Biology subjects

Yant, L.

Publications and source records attributed to Yant, L..

At least 19 recordsLinked to original sources

bioRxiv2026

A Global Genomic Resource for Outcrossing Arabidopsis lyrata and Arabidopsis arenosa

Genetic studies leveraging natural variation in Arabidopsis species have improved our understanding of evolutionary genetic processes underlying ecologically important and adaptive traits. Integrating the thorough functional knowledge accumulated in A. thaliana with the extensive natural variation in outcrossing Arabidopsis species is a powerful approach to study the basis of adaptation in natural evolutionary and ecological contexts. Here we present an integrated genomics database of sequenced genomes from several studies in A. lyrata (1018 genomes in total) and A. arenosa (736 genomes in total), spanning the geographic ranges of these two ploidy-variable, outcrossing taxa. We provide a searchable genome browser with population data mapped to respective reference genomes, an interactive geographic map of population structure clusters, and an efficient way to subsample the full dataset of genetic variation, available at arabidopsislyrata.org. To demonstrate its utility, we perform a genome-wide association study on a latitudinal cline of A. lyrata and find strong associations of several loci with latitude, including variants in key regulators of photoperiodic growth. This resource provides access to genetic diversity data in a single repository, enabling further studies of comparative genetics and local adaptation, as well as of individual genes of interest.

evolutionary biology↗

bioRxiv2026

Integrative genomic and regulatory network analysis reveals adaptive mechanisms to salt-alkalinity stress in Brassica fruticulosa

Salinity poses a widespread and increasing threat to plant fitness, ultimately constraining agricultural productivity worldwide. An inherent roadblock to understanding the precise physiological impacts of high-salinity soils is the frequent co-occurrence of multiple stressors. In calcareous soils, salinity typically coincides with alkalinity. To address this realistic combinatorial stress scenario, we deconstructed the enhanced performance of the coastally distributed, salt-tolerant Brassica fruticulosa under salt-alkaline conditions using comparative physiological, transcriptomic, and genomic analyses across major brassica crops. First, to gain a high-resolution genomic view, we generated phased, chromosome-level genome assemblies of B. fruticulosa and performed cross-species comparisons of transcriptome-derived Gene Regulatory Networks (GRNs) among important related crop models with contrasting salt tolerances. These results revealed that B. fruticulosa mounts predominantly root-centered transcriptional responses to cope with high salinity, whereas salt-sensitive species rely largely on shoot-level mechanisms to mitigate salt toxicity. Consistently, regulatory modules within GRNs diverged substantially between organs and among species, reflecting distinct adaptive programmes of varying efficacy. Functional categorisation of transcription factors with high centrality in B. fruticulosa shoot GRNs highlighted processes related to iron (Fe) homeostasis, suggesting that effective maintenance of Fe allocation to aerial tissues supports biomass retention under combined salt and alkalinity stress. Collectively, these findings establish B. fruticulosa as a valuable new model for dissecting adaptation to salinity in natural environments and provide mechanistic insight into the regulatory architecture underlying salt-alkaline tolerance.

plant biology↗

bioRxiv2025

Arabidopsis arenosa influences its microbiome as a serpentine soil adaptation strategy

There is growing evidence that microbes can facilitate plant growth in metal-rich soils. However, our current understanding of how plants recruit their microbiomes under abiotic stress remains incomplete. Serpentine soils are elementally skewed, with high concentrations of magnesium and nickel, often accompanied by other heavy metals, which can limit calcium availability and present unique challenges to plant growth. These soils are also nutrient-poor, prone to erosion, and have low water-holding capacity. To date, the mechanisms by which plants adapt to serpentine soils remain poorly understood and the role of plant-associated microbiomes in this process has not been described. Here, we focus on Arabidopsis arenosa populations adapted to serpentine conditions and investigate their bacterial and fungal microbiomes to better understand the role of plant-associated microbes in serpentine adaptation. We show that serpentine soils harbour distinct plant-associated microbiomes across different plant niches and that the plant genetic background plays a key role in shaping microbial community composition. Finally, we identify serpentine-specific bacterial and fungal variants that may contribute to plant adaptation under these challenging soil conditions.

