance of carefully considering the statistical methods applied for the hypotheses being tested in outlier analysis. Sampling design may have lower impact on results if the objective is to identify GEA loci and their population distribution. Our study provides new insights into trout populations, and results have direct management implications in serving as a tool for identification of conservation units.
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11.
  • Bishop, Anusha P., et al. (author)
  • A machine learning approach to integrating genetic and ecological data in tsetse flies (Glossina pallidipes) for spatially explicit vector control planning
  • 2021
  • In: Evolutionary Applications. - : John Wiley & Sons. - 1752-4571. ; 14:7, s. 1762-1777
  • Journal article (peer-reviewed)abstract
    • Vector control is an effective strategy for reducing vector-borne disease transmission, but requires knowledge of vector habitat use and dispersal patterns. Our goal was to improve this knowledge for the tsetse species Glossina pallidipes, a vector of human and animal African trypanosomiasis, which are diseases that pose serious health and socioeconomic burdens across sub-Saharan Africa. We used random forest regression to (i) build and integrate models of G. pallidipes habitat suitability and genetic connectivity across Kenya and northern Tanzania and (ii) provide novel vector control recommendations. Inputs for the models included field survey records from 349 trap locations, genetic data from 11 microsatellite loci from 659 flies and 29 sampling sites, and remotely sensed environmental data. The suitability and connectivity models explained approximately 80% and 67% of the variance in the occurrence and genetic data and exhibited high accuracy based on cross-validation. The bivariate map showed that suitability and connectivity vary independently across the landscape and was used to inform our vector control recommendations. Post hoc analyses show spatial variation in the correlations between the most important environmental predictors from our models and each response variable (e.g., suitability and connectivity) as well as heterogeneity in expected future climatic change of these predictors. The bivariate map suggests that vector control is most likely to be successful in the Lake Victoria Basin and supports the previous recommendation that G. pallidipes from most of eastern Kenya should be managed as a single unit. We further recommend that future monitoring efforts should focus on tracking potential changes in vector presence and dispersal around the Serengeti and the Lake Victoria Basin based on projected local climatic shifts. The strong performance of the spatial models suggests potential for our integrative methodology to be used to understand future impacts of climate change in this and other vector systems.
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12.
  • Bridle, J. R., et al. (author)
  • Local adaptation stops where ecological gradients steepen or are interrupted
  • 2019
  • In: Evolutionary Applications. - : Wiley. - 1752-4571. ; 12:7, s. 1449-1462
  • Journal article (peer-reviewed)abstract
    • Population genetic models of evolution along linear environmental gradients cannot explain why adaptation stops at ecological margins. This is because, unless models impose reductions in carrying capacity at species' edges, the dominant effect of gene flow is to increase genetic variance and adaptive potential rather than swamping local adaptation. This allows the population to match even very steep changes in trait optima. We extend our previous simulations to explore two nonlinear models of ecological gradients: (a) a sigmoid (steepening) gradient and (b) a linear gradient with a flat centre of variable width. We compare the parameter conditions that allow local adaptation and range expansion from the centre, with those that permit the persistence of a perfectly adapted population distributed across the entire range. Along nonlinear gradients, colonization is easier, and extinction rarer, than along a linear gradient. This is because the shallow environmental gradient near the range centre does not cause gene flow to increase genetic variation, and so does not result in reduced population density. However, as gradient steepness increases, gene flow inflates genetic variance and reduces local population density sufficiently that genetic drift overcomes local selection, creating a finite range margin. When a flat centre is superimposed on a linear gradient, gene flow increases genetic variation dramatically at its edges, leading to an abrupt reduction in density that prevents niche expansion. Remarkably local interruptions in a linear ecological gradient (of a width much less than the mean dispersal distance) can prevent local adaptation beyond this flat centre. In contrast to other situations, this effect is stronger and more consistent where carrying capacity is high. Practically speaking, this means that habitat improvement at patch margins will make evolutionary rescue more likely. By contrast, even small improvements in habitat at patch centres may confine populations to limited areas of ecological space.
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13.
  • Broberg, Martin, et al. (author)
  • Comparative genomics highlights the importance of drug efflux transporters during evolution of mycoparasitism in Clonostachys subgenus Bionectria (Fungi, Ascomycota, Hypocreales)
  • 2021
  • In: Evolutionary applications. - : Wiley. - 1752-4571. ; 14, s. 476-497
  • Journal article (peer-reviewed)abstract
    • Various strains of the mycoparasitic fungal speciesClonostachys roseaare used commercially as biological control agents for the control of fungal plant diseases in agricultural crop production. Further improvements of the use and efficacy ofC. roseain biocontrol require a mechanistic understanding of the factors that determines the outcome of the interaction betweenC. roseaand plant pathogenic fungi. Here, we determined the genome sequences of 11Clonostachysstrains, representing five species inClonostachyssubgenusBionectria, and performed a comparative genomic analysis with the aim to identify gene families evolving under selection for gene gains or losses. Several gene families predicted to encode proteins involved in biosynthesis of secondary metabolites, including polyketide synthases, nonribosomal peptide syntethases and cytochrome P450s, evolved under selection for gene gains (p <= .05) in theBionectriasubgenus lineage. This was accompanied with gene copy number increases (p <= .05) in ATP-binding cassette (ABC) transporters and major facilitator superfamily (MFS) transporters predicted to contribute to drug efflux. MostClonostachysspecies were also characterized by high numbers of auxiliary activity (AA) family 9 lytic polysaccharide monooxygenases, AA3 glucose-methanol-choline oxidoreductases and additional carbohydrate-active enzyme gene families with putative activity (or binding) towards xylan and rhamnose/pectin substrates. Particular features of theC. roseagenome included expansions (p <= .05) of the ABC-B4 multidrug resistance transporters, the ABC-C5 multidrug resistance-related transporters and the 2.A.1.3 drug:H + antiporter-2 MFS drug resistance transporters. The ABC-G1 pleiotropic drug resistance transporter geneabcG6inC. roseawas induced (p <= .009) by exposure to the antifungalFusariummycotoxin zearalenone (1121-fold) and various fungicides. Deletion ofabcG6resulted in mutants with reduced (p < .001) growth rates on media containing the fungicides boscalid, fenhexamid and iprodione. Our results emphasize the role of biosynthesis of, and protection against, secondary metabolites inClonostachyssubgenusBionectria.
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14.
  • Burnett, Hamish A., et al. (author)
  • Contrasting genomic consequences of anthropogenic reintroduction and natural recolonization in high-arctic wild reindeer
  • 2023
  • In: Evolutionary Applications. - 1752-4571. ; 16:9, s. 1531-1548
  • Journal article (peer-reviewed)abstract
    • Anthropogenic reintroduction can supplement natural recolonization in reestablishing a species' distribution and abundance. However, both reintroductions and recolonizations can give rise to founder effects that reduce genetic diversity and increase inbreeding, potentially causing the accumulation of genetic load and reduced fitness. Most current populations of the endemic high-arctic Svalbard reindeer (Rangifer tarandus platyrhynchus) originate from recent reintroductions or recolonizations following regional extirpations due to past overharvesting. We investigated and compared the genomic consequences of these two paths to reestablishment using whole-genome shotgun sequencing of 100 Svalbard reindeer across their range. We found little admixture between reintroduced and natural populations. Two reintroduced populations, each founded by 12 individuals around four decades (i.e. 8 reindeer generations) ago, formed two distinct genetic clusters. Compared to the source population, these populations showed only small decreases in genome-wide heterozygosity and increases in inbreeding and lengths of runs of homozygosity. In contrast, the two naturally recolonized populations without admixture possessed much lower heterozygosity, higher inbreeding and longer runs of homozygosity, possibly caused by serial population founder effects and/or fewer or more genetically related founders than in the reintroduction events. Naturally recolonized populations can thus be more vulnerable to the accumulation of genetic load than reintroduced populations. This suggests that in some organisms even small-scale reintroduction programs based on genetically diverse source populations can be more effective than natural recolonization in establishing genetically diverse populations. These findings warrant particular attention in the conservation and management of populations and species threatened by habitat fragmentation and loss. 
