Publications by authors named "Outi Savolainen"

63 Publications

Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research.

Plant J 2021 Dec 11. Epub 2021 Dec 11.

Department of Ecology and Genetics, University of Oulu, P.O. Box 3000, 90014, Oulu, Finland.

Pinus sylvestris (Scots pine) is the most widespread coniferous tree in the boreal forests of Eurasia, with major economic and ecological importance. However, its large and repetitive genome presents a challenge for conducting genome-wide analyses such as association studies, genetic mapping and genomic selection. We present a new 50K single-nucleotide polymorphism (SNP) genotyping array for Scots pine research, breeding and other applications. To select the SNP set, we first genotyped 480 Scots pine samples on a 407 540 SNP screening array and identified 47 712 high-quality SNPs for the final array (called 'PiSy50k'). Here, we provide details of the design and testing, as well as allele frequency estimates from the discovery panel, functional annotation, tissue-specific expression patterns and expression level information for the SNPs or corresponding genes, when available. We validated the performance of the PiSy50k array using samples from Finland and Scotland. Overall, 39 678 (83.2%) SNPs showed low error rates (mean = 0.9%). Relatedness estimates based on array genotypes were consistent with the expected pedigrees, and the level of Mendelian error was negligible. In addition, array genotypes successfully discriminate between Scots pine populations of Finnish and Scottish origins. The PiSy50k SNP array will be a valuable tool for a wide variety of future genetic studies and forestry applications.
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http://dx.doi.org/10.1111/tpj.15628DOI Listing
December 2021

Municipal strategies and meeting minutes' descriptions of the promotion of children's mental health: a document analysis.

Scand J Public Health 2021 Jul 8;49(5):519-528. Epub 2020 Oct 8.

Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Finland.

Aims: Little is known about how municipal strategies, programmes and plans pay attention to the promotion of children's mental health and whether it is discussed and reported in the municipal councils, boards and committees. The purpose of this study was to examine how municipalities in one Finnish region promote mental health, with a focus on the promotion of children's mental health.

Methods: Document analysis was used as a research method. Documents were selected for a one-year period (2018) from three municipalities of the North Savo region. Analysed documents (=269) were municipal strategies, programmes and plans, as well as meeting minutes of municipal councils, boards and committees. Eight domains of the structural indicators of mental health were used as an analysis frame.

Results: In total, 1169 mentions related to the structural indicators of mental health were found in the documents. In strategies, programmes and plans, parenting-related mentions were found most often. Regarding the minutes, the issues discussed and reported about the wellbeing of children focused on practical issues, such as the construction of day care buildings.

Conclusions:
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http://dx.doi.org/10.1177/1403494820961902DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8512289PMC
July 2021

Adaptive responses to temperature and precipitation variation at the early-life stages of Pinus sylvestris.

New Phytol 2021 11 6;232(4):1632-1647. Epub 2021 Sep 6.

Department of Forest Ecology & Genetics, Forest Research Centre (INIA, CSIC), Ctra. de la Coruña km 7.5, Madrid, 28040, Spain.

Early-stage fitness variation has been seldom evaluated at broad scales in forest tree species, despite the long tradition of studying climate-driven intraspecific genetic variation. In this study, we evaluated the role of climate in driving patterns of population differentiation at early-life stages in Pinus sylvestris and explored the fitness and growth consequences of seed transfer within the species range. We monitored seedling emergence, survival and growth over a 2-yr period in a multi-site common garden experiment which included 18 European populations and spanned 25° in latitude and 1700 m in elevation. Climate-fitness functions showed that populations exhibited higher seedling survival and growth at temperatures similar to their home environment, which is consistent with local adaptation. Northern populations experienced lower survival and growth at warmer sites, contrary to previous studies on later life stages. Seed mass was higher in populations from warmer areas and was positively associated with survival and growth at more southern sites. Finally, we did not detect a survival-growth trade-off; on the contrary, bigger seedlings exhibited higher survival probabilities under most climatic conditions. In conclusion, our results reveal that contrasting temperature regimes have played an important role in driving the divergent evolution of P. sylvestris populations at early-life stages.
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http://dx.doi.org/10.1111/nph.17678DOI Listing
November 2021

Public health nurses' perceptions on promotive and risk factors for children's mental health: A qualitative interview study.

J Adv Nurs 2021 Dec 28;77(12):4815-4826. Epub 2021 Jul 28.

Department of Nursing Science, University of Eastern Finland, Kuopio, Finland.

Aim: To describe promotive and risk factors for children's mental health at the individual, interpersonal, organizational, community and public policy levels of the socioecological environment.

Design: A descriptive qualitative interview study.

Methods: Data were collected in Finland during autumn 2019 via semi-structured interviews. Participants (n = 23) comprised public health nurses who worked in child health clinics and school healthcare. Data were analyzed using inductive content analysis.

Results: Several promotive and risk factors were identified to have affected children's mental health. Intra-family factors were the most important in the opinion of public health nurses, and they were most concerned about family related risk factors. In addition, the descriptions of nurses revealed that children are in a socially unequal position in terms of their place of residence. It was also uncovered that there were fewer social and healthcare and leisure services in small municipalities, the distances to services were longer, which was perceived to complicate the use of services, and the fear of stigma was greater.

Conclusion: According to public health nurses, factors at the individual, interpersonal, organizational, community and public policy levels of the socioecological environment affect children's mental health and overall well-being. Consequently, the promotion of children's mental health should be emphasized at every level of the society, considering the whole family.

