Parallel Alpine Differentiation in Arabidopsis arenosa

Parallel evolution provides powerful natural experiments for studying repeatability of evolution and genomic basis of adaptation. Well-documented examples from plants are, however, still rare, as are inquiries of mechanisms driving convergence in some traits while divergence in others. Arabidopsis arenosa, a predominantly foothill species with scattered morphologically distinct alpine occurrences is a promising candidate. Yet, the hypothesis of parallelism remained untested. We sampled foothill and alpine populations in all regions known to harbor the alpine ecotype and used SNP genotyping to test for repeated alpine colonization. Then, we combined field surveys and a common garden experiment to quantify phenotypic parallelism. Genetic clustering by region but not elevation and coalescent simulations demonstrated parallel origin of alpine ecotype in four mountain regions. Alpine populations exhibited parallelism in height and floral traits which persisted after two generations in cultivation. In contrast, leaf traits were distinctive only in certain region(s), reflecting a mixture of plasticity and genetically determined non-parallelism. We demonstrate varying degrees and causes of parallelism and non-parallelism across populations and traits within a plant species. Parallel divergence along a sharp elevation gradient makes A. arenosa a promising candidate for studying genomic basis of adaptation.

Download Full-text

Parallel alpine differentiation in Arabidopsis arenosa

10.1101/2020.02.13.948158 ◽

2020 ◽

Cited By ~ 4

Author(s):

Adam Knotek ◽

Veronika Konečná ◽

Guillaume Wos ◽

Doubravka Požárová ◽

Gabriela Šrámková ◽

...

Keyword(s):

Elevation Gradient ◽

Parallel Evolution ◽

Common Garden ◽

Leaf Traits ◽

Natural Experiments ◽

Promising Candidate ◽

Two Generations ◽

Arabidopsis Arenosa ◽

Genetic Clustering ◽

Phenotypic Parallelism

AbstractParallel evolution provides powerful natural experiments for studying repeatability of evolution. Well-documented examples from plants are, however, still rare, as are inquiries of mechanisms driving convergence in some traits while divergence in others. Arabidopsis arenosa, a predominantly foothill species with scattered morphologically distinct alpine occurrences is a promising candidate. Yet, the hypothesis of parallelism remained untested. We sampled foothill and alpine populations in all regions known to harbour the alpine ecotype and used SNP genotyping to test for repeated alpine colonisation. Then, we combined field surveys and a common garden experiment to quantify phenotypic parallelism. Genetic clustering by region but not elevation and coalescent simulations demonstrated parallel origin of alpine ecotype in four mountain regions. Alpine populations exhibited parallelism in height and floral traits which persisted after two generations in cultivation. In contrast, leaf traits were distinctive only in certain region(s), reflecting a mixture of plasticity and genetically determined non-parallelism. We demonstrate varying degrees and causes of parallelism and non-parallelism across populations and traits within a plant species. Parallel divergence along a sharp elevation gradient makes A. arenosa a promising candidate for studying genomic basis of adaptation.

Download Full-text

Genomic basis of parallel adaptation varies with divergence in Arabidopsis and its relatives

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2022713118 ◽

2021 ◽

Vol 118 (21) ◽

pp. e2022713118

Author(s):

Magdalena Bohutínská ◽

Jakub Vlček ◽

Sivan Yair ◽

Benjamin Laenen ◽

Veronika Konečná ◽

...

Keyword(s):

Genetic Divergence ◽

Parallel Evolution ◽

Valuable Insight ◽

Natural Experiments ◽

High Radiation ◽

Genome Wide ◽

Short Season ◽

Alpine Environments ◽

Genomic Basis ◽

Insight Into

Parallel adaptation provides valuable insight into the predictability of evolutionary change through replicated natural experiments. A steadily increasing number of studies have demonstrated genomic parallelism, yet the magnitude of this parallelism varies depending on whether populations, species, or genera are compared. This led us to hypothesize that the magnitude of genomic parallelism scales with genetic divergence between lineages, but whether this is the case and the underlying evolutionary processes remain unknown. Here, we resequenced seven parallel lineages of two Arabidopsis species, which repeatedly adapted to challenging alpine environments. By combining genome-wide divergence scans with model-based approaches, we detected a suite of 151 genes that show parallel signatures of positive selection associated with alpine colonization, involved in response to cold, high radiation, short season, herbivores, and pathogens. We complemented these parallel candidates with published gene lists from five additional alpine Brassicaceae and tested our hypothesis on a broad scale spanning ∼0.02 to 18 My of divergence. Indeed, we found quantitatively variable genomic parallelism whose extent significantly decreased with increasing divergence between the compared lineages. We further modeled parallel evolution over the Arabidopsis candidate genes and showed that a decreasing probability of repeated selection on the same standing or introgressed alleles drives the observed pattern of divergence-dependent parallelism. We therefore conclude that genetic divergence between populations, species, and genera, affecting the pool of shared variants, is an important factor in the predictability of genome evolution.