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15.
  • Burraco, Pablo, et al. (author)
  • Ionizing radiation and melanism in Chornobyl tree frogs
  • 2022
  • In: Evolutionary Applications. - : John Wiley & Sons. - 1752-4571. ; 15:9, s. 1469-1479
  • Journal article (peer-reviewed)abstract
    • Human actions are altering ecosystems worldwide. Among human-released pollutants, ionizing radiation arises as a rare but potentially devastating threat to natural systems. The Chornobyl accident (1986) represents the largest release of radioactive material to the environment. Our aim was to examine how exposure to radiation from the Chornobyl accident influences dorsal skin coloration of Eastern tree frog (Hyla orientalis) males sampled across a wide gradient of radioactive contamination in northern Ukraine. We assessed the relationship between skin frog coloration (which can act as a protective mechanism against ionizing radiation), radiation conditions and oxidative stress levels. Skin coloration was darker in localities closest to areas with high radiation levels at the time of the accident, whereas current radiation levels seemed not to influence skin coloration in Chornobyl tree frogs. Tree frogs living within the Chornobyl Exclusion Zone had a remarkably darker dorsal skin coloration than frogs from outside the Zone. The maintenance of dark skin coloration was not linked to physiological costs in terms of frog body condition or oxidative status, and we did not detect short-term changes in frog coloration. Dark coloration is known to protect against different sources of radiation by neutralizing free radicals and reducing DNA damage, and, particularly melanin pigmentation has been proposed as a buffering mechanism against ionizing radiation. Our results suggest that exposure to high levels of ionizing radiation, likely at the time of the accident, may have been selected for darker coloration in Chornobyl tree frogs. Further studies are needed to determine the underlying mechanisms and evolutionary consequences of the patterns found here.
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16.
  • Calosi, Piero, et al. (author)
  • Will Life find a Way? Evolution of Marine Species Under Global Change
  • 2016
  • In: Evolutionary Applications. - : Wiley. - 1752-4571. ; 9:9, s. 1035-1042
  • Journal article (peer-reviewed)abstract
    • Projections of marine biodiversity and implementation of effective actions for its maintenance in face of current rapid global environmental change are constrained by our limited understanding of species’ adaptive responses, including, transgenerational plasticity, epigenetics, natural selection. This special issue presents 13 novel studies, which employ experimental and modeling approaches to: (1) Investigate plastic and evolutionary responses of marine species to major global change drivers; (2) ask relevant broad eco-evolutionary questions, implementing well-designed multiple species and populations studies; (3) show the advantages of using advanced experimental designs and tools; (4) construct novel model organisms for marine evolution; (5) help identifying future challenges for the field, and (6) highlight the importance of incorporating existing evolutionary theory into management solutions for the marine realm. What emerges is that at least some populations of marine species are able to adapt to future global change conditions. However, marine organisms’ capacity for adaptation appears finite, due to evolutionary trade-offs and possible rapid losses in genetic diversity. This further corroborate the idea that acquiring an evolutionary perspective on how marine life will respond to the selective pressure of future global changes will guide us in better identifying which conservation efforts will be most needed, and most effective.
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17.
  • Car, Clement, et al. (author)
  • Unusual evolution of tree frog populations in the Chernobyl exclusion zone
  • 2022
  • In: Evolutionary Applications. - : John Wiley & Sons. - 1752-4571. ; 15:2, s. 203-219
  • Journal article (peer-reviewed)abstract
    • Despite the ubiquity of pollutants in the environment, their long-term ecological consequences are not always clear and still poorly studied. This is the case concerning the radioactive contamination of the environment following the major nuclear accident at the Chernobyl nuclear power plant. Notwithstanding the implications of evolutionary processes on the population status, few studies concern the evolution of organisms chronically exposed to ionizing radiation in the Chernobyl exclusion zone. Here, we examined genetic markers for 19 populations of Eastern tree frog (Hyla orientalis) sampled in the Chernobyl region about thirty years after the nuclear power plant accident to investigate microevolutionary processes ongoing in local populations. Genetic diversity estimated from nuclear and mitochondrial markers showed an absence of genetic erosion and higher mitochondrial diversity in tree frogs from the Chernobyl exclusion zone compared to other European populations. Moreover, the study of haplotype network permitted us to decipher the presence of an independent recent evolutionary history of Chernobyl exclusion zone's Eastern tree frogs caused by an elevated mutation rate compared to other European populations. By fitting to our data a model of haplotype network evolution, we suspected that Eastern tree frog populations in the Chernobyl exclusion zone have a high mitochondrial mutation rate and small effective population sizes. These data suggest that Eastern tree frog populations might offset the impact of deleterious mutations because of their large clutch size, but also question the long-term impact of ionizing radiation on the status of other species living in the Chernobyl exclusion zone.
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18.
  • Chen, Jun, et al. (author)
  • Genomic data provide new insights on the demographic history and the extent of recent material transfers in Norway spruce
  • 2019
  • In: Evolutionary Applications. - : WILEY. - 1752-4571. ; 12:8, s. 1539-1551
  • Journal article (peer-reviewed)abstract
    • Primeval forests are today exceedingly rare in Europe, and transfer of forest reproductive material for afforestation and improvement has been very common, especially over the last two centuries. This can be a serious impediment when inferring past population movements in response to past climate changes such as the last glacial maximum (LGM), some 18,000 years ago. In the present study, we genotyped 1,672 individuals from three Picea species (P. abies, P. obovata, and P. omorika) at 400K SNPs using exome capture to infer the past demographic history of Norway spruce (P. abies) and estimate the amount of recent introduction used to establish the Norway spruce breeding program in southern Sweden. Most of these trees belong to P. abies and originate from the base populations of the Swedish breeding program. Others originate from populations across the natural ranges of the three species. Of the 1,499 individuals stemming from the breeding program, a large proportion corresponds to recent introductions from mainland Europe. The split of P. omorika occurred 23 million years ago (mya), while the divergence between P. obovata and P. abies began 17.6 mya. Demographic inferences retrieved the same main clusters within P. abies than previous studies, that is, a vast northern domain ranging from Norway to central Russia, where the species is progressively replaced by Siberian spruce (P. obovata) and two smaller domains, an Alpine domain and a Carpathian one, but also revealed further subdivision and gene flow among clusters. The three main domains divergence was ancient (15 mya), and all three went through a bottleneck corresponding to the LGM. Approximately 17% of P. abies Nordic domain migrated from P. obovata ~103K years ago, when both species had much larger effective population sizes. Our analysis of genomewide polymorphism data thus revealed the complex demographic history of Picea genus in Western Europe and highlighted the importance of material transfer in Swedish breeding program.
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19.
  • Cornille, Amandine, et al. (author)
  • Anthropogenic and natural drivers of gene flow in a temperate wild fruit tree : a basis for conservation and breeding programs in apples
  • 2015
  • In: Evolutionary Applications. - : Wiley. - 1752-4571. ; 8:4, s. 373-384
  • Journal article (peer-reviewed)abstract
    • Gene flow is an essential component of population adaptation and species evolution. Understanding of the natural and anthropogenic factors affecting gene flow is also critical for the development of appropriate management, breeding, and conservation programs. Here, we explored the natural and anthropogenic factors impacting crop-to-wild and within wild gene flow in apples in Europe using an unprecedented dense sampling of 1889 wild apple (Malus sylvestris) from European forests and 339 apple cultivars (Malus domestica). We made use of genetic, environmental, and ecological data (microsatellite markers, apple production across landscapes and records of apple flower visitors, respectively). We provide the first evidence that both human activities, through apple production, and human disturbance, through modifications of apple flower visitor diversity, have had a significant impact on crop-to-wild interspecific introgression rates. Our analysis also revealed the impact of previous natural climate change on historical gene flow in the nonintrogressed wild apple M.sylvestris, by identifying five distinct genetic groups in Europe and a north-south gradient of genetic diversity. These findings identify human activities and climate as key drivers of gene flow in a wild temperate fruit tree and provide a practical basis for conservation, agroforestry, and breeding programs for apples in Europe.
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20.