Impact: This study indicated the importance of considering factors that affect children's mental health at all levels of the socioecological environment. The results can be reflected in the relation of the socioecological model of health promotion and used in planning the work of nurses in primary healthcare and other relevant nursing settings to emphasize promotive and preventive work.
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http://dx.doi.org/10.1111/jan.14987DOI Listing
December 2021

The GenTree Platform: growth traits and tree-level environmental data in 12 European forest tree species.

Gigascience 2021 03;10(3)

Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR), Ctra. de la Coruña km 7.5, 28040, Madrid, Spain.

Background: Progress in the field of evolutionary forest ecology has been hampered by the huge challenge of phenotyping trees across their ranges in their natural environments, and the limitation in high-resolution environmental information.

Findings: The GenTree Platform contains phenotypic and environmental data from 4,959 trees from 12 ecologically and economically important European forest tree species: Abies alba Mill. (silver fir), Betula pendula Roth. (silver birch), Fagus sylvatica L. (European beech), Picea abies (L.) H. Karst (Norway spruce), Pinus cembra L. (Swiss stone pine), Pinus halepensis Mill. (Aleppo pine), Pinus nigra Arnold (European black pine), Pinus pinaster Aiton (maritime pine), Pinus sylvestris L. (Scots pine), Populus nigra L. (European black poplar), Taxus baccata L. (English yew), and Quercus petraea (Matt.) Liebl. (sessile oak). Phenotypic (height, diameter at breast height, crown size, bark thickness, biomass, straightness, forking, branch angle, fructification), regeneration, environmental in situ measurements (soil depth, vegetation cover, competition indices), and environmental modeling data extracted by using bilinear interpolation accounting for surrounding conditions of each tree (precipitation, temperature, insolation, drought indices) were obtained from trees in 194 sites covering the species' geographic ranges and reflecting local environmental gradients.

Conclusion: The GenTree Platform is a new resource for investigating ecological and evolutionary processes in forest trees. The coherent phenotyping and environmental characterization across 12 species in their European ranges allow for a wide range of analyses from forest ecologists, conservationists, and macro-ecologists. Also, the data here presented can be linked to the GenTree Dendroecological collection, the GenTree Leaf Trait collection, and the GenTree Genomic collection presented elsewhere, which together build the largest evolutionary forest ecology data collection available.
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http://dx.doi.org/10.1093/gigascience/giab010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7970660PMC
March 2021

Maintenance of Adaptive Dynamics and No Detectable Load in a Range-Edge Outcrossing Plant Population.

Mol Biol Evol 2021 05;38(5):1820-1836

Institute of Botany, University of Cologne, Cologne, Germany.

During range expansion, edge populations are expected to face increased genetic drift, which in turn can alter and potentially compromise adaptive dynamics, preventing the removal of deleterious mutations and slowing down adaptation. Here, we contrast populations of the European subspecies Arabidopsis lyrata ssp. petraea, which expanded its Northern range after the last glaciation. We document a sharp decline in effective population size in the range-edge population and observe that nonsynonymous variants segregate at higher frequencies. We detect a 4.9% excess of derived nonsynonymous variants per individual in the range-edge population, suggesting an increase of the genomic burden of deleterious mutations. Inference of the fitness effects of mutations and modeling of allele frequencies under the explicit demographic history of each population predicts a depletion of rare deleterious variants in the range-edge population, but an enrichment for fixed ones, consistent with the bottleneck effect. However, the demographic history of the range-edge population predicts a small net decrease in per-individual fitness. Consistent with this prediction, the range-edge population is not impaired in its growth and survival measured in a common garden experiment. We further observe that the allelic diversity at the self-incompatibility locus, which ensures strict outcrossing and evolves under negative frequency-dependent selection, has remained unchanged. Genomic footprints indicative of selective sweeps are broader in the Northern population but not less frequent. We conclude that the outcrossing species A. lyrata ssp. petraea shows a strong resilience to the effect of range expansion.
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http://dx.doi.org/10.1093/molbev/msaa322DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8097302PMC
May 2021

Selection patterns on early-life phenotypic traits in Pinus sylvestris are associated with precipitation and temperature along a climatic gradient in Europe.

New Phytol 2021 03 22;229(5):3009-3025. Epub 2020 Nov 22.

Department of Forest Ecology & Genetics, INIA-CIFOR, Ctra. de la Coruña km 7.5, Madrid, 28040, Spain.

Understanding the dynamics of selection is key to predicting the response of tree species to new environmental conditions in the current context of climate change. However, selection patterns acting on early recruitment stages and their climatic drivers remain largely unknown in most tree species, despite being a critical period of their life cycle. We measured phenotypic selection on Pinus sylvestris seed mass, emergence time and early growth rate over 2 yr in four common garden experiments established along the latitudinal gradient of the species in Europe. Significant phenotypic plasticity and among-population genetic variation were found for all measured phenotypic traits. Heat and drought negatively affected fitness in the southern sites, but heavy rainfalls also decreased early survival in middle latitudes. Climate-driven directional selection was found for higher seed mass and earlier emergence time, while the form of selection on seedling growth rates differed among sites and populations. Evidence of adaptive and maladaptive phenotypic plasticity was found for emergence time and early growth rate, respectively. Seed mass, emergence time and early growth rate have an adaptive role in the early stages of P. sylvestris and climate strongly influences the patterns of selection on these fitness-related traits.
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http://dx.doi.org/10.1111/nph.17029DOI Listing
March 2021

Genomics of Clinal Local Adaptation in Under Continuous Environmental and Spatial Genetic Setting.

G3 (Bethesda) 2020 08 5;10(8):2683-2696. Epub 2020 Aug 5.