Download Full-text

Genomic basis of parallel adaptation varies with divergence in Arabidopsis and its relatives

10.1101/2020.03.24.005397 ◽

2020 ◽

Cited By ~ 5

Author(s):

Magdalena Bohutínská ◽

Jakub Vlček ◽

Sivan Yair ◽

Benjamin Laenen ◽

Veronika Konečná ◽

...

Keyword(s):

Genetic Divergence ◽

Parallel Evolution ◽

Pathogen Resistance ◽

Valuable Insight ◽

Natural Experiments ◽

Genome Wide ◽

Repeated Evolution ◽

Alpine Environments ◽

Genomic Basis ◽

Selection Of

AbstractParallel adaptation provides valuable insight into the predictability of evolutionary change through replicated natural experiments. A steadily increasing number of studies have demonstrated genomic parallelism, yet the magnitude of this parallelism varies depending on whether populations, species or genera are compared. This led us to hypothesize that the magnitude of genomic parallelism scales with genetic divergence between lineages, but whether this is the case and the underlying evolutionary processes remain unknown. Here, we resequenced seven parallel lineages of two Arabidopsis species which repeatedly adapted to challenging alpine environments. By combining genome-wide divergence scans with model-based approaches we detected a suite of 151 genes that show parallel signatures of positive selection associated with alpine colonization, involved in response to cold, high radiation, short season, herbivores and pathogens. We complemented these parallel candidates with published gene lists from five additional alpine Brassicaceae and tested our hypothesis on a broad scale spanning ~ 0.02 to 18 million years of divergence. Indeed, we found quantitatively variable genomic parallelism whose extent significantly decreased with increasing divergence between the compared lineages. We further modeled parallel evolution over the Arabidopsis candidate genes and showed that a decreasing probability of repeated selection of the same standing or introgressed alleles drives the observed pattern of divergence-dependent parallelism. We therefore conclude that genetic divergence between populations, species and genera, affecting the pool of shared variants, is an important factor in the predictability of genome evolution.Significance statementRepeated evolution tends to be more predictable. The impressive spectrum of recent reports on genomic parallelism, however, revealed that the fraction of the genome that evolves in parallel largely varies, possibly reflecting different evolutionary scales investigated. Here, we demonstrate divergence-dependent parallelism using a comprehensive genome-wide dataset comprising 12 cases of parallel alpine adaptation and identify decreasing probability of adaptive re-use of genetic variation as the major underlying cause. This finding empirically demonstrates that evolutionary predictability is scale dependent and suggests that availability of pre-existing variation drives parallelism within and among populations and species. Altogether, our results inform the ongoing discussion about the (un)predictability of evolution, relevant for applications in pest control, nature conservation, or the evolution of pathogen resistance.

Download Full-text

Leaf Nutrient Relations of Cycads in a Common Garden

Tropical Conservation Science ◽

10.1177/19400829211036570 ◽

2021 ◽

Vol 14 ◽

pp. 194008292110365

Author(s):

Thomas E. Marler ◽

Anders J. Lindström

Keyword(s):

Common Garden ◽

Nutrient Content ◽

Leaf Traits ◽

Botanical Garden ◽

Active Management ◽

Nitrogen And Phosphorus ◽

Representative Species ◽

Nutrient Relations ◽

Homogeneous Environment ◽

Dry Combustion

Background and Aims Research required to clarify leaf nutrient relations of cycad species has been inadequate. Common garden studies are useful for determining the influence of genetics on leaf traits because of the homogeneous environment among experimental units. To date, there have been no common garden studies which included all ten genera of cycads. The full phylogenetic breadth has, therefore, not been included in this important area of study. Methods We examined macronutrient and micronutrient content of leaves from one representative species from each of the ten cycad genera at Nong Nooch Tropical Botanical Garden in Thailand. Nitrogen content was determined by dry combustion, and the remaining nutrients were quantified by spectrometry. Results The least variable elements were nitrogen and phosphorus, and the most variable elements were boron and sodium. Nutrient content based on leaflet area was more variable than based on leaflet mass, reflecting species differences in specific leaf area. There were no universal macronutrient or micronutrient signals indicating clear phylogenetic distinctions. Implications for Conservation: Active management of threatened cycad taxa requires research to develop the knowledge to enable evidence-based decisions. This common garden study inclusive of all 10 cycad genera creates a foundation to determine leaf nutrient sufficiency ranges to inform management decisions.

