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  • 1.
    Chen, Jun
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Li, Lili
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Milesi, Pascal
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Jansson, Gunnar
    Forestry Res Inst Sweden Skogforsk, Uppsala, Sweden.
    Berlin, Mats
    Forestry Res Inst Sweden Skogforsk, Uppsala, Sweden.
    Karlsson, Bo
    Forestry Res Inst Sweden Skogforsk, Ekebo, Sweden.
    Aleksic, Jelena
    Univ Belgrade, Inst Mol Genet & Genet Engn, Belgrade, Serbia.
    Vendramin, Giovanni G.
    CNR, Natl Res Council IBBR, Div Florence, Inst Biosci & BioResources, Sesto Fiorentino, Italy.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Genomic data provide new insights on the demographic history and the extent of recent material transfers in Norway spruce2019In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571, Vol. 12, no 8, p. 1539-1551Article in journal (Refereed)
    Abstract [en]

    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.

  • 2.
    Cornille, Amandine
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Feurtey, Alice
    Gelin, Uriel
    Ropars, Jeanne
    Misvanderbrugge, Kristine
    Gladieux, Pierre
    Giraud, Tatiana
    Anthropogenic and natural drivers of gene flow in a temperate wild fruit tree: a basis for conservation and breeding programs in apples2015In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571, Vol. 8, no 4, p. 373-384Article in journal (Refereed)
    Abstract [en]

    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.

  • 3.
    Ekblom, Robert
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    A field guide to whole-genome sequencing, assembly and annotation2014In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571, Vol. 7, no 9, p. 1026-1042Article in journal (Refereed)
    Abstract [en]

    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.

  • 4.
    Feurtey, Alice
    et al.
    Univ Paris Saclay, AgroParisTech, CNRS, Ecol Systemat Evolut,Univ Paris Sud, Orsay, France..
    Cornille, Amandine
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Paris Saclay, AgroParisTech, CNRS, Ecol Systemat Evolut,Univ Paris Sud, Orsay, France.;Swiss Fed Inst Technol, Adaptat Changing Environm, Zurich, Switzerland.;Swiss Fed Inst Technol, Inst Integrat Biol, Zurich, Switzerland..
    Shykoff, Jacqui A.
    Univ Paris Saclay, AgroParisTech, CNRS, Ecol Systemat Evolut,Univ Paris Sud, Orsay, France..
    Snirc, Alodie
    Univ Paris Saclay, AgroParisTech, CNRS, Ecol Systemat Evolut,Univ Paris Sud, Orsay, France..
    Giraud, Tatiana
    Univ Paris Saclay, AgroParisTech, CNRS, Ecol Systemat Evolut,Univ Paris Sud, Orsay, France..
    Crop-to-wild gene flow and its fitness consequences for a wild fruit tree: Towards a comprehensive conservation strategy of the wild apple in Europe2017In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571, Vol. 10, no 2, p. 180-188Article in journal (Refereed)
    Abstract [en]

    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.

  • 5.
    Fountain, Toby
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ Helsinki, Dept Biosci, Helsinki, Finland.
    Husby, Arild
    Univ Helsinki, Dept Biosci, Helsinki, Finland.
    Nonaka, Etsuko
    Univ Helsinki, Dept Biosci, Helsinki, Finland;Lund Univ, Dept Biol, Lund, Sweden.
    Dileo, Michelle F.
    Univ Helsinki, Dept Biosci, Helsinki, Finland.
    Korhonen, Janne H.
    Univ Helsinki, Dept Biosci, Helsinki, Finland;Aalto Univ, Dept Comp Sci, Aalto, Finland.
    Rastas, Pasi
    Univ Helsinki, Dept Biosci, Helsinki, Finland;Univ Cambridge, Dept Zool, Cambridge, England.
    Schulz, Torsti
    Univ Helsinki, Dept Biosci, Helsinki, Finland.
    Saastamoinen, Marjo
    Univ Helsinki, Dept Biosci, Helsinki, Finland.
    Hanski, Ilkka
    Univ Helsinki, Dept Biosci, Helsinki, Finland.
    Inferring dispersal across a fragmented landscape using reconstructed families in the Glanville fritillary butterfly2018In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571, Vol. 11, no 3, p. 287-297Article in journal (Refereed)
    Abstract [en]

    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 Aland 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.

  • 6.
    Gering, Eben
    et al.
    Michigan State Univ, MI 48824 USA.
    Incorvaia, Darren
    Michigan State Univ, MI 48824 USA.
    Henriksen, Rie
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Getty, Thomas
    Michigan State Univ, MI 48824 USA.
    Maladaptation in feral and domesticated animals2019In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571, Vol. 12, no 7, p. 1274-1286Article, review/survey (Refereed)
    Abstract [en]

    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.

