scholarly journals Genomics of clinal local adaptation in Pinus sylvestris under continuous environmental and spatial genetic setting

2019 ◽  
Author(s):  
Jaakko S. Tyrmi ◽  
Jaana Vuosku ◽  
Juan J. Acosta ◽  
Zhen Li ◽  
Lieven Sterck ◽  
...  
Keyword(s):  
Pinus Sylvestris ◽  
Local Adaptation ◽  
Large Scale ◽  
Molecular Genetic ◽  
Natural Populations ◽  
Keystone Species ◽  
Evolutionary Genetics ◽  
Genomic Diversity ◽  
Landscape Genomics ◽  
Polygenic Adaptation

AbstractUnderstanding 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 background often remains elusive. We examined the patterns of genetic diversity in Pinus sylvestris, 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 P. sylvestris 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 found that several coding loci contribute to local adaptation. We also discovered a very large (ca. 300 Mbp) putative inversion with a signal of local adaptation, 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 to the need for more attention towards multi-locus analysis of polygenic adaptation.

scholarly journals Genomics of Clinal Local Adaptation in Pinus sylvestris Under Continuous Environmental and Spatial Genetic Setting

2020 ◽  
Vol 10 (8) ◽  
pp. 2683-2696 ◽  
Author(s):  
Jaakko S. Tyrmi ◽  
Jaana Vuosku ◽  
Juan J. Acosta ◽  
Zhen Li ◽  
Lieven Sterck ◽  
...  
Keyword(s):  
Pinus Sylvestris ◽  
Local Adaptation ◽  
Large Scale ◽  
Genetic Basis ◽  
Molecular Genetic ◽  
Keystone Species ◽  
Evolutionary Genetics ◽  
Genomic Diversity ◽  
Landscape Genomics ◽  
Frequency Changes

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 Pinus sylvestris, 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 P. sylvestris 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.

scholarly journals Selective Sweeps and Polygenic Adaptation Drive Local Adaptation along Moisture and Temperature Gradients in Natural Populations of Coast Redwood and Giant Sequoia

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1826
Author(s):  
Amanda R. De La Torre ◽  
Manoj K. Sekhwal ◽  
David B. Neale
Keyword(s):  
Local Adaptation ◽  
Climate Adaptation ◽  
Natural Populations ◽  
Temperature Gradients ◽  
Selective Sweeps ◽  
Coast Redwood ◽  
Giant Sequoia ◽  
Polygenic Adaptation ◽  
Genomic Regions ◽  
Genomic Basis

Dissecting the genomic basis of local adaptation is a major goal in evolutionary biology and conservation science. Rapid changes in the climate pose significant challenges to the survival of natural populations, and the genomic basis of long-generation plant species is still poorly understood. Here, we investigated genome-wide climate adaptation in giant sequoia and coast redwood, two iconic and ecologically important tree species. We used a combination of univariate and multivariate genotype–environment association methods and a selective sweep analysis using non-overlapping sliding windows. We identified genomic regions of potential adaptive importance, showing strong associations to moisture variables and mean annual temperature. Our results found a complex architecture of climate adaptation in the species, with genomic regions showing signatures of selective sweeps, polygenic adaptation, or a combination of both, suggesting recent or ongoing climate adaptation along moisture and temperature gradients in giant sequoia and coast redwood. The results of this study provide a first step toward identifying genomic regions of adaptive significance in the species and will provide information to guide management and conservation strategies that seek to maximize adaptive potential in the face of climate change.

scholarly journals Pleistocene climate changes explain large-scale genetic variation in a dominant grassland species, Lolium perenne L

2018 ◽  
Author(s):  
J.L. Blanco-Pastor ◽  
S. Manel ◽  
P. Barre ◽  
A.M. Roschanski ◽  
E. Willner ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Lolium Perenne ◽  
Large Scale ◽  
Agricultural Land ◽  
Natural Populations ◽  
Genomic Diversity ◽  
Cooling Period ◽  
Grassland Species ◽  
Continental Scale ◽  
Natural Grasslands