Department of Ecology and Genetics, University of Oulu, FI-90014 Oulu, Finland,

Understanding the consequences of local adaptation at the genomic diversity is a central goal in evolutionary genetics of natural populations. In species with large continuous geographical distributions the phenotypic signal of local adaptation is frequently clear, but the genetic basis often remains elusive. We examined the patterns of genetic diversity in , a keystone species in many Eurasian ecosystems with a huge distribution range and decades of forestry research showing that it is locally adapted to the vast range of environmental conditions. Making an even more attractive subject of local adaptation study, population structure has been shown to be weak previously and in this study. However, little is known about the molecular genetic basis of adaptation, as the massive size of gymnosperm genomes has prevented large scale genomic surveys. We generated a both geographically and genomically extensive dataset using a targeted sequencing approach. By applying divergence-based and landscape genomics methods we identified several loci contributing to local adaptation, but only few with large allele frequency changes across latitude. We also discovered a very large (ca. 300 Mbp) putative inversion potentially under selection, which to our knowledge is the first such discovery in conifers. Our results call for more detailed analysis of structural variation in relation to genomic basis of local adaptation, emphasize the lack of large effect loci contributing to local adaptation in the coding regions and thus point out the need for more attention toward multi-locus analysis of polygenic adaptation.
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http://dx.doi.org/10.1534/g3.120.401285DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7407466PMC
August 2020

Evolutionary genomics can improve prediction of species' responses to climate change.

Evol Lett 2020 Feb 14;4(1):4-18. Epub 2020 Jan 14.

Senckenberg Biodiversity and Climate Research Centre Frankfurt am Main Germany.

Global climate change (GCC) increasingly threatens biodiversity through the loss of species, and the transformation of entire ecosystems. Many species are challenged by the pace of GCC because they might not be able to respond fast enough to changing biotic and abiotic conditions. Species can respond either by shifting their range, or by persisting in their local habitat. If populations persist, they can tolerate climatic changes through phenotypic plasticity, or genetically adapt to changing conditions depending on their genetic variability and census population size to allow for de novo mutations. Otherwise, populations will experience demographic collapses and species may go extinct. Current approaches to predicting species responses to GCC begin to combine ecological and evolutionary information for species distribution modelling. Including an evolutionary dimension will substantially improve species distribution projections which have not accounted for key processes such as dispersal, adaptive genetic change, demography, or species interactions. However, eco-evolutionary models require new data and methods for the estimation of a species' adaptive potential, which have so far only been available for a small number of model species. To represent global biodiversity, we need to devise large-scale data collection strategies to define the ecology and evolutionary potential of a broad range of species, especially of keystone species of ecosystems. We also need standardized and replicable modelling approaches that integrate these new data to account for eco-evolutionary processes when predicting the impact of GCC on species' survival. Here, we discuss different genomic approaches that can be used to investigate and predict species responses to GCC. This can serve as guidance for researchers looking for the appropriate experimental setup for their particular system. We furthermore highlight future directions for moving forward in the field and allocating available resources more effectively, to implement mitigation measures before species go extinct and ecosystems lose important functions.
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http://dx.doi.org/10.1002/evl3.154DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7006467PMC
February 2020

275 years of forestry meets genomics in .

Evol Appl 2020 Jan 28;13(1):11-30. Epub 2019 Jun 28.

Department of Ecology and Genetics University of Oulu Oulu Finland.

has a long history of basic and applied research that is relevant for both forestry and evolutionary studies. Its patterns of adaptive variation and role in forest economic and ecological systems have been studied extensively for nearly 275 years, detailed demography for a 100 years and mating system more than 50 years. However, its reference genome sequence is not yet available and genomic studies have been lagging compared to, for example, and , two other economically important conifers. Despite the lack of reference genome, many modern genomic methods are applicable for a more detailed look at its biological characteristics. For example, RNA-seq has revealed a complex transcriptional landscape and targeted DNA sequencing displays an excess of rare variants and geographically homogenously distributed molecular genetic diversity. Current DNA and RNA resources can be used as a reference for gene expression studies, SNP discovery, and further targeted sequencing. In the future, specific consequences of the large genome size, such as functional effects of regulatory open chromatin regions and transposable elements, should be investigated more carefully. For forest breeding and long-term management purposes, genomic data can help in assessing the genetic basis of inbreeding depression and the application of genomic tools for genomic prediction and relatedness estimates. Given the challenges of breeding (long generation time, no easy vegetative propagation) and the economic importance, application of genomic tools has a potential to have a considerable impact. Here, we explore how genomic characteristics of , such as rare alleles and the low extent of linkage disequilibrium, impact the applicability and power of the tools.
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http://dx.doi.org/10.1111/eva.12809DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6966708PMC
January 2020

Thermospermine Synthase () and Diamine Oxidase () Expression Is Needed for Zygotic Embryogenesis and Vascular Development in Scots Pine.

Front Plant Sci 2019 20;10:1600. Epub 2019 Dec 20.

Production Systems, Natural Resources Institute Finland, Espoo, Finland.