ecology↗

bioRxiv2025

European ash pangenome reveals widespread structural variation and a diverse genetic basis for low ash dieback susceptibility

European Ash (Fraxinus excelsior) is a keystone forest tree species, whose populations are being decimated by ash dieback disease (ADB). Uncovering the genetic basis of low susceptibility to this devastating disease relies on a comprehensive understanding of genetic variation present in F. excelsior. A linear reference genome from a single individual cannot contain the total sequence variability within a species, including its genic regions; a pangenome more fully captures total sequence content. In this study, we developed a F. excelsior pangenome reference using a new chromosomal-level phased linear reference genome, and de novo assemblies and long-read data from a geographically diverse set of fifty F. excelsior samples, with particular focus on individuals showing low ADB susceptibility. We identified 362,965 structural variants (SVs) present in more than three individuals, including 174Mb of sequence absent from the linear reference genome (22% of the linear reference size). We demonstrated that failing to explicitly link SVs with gene sequences can lead to substantial overestimation of dispensable genes (those that vary in their presence/absence between individuals) due to variability in the annotation process. Controlling for this reduced the fraction of the genome estimated as dispensable from 35.9% to 8.7%, identifying 3,412 high-confidence dispensable genes, including 141 annotated with gene ontology terms associated with defence response. We used the pangenome to analyse existing genomic data from over 1,200 individuals to identify loci associated with reduced susceptibility to ADB. This revealed 220 single nucleotide polymorphisms (SNPs) showing allele frequency shifts between healthy and highly damaged pools of individuals that are broadly consistent across the mainly UK seed sources sampled, explicitly demonstrating the existence of a shared genetic component to low ADB susceptibility.

genomics↗

bioRxiv2025

Genomic basis of adaptation to serpentine soil in two Alyssum species shows convergence with Arabidopsis across 20 million years of divergence

Background and AimsSerpentine outcrops, characterized by low nutrient availability, high heavy metal concentrations, propensity to drought, and island-like distributions, offer valuable systems to study parallelisms in repeated adaptation to extreme environments. While shared phenotypic manifestation of adaptation to serpentine environments has been investigated in many species, it is still unclear whether there may be a common genetic basis underlying such responses. Here we assess local adaptation to serpentine soil and infer the parallel genetic signatures of local adaptation to serpentine environments in two thus far unexplored closely related species, Alyssum gmelinii and Alyssum spruneri (Brassicaceae). Then we measure gene- and function-level convergence with the previously explored Arabidopsis arenosa, to reveal candidate shared adaptive strategies within Brassicaceae. MethodsWe tested for adaptation using a reciprocal substrate-transplant experiment in A. gmelinii. Then, after assembling a reference genome, we generated population-level sequencing data of four population pairs and performed genome scans for directional selection to infer serpentine adaptive candidate genes in Alyssum. Finally, we compared candidate gene lists with those inferred in similar experiments in Arabidopsis arenosa and used protein-protein interaction networks to discern functional convergence in serpentine adaptation. Key ResultsIndependent colonization of serpentine environments by Alyssum populations is associated with footprints of selection on genes related to ion transport and homeostasis, nutrient and water uptake, and life-history traits related to germination and reproduction. Reciprocal transplant experiments demonstrated that adapted plants germinate sooner and exhibit better growth in serpentine conditions while excluding heavy metals and increasing Ca uptake in their tissues. Finally, a significant fraction of such genes and molecular pathways is shared with Arabidopsis arenosa. ConclusionsWe show that genetic adaptation to the multi-factorial challenge imposed by serpentine environments involves key pathways that are shared not only between closely related species, but also between Brassicaceae tribes of [~]20 Mya divergence.

