scholarly journals QTL × environment interactions underlie adaptive divergence in switchgrass across a large latitudinal gradient

2019 ◽  
Vol 116 (26) ◽  
pp. 12933-12941 ◽  
Author(s):  
David B. Lowry ◽  
John T. Lovell ◽  
Li Zhang ◽  
Jason Bonnette ◽  
Philip A. Fay ◽  
...  
Keyword(s):  
Local Adaptation ◽  
Panicum Virgatum ◽  
Environmental Gradients ◽  
Adaptive Divergence ◽  
Multiple Loci ◽  
Trade Offs ◽  
Locally Adaptive ◽  
Trait Locus ◽  
Benefits And Costs ◽  
Transplant Experiments

Local adaptation is the process by which natural selection drives adaptive phenotypic divergence across environmental gradients. Theory suggests that local adaptation results from genetic trade-offs at individual genetic loci, where adaptation to one set of environmental conditions results in a cost to fitness in alternative environments. However, the degree to which there are costs associated with local adaptation is poorly understood because most of these experiments rely on two-site reciprocal transplant experiments. Here, we quantify the benefits and costs of locally adaptive loci across 17° of latitude in a four-grandparent outbred mapping population in outcrossing switchgrass (Panicum virgatumL.), an emerging biofuel crop and dominant tallgrass species. We conducted quantitative trait locus (QTL) mapping across 10 sites, ranging from Texas to South Dakota. This analysis revealed that beneficial biomass (fitness) QTL generally incur minimal costs when transplanted to other field sites distributed over a large climatic gradient over the 2 y of our study. Therefore, locally advantageous alleles could potentially be combined across multiple loci through breeding to create high-yielding regionally adapted cultivars.

scholarly journals Combining population genomics and fitness QTLs to identify the genetics of local adaptation in Arabidopsis thaliana

2018 ◽  
Vol 115 (19) ◽  
pp. 5028-5033 ◽  
Author(s):  
Nicholas Price ◽  
Brook T. Moyers ◽  
Lua Lopez ◽  
Jesse R. Lasky ◽  
J. Grey Monroe ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Local Adaptation ◽  
Genetic Basis ◽  
Population Genomics ◽  
Frequency Spectra ◽  
Population Genomic ◽  
Trade Offs ◽  
Trait Locus ◽  
Genomic Regions ◽  
Transplant Experiments

Evidence for adaptation to different climates in the model species Arabidopsis thaliana is seen in reciprocal transplant experiments, but the genetic basis of this adaptation remains poorly understood. Field-based quantitative trait locus (QTL) studies provide direct but low-resolution evidence for the genetic basis of local adaptation. Using high-resolution population genomic approaches, we examine local adaptation along previously identified genetic trade-off (GT) and conditionally neutral (CN) QTLs for fitness between locally adapted Italian and Swedish A. thaliana populations [Ågren J, et al. (2013) Proc Natl Acad Sci USA 110:21077–21082]. We find that genomic regions enriched in high FST SNPs colocalize with GT QTL peaks. Many of these high FST regions also colocalize with regions enriched for SNPs significantly correlated to climate in Eurasia and evidence of recent selective sweeps in Sweden. Examining unfolded site frequency spectra across genes containing high FST SNPs suggests GTs may be due to more recent adaptation in Sweden than Italy. Finally, we collapse a list of thousands of genes spanning GT QTLs to 42 genes that likely underlie the observed GTs and explore potential biological processes driving these trade-offs, from protein phosphorylation, to seed dormancy and longevity. Our analyses link population genomic analyses and field-based QTL studies of local adaptation, and emphasize that GTs play an important role in the process of local adaptation.

scholarly journals Geographic variation in the genetic basis of resistance to leaf rust between locally adapted ecotypes of the biofuel crop switchgrass (Panicum virgatum)

2019 ◽  
Author(s):  
Acer VanWallendael ◽  
Jason Bonnette ◽  
Thomas E. Juenger ◽  
Felix B. Fritschi ◽  
Philip A. Fay ◽  
...  
Keyword(s):  
Panicum Virgatum ◽  
Environmental Gradients ◽  
Abiotic Factors ◽  
Pathogen Resistance ◽  
Genotype By Environment Interaction ◽  
Plant Evolution ◽  
List Type ◽  
Environment Interaction ◽  
Geographic Space ◽  
Trait Locus