Unlike in flowering plants, the detailed roles of the enzymes in the polyamine (PA) pathway in conifers are poorly known. We explored the sequence conservation of the PA biosynthetic genes and diamine oxidase () in conifers and flowering plants to reveal the potential functional diversification of the enzymes between the plant lineages. The expression of the genes showing different selective constraints was studied in Scots pine zygotic embryogenesis and early seedling development. We found that the arginine decarboxylase pathway is strongly preferred in putrescine production in the Scots pine as well as generally in conifers and that the reduced use of ornithine decarboxylase (ODC) has led to relaxed purifying selection in genes. Thermospermine synthase () genes evolve under strong purifying selection in conifers and the gene is also highly conserved in pines. In developing Scots pine seeds, the expression of both and increased as embryogenesis proceeded. Strong expression was present in the procambial cells of the embryo and in the megagametophyte cells destined to die morphologically necrotic cell death. Thus, the high sequence conservation of genes in conifers may indicate the necessity of for both embryogenesis and vascular development. Moreover, the result suggests the involvement of in morphologically necrotic cell death and supports the view of the genetic regulation of necrosis in Scots pine embryogenesis and in plant development. transcripts were located close to the cell walls and between the walls of adjacent cells in Scots pine zygotic embryos and in the roots of young seedlings. We propose that DAO, in addition to the role in Put oxidation for providing HO during the cell-wall structural processes, may also participate in cell-to-cell communication at the mRNA level. To conclude, our findings indicate that the PA pathway of Scots pines possesses several special functional characteristics which differ from those of flowering plants.
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http://dx.doi.org/10.3389/fpls.2019.01600DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6934065PMC
December 2019

The GenTree Dendroecological Collection, tree-ring and wood density data from seven tree species across Europe.

Sci Data 2020 01 2;7(1). Epub 2020 Jan 2.

Vytautas Magnus University, Studentu Street 11, 53361, Akademija, Lithuania.

The dataset presented here was collected by the GenTree project (EU-Horizon 2020), which aims to improve the use of forest genetic resources across Europe by better understanding how trees adapt to their local environment. This dataset of individual tree-core characteristics including ring-width series and whole-core wood density was collected for seven ecologically and economically important European tree species: silver birch (Betula pendula), European beech (Fagus sylvatica), Norway spruce (Picea abies), European black poplar (Populus nigra), maritime pine (Pinus pinaster), Scots pine (Pinus sylvestris), and sessile oak (Quercus petraea). Tree-ring width measurements were obtained from 3600 trees in 142 populations and whole-core wood density was measured for 3098 trees in 125 populations. This dataset covers most of the geographical and climatic range occupied by the selected species. The potential use of it will be highly valuable for assessing ecological and evolutionary responses to environmental conditions as well as for model development and parameterization, to predict adaptability under climate change scenarios.
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http://dx.doi.org/10.1038/s41597-019-0340-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6940356PMC
January 2020

Impact of demography on linked selection in two outcrossing Brassicaceae species.

Ecol Evol 2019 Sep 13;9(17):9532-9545. Epub 2019 Aug 13.

Science for Life Laboratory, Department of Ecology, Environment, and Plant Sciences Stockholm University Stockholm Sweden.

Genetic diversity is shaped by mutation, genetic drift, gene flow, recombination, and selection. The dynamics and interactions of these forces shape genetic diversity across different parts of the genome, between populations and species. Here, we have studied the effects of linked selection on nucleotide diversity in outcrossing populations of two Brassicaceae species, and , with contrasting demographic history. In agreement with previous estimates, we found evidence for a modest population size expansion thousands of generations ago, as well as efficient purifying selection in . In contrast, the population exhibited evidence for very recent strong population size decline and weaker efficacy of purifying selection. Using multiple regression analyses with recombination rate and other genomic covariates as explanatory variables, we can explain 47% of the variance in neutral diversity in the population, while in the population, only 11% of the variance was explained by the model. Recombination rate had a significant positive effect on neutral diversity in both species, suggesting that selection at linked sites has an effect on patterns of neutral variation. In line with this finding, we also found reduced neutral diversity in the vicinity of genes in the population. However, in no such reduction in diversity was evident, a finding that is consistent with expectations of the impact of a recent bottleneck on patterns of neutral diversity near genes. This study thus empirically demonstrates how differences in demographic history modulate the impact of selection at linked sites in natural populations.
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http://dx.doi.org/10.1002/ece3.5463DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6745670PMC
September 2019

Inflorescence shoot elongation, but not flower primordia formation, is photoperiodically regulated in Arabidopsis lyrata.

Ann Bot 2019 08;124(1):91-102

Department of Ecology and Genetics, University of Oulu, FIN-90014 Oulu, Finland.

Background And Aims: Photoperiod contains information about the progress of seasons. Plants use the changing photoperiod as a cue for the correct timing of important life history events, including flowering. Here the effect of photoperiod on flowering in four Arabidopsis lyrata populations originating from different latitudes was studied, as well as expression levels of candidate genes for governing the between-population differences.

Methods: Flowering of plants from four A. lyrata populations was studied in three different photoperiods after vernalization. Flowering development was separated into three steps: flower primordia formation, inflorescence shoot elongation and opening of the first flower. Circadian expression rhythms of the A. lyrata homologues of GIGANTEA (GI), FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (FKF1), CONSTANS (CO) and FLOWERING LOCUS T (FT) were studied in three of the populations in the intermediate (14 h) photoperiod treatment.

Key Results: Most plants in all populations formed visible flower primordia during vernalization. Further inflorescence development after vernalization was strongly inhibited by short days in the northern European population (latitude 61°N), only slightly in the central European population (49°N) and not at all in the North American populations (36°N and 42°N). In the 14 h daylength, where all plants from the three southernmost populations but only 60 % of the northernmost population flowered, the circadian expression rhythm of the A. lyrata FT was only detected in the southern populations, suggesting differentiation in the critical daylength for activation of the long-day pathway. However, circadian expression rhythms of A. lyrata GI, FKF1 and CO were similar between populations.