evolutionary biology↗

bioRxiv2025

Whole-genome duplication increases genetic diversity and load in outcrossing Arabidopsis

Genetic variation underpins evolutionary change, but accumulation of slightly deleterious mutations also increases mutation load. There are multiple factors affecting the extent of load such as population size and breeding system, yet other potential determinants remain unexplored. A common macromutation, whole-genome duplication (WGD) occurs broadly across Eukaryotes, yet we lack a clear understanding of how WGD impacts neutral and selective processes within a population. Using forward simulations and empirical analysis of 632 short- and 16 long-read sequenced individuals of Arabidopsis arenosa (23 diploid and 42 natural autotetraploid populations), we test for the effects of WGD on genome-wide diversity and mutation load. Our simulations show how genetic variation gradually rises in autotetraploids due to increase of mutational target size. Moreover, mutation load increases due to relaxed purifying selection when deleterious mutations are masked by additional chromosome copies. Empirical data confirm these patterns, showing significant increase in nucleotide diversity, ratios of non-synonymous to synonymous SNPs, and number of indels and large structural variants in A. arenosa autotetraploids. However, a rather modest increase in load proxies together with a broad distribution and niche of autotetraploids suggests load accumulation has not (yet) limited their successful expansion. Overall, we demonstrate a complex interplay between neutral processes and purifying selection in shaping genetic variation following WGD and highlight ploidy as an important determinant of genetic diversity and mutation load in natural populations.

evolutionary biology↗

bioRxiv2024

An ecological, phenotypic and genomic survey of duckweeds with their associated aquatic environments in the United Kingdom

The duckweeds feature global distributions and diverse applications in phytoremediation and nutrition, as well as use in fundamental studies of development. Existing collections have minimal environmental data linked to natural habitats. Thus, there is a lack of understanding of natural variation in the context of native habitats. Here, a novel collection of 124 duckweed accessions from 115 sites across the United Kingdom were characterised by genome sequencing and ionomics. In nutrient-replete conditions all accessions hyperaccumulated P, K, Mg and Ca. Local but not large-scale associations were revealed between elemental composition of duckweed in common, replete conditions and native water profiles. Lemna minor was the most prevalent species in the UK, with a closely related hybrid L. japonica frequently found in waters with higher micronutrient concentrations. Invasive L. minuta was common in the southern and midland regions, but restricted in Scotland. Lemna accessions accumulated heavy metal contaminants typically together with macronutrients, suggesting phytoremediation potential, but some limitations as food. Furthermore, monitoring the ecological interactions between native, hybrid and invasive Lemna species should be ongoing in the interest of biodiversity.

ecology↗

bioRxiv2024

Local cryptic diversity in salinity adaptation mechanisms in a wild outcrossing Brassica

It is generally assumed that populations of the same species should evolve shared mechanisms of adaptation to common stressors due to evolutionary constraint. Here, we describe a novel system of within-species local adaptation to coastal habitats, Brassica fruticulosa, and detail surprising mechanistic variability in adaptive responses to extreme salinity. These radically different adaptive responses in neighbouring populations are evidenced by transcriptomes, diverse physiological outputs, and completely distinct genomic selective landscapes. In response to high salinity Northern Catalonian populations restrict root-to-shoot Na+ transport, favouring K+ uptake. Contrastingly, Central Catalonian populations accumulate Na+ in leaves and compensate for the osmotic imbalance with compatible solutes such as proline and elevated Ca2+. Despite contrasting responses, both metapopulations were salinity tolerant relative to all inland accessions. To characterise the genomic basis of these two divergent adaptive strategies in an otherwise non-saline-tolerant endemic, we generate a long-read-based genome and population sequencing of 18 populations (9 inland, 9 coastal) across the B. fruticulosa species range. Results of genomic and transcriptomic approaches confirm the physiological observations of completely distinct underlying mechanisms of adaptation to extreme salinity and reveal potential genetic targets of these two recently evolved salinity adaptations. We therefore provide a new model of within-species salinity adaptation and reveal cryptic variation in neighbouring plant populations in the mechanisms of adaptation to an important natural stressor highly relevant to agriculture. SignificanceIts usually expected that closely related populations of a given species should adapt to the same environmental stressor in the same way due to genetic or physiological constraints. However, this is not commonly tested due to practical constraints. Here we show that, even at the level of neighbouring populations, contrasting adaptive mechanisms control adaptive responses to extreme coastal salinity in a new plant model, Brassica fruticulosa, a close wild relative of many crops of worldwide importance. This indicates multiple options for engineering an agriculturally crucial adaptation: soil salinization. These results will be of great interest to not only those studying fundamental mechanisms of adaptation, but also resilience improvement in Brassica species.