Download Full-text

Transcriptional activity of transposable elements along an elevational gradient in Arabidopsis arenosa

Mobile DNA ◽

10.1186/s13100-021-00236-0 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Guillaume Wos ◽

Rimjhim Roy Choudhury ◽

Filip Kolář ◽

Christian Parisod

Keyword(s):

Transposable Elements ◽

Environmental Changes ◽

Common Garden ◽

Elevational Gradient ◽

Mountain Regions ◽

Transcriptomic Response ◽

Genetic Lineages ◽

Two Factors ◽

Arabidopsis Arenosa ◽

Expression Response

Abstract Background Plant genomes can respond rapidly to environmental changes and transposable elements (TEs) arise as important drivers contributing to genome dynamics. Although some elements were reported to be induced by various abiotic or biotic factors, there is a lack of general understanding on how environment influences the activity and diversity of TEs. Here, we combined common garden experiment with short-read sequencing to investigate genomic abundance and expression of 2245 consensus TE sequences (containing retrotransposons and DNA transposons) in an alpine environment in Arabidopsis arenosa. To disentangle general trends from local differentiation, we leveraged four foothill-alpine population pairs from different mountain regions. Seeds of each of the eight populations were raised under four treatments that differed in temperature and irradiance, two factors varying with elevation. RNA-seq analysis was performed on leaves of young plants to test for the effect of elevation and subsequently of temperature and irradiance on expression of TE sequences. Results Genomic abundance of the 2245 consensus TE sequences varied greatly between the mountain regions in line with neutral divergence among the regions, representing distinct genetic lineages of A. arenosa. Accounting for intraspecific variation in abundance, we found consistent transcriptomic response for some TE sequences across the different pairs of foothill-alpine populations suggesting parallelism in TE expression. In particular expression of retrotransposon LTR Copia (e.g. Ivana and Ale clades) and LTR Gypsy (e.g. Athila and CRM clades) but also non-LTR LINE or DNA transposon TIR MuDR consistently varied with elevation of origin. TE sequences responding specifically to temperature and irradiance belonged to the same classes as well as additional TE clades containing potentially stress-responsive elements (e.g. LTR Copia Sire and Tar, LTR Gypsy Reina). Conclusions Our study demonstrated that the A. arenosa genome harbours a considerable diversity of TE sequences whose abundance and expression response varies across its native range. Some TE clades may contain transcriptionally active elements responding to a natural environmental gradient. This may further contribute to genetic variation between populations and may ultimately provide new regulatory mechanisms to face environmental challenges.

Download Full-text

Contrasting patterns in leaf traits of Mediterranean shrub communities along an elevation gradient: measurements matter

Plant Ecology ◽

10.1007/s11258-019-00951-y ◽

2019 ◽

Vol 220 (7-8) ◽

pp. 765-776 ◽

Cited By ~ 1

Author(s):

Giandiego Campetella ◽

Stefano Chelli ◽

Camilla Wellstein ◽

Emmanuele Farris ◽

Giacomo Calvia ◽

...

Keyword(s):

Elevation Gradient ◽

Leaf Traits ◽

Gradient Measurements ◽

Mediterranean Shrub

Download Full-text

Leaf Canopy Layers Affect Spectral Reflectance in Silver Birch

Remote Sensing ◽

10.3390/rs11242884 ◽

2019 ◽

Vol 11 (24) ◽

pp. 2884 ◽

Cited By ~ 5

Author(s):

Maya Deepak ◽

Sarita Keski-Saari ◽

Laure Fauch ◽

Lars Granlund ◽

Elina Oksanen ◽

...

Keyword(s):

Principal Component ◽

Common Garden ◽

Dry Weight ◽

Leaf Traits ◽

Tree Canopy ◽

Canopy Reflectance ◽

Canopy Layer ◽

Leaf Reflectance ◽

Individual Trees ◽

Reflectance Indices

The availability of light within the tree canopy affects various leaf traits and leaf reflectance. We determined the leaf reflectance variation from 400 nm to 2500 nm among three canopy layers and cardinal directions of three genetically identical cloned silver birches growing at the same common garden site. The variation in the canopy layer was evident in the principal component analysis (PCA), and the influential wavelengths responsible for variation were identified using the variable importance in projection (VIP) based on partial least squares discriminant analysis (PLS-DA). Leaf traits, such as chlorophyll, nitrogen, dry weight, and specific leaf area (SLA), also showed significant variation among the canopy layers. We found a shift in the red edge inflection point (REIP) for the canopy layers. The canopy layers contribute to the variability in the reflectance indices. We conclude that the largest variation was among the canopy layers, whereas the differences among individual trees to the leaf reflectance were relatively small. This implies that within-tree variation due to the canopy layer should be taken into account in the estimation of intraspecific variation in the canopy reflectance.