Conclusions: The results indicate that in A. lyrata, transition to flowering can occur through pathways independent of long days, but elongation of inflorescences is photoperiodically regulated.
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http://dx.doi.org/10.1093/aob/mcz035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6676387PMC
August 2019

Genomic patterns of local adaptation under gene flow in Arabidopsis lyrata.

Mol Biol Evol 2019 Jun 25. Epub 2019 Jun 25.

Department of Ecology and Genetics, University of Oulu, FI-90014 Oulu, Finland.

Short-scale local adaptation is a complex process involving selection, migration and drift. The expected effects on the genome are well grounded in theory but examining these on an empirical level has proven difficult, as it requires information about local selection, demographic history and recombination rate variation. Here, we use locally adapted and phenotypically differentiated Arabidopsis lyrata populations from two altitudinal gradients in Norway to test these expectations at the whole-genome level. Demography modelling indicates that populations within the gradients diverged less than 2 kya and that the sites are connected by gene flow. The gene flow estimates are, however, highly asymmetric with migration from high to low altitudes being several times more frequent than vice versa. To detect signatures of selection for local adaptation, we estimate patterns of lineage specific differentiation among these populations. Theory predicts that gene flow leads to concentration of adaptive loci in areas of low recombination; a pattern we observe in both lowland-alpine comparisons. Although most selected loci display patterns of conditional neutrality, we found indications of genetic trade-offs, with one locus particularly showing high differentiation and signs of selection in both populations. Our results further suggest that resistance to solar radiation is an important adaptation to alpine environments, while vegetative growth and bacterial defense are indicated as selected traits in the lowland habitats. These results provide insights into genetic architectures and evolutionary processes driving local adaptation under gene flow. We also contribute to understanding of traits and biological processes underlying alpine adaptation in northern latitudes.
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http://dx.doi.org/10.1093/molbev/msz149DOI Listing
June 2019

Local adaptation and ecological differentiation under selection, migration, and drift in Arabidopsis lyrata.

Evolution 2018 May 9. Epub 2018 May 9.

Department of Ecology and Genetics, University of Oulu, FI-90014 Oulu, Finland.

How the balance between selection, migration, and drift influences the evolution of local adaptation has been under intense theoretical scrutiny. Yet, empirical studies that relate estimates of local adaptation to quantification of gene flow and effective population sizes have been rare. Here, we conducted a reciprocal transplant trial, a common garden trial, and a whole-genome-based demography analysis to examine these effects among Arabidopsis lyrata populations from two altitudinal gradients in Norway. Demography simulations indicated that populations within the two gradients are connected by gene flow (0.1 < 4N m < 11) and have small effective population sizes (N 6000), suggesting that both migration and drift can counteract local selection. However, the three-year field experiments showed evidence of local adaptation at the level of hierarchical multiyear fitness, attesting to the strength of differential selection. In the lowland habitat, local superiority was associated with greater fecundity, while viability accounted for fitness differences in the alpine habitat. We also demonstrate that flowering time differentiation has contributed to adaptive divergence between these locally adapted populations. Our results show that despite the estimated potential of gene flow and drift to hinder differentiation, selection among these A. lyrata populations has resulted in local adaptation.
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http://dx.doi.org/10.1111/evo.13502DOI Listing
May 2018

Scots pine aminopropyltransferases shed new light on evolution of the polyamine biosynthesis pathway in seed plants.

Ann Bot 2018 05;121(6):1243-1256

Natural Resources Institute Finland, Bio-based Business and Industry, Parkano, Finland.

Background And Aims: Polyamines are small metabolites present in all living cells and play fundamental roles in numerous physiological events in plants. The aminopropyltransferases (APTs), spermidine synthase (SPDS), spermine synthase (SPMS) and thermospermine synthase (ACL5), are essential enzymes in the polyamine biosynthesis pathway. In angiosperms, SPMS has evolved from SPDS via gene duplication, whereas in gymnosperms APTs are mostly unexplored and no SPMS gene has been reported. The present study aimed to investigate the functional properties of the SPDS and ACL5 proteins of Scots pine (Pinus sylvestris L.) in order to elucidate the role and evolution of APTs in higher plants.

Methods: Germinating Scots pine seeds and seedlings were analysed for polyamines by high-performance liquid chromatography (HPLC) and the expression of PsSPDS and PsACL5 genes by in situ hybridization. Recombinant proteins of PsSPDS and PsACL5 were produced and investigated for functional properties. Also gene structures, promoter regions and phylogenetic relationships of PsSPDS and PsACL5 genes were analysed.

Key Results: Scots pine tissues were found to contain spermidine, spermine and thermospermine. PsSPDS enzyme catalysed synthesis of both spermidine and spermine. PsACL5 was found to produce thermospermine, and PsACL5 gene expression was localized in the developing procambium in embryos and tracheary elements in seedlings.

Conclusions: Contrary to previous views, our results demonstrate that SPMS activity is not a novel feature developed solely in the angiosperm lineage of seed plants but also exists as a secondary property in the Scots pine SPDS enzyme. The discovery of bifunctional SPDS from an evolutionarily old conifer reveals the missing link in the evolution of the polyamine biosynthesis pathway. The finding emphasizes the importance of pre-existing secondary functions in the evolution of new enzyme activities via gene duplication. Our results also associate PsACL5 with the development of vascular structures in Scots pine.
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http://dx.doi.org/10.1093/aob/mcy012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5946884PMC
May 2018

High rate of adaptive evolution in two widespread European pines.

Mol Ecol 2017 12 2;26(24):6857-6870. Epub 2017 Dec 2.

Department of Forest Ecology and Genetics, Forest Research Centre, INIA-CIFOR, Madrid, Spain.