evolutionary biology↗

bioRxiv2024

Chromosome-level baobab (Adansonia digitata) genome illuminates its evolutionary insights

AbstractBaobab, Adansonia digitata, is a long-lived tree endemic to Africa that holds great economic, ecological, and cultural value. However, our knowledge of its genomic features, evolutionary history, and diversity is limited, rendering it orphaned scientifically. We generated a haploid chromosome-level reference genome anchored into 42 chromosomes for A. digitata, as well as draft assemblies for a sibling tree, two trees from distinct locations in Africa, and a related species, A. za from Madagascar. Unlike any other plant to date, DNA transposable elements (TEs) make up 33% of the A. digitata genome compared to only 10% long terminal repeat retrotransposons (LTR-RTs), which are usually predominant in plant genomes. Baobab has undergone a whole genome duplication (WGD) shared with the Malvoideae [~]30 million years ago (MYA), as well as a confirmed autotetraplody event 3-4 million MYA that coincides with the most recent burst of TE insertions. Resequencing 25 A. digitata trees from Africa revealed three subpopulations that suggest gene flow through most of West Africa but separated from East Africa. Gene enrichment analysis for baobab-specific and high fixation index (Fst) suggested baobab may have retained multiple copies of circadian, light and growth genes to coordinate genome protection for longevity through the UV RESISTANCE LOCUS 8 (UVR8) and synchronizing flower development with pollinators. This study lays the groundwork for the creation of breeding resources and the conservation of baobab biodiversity.

genomics↗

bioRxiv2024

Chromosome-scale genome assembly of bread wheat's wild relative Triticum timopheevii

Wheat (Triticum aestivum) is one of the most important food crops with an urgent need for increase in its production to feed the growing world. Triticum timopheevii (2n = 4x = 28) is an allotetraploid wheat wild relative species containing the At and G genomes that has been exploited in many pre-breeding programmes for wheat improvement. In this study, we report the generation of a chromosome-scale reference genome assembly of T. timopheevii accession PI 94760 based on PacBio HiFi reads and chromosome conformation capture (Hi-C). The assembly comprised a total size of 9.35 Gb, featuring a contig N50 of 42.4 Mb, and 166,325 predicted gene models. DNA methylation analysis showed that the G genome had on average more methylated bases than the At genome. The G genome was also more closely related to the S genome of Aegilops speltoides than to the B genome of hexaploid or tetraploid wheat. In summary, the T. timopheevii genome assembly provides a valuable resource for genome-informed discovery of agronomically important genes for food security.

plant biology↗

bioRxiv2023

Impact of whole-genome duplications on structural variant evolution in the plant genus Cochlearia

