Biology subjects

Birkeland, S.

Publications and source records attributed to Birkeland, S..

7 recordsLinked to original sources

bioRxiv2026

Shared genomic signatures of Arctic adaptation among distantly related plant lineages

Extreme environments impose strong selection pressures that can drive convergent adaptation among distantly related species. Arctic plants survive low temperatures, 24-hour light in summer and darkness in winter, short growing seasons, limited precipitation, nutrient-poor soils, and extreme seasonal variation. To test if these conditions are associated with shared genomic signatures, we generated a chromosome-level genome assembly for Oxyria digyna and compared it with existing reference genomes for three distantly related Arctic species (Cochlearia groenlandica, Draba nivalis, Dryas octopetala) and for 16 non-Arctic species from the same families. We identified 214 orthogroups with signatures of positive selection in all Arctic species, 1.6 times the number shared among the non-Arctic species. Although no gene ontology (GO) categories remained significantly enriched after multiple-testing correction, descriptive annotations included genes involved in general functions including protein folding, glycolysis, transcription, and oxidative-stress responses. Orthogroups showing copy number variation were associated with biotic interactions, sexual reproduction, and nutrient acquisition, suggesting that species may respond to biotic and nutrient stresses by shifts in gene copy number. Arctic and alpine genomes contained lower proportions of some repetitive elements, including terminal inverted repeats, and smaller regions of centromeric repeats than non-Arctic genomes. Overall, we see shared genes under positive selection, similar functions of genes with high copy number variation, and lower counts of some repetitive elements in the Arctic plant genomes. Our findings reveal a shared genomic signature of Arctic adaptation across deeply diverged plant lineages, suggesting that evolution in extreme environments repeatedly targets similar genomic features.

genomics↗

bioRxiv2025

Vascular plant extinctions outpace colonizations under climate change

Climate change is expected to shift plant distributions poleward and upslope, yet requires global empirical evidence. Using historical range shifts from global herbarium specimens for 109,242 vascular plant species over the past 28 years as baseline, we fit 1.8 million species distribution models on a global dataset of 184,545 vascular plant species to project future range shifts over an equivalent period, the next 20 years (2021-2040). We find that plant species have already shifted their distribution centroids at a median velocity of 5.6 km per year globally, exceeding projected future velocities of 3.27 km yr per year. Projected shifts will vary widely in direction and magnitude, with varied velocities, colonization and extinction rates. Shifts will vary across clades with Superasteridae, Gymnosperms and Monocots moving at slower velocities, and Ferns, Chloranthales, and Magnoliidae with faster velocities. Although most clades will shift polewards, velocities will be highest in temperate and boreal regions, while shifts will be slower in regions of high topographic variation in the tropics. High latitude species will trend poleward and upslope, while desert shrubs, and tropical conifer forests will show slower and directional shifts. Extinctions will outpace colonizations, confirming that climate change will be a driver of biodiversity loss. Colonization will be frequent in protected areas, higher elevations, and among threatened species whereas extinctions will cluster near species historical ranges and at lower elevations. Our findings show the complexity of climate-driven range shifts and emphasize the importance of considering multiple interacting processes beyond simple latitudinal or elevational movements.

ecology↗

bioRxiv2025

Comparative regulomics provides novel insight into the evolution of wood formation across dicot and conifer trees

Understanding the regulatory program underlying wood formation is key to improving biomass production and carbon sequestration in trees. However, how wood formation evolved and how these programs have been rewired across lineages remains unclear. Here, we present the first high-spatial-resolution evo-devo resource spanning the wood transcriptomes of six tree species - three dicots and three conifers - capturing 250 million years of evolutionary divergence. Using orthology-aware co-expression network analysis, we identified genes with conserved and lineage-specific expression patterns. By integrating chromatin accessibility data and transcription factor motif analysis, we further inferred regulatory networks for xylem differentiation and secondary cell wall formation. We demonstrate how this dataset can be used to answer long standing questions in wood biology related to differences in acetylation of cell wall polymers and master regulators of xylem specification across dicot and conifer tree species. The data offer a foundational resource for the tree biology and evo-devo communities, and are publicly available at PlantGenIE.org.

genomics↗

bioRxiv2024

Maize genetic diversity identifies moisture-dependent root-branch signaling pathways

Plants grow complex root systems to extract unevenly distributed resources from soils. Spatial differences in soil moisture are perceived by root tips leading to the patterning of new root branches towards available water, a process called hydropatterning. Little is known about hydropatterning behavior and its genetic basis in crops plants. Here, we develop an assay to measure hydropatterning in maize and reveal substantial differences between tropical/subtropical and temperate maize breeding germplasm that likely resulted from divergent selection. Genetic dissection of hydropatterning confirmed the regulatory role of auxin and revealed that the gaseous hormone ethylene acts to locally inhibit root branching from air-exposed tissues. These findings demonstrate the crop relevance of hydropatterning and establish its genetic basis.

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↗

bioRxiv2022

The genomic basis of the plant island syndrome in Darwin's giant daisies

Oceanic archipelagos comprise multiple disparate environments over small geographic areas and are isolated from other biotas. These conditions have led to some of the most spectacular adaptive radiations, which have been key to our understanding of evolution, and offer a unique chance to characterise the genomic basis underlying rapid and pronounced phenotypic changes. Repeated patterns of evolutionary change in plants on oceanic archipelagos, i.e. the plant island syndrome, include changes in leaf morphology, acquisition of perennial life-style, and change of ploidy. Here, we describe the genome of the critically endangered and Galapagos endemic Scalesia atractyloides Arnot., obtaining a chromosome-resolved 3.2-Gbp assembly with 43,093 candidate gene models. Using a combination of fossil transposable elements, k-mer spectra analyses and orthologue assignment, we identify the two ancestral subgenomes and date their divergence and the polyploidization event, concluding that the ancestor of all Scalesia species on the Galapagos was an allotetraploid. There are a comparable number of genes and transposable elements across the two subgenomes, and while their synteny has been mostly conserved, we find multiple inversions that may have facilitated adaptation. We identify clear signatures of selection across genes associated with vascular development, life-growth, adaptation to salinity and changes in flowering time, thus finding compelling evidence for a genomic basis of island syndrome in Darwins giant daisy radiation. This work advances understanding of factors influencing subgenome divergence in polyploid genomes, and characterizes the quick and pronounced genomic changes in a specular and diverse radiation of an iconic island plant radiation.

evolutionary biology↗

bioRxiv2021

What can the cold-induced transcriptomes of Arctic Brassicaceae tell us about the evolution of cold tolerance?

O_LILittle is known about the evolution of cold tolerance in polar plant species and how they differ from their temperate relatives. To gain insight into their biology and the evolution of cold tolerance, we compared the molecular basis of cold response in three Arctic Brassicaceae species. C_LIO_LIWe conducted a comparative time series experiment to examine transcriptional responses to low temperature. RNA was sampled at 22 {degrees}C, and after 3h, 6h, and 24h at 2 {degrees}C. We then identified sets of genes that were differentially expressed in response to cold and compared them between species, as well as to published data from the temperate Arabidopsis thaliana. C_LIO_LIMost differentially expressed genes were species-specific, but a significant portion of the cold response was also shared among species. Among thousands of differentially expressed genes, [~]200 were shared among the three Arctic species and A. thaliana, while [~]100 were exclusively shared among the three Arctic species. C_LIO_LIOur results show that cold response differs markedly between Arctic Brassicaceae species, but likely builds on a conserved basis found across the family. They also confirm that highly polygenic traits such as cold tolerance may show little repeatability in their patterns of adaptation. C_LI

evolutionary biology↗