  • Cros, Emilie, et al. (author)
  • Fine‐scale barriers to connectivity across a fragmented South‐East Asian landscape in six songbird species
  • 2020
  • In: Evolutionary Applications. - 1752-4571. ; 13:5, s. 1026-1036
  • Journal article (peer-reviewed)abstract
    • Habitat  fragmentation  is  a major  extinction  driver.  Despite  dramatically  increas-ing fragmentation across the globe, its specific impacts on population connectivityacross species with differing life histories remain difficult to characterize, let alonequantify. Here, we investigate patterns of population connectivity in six songbirdspecies from Singapore, a highly fragmented tropical rainforest island. Using massivepanels of genome-wide single nucleotide polymorphisms across dozens of samplesper species, we examined population genetic diversity, inbreeding, gene flow andconnectivity among species along a spectrum of ecological specificities. We found ahigher resilience to habitat fragmentation in edge-tolerant and forest-canopy speciesas compared to forest-dependent understorey insectivores. The latter exhibited lev-els of genetic diversity up to three times lower in Singapore than in populations fromcontiguous forest elsewhere. Using dense genomic and geographic sampling, weidentified individual barriers such as reservoirs that effectively minimize gene flowin sensitive understorey birds, revealing that terrestrial forest species may exhibitlevels of sensitivity to fragmentation far greater than previously expected. This studyprovides a blueprint for conservation genomics at small scales with a view to iden-tifying preferred locations for habitat corridors, flagging candidate populations forrestocking with translocated individuals and improving the design of future reserves.
  •  
21.
  • De Jode, Aurélien, et al. (author)
  • Ten years of demographic modelling of divergence and speciation in the sea
  • 2022
  • In: Evolutionary Applications. - : Wiley. - 1752-4571. ; 16:2, s. 542-59
  • Journal article (peer-reviewed)abstract
    • Understanding population divergence that eventually leads to speciation is essential for evolutionary biology. High species diversity in the sea was regarded as a paradox when strict allopatry was considered necessary for most speciation events because geographical barriers seemed largely absent in the sea, and many marine species have high dispersal capacities. Combining genome-wide data with demographic modelling to infer the demographic history of divergence has introduced new ways to address this classical issue. These models assume an ancestral population that splits into two subpopulations diverging according to different scenarios that allow tests for periods of gene flow. Models can also test for heterogeneities in population sizes and migration rates along the genome to account, respectively, for background selection and selection against introgressed ancestry. To investigate how barriers to gene flow arise in the sea, we compiled studies modelling the demographic history of divergence in marine organisms and extracted preferred demographic scenarios together with estimates of demographic parameters. These studies show that geographical barriers to gene flow do exist in the sea but that divergence can also occur without strict isolation. Heterogeneity of gene flow was detected in most population pairs suggesting the predominance of semipermeable barriers during divergence. We found a weak positive relationship between the fraction of the genome experiencing reduced gene flow and levels of genome-wide differentiation. Furthermore, we found that the upper bound of the ‘grey zone of speciation’ for our dataset extended beyond that found before, implying that gene flow between diverging taxa is possible at higher levels of divergence than previously thought. Finally, we list recommendations for further strengthening the use of demographic modelling in speciation research. These include a more balanced representation of taxa, more consistent and comprehensive modelling, clear reporting of results and simulation studies to rule out nonbiological explanations for general results.
  •  
22.
  • De Wit, Pierre, 1978, et al. (author)
  • A decade of progress in marine evolutionary biology
  • 2022
  • In: Evolutionary Applications. - : Wiley. - 1752-4571. ; 16:2, s. 193-201
  • Journal article (other academic/artistic)abstract
    • This article summarizes the Evolutionary Applications Special Issue, “A decade of progress in Marine Evolutionary Biology.” The globally connected ocean, from its pelagic depths to its highly varied coastlines, inspired Charles Darwin to develop the theory of evolution during the voyage of the Beagle. As technology has developed, there has been a dramatic increase in our knowledge about life on our blue planet. This Special Issue, composed of 19 original papers and seven reviews, represents a small contribution to the larger picture of recent research in evolutionary biology, and how such advancements come about through the connection of researchers, their fields, and their knowledge. The first European network for marine evolutionary biology, the Linnaeus Centre for Marine Evolutionary Biology (CeMEB), was developed to study evolutionary processes in the marine environment under global change. Though hosted by the University of Gothenburg in Sweden, the network quickly grew to encompass researchers throughout Europe and beyond. Today, more than a decade after its foundation, CeMEB's focus on the evolutionary consequences of global change is more relevant than ever, and knowledge gained from marine evolution research is urgently needed in management and conservation. This Special Issue, organized and developed through the CeMEB network, contains contributions from all over the world and provides a snapshot of the current state of the field, thus forming an important basis for future research directions.
  •  
23.
  • De Wit, Pierre, 1978, et al. (author)
  • Selection on oxidative phosphorylation and ribosomal structure as a multigenerational response to ocean acidification in the common copepod Pseudocalanus acuspes
  • 2016
  • In: Evolutionary Applications. - : Wiley. - 1752-4571. ; 9:9, s. 1112-1223
  • Journal article (peer-reviewed)abstract
    • Ocean acidification is expected to have dramatic impacts on oceanic ecosystems, yet surprisingly few studies currently examine long-term adaptive and plastic responses of marine invertebrates to pCO2 stress. Here, we exposed populations of the common copepod Pseudocalanus acuspes to three pCO2 regimes (400, 900 and 1550 μatm) for two generations, after which we conducted a reciprocal transplant experiment. A de novo transcriptome was assembled, annotated, and gene expression data revealed that genes involved in RNA transcription were strongly down-regulated in populations with long-term exposure to a high pCO2 environment, even after transplantation back to control levels. In addition, 747,000 SNPs were identified, out of which 1513 showed consistent changes in nucleotide frequency between replicates of control and high pCO2 populations. Functions involving RNA transcription and ribosomal function, as well as ion transport and oxidative phosphorylation were highly overrepresented. We thus conclude that pCO2 stress appears to impose selection in copepods on RNA synthesis and translation, possibly modulated by helicase expression. Using a physiological hypothesis-testing strategy to mine gene expression data, we herein increase the power to detect cellular targets of ocean acidification. This novel approach seems promising for future studies of effects of environmental changes in ecologically important non- model organisms.
  •  
24.
  • Durland, Evan, et al. (author)
  • Larval development in the Pacific oyster and the impacts of ocean acidification: Differential genetic effects in wild and domesticated stocks
  • 2021
  • In: Evolutionary Applications. - : Wiley. - 1752-4571. ; 14:9, s. 2258-2272
  • Journal article (peer-reviewed)abstract
    • The adaptive capacity of marine calcifiers to ocean acidification (OA) is a topic of great interest to evolutionary biologists and ecologists. Previous studies have provided evidence to suggest that larval resilience to high pCO2 seawater for these species is a trait with a genetic basis and variability in natural populations. To date, however, it remains unclear how the selective effects of OA occur within the context of complex genetic interactions underpinning larval development in many of the most vulnerable taxa. Here we evaluated phenotypic and genetic changes during larval development of Pacific oysters (Crassostrea gigas) reared in ambient (~400 µatm) and high (~1600 µatm) pCO2 conditions, both in domesticated and naturalized “wild” oysters from the Pacific Northwest, USA. Using pooled DNA samples, we determined changes in allele frequencies across larval development, from early “D-stage” larvae to metamorphosed juveniles (spat), in both groups and environments. Domesticated larvae had ~26% fewer loci with changing allele frequencies across developmental stages and <50% as many loci affected by acidified culture conditions, compared to larvae from wild broodstock. Functional enrichment analyses of genetic markers with significant changes in allele frequency revealed that the structure and function of cellular membranes were disproportionately affected by high pCO2 conditions in both groups. These results indicate the potential for a rapid adaptive response of oyster populations to OA conditions; however, underlying genetic changes associated with larval development differ between these wild and domesticated oyster stocks and influence their adaptive responses to OA conditions.
  •  
25.