  • 7.
    Henriques, Dora
    et al.
    Univ Minho, Ctr Mol & Environm Biol CBMA, Braga, Portugal;Polytech Inst Braganca, Mt Res Ctr CIMO, Braganca, Portugal.
    Parejo, Melanie
    Agroscope, Swiss Bee Res Ctr, Bern, Switzerland;Univ Bern, Vetsuisse Fac, Inst Bee Hlth, Bern, Switzerland.
    Vignal, Alain
    Univ Toulouse, GenPhySE, INRA, INPT,INP ENVT, Castanet Tolosan, France.
    Wragg, David
    Univ Edinburgh, Roslin Inst, Edinburgh, Midlothian, Scotland.
    Wallberg, Andreas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Webster, Matthew Thomas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Pinto, M. Alice
    Polytech Inst Braganca, Mt Res Ctr CIMO, Braganca, Portugal.
    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)2018In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571, Vol. 11, no 8, p. 1270-1282Article in journal (Refereed)
    Abstract [en]

    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.

  • 8. Jia, Kai-Hua
    et al.
    Zhao, Wei
    Maier, Paul Andrew
    Hu, Xian-Ge
    Jin, Yuqing
    Zhou, Shan-Shan
    Jiao, Si-Qian
    El-Kassaby, Yousry A.
    Wang, Tongli
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
    Mao, Jian-Feng
    Landscape genomics predicts climate change-related genetic offset for the widespread Platycladus orientalis (Cupressaceae)2019In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571Article in journal (Refereed)
    Abstract [en]

    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.

  • 9.
    Kardos, Marty
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Taylor, Helen R.
    Univ Otago, Dept Anat, Dunedin, New Zealand..
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Luikart, Gordon
    Univ Montana, Div Biol Sci, Missoula, MT 59812 USA.;Univ Montana, Flathead Lake Biol Stn, Div Biol Sci, Polson, MT 59860 USA..
    Allendorf, Fred W.
    Univ Montana, Div Biol Sci, Missoula, MT 59812 USA..
    Genomics advances the study of inbreeding depression in the wild2016In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571, Vol. 9, no 10, p. 1205-1218Article, review/survey (Refereed)
    Abstract [en]

    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.

  • 10.
    Martinossi-Allibert, Ivain
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Thilliez, Emma
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Arnqvist, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Berger, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Sexual selection, environmental robustness and evolutionary demography of maladapted populations: a test using experimental evolution in seed beetles2019In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571, Vol. 12, no 7, p. 1371-1384Article in journal (Refereed)
    Abstract [en]

    Whether sexual selection impedes or aids adaptation has become an outstanding question in times of rapid environmental change and parallels the debate about how the evolution of individual traits impacts on population dynamics. The net effect of sexual selection on population viability results from a balance between genetic benefits of “good‐genes” effects and costs of sexual conflict. Depending on how these facets of sexual selection are affected under environmental change, extinction of maladapted populations could be either avoided or accelerated. Here, we evolved seed beetles under three alternative mating regimes to disentangle the contributions of sexual selection, fecundity selection, and male–female coevolution to individual reproductive success and population fitness. We compared these contributions between the ancestral environment and two stressful environments (elevated temperature and a host plant shift). We found evidence that sexual selection on males had positive genetic effects on female fitness components across environments, supporting good‐genes sexual selection. Interestingly, however, when males evolved under sexual selection with fecundity selection removed, they became more robust to both temperature and host plant stress compared to their conspecific females and males from the other evolution regimes that applied fecundity selection. We quantified the population‐level consequences of this sex‐specific adaptation and found evidence that the cost of sociosexual interactions in terms of reduced offspring production was higher in the regime applying only sexual selection to males. Moreover, the cost tended to be more pronounced at the elevated temperature to which males from the regime were more robust compared to their conspecific females. These results illustrate the tension between individual‐level adaptation and population‐level viability in sexually reproducing species and suggest that the relative efficacies of sexual selection and fecundity selection can cause inherent sex differences in environmental robustness that may impact demography of maladapted populations.