AbstractAimGrasslands have been pivotal in the development of herbivore breeding since the Neolithic and are still nowadays the most widespread agricultural land-use across Europe. However, it remains unclear whether the current large-scale genetic variation of plant species found in natural grasslands of Europe is the result of human activities or natural processes.LocationEurope.TaxonLolium perenne L (perennial ryegrass).MethodsWe reconstructed the phylogeographic history of L. perenne, a dominant grassland species, using 481 natural populations including 11 populations from closely related taxa. We combined the Genotyping-by-Sequencing (GBS) and Pool-sequencing (Pool-seq) methods to obtain high-quality allele frequency calls of ~ 500 k SNP loci. We performed genetic structure analyses and demographic reconstructions based on the site frequency spectrum (SFS). We additionally used the same genotyping protocol to assess the genomic diversity of a set of 32 cultivars representative of the L. perenne cultivars widely used for forage purposes.ResultsExpansion across Europe took place during the Würm glaciation (12-110 kya), a cooling period that decreased the dominance of trees in favour of grasses. Splits and admixtures in L. perenne fit historical sea level changes in the Mediterranean basin. The development of agriculture in Europe (7-3.5 kya), that caused an increase in the abundance of grasslands, did not have an effect on the demographic patterns of L. perenne. We found little differentiation between modern cultivars and certain natural variants. However, modern cultivars do not represent the wide genetic variation found in natural populations.Main conclusionsDemographic events in L. perenne can be explained by the changing climatic conditions during the Pleistocene. Natural populations maintain a wide genomic variability at continental scale that has been underused by recent breeding activities. This variability constitutes valuable standing genetic variation for future adaptation of grasslands to climate change, safeguarding the agricultural services they provide.

scholarly journals Measuring recent effective gene flow among large populations in Pinus sylvestris: Local pollen shedding does not preclude substantial long-distance pollen immigration

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0255776
Author(s):  
Azucena Jiménez-Ramírez ◽  
Delphine Grivet ◽  
Juan José Robledo-Arnuncio
Keyword(s):  
Gene Flow ◽  
Pinus Sylvestris ◽  
Molecular Genetic ◽  
Natural Populations ◽  
Common Garden ◽  
Long Distance ◽  
Chloroplast Microsatellite ◽  
Flow Rates ◽  
Recent Gene Flow ◽  
Large Tree

The estimation of recent gene flow rates among vast and often weakly genetically differentiated tree populations remains a great challenge. Yet, empirical information would help understanding the interaction between gene flow and local adaptation in present-day non-equilibrium forests. We investigate here recent gene flow rates between two large native Scots pine (Pinus sylvestris L.) populations in central Iberian Peninsula (Spain), which grow on contrasting edaphic conditions six kilometers apart from each other and show substantial quantitative trait divergence in common garden experiments. Using a sample of 1,200 adult and offspring chloroplast-microsatellite haplotypes and a Bayesian inference model, we estimated substantial male gametic gene flow rates (8 and 21%) between the two natural populations, and even greater estimated immigration rates (42 and 64%) from nearby plantations into the two natural populations. Our results suggest that local pollen shedding within large tree populations does not preclude long-distance pollen immigration from large external sources, supporting the role of gene flow as a homogenizing evolutionary force contributing to low molecular genetic differentiation among populations of widely distributed wind-pollinated species. Our results also indicate the high potential for reproductive connectivity in large fragmented populations of wind-pollinated trees, and draw attention to a potential scenario of adaptive genetic divergence in quantitative traits under high gene flow.

scholarly journals Selecting of Polymorphic Loci of Genome for Identification of Populations of Pinus sylvestris L. on East-Europe Plain

2019 ◽  
Vol 5 (5) ◽  
pp. 25-30
Author(s):  
Ya. Prishnivskaya ◽  
E. Nassonova ◽  
Yu. Vasileva ◽  
S. Boronnikova
Keyword(s):  
Pinus Sylvestris ◽  
Molecular Genetic ◽  
Genetic Identification ◽  
East European Plain ◽  
Data Bases ◽  
East Europe ◽  
Polymorphic Loci ◽  
East European ◽  
Molecular Genetic Identification

10 pairs of primers from 8 related Pinus sylvestris L. populations collected on East-European plain to 10 genes and 4 primer’s pairs to 4 loci of uncoding clDNA regions. 2 loci of uncoding clDNA regions (psbA-trnH, trnL-trnF) were selected from tested 14 primer’s pairs. These two loci are most polymorphic and has homologous consistencies in data bases. Therefore, these loci is recommended for molecular–genetic identification of related Pinus sylvestris L. populations on East–European plain.

scholarly journals Sexual and vegetative propagation of the medicinal Mexican species Phyllonoma laticuspis (Phyllonomaceae)