Polyploidy, the result of whole-genome duplication (WGD), is a major driver of eukaryote evolution. All angiosperms have undergone ancient WGDs, and today stable polyploids account for a substantial portion of both wild and domesticated plant species. Despite its centrality in evolution, WGD is a hugely disruptive mutation, and we still lack a clear understanding of its fitness consequences. Here, we study whether WGD results in greater diversity of genomic structural variants (SVs) and how this influences evolutionary dynamics in nature. Using a set of long-read sequenced samples from the plant genus Cochlearia (Brassicaceae), which contains diploids and a recent ploidy series up to octoploid, we show that masking of recessive mutations due to WGD has led to a substantial and progressive accumulation of genic SVs across four ploidy levels. Such SVs likely constitute a genetic load and thus reduce the adaptive potential of polyploid populations. However, this SV accumulation also provides a rich pool of standing genetic variation upon which selection may act in novel environments. By constructing a graph-based pangenome for Cochlearia, we identify SVs in hundreds of samples and study the genomic basis of environmental adaptation. We find putatively beneficial SVs involved in pathogen resistance, root development, and salt tolerance, many of which are unique to polyploids. Finally, we explore the adaptive landscapes of SVs and SNPs, identify geographical regions where SVs make novel contributions to adaptive variation, and predict that the role of SVs in environmental adaptation increases due to rapid climate change.

evolutionary biology↗

bioRxiv2023

Kinetochore and ionomic adaptation to whole genome duplication

Transforming genomic and cellular landscapes in a single generation, whole genome duplication (WGD) brings fundamental challenges, but is also associated with diversification. How is WGD tolerated, and what processes commonly evolve to stabilize the resulting polyploid? Here we study this in Cochlearia spp., which have experienced multiple WGDs in the last 300,000 years. We first generate a chromosome-scale genome and sequence 113 individuals from 33 diploid, tetraploid, hexaploid, and outgroup populations. We detect the clearest post-WGD selection signatures in functionally interacting kinetochore components and ion transporters. We structurally model these derived selected alleles, identifying striking WGD-relevant functional variation, and then compare these results to independent recent post-WGD selection in Arabidopsis arenosa and Cardamine amara. Most prominent in these results is genetic evidence of at least four functionally interacting kinetochore complex subunits in adaptation to WGD at the centromere among our very top selective sweep outliers. In addition, some of the same biological processes evolve in all three WGDs, but specific genes recruited are flexible. This points to a polygenic basis for modifying systems that control the kinetochore, meiotic crossover number, DNA repair, ion homeostasis, and cell cycle. Given that DNA management (especially repair) is the most salient category with the strongest selection signal, we speculate that the generation rate of structural genomic variants may be altered by WGD in young polyploids, contributing to their occasionally spectacular adaptability observed across kingdoms. Significance StatementWhole-genome duplication (WGD) occurs in all kingdoms and is linked to adaptation, speciation, domestication, and even cancer outcome. But WGD is a shock to the system, and commonly disrupts cell division due to increased DNA management burden and transformed cell physiology. Nevertheless, the hopeful monster that survives WGD is special, occasionally experiencing runaway success. Why do some thrive but others die? Here we introduce a powerful new model, Cochlearia, which has benefitted from multiple WGDs, and we provide the first genetic evidence of rapid adaptation of functionally interacting components of the cell division machinery, the kinetochore. We also compare which processes and genes evolve to stabilize the new polyploid in three independent cases and highlight common mechanisms.