  • Egan, Paul, et al. (author)
  • Capturing genetic variation in crop wild relatives: An evolutionary approach
  • 2018
  • In: Evolutionary applications. - : Wiley. - 1752-4571. ; 11, s. 1293-1304
  • Journal article (peer-reviewed)abstract
    • Crop wild relatives (CWRs) offer novel genetic resources for crop improvement. To assist in the urgent need to collect and conserve CWR germplasm, we advance here the concept of an evolutionary approach. Central to this approach is the predictive use of spatial proxies of evolutionary processes (natural selection, gene flow and genetic drift) to locate and capture genetic variation. As a means to help validate this concept, we screened wild-collected genotypes of woodland strawberry (Fragaria vesca) in a common garden. A quantitative genetic approach was then used to test the ability of two such proxiesmesoclimatic variation (a proxy of natural selection) and landscape isolation and geographic distance between populations (proxies of gene flow potential)to predict spatial genetic variation in three quantitative traits (plant size, early season flower number and flower frost tolerance). Our results indicated a significant but variable effect of mesoclimatic conditions in structuring genetic variation in the wild, in addition to other undetermined regional scale processes. As a proxy of gene flow potential, landscape isolation was also a likely determinant of observed patternsas opposed to, and regardless of, geographic distance between populations. We conclude that harnessing proxies of adaptive and nonadaptive evolutionary processes could provide a robust and valuable means to identify genetic variation in CWRs. We thus advocate wider use and development of this approach amongst researchers, breeders and practitioners, to expedite the capture and in situ conservation of genetic resources provided by crop wild relatives.
  •  
26.
  • Ekblom, Robert, et al. (author)
  • A field guide to whole-genome sequencing, assembly and annotation
  • 2014
  • In: Evolutionary Applications. - : Wiley. - 1752-4571. ; 7:9, s. 1026-1042
  • Journal article (peer-reviewed)abstract
    • Genome sequencing projects were long confined to biomedical model organisms and required the concerted effort of large consortia. Rapid progress in high-throughput sequencing technology and the simultaneous development of bioinformatic tools have democratized the field. It is now within reach for individual research groups in the eco-evolutionary and conservation community to generate de novo draft genome sequences for any organism of choice. Because of the cost and considerable effort involved in such an endeavour, the important first step is to thoroughly consider whether a genome sequence is necessary for addressing the biological question at hand. Once this decision is taken, a genome project requires careful planning with respect to the organism involved and the intended quality of the genome draft. Here, we briefly review the state of the art within this field and provide a step-by-step introduction to the workflow involved in genome sequencing, assembly and annotation with particular reference to large and complex genomes. This tutorial is targeted at scientists with a background in conservation genetics, but more generally, provides useful practical guidance for researchers engaging in whole-genome sequencing projects.
  •  
27.
  • Eriksson, Martin, et al. (author)
  • Adaptive, maladaptive, neutral, or absent plasticity: Hidden caveats of reaction norms
  • 2022
  • In: Evolutionary Applications. - : Wiley. - 1752-4571. ; 16:2, s. 486-503
  • Journal article (peer-reviewed)abstract
    • Adaptive phenotypic plasticity may improve the response of individuals when faced with new environmental conditions. Typically, empirical evidence for plasticity is based on phenotypic reaction norms obtained in reciprocal transplant experiments. In such experiments, individuals from their native environment are transplanted into a different environment, and a number of trait values, potentially implicated in individuals' response to the new environment, are measured. However, the interpretations of reaction norms may differ depending on the nature of the assessed traits, which may not be known beforehand. For example, for traits that contribute to local adaptation, adaptive plasticity implies nonzero slopes of reaction norms. By contrast, for traits that are correlated to fitness, high tolerance to different environments (possibly due to adaptive plasticity in traits that contribute to adaptation) may, instead, result in flat reaction norms. Here we investigate reaction norms for adaptive versus fitness-correlated traits and how they may affect the conclusions regarding the contribution of plasticity. To this end, we first simulate range expansion along an environmental gradient where plasticity evolves to different values locally and then perform reciprocal transplant experiments in silico. We show that reaction norms alone cannot inform us whether the assessed trait exhibits locally adaptive, maladaptive, neutral, or no plasticity, without any additional knowledge of the traits assessed and species' biology. We use the insights from the model to analyse and interpret empirical data from reciprocal transplant experiments involving the marine isopod Idotea balthica sampled from two geographical locations with different salinities, concluding that the low-salinity population likely has reduced adaptive plasticity relative to the high-salinity population. Overall, we conclude that, when interpreting results from reciprocal transplant experiments, it is necessary to consider whether traits assessed are locally adaptive with respect to the environmental variable accounted for in the experiments or correlated to fitness.
  •  
28.
  • Erlichman, Adèle, et al. (author)
  • Planting long-lived trees in a warming climate : Theory shows the importance of stage-dependent climatic tolerance
  • 2024
  • In: Evolutionary Applications. - : John Wiley & Sons. - 1752-4571. ; 17:6
  • Journal article (peer-reviewed)abstract
    • Climate change poses a particular threat to long-lived trees, which may not adapt or migrate fast enough to keep up with rising temperatures. Assisted gene flow could facilitate adaptation of populations to future climates by using managed translocation of seeds from a warmer location (provenance) within the current range of a species. Finding the provenance that will perform best in terms of survival or growth is complicated by a trade-off. Because trees face a rapidly changing climate during their long lives, the alleles that confer optimal performance may vary across their lifespan. For instance, trees from warmer provenances could be well adapted as adults but suffer from colder temperatures while juvenile. Here we use a stage-structured model, using both analytical predictions and numerical simulations, to determine which provenance would maximize the survival of a cohort of long-lived trees in a changing climate. We parameterize our simulations using empirically estimated demographic transition matrices for 20 long-lived tree species. Unable to find reliable quantitative estimates of how climatic tolerance changes across stages in these same species, we varied this parameter to study its effect. Both our mathematical model and simulations predict that the best provenance depends strongly on how fast the climate changes and also how climatic tolerance varies across the lifespan of a tree. We thus call for increased empirical efforts to measure how climate tolerance changes over life in long-lived species, as our model suggests that it should strongly influence the best provenance for assisted gene flow.
  •  
29.
  • Faust, Ellika, et al. (author)
  • Not that clean: Aquaculture-mediated translocation of cleaner fish has led to hybridization on the northern edge of the species' range
  • 2021
  • In: Evolutionary Applications. - : Wiley. - 1752-4571. ; 14:6, s. 1572-87
  • Journal article (peer-reviewed)abstract
    • Translocation and introduction of non-native organisms can have major impacts on local populations and ecosystems. Nevertheless, translocations are common practices in agri- and aquaculture. Each year, millions of wild-caught wrasses are transported large distances to be used as cleaner fish for parasite control in marine salmon farms. Recently, it was documented that translocated cleaner fish are able to escape and reproduce with local wild populations. This is especially a challenge in Norway, which is the world's largest salmon producer. Here, a panel of 84 informative SNPs was developed to identify the presence of nonlocal corkwing wrasse (Symphodus melops) escapees and admixed individuals in wild populations in western Norway. Applying this panel to ~2000 individuals, escapees and hybrids were found to constitute up to 20% of the local population at the northern edge of the species’ distribution. The introduction of southern genetic material at the northern edge of the species distribution range has altered the local genetic composition and could obstruct local adaptation and further range expansion. Surprisingly, in other parts of the species distribution where salmon farming is also common, few escapees and hybrids were found. Why hybridization seems to be common only in the far north is discussed in the context of demographic and transport history. However, the current lack of reporting of escapes makes it difficult to evaluate possible causes for why some aquaculture-dense areas have more escapees and hybrids than others. The results obtained in this study, and the observed high genomic divergence between the main export and import regions, puts the sustainability of mass translocation of nonlocal wild wrasse into question and suggests that the current management regime needs re-evaluation.
  •  
30.