2016 ◽  
Vol 65 (1) ◽  
pp. 9
Author(s):  
Ela Alcántara-Flores ◽  
Alicia Enriqueta Brechú-Franco ◽  
Angel Villegas-Monter ◽  
Guillermo Laguna-Hernández ◽  
Armando Gómez-Campos
Keyword(s):  
Vegetative Propagation ◽  
Large Scale ◽  
Seed Quality ◽  
Natural Populations ◽  
Skin Lesions ◽  
Control Treatment ◽  
Indole Butyric Acid ◽  
Randomized Design ◽  
Air Layers ◽  
Dark Conditions

Phyllonoma laticuspis leaves are used in Carrizal de Bravo, Guerrero, Mexico, to heal skin lesions such as injuries and smallpox sequelae and to treat diabetes mellitus type 2, and organic extracts of these leaves have been reported to exert antibacterial effects. High demand of P. laticuspis as a medicinal plant has decreased its natural populations, and propagation of the species has not yet been reported. Therefore, the purpose of this study was to assess the vegetative propagation of the species through cutting and air layering, as well as its sexual propagation in a preserved population. For this, concentrations of 1 000, 4 000 and 6 000 ppm of a commercial root enhancer, with indole butyric acid (IBA), and a control treatment without IBA, were applied to the cuttings and air layers. Germination was evaluated under light and dark conditions using lots of freshly collected seeds and lots of seeds that had been stored for three months at 4 °C or 24 ± 2 °C. All experiments were performed in a completely randomized design. The cuttings did not develop roots in any concentration, whereas 100 % of the air layers rooted, displaying vigorous roots in the presence of 4 000 ppm IBA, after four month of treatment application. Regarding germination, more than 60 % of the freshly collected seeds germinated, whereas less than 20 % of the seeds stored at 4 °C, and close to 50 % of the seeds stored at 24 ± 2 °C germinated under light and dark conditions. No significant differences were observed between light and dark conditions, so they were categorized as indifferent photoblastic seeds. The observed moisture content of 13.5 % and germination behaviour as the response to cold storage, suggest that the resultant seed quality was intermediate. P. laticuspis propagation for short-term foliage production can be carried out in air layers, in populations with a high density of adult plants as a source of plant material and for the restoration of disturbed areas, in the same locality. On the other hand, large-scale seedling production, medium-term foliage production and preservation of species variability can be achieved using seeds.

scholarly journals Evolutionary inference from QST-FST comparisons: disentangling local adaptation from altitudinal gradient selection in snapdragon plants

2018 ◽  
Author(s):  
Sara Marin ◽  
Juliette Archambeau ◽  
Vincent Bonhomme ◽  
Mylène Lascoste ◽  
Benoit Pujol
Keyword(s):  
Local Adaptation ◽  
Natural Populations ◽  
Common Garden ◽  
Global Scale ◽  
Structured Populations ◽  
Adaptive Divergence ◽  
Adaptation To Climate Change ◽  
Phenotypic Differentiation ◽  
Multiple Populations ◽  
Environmental Demand

ABSTRACTPhenotypic differentiation among natural populations can be explained by natural selection or by neutral processes such as drift. There are many examples in the literature where comparing the effects of these processes on multiple populations has allowed the detection of local adaptation. However, these studies rarely identify the agents of selection. Whether population adaptive divergence is caused by local features of the environment, or by the environmental demand emerging at a more global scale, for example along altitudinal gradients, is a question that remains poorly investigated. Here, we measured neutral genetic (FST) and quantitative genetic (QST) differentiation among 13 populations of snapdragon plants (Antirrhinum majus) in a common garden experiment. We found low but significant genetic differentiation at putatively neutral markers, which supports the hypothesis of either ongoing pervasive homogenisation via gene flow between diverged populations or reproductive isolation between disconnected populations. Our results also support the hypothesis of local adaptation involving phenological, morphological, reproductive and functional traits. They also showed that phenotypic differentiation increased with altitude for traits reflecting the reproduction and the phenology of plants, thereby confirming the role of such traits in their adaptation to environmental differences associated with altitude. Our approach allowed us to identify candidate traits for the adaptation to climate change in snapdragon plants. Our findings imply that environmental conditions changing with altitude, such as the climatic envelope, influenced the adaptation of multiple populations of snapdragon plants on the top of their adaptation to local environmental features. They also have implications for the study of adaptive evolution in structured populations because they highlight the need to disentangle the adaptation of plant populations to climate envelopes and altitude from the confounding effects of selective pressures acting specifically at the local scale of a population.

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