Biology subjects

Eriksson, M.

Publications and source records attributed to Eriksson, M..

7 recordsLinked to original sources

bioRxiv2024

Ecological divergence is marked by specific plastic gene expression and distinct rhizosphere among sibling allopolyploid marsh orchids (Dactylorhiza)

Phenotypic plasticity, the dynamic adjustment of traits to environmental variations, is crucial for enabling species to exploit broader niches and withstand suboptimal conditions. This adaptability is particularly relevant for newly formed allopolyploids, which possess redundant gene copies and must become established in diverse environments distinct from their parents and other relatives. By evaluating gene expression and root mycobiome among two ecologically divergent sibling allopolyploid marsh orchids (Dactylorhiza majalis and D. traunsteineri) in reciprocal transplants at localities where both species are native, we aimed to understand the drivers of species persistence in the face of interspecific gene flow. Despite consistent abiotic differences characterising the alternative environments at each locality, the majority of gene expression differences between the allopolyploids appears to be plastic. Ecologically relevant processes, such as photosynthesis and transmembrane transport, include some genes that are differentially expressed between the two orchids regardless of the environment, while others change their activity plastically in one species or the other. This suggests that although plasticity helps define the specific ecological range of each sibling allopolyploid, it also mediates gene flow between them, thereby preventing differentiation. Extending our investigations to the root mycobiome, we uncover more diverse fungal communities for either species when grown in the environment with nutrient-poor soils, indicating that both abiotic and biotic factors drive the distribution of sibling marsh orchids. Altogether, our results indicate that plasticity can simultaneously promote diversification and homogenization of lineages, influencing the establishment and persistence of recurrently formed allopolyploid species. Significance statementThis study highlights the role of phenotypic plasticity in the persistence and distribution of sibling allopolyploid marsh orchids (Dactylorhiza majalis s.l.). By examining gene expression and the diversity of root mycobiome across reciprocal transplantations in native environments, we uncover high plasticity that facilitates adaptation and gene flow, thereby promoting both diversification and homogenization. These findings underscore the importance of plasticity in the establishment and long-term survival of allopolyploid species across the landscape.

evolutionary biology↗

bioRxiv2022

Adaptive, maladaptive, neutral, or absent plasticity: Hidden caveats of reaction norms

Adaptive phenotypic plasticity may improve the response of individuals when faced with new environmental conditions. Typically, empirical evidence for plasticity is based on phenotypic reaction norms obtained in reciprocal transplant experiments. In such experiments, individuals from their native environment are transplanted into a different environment, and a number of trait values, potentially implicated in individuals response to the new environment, are measured. However, the interpretations of reaction norms may differ depending on the nature of the assessed traits, which may not be known beforehand. For example, for traits that contribute to local adaptation, adaptive plasticity implies non-zero slopes of reaction norms. By contrast, for traits that are correlated to fitness, high tolerance to different environments (possibly due to adaptive plasticity in traits that contribute to adaptation) may, instead, result in flat reaction norms. Here we investigate reaction norms for adaptive versus fitness-correlated traits, and how they may affect the conclusions regarding the contribution of plasticity. To this end, we first simulate range expansion along an environmental gradient where plasticity evolves to different values locally and then perform reciprocal transplant experiments in silico. We show that reaction norms alone cannot inform us whether the assessed trait exhibits locally adaptive, maladaptive, neutral or no plasticity, without any additional knowledge of the traits assessed and species biology. We use the insights from the model to analyse and interpret empirical data from reciprocal transplant experiments involving the marine isopod Idotea balthica sampled from two geographical locations with different salinities, concluding that the low-salinity population likely has reduced adaptive plasticity relative to the high-salinity population. Overall, we conclude that, when interpreting results from reciprocal transplant experiments, it is necessary to consider whether traits assessed are locally adaptive with respect to the environmental variable accounted for in the experiments, or correlated to fitness.

evolutionary biology↗

bioRxiv2022

Species' ranges and the steepening-gradient hypothesis

One hypothesis invoked to explain limits to species ranges is a mismatch in environmental conditions between the central and marginal areas of species ranges. Low population size at the margins causes genetic drift to outplay selection locally, and limits the accumulation of genetic variance, so that adaptation is hindered locally. Earlier theoretical work shows that, for a population expanding over a spatially heterogeneous environment without any geographical barriers, adaptation will fail abruptly and sharp range margins will establish only when the underlying environmental conditions change more and more severely across space, whereas an environment changing constantly will result either in infinite expansion or rapid global extinction. Here, we extend this "steepening-gradient hypothesis" to encompass situations when multiple (up to three) environmental factors impose selection on separate adaptive traits. We show that multiple selection gradients steepen each other and that it is sufficient that just one of the gradients steepen in space for sharp range margins to form. This is true even if this gradient is shallow throughout the realised range. Thus, despite its detrimental role in forming range margins, it could be overlooked in field studies. Finally, by decomposing an environmental gradient to selection on two (or three) adaptive traits, we show that a population can withstand harsher environmental conditions than when selection acts on one adaptive trait alone. This finding argues for the evolution of novel traits in harsh environments.