SummaryLocal adaptation is an important process in plant evolution, which can be impacted by differential pathogen pressures along environmental gradients. However, the degree to which pathogen resistance loci vary in effect across space and time is incompletely described.To understand how the genetic architecture of resistance varies across time and geographic space, we quantified rust (Puccinia spp.) severity in switchgrass (Panicum virgatum) plantings at eight locations across the central United States for three years and conducted quantitative trait locus (QTL) mapping for rust progression.We mapped several variable QTLs, but two large-effect QTLs which we have named Prr1 and Prr2 were consistently associated with rust severity in multiple sites and years, particularly in northern sites. In contrast, there were numerous small-effect QTLs at southern sites, indicating a genotype-by-environment interaction in rust resistance loci. Interestingly, Prr1 and Prr2 had a strong epistatic interaction, which also varied in strength and direction of effect across space.Our results suggest that abiotic factors covarying with latitude interact with the genetic loci underlying plant resistance to control rust infection severity. Further, our results indicate that segregating genetic variation in epistatically interacting loci may play a key role in determining response to infection across geographic space.

scholarly journals Adaptive divergence in shoot gravitropism creates intrinsic reproductive isolation in an Australian wildflower

2019 ◽  
Author(s):  
Melanie J. Wilkinson ◽  
Federico Roda ◽  
Greg M. Walter ◽  
Maddie E. James ◽  
Rick Nipper ◽  
...  
Keyword(s):  
Natural Selection ◽  
Reproductive Isolation ◽  
Plant Height ◽  
Hybrid Sterility ◽  
Local Environment ◽  
Adaptive Divergence ◽  
Reciprocal Transplant ◽  
Locally Adaptive ◽  
Shoot Gravitropism ◽  
Transplant Experiments

AbstractAdaptation to the local environment is a major driver of speciation. Yet, it remains largely unknown whether natural selection directly causes intrinsic reproductive isolation (hybrid sterility or inviability) between locally adapted populations. Here, we show that adaptive divergence in shoot gravitropism, the ability of a plant’s shoot to bend upwards in response to the downward pull of gravity, contributes to the evolution of intrinsic reproductive isolation in an Australian wildflower, Senecio lautus. We find that shoot gravitropism has evolved multiple times in association with plant height between adjacent populations inhabiting contrasting environments, suggesting that these traits have evolved by natural selection. We directly tested this prediction in multi-year reciprocal transplant experiments using hybrid populations. We show that shoot gravitropism and plant height respond to natural selection in the expected direction of the locally adapted population. Remarkably, we find that crossing F11 hybrid individuals with extreme differences in gravitropism significantly reduces their ability to produce seeds, providing strong evidence that this adaptive trait is genetically correlated with intrinsic reproductive isolation. Our results suggest that natural selection can drive the evolution of locally adaptive traits that incidentally create intrinsic reproductive isolation, thus increasing our understanding of the origin and maintenance of new species.

scholarly journals Low genomic divergence and high gene flow between locally adapted populations of the swamp sparrow

2018 ◽  
Author(s):  
P. Deane-Coe ◽  
R. Greenberg ◽  
I. J. Lovette ◽  
R. G. Harrison
Keyword(s):  
Gene Flow ◽  
Natural Selection ◽  
Local Adaptation ◽  
Environmental Gradients ◽  
Divergence Time ◽  
Sequence Divergence ◽  
Genetic Admixture ◽  
Adaptive Divergence ◽  
Swamp Sparrow ◽  
Contemporary Gene Flow

AbstractPopulations that have recently diverged across sharp environmental gradients provide an opportunity to study the mechanisms by which natural selection drives adaptive divergence. Inland and coastal populations of the North American swamp sparrow have become an emerging model system for studies of natural selection because they are morphologically and behaviourally distinct despite a very recent divergence time (<15,000 years), yet common garden experiments have demonstrated a genetic basis for their phenotypic differences. We characterized genomic patterns of variation within and between inland and coastal swamp sparrows via reduced representation sequencing in order to reconstruct the contributions of demography, gene flow and selection to this case of recent adaptive divergence. Compared to inland swamp sparrows, coastal swamp sparrows exhibited fewer polymorphic sites and reduced nucleotide diversity at those sites, indicating that a bottleneck and/or recent selective sweeps occurred in that population during coastal colonization and local adaptation. Estimates of genome-wide differentiation (FST=0.02) and sequence divergence (ΦST=0.05) between inland and coastal populations were very low, consistent with postglacial divergence. A small number of SNPs were strongly differentiated (max FST=0.8) suggesting selection at linked sites. Swamp sparrows sampled from breeding sites at the habitat transition between freshwater and brackish marshes exhibited high levels of genetic admixture. Such evidence of active contemporary gene flow makes the evolution and maintenance of local adaptation in these two populations even more notable. We summarize several features of the swamp sparrow system that may facilitate the maintenance of adaptive diversity despite gene flow, including the presence of a magic trait.