Comparing related organisms with differing ecological requirements and evolutionary histories can shed light on the mechanisms and drivers underlying genetic adaptation. Here, by examining a common set of hundreds of loci, we compare patterns of nucleotide diversity and molecular adaptation of two European conifers (Scots pine and maritime pine) living in contrasted environments and characterized by distinct population genetic structure (low and clinal in Scots pine, high and ecotypic in maritime pine) and demographic histories. We found higher nucleotide diversity in Scots pine than in maritime pine, whereas rates of new adaptive substitutions (ω ), as estimated from the distribution of fitness effects, were similar across species and among the highest found in plants. Sample size and population genetic structure did not appear to have resulted in significant bias in estimates of ω . Moreover, population contraction-expansion dynamics for each species did not affect differentially the rate of adaptive substitution in these two pines. Several methodological and biological factors may underlie the unusually high rate of adaptive evolution of Scots pine and maritime pine. By providing two new case studies with contrasting evolutionary histories, we contribute to disentangling the multiple factors potentially affecting adaptive evolution in natural plant populations.
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http://dx.doi.org/10.1111/mec.14402DOI Listing
December 2017

Genome-Wide Analysis of Colonization History and Concomitant Selection in Arabidopsis lyrata.

Mol Biol Evol 2017 10;34(10):2665-2677

Department of Ecology and Genetics, University of Oulu, Oulu, Finland.

The high climatic variability in the past hundred thousand years has affected the demographic and adaptive processes in many species, especially in boreal and temperate regions undergoing glacial cycles. This has also influenced the patterns of genome-wide nucleotide variation, but the details of these effects are largely unknown. Here we study the patterns of genome-wide variation to infer colonization history and patterns of selection of the perennial herb species Arabidopsis lyrata, in locally adapted populations from different parts of its distribution range (Germany, UK, Norway, Sweden, and USA) representing different environmental conditions. Using site frequency spectra based demographic modeling, we found strong reduction in the effective population size of the species in general within the past 100,000 years, with more pronounced effects in the colonizing populations. We further found that the northwestern European A. lyrata populations (UK and Scandinavian) are more closely related to each other than with the Central European populations, and coalescent based population split modeling suggests that western European and Scandinavian populations became isolated relatively recently after the glacial retreat. We also highlighted loci showing evidence for local selection associated with the Scandinavian colonization. The results presented here give new insights into postglacial Scandinavian colonization history and its genome-wide effects.
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http://dx.doi.org/10.1093/molbev/msx193DOI Listing
October 2017

Role of seed germination in adaptation and reproductive isolation in Arabidopsis lyrata.

Mol Ecol 2017 Jul 5;26(13):3484-3496. Epub 2017 May 5.

Department of Ecology and Genetics, University of Oulu, Oulu, Finland.

Seed germination is an important developmental and life history stage. Yet, the evolutionary impact of germination has mainly been studied in the context of dormancy, or for its role in reproductive isolation between species. Here, we aim to examine multiple consequences of genetic divergence on germination traits between two Arabidopsis lyrata subspecies: ssp. petraea (Eurasia) and ssp. lyrata (North America). Postdormancy germination time, a potentially adaptive trait, showed differentiation between the populations, and quantitative trait loci (QTL) mapping revealed that the trait variation is mainly controlled by two antagonistic loci. These QTL areas contain several candidate genes with known function in postdormancy germination in A. thaliana. The sequence variation of three genes was consistent with differential selection, and they also included fixed nonsynonymous substitutions with potential to account for the phenotypic differentiation. We further show that the divergence between the subspecies has led to a slight but significant reduction in hybrid germination proportions, indicating incipient reproductive isolation. Comparison of reciprocal F and F progenies suggests that Bateson-Dobzhansky-Muller incompatibilities likely act through uniparentally inherited factors. Examination of genomewide transmission ratio distortion further revealed that cytonuclear interactions cause substantial pregermination inviability in the hybrids. These results confirm that seed germination has adaptive potential beyond the dormancy stage and that hybrid seed inviability can be one of the first reproductive barriers to arise during divergence.
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http://dx.doi.org/10.1111/mec.14135DOI Listing
July 2017

Genomics: Geography matters for Arabidopsis.

Nature 2016 09 7;537(7620):314-315. Epub 2016 Sep 7.

Department of Genetics and Physiology, and in Biocenter Oulu, University of Oulu, 90014 Oulu, Finland.

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http://dx.doi.org/10.1038/nature19466DOI Listing
September 2016

Selection for population-specific adaptation shaped patterns of variation in the photoperiod pathway genes in Arabidopsis lyrata during post-glacial colonization.

Mol Ecol 2016 01 18;25(2):581-97. Epub 2016 Jan 18.

Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland.

Spatially varying selection can lead to population-specific adaptation, which is often recognized at the phenotypic level; however, the genetic evidence is weaker in many groups of organisms. In plants, environmental shifts that occur due to colonization of a novel environment may require adaptive changes in the timing of growth and flowering, which are often governed by location-specific environmental cues such as day length. We studied locally varying selection in 19 flowering time loci in nine populations of the perennial herb Arabidopsis lyrata, which has a wide but patchy distribution in temperate and boreal regions of the northern hemisphere. The populations differ in their recent population demographic and colonization histories and current environmental conditions, especially in the growing season length. We searched for population-specific molecular signatures of directional selection by comparing a set of candidate flowering time loci with a genomic reference set within each population using multiple approaches and contrasted the patterns of different populations. The candidate loci possessed approximately 20% of the diversity of the reference loci. On average the flowering time loci had more rare alleles (a smaller Tajima's D) and an excess of highly differentiated sites relative to the reference, suggesting positive selection. The strongest signal of selection was detected in photoperiodic pathway loci in the colonizing populations of Northwestern Europe, whereas no evidence of positive selection was detected in the Central European populations. These findings emphasized the population-specific nature of selection and suggested that photoperiodic adaptation was important during postglacial colonization of the species.
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http://dx.doi.org/10.1111/mec.13489DOI Listing
January 2016

Evolutionary conservation of cold-induced antisense RNAs of FLOWERING LOCUS C in Arabidopsis thaliana perennial relatives.