  • Feurtey, Alice, et al. (author)
  • 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
  • 2017
  • In: Evolutionary Applications. - : WILEY. - 1752-4571. ; 10:2, s. 180-188
  • Journal article (peer-reviewed)abstract
    • Crop-to-wild gene flow can reduce the fitness and genetic integrity of wild species. Malus sylvestris, the European crab-apple fruit tree in particular, is threatened by the disappearance of its habitat and by gene flow from its domesticated relative, Malus domestica. With the aims of evaluating threats for M.sylvestris and of formulating recommendations for its conservation, we studied here, using microsatellite markers and growth experiments: (i) hybridization rates in seeds and trees from a French forest and in seeds used for replanting crab apples in agrosystems and in forests, (ii) the impact of the level of M.domestica ancestry on individual tree fitness and (iii) pollen dispersal abilities in relation to crop-to-wild gene flow. We found substantial contemporary crop-to-wild gene flow in crab-apple tree populations and superior fitness of hybrids compared to wild seeds and seedlings. Using paternity analyses, we showed that pollen dispersal could occur up to 4km and decreased with tree density. The seed network furnishing the wild apple reintroduction agroforestry programmes was found to suffer from poor genetic diversity, introgressions and species misidentification. Overall, our findings indicate supported threats for the European wild apple steering us to provide precise recommendations for its conservation.
  •  
31.
  • Fountain, Toby, et al. (author)
  • Inferring dispersal across a fragmented landscape using reconstructed families in the Glanville fritillary butterfly
  • 2018
  • In: Evolutionary Applications. - : Wiley. - 1752-4571. ; 11:3, s. 287-297
  • Journal article (peer-reviewed)abstract
    • Dispersal is important for determining both species ecological processes, such as population viability, and its evolutionary processes, like gene flow and local adaptation. Yet obtaining accurate estimates in the wild through direct observation can be challenging or even impossible, particularly over large spatial and temporal scales. Genotyping many individuals from wild populations can provide detailed inferences about dispersal. We therefore utilized genomewide marker data to estimate dispersal in the classic metapopulation of the Glanville fritillary butterfly (Melitaea cinxia L.), in the Åland Islands in SW Finland. This is an ideal system to test the effectiveness of this approach due to the wealth of information already available covering dispersal across small spatial and temporal scales, but lack of information at larger spatial and temporal scales. We sampled three larvae per larval family group from 3732 groups over a six-year period and genotyped for 272 SNPs across the genome. We used this empirical data set to reconstruct cases where full-sibs were detected in different local populations to infer female effective dispersal distance, that is, dispersal events directly contributing to gene flow. On average this was one kilometre, closely matching previous dispersal estimates made using direct observation. To evaluate our power to detect full-sib families, we performed forward simulations using an individual-based model constructed and parameterized for the Glanville fritillary metapopulation. Using these simulations, 100% of predicted full-sibs were correct and over 98% of all true full-sib pairs were detected. We therefore demonstrate that even in a highly dynamic system with a relatively small number of markers, we can accurately reconstruct full-sib families and for the first time make inferences on female effective dispersal. This highlights the utility of this approach in systems where it has previously been impossible to obtain accurate estimates of dispersal over both ecological and evolutionary scales.
  •  
32.
  • Fuentes Pardo, Angela P., et al. (author)
  • Adaptation to seasonal reproduction and environment-associated factors drive temporal and spatial differentiation in northwest Atlantic herring despite gene flow
  • 2024
  • In: Evolutionary Applications. - : John Wiley & Sons. - 1752-4571. ; 17:3
  • Journal article (peer-reviewed)abstract
    • Understanding how marine organisms adapt to local environments is crucial for predicting how populations will respond to global climate change. The genomic basis, environmental factors and evolutionary processes involved in local adaptation are however not well understood. Here we use Atlantic herring, an abundant, migratory and widely distributed marine fish with substantial genomic resources, as a model organism to evaluate local adaptation. We examined genomic variation and its correlation with environmental variables across a broad environmental gradient, for 15 spawning aggregations in Atlantic Canada and the United States. We then compared our results with available genomic data of northeast Atlantic populations. We confirmed that population structure lies in a fraction of the genome including likely adaptive genetic variants of functional importance. We discovered 10 highly differentiated genomic regions distributed across four chromosomes. Nine regions show strong association with seasonal reproduction. One region, corresponding to a known inversion on chromosome 12, underlies a latitudinal pattern discriminating populations north and south of a biogeographic transition zone on the Scotian Shelf. Genome-environment associations indicate that winter seawater temperature best correlates with the latitudinal pattern of this inversion. The variation at two so-called 'islands of divergence' related to seasonal reproduction appear to be private to the northwest Atlantic. Populations in the northwest and northeast Atlantic share variation at four of these divergent regions, simultaneously displaying significant diversity in haplotype composition at another four regions, which includes an undescribed structural variant approximately 7.7 Mb long on chromosome 8. Our results suggest that the timing and geographic location of spawning and early development may be under diverse selective pressures related to allelic fitness across environments. Our study highlights the role of genomic architecture, ancestral haplotypes and selection in maintaining adaptive divergence in species with large population sizes and presumably high gene flow.
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33.
  • Fuentes-Pardo, Angela P., et al. (author)
  • The genomic basis and environmental correlates of local adaptation in the Atlantic horse mackerel (Trachurus trachurus)
  • 2023
  • In: Evolutionary Applications. - : John Wiley & Sons. - 1752-4571. ; 16:6, s. 1201-1219
  • Journal article (peer-reviewed)abstract
    • Understanding how populations adapt to their environment is increasingly important to prevent biodiversity loss due to overexploitation and climate change. Here we studied the population structure and genetic basis of local adaptation of Atlantic horse mackerel, a commercially and ecologically important marine fish that has one of the widest distributions in the eastern Atlantic. We analyzed whole-genome sequencing and environmental data of samples collected from the North Sea to North Africa and the western Mediterranean Sea. Our genomic approach indicated low population structure with a major split between the Mediterranean Sea and the Atlantic Ocean and between locations north and south of mid-Portugal. Populations from the North Sea are the most genetically distinct in the Atlantic. We discovered that most population structure patterns are driven by a few highly differentiated putatively adaptive loci. Seven loci discriminate the North Sea, two the Mediterranean Sea, and a large putative inversion (9.9 Mb) on chromosome 21 underlines the north-south divide and distinguishes North Africa. A genome-environment association analysis indicates that mean seawater temperature and temperature range, or factors correlated to them, are likely the main environmental drivers of local adaptation. Our genomic data broadly support the current stock divisions, but highlight areas of potential mixing, which require further investigation. Moreover, we demonstrate that as few as 17 highly informative SNPs can genetically discriminate the North Sea and North African samples from neighboring populations. Our study highlights the importance of both, life history and climate-related selective pressures in shaping population structure patterns in marine fish. It also supports that chromosomal rearrangements play a key role in local adaptation with gene flow. This study provides the basis for more accurate delineation of the horse mackerel stocks and paves the way for improving stock assessments.
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34.
  • Gering, Eben, et al. (author)
  • Maladaptation in feral and domesticated animals
  • 2019
  • In: Evolutionary Applications. - : WILEY. - 1752-4571. ; 12:7, s. 1274-1286
  • Research review (peer-reviewed)abstract
    • Selection regimes and population structures can be powerfully changed by domestication and feralization, and these changes can modulate animal fitness in both captive and natural environments. In this review, we synthesize recent studies of these two processes and consider their impacts on organismal and population fitness. Domestication and feralization offer multiple windows into the forms and mechanisms of maladaptation. Firstly, domestic and feral organisms that exhibit suboptimal traits or fitness allow us to identify their underlying causes within tractable research systems. This has facilitated significant progress in our general understandings of genotype-phenotype relationships, fitness trade-offs, and the roles of population structure and artificial selection in shaping domestic and formerly domestic organisms. Additionally, feralization of artificially selected gene variants and organisms can reveal or produce maladaptation in other inhabitants of an invaded biotic community. In these instances, feral animals often show similar fitness advantages to other invasive species, but they are also unique in their capacities to modify natural ecosystems through introductions of artificially selected traits. We conclude with a brief consideration of how emerging technologies such as genome editing could change the tempos, trajectories, and ecological consequences of both domestication and feralization. In addition to providing basic evolutionary insights, our growing understanding of mechanisms through which artificial selection can modulate fitness has diverse and important applications-from enhancing the welfare, sustainability, and efficiency of agroindustry, to mitigating biotic invasions.