  • 11. McMahon, Barry J.
    et al.
    Teeling, Emma C.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    How and why should we implement genomics into conservation?2014In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571, Vol. 7, no 9, p. 999-1007Article, review/survey (Refereed)
    Abstract [en]

    Conservation genetics has provided important information into the dynamics of endangered populations. The rapid development of genomic methods has posed an important question, namely where do genetics and genomics sit in relation to their application in the conservation of species? Although genetics can answer a number of relevant questions related to conservation, the argument for the application of genomics is not yet fully exploited. Here, we explore the transition and rationale for the move from genetic to genomic research in conservation biology and the utility of such research. We explore the idea of a conservation prior' and how this can be determined by genomic data and used in the management of populations. We depict three different conservation scenarios and describe how genomic data can drive management action in each situation. We conclude that the most effective applications of genomics will be to inform stakeholders with the aim of avoiding emergency room conservation'.

  • 12.
    Milesi, Pascal
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Berlin, Mats
    The Forestry Research Institute of Sweden (Skogforsk), Uppsala, Sweden.
    Chen, Jun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Orsucci, Marion
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Li, Lili
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Jansson, Gunnar
    The Forestry Research Institute of Sweden (Skogforsk), Uppsala, Sweden.
    Karlsson, Bo
    The Forestry Research Institute of Sweden (Skogforsk), Ekebo, Sweden.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Assessing the potential for assisted gene flow using past introduction of Norway spruce in southern Sweden: Local adaptation and genetic basis of quantitative traits in trees2019In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571, Vol. 12, no 10, p. 1946-1959Article in journal (Refereed)
    Abstract [en]

    Norway spruce (Picea abies) is a dominant conifer species of major economic importance in northern Europe. Extensive breeding programs were established to improve phenotypic traits of economic interest. In southern Sweden, seeds used to create progeny tests were collected on about 3,000 trees of outstanding phenotype (‘plus’ trees) across the region. In a companion paper, we showed that some were of local origin but many were recent introductions from the rest of the natural range. The mixed origin of the trees together with partial sequencing of the exome of >1,500 of these trees and phenotypic data retrieved from the Swedish breeding program offered a unique opportunity to dissect the genetic basis of local adaptation of three quantitative traits (height, diameter and bud-burst) and assess the potential of assisted gene flow. Through a combination of multivariate analyses and genome-wide association studies, we showed that there was a very strong effect of geographical origin on growth (height and diameter) and phenology (bud-burst) with trees from southern origins outperforming local provenances. Association studies revealed that growth traits were highly polygenic and bud-burst somewhat less. Hence, our results suggest that assisted gene flow and genomic selection approaches could help to alleviate the effect of climate change on P. abies breeding programs in Sweden.

  • 13. Northrup, Joseph M.
    et al.
    Shafer, Aaron B. A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Anderson, Charles R., Jr.
    Coltman, David W.
    Wittemyer, George
    Fine-scale genetic correlates to condition and migration in a wild cervid2014In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571, Vol. 7, no 8, p. 937-948Article in journal (Refereed)
    Abstract [en]

    The relationship between genetic variation and phenotypic traits is fundamental to the study and management of natural populations. Such relationships often are investigated by assessing correlations between phenotypic traits and heterozygosity or genetic differentiation. Using an extensive data set compiled from free-ranging mule deer (Odocoileus hemionus), we combined genetic and ecological data to (i) examine correlations between genetic differentiation and migration timing, (ii) screen for mitochondrial haplotypes associated with migration timing, and (iii) test whether nuclear heterozygosity was associated with condition. Migration was related to genetic differentiation (more closely related individuals migrated closer in time) and mitochondrial haplogroup. Body fat was related to heterozygosity at two nuclear loci (with antagonistic patterns), one of which is situated near a known fat metabolism gene in mammals. Despite being focused on a widespread panmictic species, these findings revealed a link between genetic variation and important phenotypes at a fine scale. We hypothesize that these correlations are either the result of mixing refugial lineages or differential mitochondrial haplotypes influencing energetics. The maintenance of phenotypic diversity will be critical to enable the potential tracking of changing climatic conditions, and these correlates highlight the need to consider evolutionary mechanisms in management, even in widely distributed panmictic species.

  • 14.
    Orizaola, German
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Laurila, Anssi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Developmental plasticity increases at the northern range margin in a warm-dependent amphibian2016In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571, Vol. 9, no 3, p. 471-478Article in journal (Refereed)
    Abstract [en]

    Accurate predictions regarding how climate change affects species and populations are crucial for the development of effective conservation measures. However, models forecasting the impact of climate change on natural environments do not often consider the geographic variation of an organism's life history. We examined variation in developmental plasticity to changing temperature in the pool frog (Pelophylax lessonae) across its distribution by studying populations from central areas (Poland), edge populations (Latvia) and northern marginal populations (Sweden). Relative to central and edge populations, northern populations experience lower and less variable temperature and fewer episodes of warm weather during larval development. Plasticity in larval life-history traits was highest at the northern range margin: larvae from marginal populations shortened larval period and increased growth rate more than larvae from central and edge populations when reared at high temperature. Maintaining high growth and development under the scarce spells of warm weather is likely adaptive for high-latitude populations. The detection of high levels of developmental plasticity in isolated, marginal populations suggests that they may be better able to respond to the temperature regimes expected under climate change than often predicted, reflecting the need to incorporate geographic variation in life-history traits into models forecasting responses to environmental change.