Nat Commun 2014 Jul 17;5:4457. Epub 2014 Jul 17.

Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10, D-50829 Cologne, Germany.

Antisense RNA (asRNA) COOLAIR is expressed at A. thaliana FLOWERING LOCUS C (FLC) in response to winter temperatures. Its contribution to cold-induced silencing of FLC was proposed but its functional and evolutionary significance remain unclear. Here we identify a highly conserved block containing the COOLAIR first exon and core promoter at the 3' end of several FLC orthologues. Furthermore, asRNAs related to COOLAIR are expressed at FLC loci in the perennials A. alpina and A. lyrata, although some splicing variants differ from A. thaliana. Study of the A. alpina orthologue, PERPETUAL FLOWERING 1 (PEP1), demonstrates that AaCOOLAIR is induced each winter of the perennial life cycle. Introduction of PEP1 into A. thaliana reveals that AaCOOLAIR cis-elements confer cold-inducibility in this heterologous species while the difference between PEP1 and FLC mRNA patterns depends on both cis-elements and species-specific trans-acting factors. Thus, expression of COOLAIR is highly conserved, supporting its importance in FLC regulation.
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http://dx.doi.org/10.1038/ncomms5457DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4109010PMC
July 2014

Association of FLOWERING LOCUS T/TERMINAL FLOWER 1-like gene FTL2 expression with growth rhythm in Scots pine (Pinus sylvestris).

New Phytol 2014 Oct 18;204(1):159-170. Epub 2014 Jun 18.

Department of Biology, University of Oulu, PO Box 3000, FIN-90014, Oulu, Finland.

Understanding the genetic basis of the timing of bud set, an important trait in conifers, is relevant for adaptation and forestry practice. In common garden experiments, both Scots pine (Pinus sylvestris) and Norway spruce (Picea abies) show a latitudinal cline in the trait. We compared the regulation of their bud set biology by examining the expression of PsFTL2, a Pinus sylvestris homolog to PaFTL2, a FLOWERING LOCUS T/TERMINAL FLOWER 1 (FT/TFL1)-like gene, the expression levels of which have been found previously to be associated with the timing of bud set in Norway spruce. In a common garden study, we analyzed the relationship of bud phenology under natural and artificial photoperiods and the expression of PsFTL2 in a set of Scots pine populations from different latitudes. The expression of PsFTL2 increased in the needles preceding bud set and decreased during bud burst. In the northernmost population, even short night periods were efficient to trigger this expression, which also increased earlier under all photoperiodic regimes compared with the southern populations. Despite the different biology, with few limitations, the two conifers that diverged 140 million yr ago probably share an association of FTL2 with bud set, pointing to a common mechanism for the timing of growth cessation in conifers.
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http://dx.doi.org/10.1111/nph.12901DOI Listing
October 2014

Climatic adaptation and ecological divergence between two closely related pine species in Southeast China.

Mol Ecol 2014 Jul;23(14):3504-22

State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, China; Plant Genetics Group, Department of Biology, University of Oulu, 90014, Oulu, Finland.

Climate is one of the most important drivers for adaptive evolution in forest trees. Climatic selection contributes greatly to local adaptation and intraspecific differentiation, but this kind of selection could also have promoted interspecific divergence through ecological speciation. To test this hypothesis, we examined intra- and interspecific genetic variation at 25 climate-related candidate genes and 12 reference loci in two closely related pine species, Pinus massoniana Lamb. and Pinus hwangshanensis Hisa, using population genetic and landscape genetic approaches. These two species occur in Southeast China but have contrasting ecological preferences in terms of several environmental variables, notably altitude, although hybrids form where their distributions overlap. One or more robust tests detected signals of recent and/or ancient selection at two-thirds (17) of the 25 candidate genes, at varying evolutionary timescales, but only three of the 12 reference loci. The signals of recent selection were species specific, but signals of ancient selection were mostly shared by the two species likely because of the shared evolutionary history. FST outlier analysis identified six SNPs in five climate-related candidate genes under divergent selection between the two species. In addition, a total of 24 candidate SNPs representing nine candidate genes showed significant correlation with altitudinal divergence in the two species based on the covariance matrix of population history derived from reference SNPs. Genetic differentiation between these two species was higher at the candidate genes than at the reference loci. Moreover, analysis using the isolation-with-migration model indicated that gene flow between the species has been more restricted for climate-related candidate genes than the reference loci, in both directions. Taken together, our results suggest that species-specific and divergent climatic selection at the candidate genes might have counteracted interspecific gene flow and played a key role in the ecological divergence of these two closely related pine species.
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http://dx.doi.org/10.1111/mec.12830DOI Listing
July 2014

A recent local sweep at the PHYA locus in the Northern European Spiterstulen population of Arabidopsis lyrata.

Mol Ecol 2014 Mar 19;23(5):1040-52. Epub 2014 Feb 19.

Department of Biology, University of Oulu, Oulu, 90014, Finland; Biocenter Oulu, University of Oulu, Oulu, 90014, Finland.