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35.
  • Green, Leon, et al. (author)
  • Evidence of rapid adaptive trait change to local salinity in the sperm of an invasive fish
  • 2020
  • In: Evolutionary Applications. - : Wiley. - 1752-4571. ; 13:3, s. 533-544
  • Journal article (peer-reviewed)abstract
    • Invasive species may quickly colonize novel environments, which could be attributed to both phenotypic plasticity and an ability to locally adapt. Reproductive traits are expected to be under strong selection when the new environment limits reproductive success of the invading species. This may be especially important for external fertilizers, which release sperm and eggs into the new environment. Despite adult tolerance to high salinity, the invasive fish Neogobius melanostomus (round goby) is absent from fully marine regions of the Baltic Sea, raising the possibility that its distribution is limited by tolerance during earlier life stages. Here, we investigate the hypothesis that the spread of N. melanostomus is limited by sperm function in novel salinities. We sampled sperm from two invasion fronts with higher and lower salinities in the Baltic Sea and tested them across a range of salinity levels. We found that sperm velocity and percentage of motile sperm declined in salinity levels higher and lower than those currently experienced by the Baltic Sea populations, with different performance curves for the two fronts. Sperm velocity also peaked closer to the home salinity conditions in each respective invasion front, with older localities showing an increased fit to local conditions. By calculating how the sperm velocity has changed over generations, we show this phenotypic shift to be in the range of other fish species under strong selection, indicating ongoing local adaptation or epigenetic acclimation to their novel environment. These results show that while immigrant reproductive dysfunction appears to at least partly limit the distribution of invasive N. melanostomus in the Baltic Sea, local adaptation to novel environments could enable future spread beyond their current boundaries.
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36.
  • Green, Leon, et al. (author)
  • Invader at the edge - Genomic origins and physiological differences of round gobies across a steep urban salinity gradient
  • 2023
  • In: Evolutionary Applications. - : Wiley. - 1752-4571. ; 16:2, s. 321-37
  • Journal article (peer-reviewed)abstract
    • Species invasions are a global problem of increasing concern, especially in highly connected aquatic environments. Despite this, salinity conditions can pose physiological barriers to their spread, and understanding them is important for management. In Scandinavia's largest cargo port, the invasive round goby (Neogobius melanostomus) is established across a steep salinity gradient. We used 12,937 SNPs to identify the genetic origin and diversity of three sites along the salinity gradient and round goby from western, central and northern Baltic Sea, as well as north European rivers. Fish from two sites from the extreme ends of the gradient were also acclimated to freshwater and seawater, and tested for respiratory and osmoregulatory physiology. Fish from the high-salinity environment in the outer port showed higher genetic diversity, and closer relatedness to the other regions, compared to fish from lower salinity upstream the river. Fish from the high-salinity site also had higher maximum metabolic rate, fewer blood cells and lower blood Ca2+. Despite these genotypic and phenotypic differences, salinity acclimation affected fish from both sites in the same way: seawater increased the blood osmolality and Na+ levels, and freshwater increased the levels of the stress hormone cortisol. Our results show genotypic and phenotypic differences over short spatial scales across this steep salinity gradient. These patterns of the physiologically robust round goby are likely driven by multiple introductions into the high-salinity site, and a process of sorting, likely based on behaviour or selection, along the gradient. This euryhaline fish risks spreading from this area, and seascape genomics and phenotypic characterization can inform management strategies even within an area as small as a coastal harbour inlet.
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37.
  • Guo, Ying, et al. (author)
  • Researching on the fine structure and admixture of the worldwide chicken population reveal connections between populations and important events in breeding history
  • 2021
  • In: Evolutionary Applications. - : John Wiley & Sons. - 1752-4571.
  • Journal article (peer-reviewed)abstract
    • Here, we have evaluated the general genomic structure and diversity and studied the divergence resulting from selection and historical admixture events for a collection of worldwide chicken breeds. In total, 636 genomes (43 populations) were sequenced from chickens of American, Chinese, Indonesian, and European origin. Evaluated populations included wild junglefowl, rural indigenous chickens, breeds that have been widely used to improve modern western poultry populations and current com-mercial stocks bred for efficient meat and egg production. In-depth characteriza-tions of the genome structure and genomic relationships among these populations were performed, and population admixture events were investigated. In addition, the genomic architectures of several domestication traits and central documented events in the recent breeding history were explored. Our results provide detailed insights into the contributions from population admixture events described in the historical literature to the genomic variation in the domestic chicken. In particular, we find that the genomes of modern chicken stocks used for meat production both in eastern (Asia) and western (Europe/US) agriculture are dominated by contributions from heavy Asian breeds. Further, by exploring the link between genomic selective divergence and pigmentation, connections to functional genes feather coloring were confirmed.
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38.
  • Gustafsson, Malin, et al. (author)
  • Unlocking the secret life of blue mussels: Exploring connectivity in the Skagerrak through biophysical modeling and population genomics
  • 2024
  • In: Evolutionary Applications. - 1752-4571. ; 17
  • Journal article (peer-reviewed)abstract
    • Knowledge of functional dispersal barriers in the marine environment can be used to inform a wide variety of management actions, such as marine spatial planning, restoration efforts, fisheries regulations, and invasive species management. Locations and causes of dispersal barriers can be studied through various methods, including movement tracking, biophysical modeling, demographic models, and genetics. Combining methods illustrating potential dispersal, such as biophysical modeling, with realized dispersal through, e.g., genetic connectivity estimates, provides particularly useful information for teasing apart potential causes of observed barriers. In this study, we focus on blue mussels (Mytilus edulis) in the Skagerrak—a marginal sea connected to the North Sea in Northern Europe—and combine biophysical models of larval dispersal with genomic data to infer locations and causes of dispersal barriers in the area. Results from both methods agree; patterns of ocean currents are a major structuring factor in the area. We find a complex pattern of source-sink dynamics with several dispersal barriers and show that some areas can be isolated despite an overall high dispersal capability. Finally, we translate our finding into management advice that can be used to sustainably manage this ecologically and economically important species in the future.
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39.
  • Helmerson, C., et al. (author)
  • Evidence of hybridization between genetically distinct Baltic cod stocks during peak population abundance(s)
  • 2023
  • In: Evolutionary Applications. - 1752-4571. ; 16:7, s. 1359-1376
  • Journal article (peer-reviewed)abstract
    • Range expansions can lead to increased contact of divergent populations, thus increasing the potential of hybridization events. Whether viable hybrids are produced will most likely depend on the level of genomic divergence and associated genomic incompatibilities between the different entities as well as environmental conditions. By taking advantage of historical Baltic cod (Gadus morhua) otolith samples combined with genotyping and whole genome sequencing, we here investigate the genetic impact of the increased spawning stock biomass of the eastern Baltic cod stock in the mid 1980s. The eastern Baltic cod is genetically highly differentiated from the adjacent western Baltic cod and locally adapted to the brackish environmental conditions in the deeper Eastern basins of the Baltic Sea unsuitable for its marine counterparts. Our genotyping results show an increased proportion of eastern Baltic cod in western Baltic areas (Mecklenburg Bay and Arkona Basin)-indicative of a range expansion westwards-during the peak population abundance in the 1980s. Additionally, we detect high frequencies of potential hybrids (including F1, F2 and backcrosses), verified by whole genome sequencing data for a subset of individuals. Analysis of mitochondrial genomes further indicates directional gene flow from eastern Baltic cod males to western Baltic cod females. Our findings unravel that increased overlap in distribution can promote hybridization between highly divergent populations and that the hybrids can be viable and survive under specific and favourable environmental conditions. However, the observed hybridization had seemingly no long-lasting impact on the continuous separation and genetic differentiation between the unique Baltic cod stocks.
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40.