  • 15.
    Qvarnström, Anna
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Ålund, Murielle
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    McFarlane, Eryn S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Sirkiä, Päivi M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Univ Helsinki, Finnish Museum Nat Hist, Zool Unit, Helsinki, Finland.
    Climate adaptation and speciation: particular focus on reproductive barriers in Ficedula flycatchers2015In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571, Vol. 9, no 1, p. 119-134Article, review/survey (Refereed)
    Abstract [en]

    Climate adaptation is surprisingly rarely reported as a cause for the build-up of reproductive isolation between diverging populations. In this review, we summarize evidence for effects of climate adaptation on pre- and postzygotic isolation between emerging species with a particular focus on pied (Ficedula hypoleuca) and collared (Ficedula albicollis) flycatchers as a model for research on speciation. Effects of climate adaptation on prezygotic isolation or extrinsic selection against hybrids have been documented in several taxa, but the combined action of climate adaptation and sexual selection is particularly well explored in Ficedula flycatchers. There is a general lack of evidence for divergent climate adaptation causing intrinsic postzygotic isolation. However, we argue that the profound effects of divergence in climate adaptation on the whole biochemical machinery of organisms and hence many underlying genes should increase the likelihood of genetic incompatibilities arising as side effects. Fast temperature-dependent co-evolution between mitochondrial and nuclear genomes may be particularly likely to lead to hybrid sterility. Thus, how climate adaptation relates to reproductive isolation is best explored in relation to fast-evolving barriers to gene flow, while more research on later stages of divergence is needed to achieve a complete understanding of climate-driven speciation.

  • 16.
    Shafer, Aaron B. A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Nielsen, Scott E.
    Northrup, Joseph M.
    Stenhouse, Gordon B.
    Linking genotype, ecotype, and phenotype in an intensively managed large carnivore2014In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571, Vol. 7, no 2, p. 301-312Article in journal (Refereed)
    Abstract [en]

    Numerous factors influence fitness of free-ranging animals, yet often these are uncharacterized. We integrated GPS habitat use data and genetic profiling to determine their influence on fitness proxies (mass, length, and body condition) in a threatened population of grizzly bears (Ursus arctos) in Alberta, Canada. We detected distinct genetic and habitat use (ecotype) clusters, with individual cluster assignments, or genotype/ecotype, being correlated (Pearson r=0.34, P<0.01). Related individuals showed evidence of similar habitat use patterns, irrespective of geographic distance and sex. Fitness proxies were influenced by sex, age, and habitat use, and homozygosity had a positive effect on these proxies that could be indicative of outbreeding depression. We further documented over 300 translocations occurring in the province since the 1970s, often to areas with significantly different habitat. We argue this could be unintentionally causing the pattern of outbreeding, although the heterozygosity correlation may instead be explained by the energetic costs associated with larger body size. The observed patterns, together with the unprecedented human-mediated migrations, make understanding the link between genotype, ecotype, and phenotype and mechanisms behind the negative heterozygosity-fitness correlations critical for management and conservation of this species.

  • 17. Sudo, Masaaki
    et al.
    Takahashi, Daisuke
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Andow, David A.
    Suzuki, Yoshito
    Yamanaka, Takehiko
    Optimal management strategy of insecticide resistance under various insect life histories: heterogeneous timing of selection and interpatch dispersal2018In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571, Vol. 11, no 2, p. 271-283, article id GENTINE JA, 1994, JOURNAL OF AGRICULTURAL ENTOMOLOGY, V11, P137 elza Pablo, 2008, PEST MANAGEMENT SCIENCE1st Global Workshop on Stewardship of Neonicotinoid secticides, JUN 05-SEP 09, 2008, Honolulu, HI, V64, P1131Article in journal (Refereed)
    Abstract [en]

    Although theoretical studies have shown that the mixture strategy, which uses multiple toxins simultaneously, can effectively delay the evolution of insecticide resistance, whether it is the optimal management strategy under different insect life histories and insecticide types remains unknown. To test the robustness of this management strategy over different life histories, we developed a series of simulation models that cover almost all the diploid insect types and have the same basic structure describing pest population dynamics and resistance evolution with discrete time steps. For each of two insecticidal toxins, independent one-locus two-allele autosomal inheritance of resistance was assumed. The simulations demonstrated the optimality of the mixture strategy either when insecticide efficacy was incomplete or when some part of the population disperses between patches before mating. The rotation strategy, which uses one insecticide on one pest generation and a different one on the next, did not differ from sequential usage in the time to resistance, except when dominance was low. It was the optimal strategy when insecticide efficacy was high and premating selection and dispersal occur.