Download Full-text

Do leaf traits in two Dalbergia species present differential plasticity in relation to light according to their habitat of origin?

Australian Journal of Botany ◽

10.1071/bt13248 ◽

2013 ◽

Vol 61 (8) ◽

pp. 592 ◽

Cited By ~ 5

Author(s):

Ana Silvia Franco Pinheiro Moreira ◽

Ana Clara Luppi Queiroz ◽

Fernanda de Vasconcelos Barros ◽

Maíra Figueiredo Goulart ◽

José Pires de Lemos-Filho

Keyword(s):

Phenotypic Plasticity ◽

Gas Exchange ◽

Stomatal Density ◽

Common Garden ◽

Leaf Traits ◽

Light Interception ◽

High Plasticity ◽

Forest Species ◽

Palisade And Spongy Parenchyma ◽

Changing Light

The phenotypic plasticity to light of two congeneric species of leguminous trees from distinct habitats was evaluated in a common-garden experiment. For that, we assessed the following two groups of leaf morphological and anatomical traits of 1-year-old seedlings: (1) traits related to light interception (tissues thickness and leaflet mass per area), and (2) traits related to gas exchange (number of leaflets per leaf and measurements of stomatal size and density). Dalbergia nigra (Vell.) Allemão ex Benth. is an endemic Atlantic forest species, and D. miscolobium Benth. is a typical cerrado species. Both were grown under shade and full-sunlight conditions. The phenotypic plasticity of leaves was determined by a relative distance plasticity index (RDPI). For both species, sun leaflets were thicker than shade ones, and only D. nigra presented lower values for stomatal density (nst), percentage of the leaflet area occupied by stomatal pores (nast) and estimated stomatal conductance (gst) under shade conditions. The forest species (D. nigra) had higher plasticity for variables related to gas exchange (number of leaflets per leaf, nst, ast, nast and gst), whereas the cerrado species (D. miscolobium) had higher plasticity for variables related to light interception, such as leaflet mass per area, leaflet thickness and palisade and spongy parenchyma thickness. The degree of plasticity was different for each analysed parameter, and not used to define which species is more plastic. The leaf traits of D. nigra and D. miscolobium that showed high plasticity were related to resources that are not limiting to improve its photosynthesis in a changing light environment.

Download Full-text

Diversity begets diversity through shared adaptive genetic variation: discovery of a cryptic wide-mouthed scale-eater

10.1101/2021.07.01.450755 ◽

2021 ◽

Author(s):

Emilie Richards ◽

Christopher Herbert Martin

Keyword(s):

Parallel Evolution ◽

Common Garden ◽

Selective Sweeps ◽

Adaptive Genetic Variation ◽

San Salvador ◽

Wide Mouth ◽

Rapid Divergence ◽

Dietary Niche ◽

San Salvador Island ◽

Ecological Transition

Adaptive radiations involve astounding bursts of phenotypic, ecological, and species diversity. However, the microevolutionary processes that underlie the origins of these bursts are still poorly understood. We report the discovery of a cryptic intermediate wide-mouth scale-eating ecomorph in a recent radiation of Cyprinodon pupfishes which provides crucial information about the evolutionary and ecological transition from a widespread algae-eating generalist to a novel microendemic scale-eating specialist. We first show that this ecomorph occurs in sympatry with generalist C. variegatus and scale-eating specialist C. desquamator across several hypersaline lakes on San Salvador Island, Bahamas, but is genetically differentiated, morphologically distinct when reared in a common garden, and sometimes consumes scales. We then compared the timing of selective sweeps on shared and unique adaptive variants in both scale-eating species to characterize the evolutionary path to scale-eating. We predicted that adaptation to the intermediate wide-mouth scale-eating niche aided in the rapid divergence of the more specialized scale-eater C. desquamator. Therefore, selection for shared adaptive variants would occur first in wide-mouth. Contrary to our prediction, four of the six sets of shared adaptive alleles in both scale-eating species swept significantly earlier in C. desquamator. Adaptive introgression from the specialist into the wide-mouth ancestor may have resulted in parallel evolution of their dietary niche. Conversely, no adaptive alleles for scale-eating were reused in a third sympatric specialist C. brontotheriodes, despite sharing 9% of hard selective sweeps. Our work provides a microevolutionary framework for investigating how diversity begets diversity during adaptive radiation.

Download Full-text