  • Henriques, Dora, et al. (author)
  • Developing reduced SNP assays from whole-genome sequence data to estimate introgression in an organism with complex genetic patterns, the Iberian honeybee (Apis mellifera iberiensis)
  • 2018
  • In: Evolutionary Applications. - : WILEY. - 1752-4571. ; 11:8, s. 1270-1282
  • Journal article (peer-reviewed)abstract
    • The most important managed pollinator, the honeybee (Apis mellifera L.), has been subject to a growing number of threats. In western Europe, one such threat is large-scale introductions of commercial strains (C-lineage ancestry), which is leading to introgressive hybridization and even the local extinction of native honeybee populations (M-lineage ancestry). Here, we developed reduced assays of highly informative SNPs from 176 whole genomes to estimate C-lineage introgression in the most diverse and evolutionarily complex subspecies in Europe, the Iberian honeybee (Apis mellifera iberiensis). We started by evaluating the effects of sample size and sampling a geographically restricted area on the number of highly informative SNPs. We demonstrated that a bias in the number of fixed SNPs (F-ST=1) is introduced when the sample size is small (N10) and when sampling only captures a small fraction of a population's genetic diversity. These results underscore the importance of having a representative sample when developing reliable reduced SNP assays for organisms with complex genetic patterns. We used a training data set to design four independent SNP assays selected from pairwise F-ST between the Iberian and C-lineage honeybees. The designed assays, which were validated in holdout and simulated hybrid data sets, proved to be highly accurate and can be readily used for monitoring populations not only in the native range of A.m.iberiensis in Iberia but also in the introduced range in the Balearic islands, Macaronesia and South America, in a time- and cost-effective manner. While our approach used the Iberian honeybee as model system, it has a high value in a wide range of scenarios for the monitoring and conservation of potentially hybridized domestic and wildlife populations.
  •  
41.
  • Heymans, Adrien (author)
  • Evidence that variation in root anatomy contributes to local adaptation in Mexican native maize
  • 2024
  • In: Evolutionary applications. - 1752-4571. ; 17
  • Journal article (peer-reviewed)abstract
    • Mexican native maize (Zea mays ssp. mays) is adapted to a wide range of climatic and edaphic conditions. Here, we focus specifically on the potential role of root anatomical variation in this adaptation. Given the investment required to characterize root anatomy, we present a machine-learning approach using environmental descriptors to project trait variation from a relatively small training panel onto a larger panel of genotyped and georeferenced Mexican maize accessions. The resulting models defined potential biologically relevant clines across a complex environment that we used subsequently for genotype-environment association. We found evidence of systematic variation in maize root anatomy across Mexico, notably a prevalence of trait combinations favoring a reduction in axial hydraulic conductance in varieties sourced from cooler, drier highland areas. We discuss our results in the context of previously described water-banking strategies and present candidate genes that are associated with both root anatomical and environmental variation. Our strategy is a refinement of standard environmental genome-wide association analysis that is applicable whenever a training set of georeferenced phenotypic data is available.
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42.
  • Hudson, J., et al. (author)
  • Secondary contacts and genetic admixture shape colonization by an amphiatlantic epibenthic invertebrate
  • 2020
  • In: Evolutionary Applications. - : Wiley. - 1752-4571. ; 13:3, s. 600-612
  • Journal article (peer-reviewed)abstract
    • Research on the genetics of invasive species often focuses on patterns of genetic diversity and population structure within the introduced range. However, a growing body of literature is demonstrating the need to study how native genotypes affect both ecological and evolutionary mechanisms within the introduced range. Here, we used genotyping-by-sequencing to study both native and introduced ranges [based on 1,653 single nucleotide polymorphisms (SNPs)] of the amphiatlantic marine invertebrate Ciona intestinalis. A previous study using microsatellites analysed samples collected along the Swedish west coast and showed the presence of genetically distinct lineages in deep and shallow waters. Using 1,653 single nucleotide polymorphisms (SNPs) from newly collected samples (285 individuals), we first confirmed the presence of this depth-defined genomic divergence along the Swedish coast. We then used approximate Bayesian computation to infer the historical relationship among sites from the North Sea, the English Channel and the northwest Atlantic and found evidence of ancestral divergence between individuals from deep waters off Sweden and individuals from the English Channel. This divergence was followed by a secondary contact that led to a genetic admixture between the ancestral populations (i.e., deep Sweden and English Channel), which originated the genotypes found in shallow Sweden. We then revealed that the colonization of C. intestinalis in the northwest Atlantic was as a result of an admixture between shallow Sweden and the English Channel genotypes across the introduced range. Our results showed the presence of both past and recent genetic admixture events that together may have promoted the successful colonizations of C. intestinalis. Our study suggests that secondary contacts potentially reshape the evolutionary trajectories of invasive species through the promotion of intraspecific hybridization and by altering both colonization patterns and their ecological effects in the introduced range.
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43.
  • Ingvarsson, Par K., et al. (author)
  • Genome-wide signatures of environmental adaptation in European aspen (Populus tremula) under current and future climate conditions
  • 2020
  • In: Evolutionary Applications. - : John Wiley & Sons. - 1752-4571. ; 13:1, s. 132-142
  • Journal article (peer-reviewed)abstract
    • Future climate change has been predicted to disrupt local adaptation in many perennial plants, such as forest trees, but the magnitude and location of these effects are thus far poorly understood. Here, we assess local adaptation to current climate in European aspen (Populus tremula) by using environmental association analyses to identify genetic variants associated with two representative climate variables describing current day variation in temperature and precipitation. We also analysed patterns of genetic differentiation between southern and northern populations and observe that regions of high genetic differentiation are enriched for SNPs that are significantly associated with climate. Using variants associated with climate, we examined patterns of isolation by distance and environment and used spatial modelling to predict the geographic distribution of genomic variation in response to two scenarios of future climate change. We show that climate conditions at a northern reference site will correspond to climate conditions experienced by current day populations located 4-8 latitude degrees further south. By assessing the relationship between phenotypic traits and vegetative fitness, we also demonstrate that southern populations harbour genetic variation that likely would be adaptive further north under both climate change scenarios. Current day populations at the lagging edge of the distribution in Sweden can therefore serve as sources for introducing adaptive alleles onto northern populations, but the likelihood of this largely depends on naturally occurring levels of gene flow.
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44.
  • Iqbal, Mudassir, et al. (author)
  • Natural variation of root lesion nematode antagonism in the biocontrol fungus Clonostachys rosea and identification of biocontrol factors through genome-wide association mapping
  • 2020
  • In: Evolutionary applications. - : Wiley. - 1752-4571. ; 13, s. 2264-2283
  • Journal article (peer-reviewed)abstract
    • Biological control is a promising approach to reduce plant diseases caused by nematodes to ensure high productivity in agricultural production. Large-scale analyses of genetic variation in fungal species used for biocontrol can generate knowledge regarding interaction mechanisms that can improve efficacy of biocontrol applications. In this study, we performed a genome-wide association study (GWAS) for in vitro antagonism against the root lesion nematode Pratylenchus penetrans in 53 previously genome re-sequenced strains of the biocontrol fungus Clonostachys rosea. Nematode mortality in C. rosea potato dextrose broth (PDB) culture filtrates was highly variable and showed continuous variation (p < .001) between strains, indicating a polygenic inheritance. Twenty-one strains produced culture filtrates with higher (p <= .05) nematode mortality compared with the PDB control treatment, while ten strains lowered (p <= .05) the mortality. The difference in in vitro antagonism against P. penetrans correlated with antagonism against the soybean cyst nematode Heterodera glycines, indicating lack of host specificity in C. rosea. An empirical Bayesian multiple hypothesis testing approach identified 279 single nucleotide polymorphism markers significantly (local false sign rate < 10(-10)) associated with the trait. Genes present in the genomic regions associated with nematicidal activity included several membrane transporters, a chitinase and genes encoding proteins predicted to biosynthesize secondary metabolites. Gene deletion strains of the predicted nonribosomal peptide synthetase genes nps4 and nps5 were generated and showed increased (p <= .001) fungal growth and conidiation rates compared to the wild type. Deletion strains also exhibited reduced (p < .001) nematicidal activity and reduced (p <= .05) biocontrol efficacy against nematode root disease and against fusarium foot rot on wheat. In summary, we show that the GWAS approach can be used to identify biocontrol factors in C. rosea, specifically the putative nonribosomal peptide synthetases NPS4 and NPS5.
  •  
45.