  • 18.
    Walters, Richard J.
    et al.
    Lund Univ, Ctr Environm & Climate Res, Solvegatan 37, S-22362 Lund, Sweden;Univ Reading, Sch Biol Sci, Reading, Berks, England.
    Berger, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Implications of existing local (mal)adaptations for ecological forecasting under environmental change2019In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571, Vol. 12, no 7, p. 1487-1502Article in journal (Refereed)
    Abstract [en]

    Standing genetic variation represents a genetic load on population fitness but can also support a rapid response to short-term environmental change, and the greatest potential source of such standing genetic variation typically exists among locally adapted populations living along an environmental gradient. Here, we develop a spatially explicit simulation model to quantify the contribution of existing genetic variation arising from migration-mutation-selection-drift balance to time to extinction under environmental change. Simulations reveal that local adaptation across a species range associated with an underlying environmental gradient could extend time to extinction by nearly threefold irrespective of the rate of environmental change. The potential for preadapted alleles to increase the rate of adaptation changes the relative importance of established extinction risk factors; in particular, it reduced the importance of the breadth of environmental tolerance and it increased the relative importance of fecundity. Although migration of preadapted alleles generally increased persistence time, it decreased it at rates of environmental change close to the critical rate of change by creating a population bottleneck, which ultimately limited the rate at which de novo mutations could arise. An analysis of the extinction dynamics further revealed that one consequence of gene flow is the potential to maximize population growth rate in at least part of the species range, which is likely to have consequences for forecasting the consequences of ecological interactions. Our study shows that predictions of persistence time change fundamentally when existing local adaptations are explicitly taken into account, underscoring the need to preserve and manage genetic diversity.

  • 19. Weeks, Andrew R.
    et al.
    Sgro, Carla M.
    Young, Andrew G.
    Frankham, Richard
    Mitchell, Nicki J.
    Miller, Kim A.
    Byrne, Margaret
    Coates, David J.
    Eldridge, Mark D. B.
    Sunnucks, Paul
    Breed, Martin F.
    Australian Centre for Evolutionary Biology and Biodiversity, and School of Earth and Environmental Science, University of Adelaide.
    James, Elizabeth A.
    Hoffmann, Ary A.
    Assessing the benefits and risks of translocations in changing environments: a genetic perspective2011In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571, Vol. 4, no 6, p. 709-725Article in journal (Refereed)
    Abstract [en]

    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.

  • 20. Xia, Hanhan
    et al.
    Wang, Baosheng
    Zhao, Wei
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Pan, Jin
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Mao, Jian-Feng
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
    Combining mitochondrial and nuclear genome analyses to dissect the effects of colonization, environment, and geography on population structure in Pinus tabuliformis2018In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571, Vol. 11, no 10, p. 1931-1945Article in journal (Refereed)
    Abstract [en]

    The phylogeographic histories of plants in East Asia are complex and shaped by both past large‐scale climatic oscillations and dramatic tectonic events. The impact of these historic events, as well as ecological adaptation, on the distribution of biodiversity remains to be elucidated. Pinus tabuliformis is the dominant coniferous tree in northern China, with a large distribution across wide environmental gradients. We examined genetic variation in this species using genotyping‐by‐sequencing and mitochondrial (mt) DNA markers. We found population structure on both nuclear and mt genomes with a geographic pattern that corresponds well with the landscape of northern China. To understand the contributions of environment, geography, and colonization history to the observed population structure, we performed ecological niche modeling and partitioned the among‐population genomic variance into isolation by environment (IBE), isolation by distance (IBD), and isolation by colonization (IBC). We used mtDNA, which is transmitted by seeds in pine, to reflect colonization. We found little impact of IBE, IBD, and IBC on variation in neutral SNPs, but significant impact of IBE on a group of outlier loci. The lack of IBC illustrates that the maternal history can be quickly eroded from the nuclear genome by high rates of gene flow. Our results suggest that genomic variation in P. tabuliformis is largely affected by neutral and stochastic processes, and the signature of local adaptation is visible only at robust outlier loci. This study enriches our understanding on the complex evolutionary forces that shape the distribution of genetic variation in plant taxa in northern China, and guides breeding, conservation, and reforestation programs for P. tabuliformis.

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