Northern and central European Arabidopsis lyrata ssp. petraea populations are locally adapted to prevailing climatic conditions through differences in timing of life history events. The timing of flowering and, in perennials, the timing of growth cessation influence fitness. Phytochrome A may have an important role in regulating these life history traits as it perceives changes in daylength. We asked whether PHYA has contributed to local adaptation to the northern conditions in A. l. petraea. To search for signals of directional selection at the PHYA locus, we resequenced PHYA and 9 short fragments around PHYA from a 57-kb region from a German (Plech) and a Norwegian (Spiterstulen) population and compared patterns of differentiation and diversity to a set of 19 reference loci around the genome. First, we found that the populations were highly differentiated: there were three nonsynonymous fixed differences at the PHYA locus, which was in stark contrast with the total four fixed differences in the 19 reference loci. Compatible with a sweep hypothesis, variation was almost completely removed from the 9.4-kb region around PHYA in the northern Spiterstulen population. The overall level of linkage disequilibrium (LD) was higher in Spiterstulen, but there was no LD across the PHYA locus in the population, which is also a known consequence of a selective sweep. The sweep has likely occurred after the last glacial maximum, which suggests that it has contributed to adaptation to the northern conditions.
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http://dx.doi.org/10.1111/mec.12682DOI Listing
March 2014

Ecological genomics of local adaptation.

Nat Rev Genet 2013 Nov;14(11):807-20

Department of Biology and Biocenter Oulu, University of Oulu, FIN-90014 Oulu, Finland.

It is increasingly important to improve our understanding of the genetic basis of local adaptation because of its relevance to climate change, crop and animal production, and conservation of genetic resources. Phenotypic patterns that are generated by spatially varying selection have long been observed, and both genetic mapping and field experiments provided initial insights into the genetic architecture of adaptive traits. Genomic tools are now allowing genome-wide studies, and recent theoretical advances can help to design research strategies that combine genomics and field experiments to examine the genetics of local adaptation. These advances are also allowing research in non-model species, the adaptation patterns of which may differ from those of traditional model species.
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http://dx.doi.org/10.1038/nrg3522DOI Listing
November 2013

Complex genetic effects on early vegetative development shape resource allocation differences between Arabidopsis lyrata populations.

Genetics 2013 Nov 26;195(3):1087-102. Epub 2013 Aug 26.

Department of Biology, University of North Carolina, Greensboro, North Carolina 27402.

Costs of reproduction due to resource allocation trade-offs have long been recognized as key forces in life history evolution, but little is known about their functional or genetic basis. Arabidopsis lyrata, a perennial relative of the annual model plant A. thaliana with a wide climatic distribution, has populations that are strongly diverged in resource allocation. In this study, we evaluated the genetic and functional basis for variation in resource allocation in a reciprocal transplant experiment, using four A. lyrata populations and F2 progeny from a cross between North Carolina (NC) and Norway parents, which had the most divergent resource allocation patterns. Local alleles at quantitative trait loci (QTL) at a North Carolina field site increased reproductive output while reducing vegetative growth. These QTL had little overlap with flowering date QTL. Structural equation models incorporating QTL genotypes and traits indicated that resource allocation differences result primarily from QTL effects on early vegetative growth patterns, with cascading effects on later vegetative and reproductive development. At a Norway field site, North Carolina alleles at some of the same QTL regions reduced survival and reproductive output components, but these effects were not associated with resource allocation trade-offs in the Norway environment. Our results indicate that resource allocation in perennial plants may involve important adaptive mechanisms largely independent of flowering time. Moreover, the contributions of resource allocation QTL to local adaptation appear to result from their effects on developmental timing and its interaction with environmental constraints, and not from simple models of reproductive costs.
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http://dx.doi.org/10.1534/genetics.113.151803DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813839PMC
November 2013

Cytoplasmic male sterility contributes to hybrid incompatibility between subspecies of Arabidopsis lyrata.

G3 (Bethesda) 2013 Oct 3;3(10):1727-40. Epub 2013 Oct 3.

Department of Biology, University of Oulu, FIN-90014 Oulu, Finland.

In crosses between evolutionarily diverged populations, genomic incompatibilities may result in sterile hybrids, indicating evolution of reproductive isolation. In several plant families, crosses within a population can also lead to male sterile progeny because of conflict between the maternally and biparentally inherited genomes. We examined hybrid fertility between subspecies of the perennial outcrossing self-incompatible Lyrate rockcress (Arabidopsis lyrata) in large reciprocal F2 progenies and three generations of backcrosses. In one of the reciprocal F2 progenies, almost one-fourth of the plants were male-sterile. Correspondingly, almost one-half of the plants in one of the four reciprocal backcross progenies expressed male sterility. In an additional four independent F2 and backcross families, three segregated male sterility. The observed asymmetrical hybrid incompatibility is attributable to male sterility factors in one cytoplasm, for which the other population lacks effective fertility restorers. Genotyping of 96 molecular markers and quantitative trait locus mapping revealed that only 60% of the plants having the male sterile cytoplasm and lacking the corresponding restorers were phenotypically male-sterile. Genotyping data showed that there is only one restorer locus, which mapped to a 600-kb interval at the top of chromosome 2 in a region containing a cluster of pentatricopeptide repeat genes. Male fertility showed no trade-off with seed production. We discuss the role of cytoplasm and genomic conflict in incipient speciation and conclude that cytoplasmic male sterility-lowering hybrid fitness is a transient effect with limited potential to form permanent reproductive barriers between diverged populations of hermaphrodite self-incompatible species.
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http://dx.doi.org/10.1534/g3.113.007815DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3789797PMC
October 2013
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