  • Jia, Kai-Hua, et al. (author)
  • Landscape genomics predicts climate change-related genetic offset for the widespread Platycladus orientalis (Cupressaceae)
  • 2020
  • In: Evolutionary Applications. - : John Wiley & Sons. - 1752-4571. ; 13:4, s. 665-676
  • Journal article (peer-reviewed)abstract
    • Understanding and quantifying populations' adaptive genetic variation and their response to climate change are critical to reforestation's seed source selection, forest management decisions, and gene conservation. Landscape genomics combined with geographic and environmental information provide an opportunity to interrogate forest populations' genome-wide variation for understanding the extent to which evolutionary forces shape past and contemporary populations' genetic structure, and identify those populations that may be most at risk under future climate change. Here, we used genotyping by sequencing to generate over 11,000 high-quality variants from Platycladus orientalis range-wide collection to evaluate its diversity and to predict genetic offset under future climate scenarios. Platycladus orientalis is a widespread conifer in China with significant ecological, timber, and medicinal values. We found population structure and evidences of isolation by environment, indicative of adaptation to local conditions. Gradient forest modeling identified temperature-related variables as the most important environmental factors influencing genetic variation and predicted areas with higher risk under future climate change. This study provides an important reference for forest resource management and conservation for P. orientalis.
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46.
  • Johannesson, Kerstin, 1955, et al. (author)
  • Ten years of marine evolutionary biology - challenges and achievements of a multidisciplinary research initiative
  • 2023
  • In: Evolutionary Applications. - : Wiley. - 1752-4571. ; 16:2, s. 530-41
  • Journal article (peer-reviewed)abstract
    • The Centre for Marine Evolutionary Biology (CeMEB) at the University of Gothenburg, Sweden, was established in 2008 through a 10-year research grant of 8.7 m€ to a team of senior researchers. Today, CeMEB members have contributed >500 scientific publications, 30 PhD theses and have organised 75 meetings and courses, including 18 three-day meetings and four conferences. What are the footprints of CeMEB, and how will the centre continue to play a national and international role as an important node of marine evolutionary research? In this perspective arcticle we first look back over the 10 years of CeMEB activities and briefly survey some of the many achievements of CeMEB. We furthermore compare the initial goals, as formulated in the grant application, with what has been achieved, and discuss challenges and milestones along the way. Finally, we bring forward some general lessons that can be learnt from a research funding of this type, and we take also look ahead, discussing how CeMEB’s achievements and lessons can be used as a springboard to the future of marine evolutionary biology.
  •  
47.
  • Johannesson, Kerstin, 1955 (author)
  • What can be learnt from a snail?
  • 2016
  • In: Evolutionary Applications. - : Wiley. - 1752-4571. ; 9:1, s. 153-165
  • Journal article (peer-reviewed)abstract
    • The marine snail Littorina saxatilis is a common inhabitant of intertidal shores of the north Atlantic. It is amazingly polymorphic and forms reproductively isolated ecotypes in microhabitats where crabs are either present and wave action is less furious, or where waves are strong and crabs are absent. Decades of research have unveiled much of the ecological and demographic context of the formation of crab- and wave-ecotype snails showing important phenotypic differences being inherited, differential selection being strong over adjacent microhabitats, local dispersal being restricted, and long-distance transports of individuals being rare. In addition, strong assortative mating of ecotypes has been shown to include a component of male mate preference based on female size. Several studies support ecotypes being diverged locally and under gene flow in a parallel and highly replicated fashion. The high level of replication at various levels of independence (from local to pan-European scale) provides excellent opportunities to investigate the detailed mechanisms of microevolution, including the formation of barriers to gene flow. Current investigations benefit from a draft reference genome and an integration of genomic approaches, modelling and experiments to unveil molecular and ecological components of speciation and their interactions.
  •  
48.
  • Kardos, Marty, et al. (author)
  • Genomics advances the study of inbreeding depression in the wild
  • 2016
  • In: Evolutionary Applications. - : Wiley. - 1752-4571. ; 9:10, s. 1205-1218
  • Research review (peer-reviewed)abstract
    • Inbreeding depression (reduced fitness of individuals with related parents) has long been a major focus of ecology, evolution, and conservation biology. Despite decades of research, we still have a limited understanding of the strength, underlying genetic mechanisms, and demographic consequences of inbreeding depression in the wild. Studying inbreeding depression in natural populations has been hampered by the inability to precisely measure individual inbreeding. Fortunately, the rapidly increasing availability of high-throughput sequencing data means it is now feasible to measure the inbreeding of any individual with high precision. Here, we review how genomic data are advancing our understanding of inbreeding depression in the wild. Recent results show that individual inbreeding and inbreeding depression can be measured more precisely with genomic data than via traditional pedigree analysis. Additionally, the availability of genomic data has made it possible to pinpoint loci with large effects contributing to inbreeding depression in wild populations, although this will continue to be a challenging task in many study systems due to low statistical power. Now that reliably measuring individual inbreeding is no longer a limitation, a major focus of future studies should be to more accurately quantify effects of inbreeding depression on population growth and viability.
  •  
49.
  • Kardum Hjort, Cecilia, et al. (author)
  • Genomic divergence and a lack of recent introgression between commercial and wild bumblebees (Bombus terrestris)
  • 2022
  • In: Evolutionary Applications. - : Wiley. - 1752-4571. ; 15:3, s. 365-382
  • Journal article (peer-reviewed)abstract
    • The global movement of bees for agricultural pollination services can affect local pollinator populations via hybridization. When commercial bumblebees are of the same species but of different geographic origin, intraspecific hybridization may result in beneficial integration of new genetic variation, or alternatively may disrupt locally adapted gene complexes. However, neither the existence nor the extent of genomic introgression and evolutionary divergence between wild and commercial bumblebees is fully understood. We obtained whole-genome sequencing data from wild and commercial Bombus terrestris collected from sites in Southern Sweden with and without long-term use of commercially imported B. terrestris. We search for evidence of introgression, dispersal and genome-wide differentiation in a comparative genomic analysis of wild and commercial bumblebees. Commercial B. terrestris were found in natural environments near sites where commercial bumblebees were used, as well as drifting wild B. terrestris in commercial bumblebee colonies. However, we found no evidence for widespread, recent genomic introgression of commercial B. terrestris into local wild conspecific populations. We found that wild B. terrestris had significantly higher nucleotide diversity (Nei's pi, π), while the number of segregating sites (Watterson's theta, θw) was higher in commercial B. terrestris. A highly divergent region on chromosome 11 was identified in commercial B. terrestris and found to be enriched with structural variants. The genes present in this region are involved in flight muscle contraction and structure and pathogen immune response, providing evidence for differing evolutionary processes operating in wild and commercial B. terrestris. We did not find evidence for recent introgression, suggesting that co-occurring commercial B. terrestris have not disrupted evolutionary processes in wild B. terrestris populations.
  •  
50.
  • Karlsson Green, Kristina, et al. (author)
  • Making sense of Integrated Pest Management (IPM) in the light of evolution
  • 2020
  • In: Evolutionary applications. - : Wiley. - 1752-4571. ; 13, s. 1791-1805
  • Journal article (peer-reviewed)abstract
    • Integrated Pest Management (IPM) is a holistic approach to combat pests (including herbivores, pathogens, and weeds) using a combination of preventive and curative actions, and only applying synthetic pesticides when there is an urgent need. Just as the recent recognition that an evolutionary perspective is useful in medicine to understand and predict interactions between hosts, diseases, and medical treatments, we argue that it is crucial to integrate an evolutionary framework in IPM to develop efficient and reliable crop protection strategies that do not lead to resistance development in herbivores, pathogens, and weeds. Such a framework would not only delay resistance evolution in pests, but also optimize each element of the management and increase the synergies between them. Here, we outline key areas within IPM that would especially benefit from a thorough evolutionary understanding. In addition, we discuss the difficulties and advantages of enhancing communication among research communities rooted in different biological disciplines and between researchers and society. Furthermore, we present suggestions that could advance implementation of evolutionary principles in IPM and thus contribute to the development of sustainable agriculture that is resilient to current and emerging pests.
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