evolutionary biology↗

bioRxiv2023

The evolution of the duckweed ionome mirrors losses in structural complexity

Background and AimsThe duckweeds consist of 36 species exhibiting impressive phenotypic variation, including the progressive evolutionary loss of a fundamental plant organ, the root. Loss of roots and reduction of vascular tissues in recently derived taxa occur in concert with genome expansions of up to 14-fold. Given the paired loss of roots and reduction in structural complexity in derived taxa, we focus on the evolution of the ionome (whole-plant elemental contents) in the context of these fundamental body plan changes. We expect that progressive vestigiality and eventual loss of roots may have both adaptive and maladaptive consequences which are hitherto unknown. MethodsWe quantify the ionomes of 34 accessions in 21 species across all duckweed genera, spanning 70 million years in this rapid cycling plant (doubling times are as low as 24 hours). We relate both micro- and macroevolutionary ionome contrasts to body plan remodelling and show nimble microevolutionary shifts in elemental accumulation and exclusion in novel accessions. Key ResultsWe observe a robust directional trend in calcium and magnesium levels decreasing from the ancestral representative Spirodela genus towards the derived rootless Wolffia, with the latter also accumulating cadmium. We also identify abundant within-species variation and hyperaccumulators of specific elements, with this extensive variation at the fine- as opposed to broad-scale. ConclusionsThese data underscore the impact of root loss, and reveal the very fine scale of microevolutionary variation in hyperaccumulation and exclusion of a wide range of elements. Broadly, they may point to trade-offs not well recognized in ionomes.

plant biology↗

bioRxiv2023

Repeated adaptation to whole genome duplication in outcrossing Arabidopsis is mediated by mosaic adaptive haplotypes

Polyploidy, the result of whole genome duplication (WGD), is widespread across the tree of life and is often associated with speciation or adaptability. It is thought that adaptation in autopolyploids (within-species polyploids) may be facilitated by increased access to genetic variation. This variation may be sourced from gene flow with sister diploids and new access to other tetraploid lineages, as well as from increased mutational targets provided by doubled DNA content. Here we deconstruct the origins of haplotype blocks displaying the strongest selection signals in established, successful autopolyploids, Arabidopsis lyrata and Arabidopsis arenosa. We see strong signatures of selection in 17 genes implied in meiosis, cell cycle, and transcription across all four autotetraploid lineages present in our expanded sampling of 983 sequenced genomes. Most prominent in our results is the finding that the tetraploid-characteristic haplotype blocks with the most robust signals of selection were completely absent in diploid sisters. In contrast, the fine-scaled variant mosaics in the tetraploids originated from highly diverse evolutionary sources. These include novel reassortments of trans-specific polymorphism from diploids, new mutations, and tetraploid-specific inter-species hybridization. We speculate that this broad-scale allele acquisition and re-shuffling enabled the autotetraploids to rapidly adapt to the challenges inherent to WGD, and may further promote their adaptation to environmental challenges. Lay summaryPolyploidy, the result of whole genome duplication, is associated with speciation and adaptation. To fuel their often remarkable adaptations, polyploids may access and maintain adaptive alleles more readily than diploids. Here we identify repeated signals of selection on genes that are thought to mediate adaptation to whole genome duplication in two Arabidopsis species. We found that the tetraploid-characteristic haplotype blocks, found in genes exhibiting the most robust signals of selection, were never present in their diploid relatives. Instead, these blocks were made of mosaics forged from multiple allelic sources. We hypothesize that this increased variation helped polyploids to adapt to the process that caused this increase - genome duplication - and may also help them adapt to novel environments.

evolutionary biology↗

bioRxiv2022

Genome of selfing Siberian Arabidopsis lyrata explains establishment of allopolyploid Arabidopsis kamchatica

A transition to selfing can be beneficial when mating partners are scarce, for example, due to ploidy changes or at species range edges. Here we explain how self-compatibility evolved in diploid Siberian Arabidopsis lyrata, and how it contributed to the establishment of allotetraploid A. kamchatica. First, we provide chromosome-level genome assemblies for two self-fertilizing diploid A. lyrata accessions, one from North America and one from Siberia, including a fully assembled S-locus for the latter. We then propose a sequence of events leading to the loss of self-incompatibility in Siberian A. lyrata, date this independent transition to [~]90 Kya, and infer evolutionary relationships between Siberian and North American A. lyrata, showing an independent transition to selfing in Siberia. Finally, we provide evidence that this selfing Siberian A. lyrata lineage contributed to the formation of the allotetraploid A. kamchatica and propose that the selfing of the latter is mediated by the loss-of-function mutation in a dominant S-allele inherited from A. lyrata.