evolutionary biology↗

bioRxiv2021

The role of phenotypic plasticity in the establishment of range margins

It has been argued that adaptive phenotypic plasticity may facilitate range expansions over spatially and temporally variable environments. However, plasticity may induce fitness costs. This may hinder the evolution of plasticity. Earlier modelling studies examined the role of plasticity during range expansions of populations with fixed genetic variance. However, genetic variance evolves in natural populations. This may critically alter model outcomes. We ask: How does the capacity for plasticity in populations with evolving genetic variance alter range margins that populations without the capacity for plasticity are expected to attain? We answered this question using computer simulations and analytical approximations. We found a critical plasticity cost above which the capacity for plasticity has no impact on the expected range of the population. Below the critical cost, by contrast, plasticity facilitates range expansion, extending the range in comparison to that expected for populations without plasticity. We further found that populations may evolve plasticity to buffer temporal environmental fluctuations, but only when the plasticity cost is below the critical cost. Thus, the cost of plasticity is a key factor involved in range expansions of populations with the potential to express plastic response in the adaptive trait.

evolutionary biology↗

bioRxiv2021

Rare copy number variants (CNVs) and breast cancer risk

BackgroundCopy number variants (CNVs) are pervasive in the human genome but potential disease associations with rare CNVs have not been comprehensively assessed in large datasets. We analysed rare CNVs in genes and non-coding regions for 86,788 breast cancer cases and 76,122 controls of European ancestry with genome-wide array data. ResultsGene burden tests detected the strongest association for deletions in BRCA1 (P= 3.7E-18). Nine other genes were associated with a p-value < 0.01 including known susceptibility genes CHEK2 (P= 0.0008), ATM (P= 0.002) and BRCA2 (P= 0.008). Outside the known genes we detected associations with p-values < 0.001 for either overall or subtype-specific breast cancer at nine deletion regions and four duplication regions. Three of the deletion regions were in established common susceptibility loci. ConclusionsThis is the first genome-wide analysis of rare CNVs in a large breast cancer case-control dataset. We detected associations with exonic deletions in established breast cancer susceptibility genes. We also detected suggestive associations with non-coding CNVs in known and novel loci with large effects sizes. Larger sample sizes will be required to reach robust levels of statistical significance.

genetics↗

bioRxiv2020

The effect of genetic architecture and selfing on the capacity of a population to expand its range

Previous theoretical work on range expansions over heterogeneous environments showed that there is a critical environmental gradient where range expansion stops. For populations with freely recombining loci underlying the trait under selection (hereafter adaptive loci), the critical gradient in one-dimensional habitats depends on the fitness cost of dispersal, and the strength of selection relative to genetic drift. Here, we extend the previous work in two directions and ask: What is the role of the genetic architecture of adaptive loci during range expansions? And what effect does the ability of selfing have on range expansions? To answer these questions, we use computer simulations. We demonstrate that, while reduced recombination rates between adaptive loci slow down range expansions due to poor purging of locally deleterious alleles at the expansion front, they may also allow a species to occupy a greater range. In fact, for some parameter values, we find that a population with freely recombining adaptive loci experiences global extinction, whereas reduced recombination rates allow for a successful expansion over a wide geographic range. In addition, we find that allowance of selfing may improve the ability of populations to expand their ranges. We discuss the mechanisms underlying these results.

evolutionary biology↗

bioRxiv2018

Taxonomic identification from metagenomic and metabarcoding data using any genetic marker

Correct taxonomic identification of DNA sequences is central to studies of biodiversity using both shotgun metagenomic and metabarcoding approaches. However, there is no genetic marker that gives sufficient performance across all the biological kingdoms, hampering studies of taxonomic diversity in many groups of organisms. We here present a major update to Metaxa2 (http://microbiology.se/software/metaxa2/) that enables the use of any genetic marker for taxonomic classification of metagenome and amplicon sequence data.

bioinformatics↗