Global Banking: Toward an Assessment of Benefits and Costs

2020 ◽  
Vol 12 (1) ◽  
pp. 141-175
Author(s):  
Claudia M. Buch ◽  
Linda S. Goldberg
Keyword(s):  
Evaluation Studies ◽  
Cost And Benefit ◽  
Theoretical Literature ◽  
Trade Offs ◽  
Global Banking ◽  
Policy Frameworks ◽  
Key Dimensions ◽  
Benefits And Costs ◽  
Global Banks ◽  
Empirical Analyses

Global activities of banks are a core manifestation of broader patterns of globalization of production, trade, and finance. This article reviews the extensive recent empirical and theoretical literature on global banking, emphasizing the careful empirical analyses that incorporate key dimensions of heterogeneity among borrowers and lenders, and across activities. The actions of globally active banks are consequential, with cost and benefit trade-offs that differ during their lifetimes and at times of stress. Both research and policymaking around global banking benefit from improved infrastructures around collection of and access to granular data and repositories of evaluation studies. Although overall positive contributions from welfare perspectives arise from the activities of global banks, these organizations require appropriately targeted policy frameworks and oversight.

scholarly journals Gene expression clines reveal local adaptation and associated trade-offs at a continental scale

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Damiano Porcelli ◽  
Anja M. Westram ◽  
Marta Pascual ◽  
Kevin J. Gaston ◽  
Roger K. Butlin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Local Adaptation ◽  
Continental Scale ◽  
Trade Offs

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.

scholarly journals Evolutionary trade-offs between unicellularity and multicellularity in budding yeast

2018 ◽  
Author(s):  
Jennie J. Kuzdzal-Fick ◽  
Lin Chen ◽  
Gábor Balázsi
Keyword(s):  
Mitotic Exit ◽  
Fundamental Question ◽  
Bet Hedging ◽  
Evolutionary Transitions ◽  
Wild Yeast ◽  
Yeast Strains ◽  
Trade Offs ◽  
Mitotic Exit Network ◽  
Multicellular Organisms ◽  
Benefits And Costs

ABSTRACTMulticellular organisms appeared on Earth through several independent major evolutionary transitions. Are such transitions reversible? Addressing this fundamental question entails understanding the benefits and costs of multicellularity versus unicellularity. For example, some wild yeast strains form multicellular clumps, which might be beneficial in stressful conditions, but this has been untested. Here we show that unicellular yeast evolves from clump-forming ancestors by propagating samples from suspension after larger clumps have settled. Unicellular yeast strains differed from their clumping ancestors mainly by mutations in the AMN1 (Antagonist of Mitotic exit Network) gene. Ancestral yeast clumps were more resistant to freeze/thaw, hydrogen peroxide, and ethanol stressors than their unicellular counterparts, while unicellularity was advantageous without stress. These findings inform mathematical models, jointly suggesting a trade-off between the benefits and downsides of multicellularity, causing bet-hedging by regulated phenotype switching as a survival strategy in unexpected stress.

scholarly journals Nanopore amplicon sequencing reveals molecular convergence and local adaptation of opsin genes

2020 ◽  
Author(s):  
Katherine M. Eaton ◽  
Moisés A. Bernal ◽  
Nathan J.C. Backenstose ◽  
Trevor J. Krabbenhoft
Keyword(s):  
Local Adaptation ◽  
Environmental Gradients ◽  
Parallel Evolution ◽  
Amplicon Sequencing ◽  
Species Flock ◽  
Closely Related Species ◽  
Oxford Nanopore ◽  
Opsin Genes ◽  
Potential Case ◽  
Species Specific

AbstractLocal adaptation can drive diversification of closely related species across environmental gradients and promote convergence of distantly related taxa that experience similar conditions. We examined a potential case of adaptation to novel visual environments in a species flock (Great Lakes salmonids, genus Coregonus) using a new amplicon genotyping protocol on the Oxford Nanopore Flongle. Five visual opsin genes were amplified for individuals of C. artedi, C. hoyi, C. kiyi, and C. zenithicus. Comparisons revealed species-specific differences in the coding sequence of rhodopsin (Tyr261Phe substitution), suggesting local adaptation by C. kiyi to the blue-shifted depths of Lake Superior. Parallel evolution and “toggling” at this amino acid residue has occurred several times across the fish tree of life, resulting in identical changes to the visual systems of distantly related taxa across replicated environmental gradients. Our results suggest that ecological differences and local adaptation to distinct visual environments are strong drivers of both evolutionary parallelism and diversification.

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