plant biology↗

bioRxiv2022

Duckweed roots are dispensable and are on a trajectory toward vestigiality

Duckweeds are morphologically simplified, free floating aquatic monocots comprising both rooted and rootless genera. This has led to the idea that roots in these species may be vestigial, but empirical evidence supporting this is lacking. Here we show that duckweed roots are no longer required for their ancestral role of nutrient uptake. Comparative analyses of nearly all rooted duckweed species revealed a highly reduced anatomy, with greater simplification in the more recently diverged genus Lemna. A series of root excision experiments demonstrated that roots are dispensable for normal growth in Spirodela polyrhiza and Lemna minor. Furthermore, ionomic analyses of fronds in these two species showed little difference in the elemental composition of plants in rooted versus root-excised samples. In comparison, another free-floating member of the Araceae, Pistia stratiotes, which colonized the aquatic environment independently of duckweeds, has retained a more complex root anatomy. Whilst Pistia roots were not absolutely required for growth, their removal inhibited plant growth and resulted in a broad change in the mineral profile of aerial tissues. Collectively, these observations suggest that duckweeds and Pistia may be different stages along a trajectory towards root vestigialization Given this, along with the striking diversity of root phenotypes, culminating in total loss in the most derived species, we propose that duckweed roots are a powerful system with which to understand organ loss and vestigiality. One sentence summaryThrough their adaption to the aquatic environment, duckweed roots have progressively become structurally reduced making them an ideal plant model with which to study vestigiality.

evolutionary biology↗

bioRxiv2021

Evolutionary footprints of a cold relic in a rapidly warming world

With accelerating global warming, understanding the evolutionary dynamics of plant adaptation to environmental change is increasingly urgent. Here we reveal the enigmatic history of the genus Cochlearia (Brassicaceae), a Pleistocene relic that originated from a drought-adapted Mediterranean sister genus during the Miocene. Cochlearia rapidly diversified and adapted to circum-Arctic regions and other cold-characterized habitat types during the Pleistocene. This rapid change in ecological preferences was accompanied by a highly complex, reticulate polyploid evolution, which was apparently triggered by the impact of repeated Pleistocene glaciation cycles. Our results illustrate that two early diversified arctic-alpine diploid gene pools contributed differently to the evolution of this young polyploid genus now captured in a cold-adapted niche. Metabolomics revealed ancestral central carbon metabolism responses to cold in diverse ecotypes, likely due to continuous connections to cold habitats that we hypothesize facilitated widespread parallel adaptation to alpine and subalpine habitats, and which we speculate were coopted from existing drought adaptations. Given the growing scientific interest in adaptive evolution of temperature-related traits, our results provide much-needed taxonomic and phylogenomic resolution of a model system as well as first insights into the origins of its adaptation to cold.

evolutionary biology↗

bioRxiv2021

Parallel adaptation in autopolyploid Arabidopsis arenosa is dominated by repeated recruitment of shared alleles

Relative contributions of pre-existing vs de novo genomic variation to adaptation are poorly understood, especially in polyploid organisms, which maintain increased variation. We assess this in high resolution using autotetraploid Arabidopsis arenosa, which repeatedly adapted to toxic serpentine soils that exhibit skewed elemental profiles. Leveraging a fivefold replicated serpentine invasion, we assess selection on SNPs and structural variants (TEs) in 78 resequenced individuals and discovered substantial parallelism in candidate genes involved in ion homeostasis. We further modelled parallel selection and inferred repeated sweeps on a shared pool of variants in nearly all these loci, supporting theoretical expectations. A single, striking exception is represented by TWO PORE CHANNEL 1, which exhibits convergent evolution from independent de novo mutations at an identical, otherwise conserved site at the calcium channel selectivity gate. Taken together, this suggests that polyploid populations can rapidly adapt to environmental extremes, calling on both pre-existing variation and novel polymorphisms.

evolutionary biology↗