On the use of population genomic time series for environmental monitoring

Pfenninger, Markus; Bálint, Miklós

doi:10.1002/ajb2.1836

Cited by 4 publications

(1 citation statement)

References 20 publications

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“…Beyond these important scientific questions, the presented framework opens the possibility to use population genomic time series for applied functional environmental monitoring (Pfenninger & Bálint, 2022). While currently rather the presence or absence of species is used to evaluate the state of environments, the monitoring of selective changes associated with certain anthropogenic or environmental factors could serve as an early warning system before any community change would be visible.…”

Section: Discussionmentioning

confidence: 99%

Population genomic time series data of a natural population suggests adaptive tracking of environmental changes

Pfenninger

Foucault

2020

Preprint

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14While the evolutionary fitness of natural populations is affected by a multitude of environmental 15 factors, theory predicts that selective responses are in principle limited. However, we lack empirical 16 knowledge on the magnitude of different selection pressures natural populations adaptively track. 17Here, we developed a framework to investigate the quantitative and qualitative complexity of the 18 effectively acting selection regime using population genomic time series data. We applied the 19 approach to a natural population of the multivoltine midge Chironomus riparius. Using six seasonal 20 samples over three years from the same natural population, we could show with fitness experiments 21 that the population continuously evolved in response to a highly variable environment. Analyses of 22 genome-wide allele-frequencies revealed that tens of thousands of haplotypes responded at least 23 once to selection during the monitored period. Clustering the temporal haplotype frequency 24 trajectories revealed 46 different patterns, i.e. selection pressures. Some of these co-varied with 25 measured environmental variables known to be selective factors for the species. Our results 26 demonstrate that 1) adaptive tracking of multiple fluctuating selection pressures occurs in natural 27 populations, 2) the estimated minimum number of simultaneously acting selective pressures is quite 28 high but appears to be limited and 3) changes in intensity and direction of selective responses can be 29 frequent. This shows that adaptation in natural populations can be rapid, pervasive and complex 30

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Section: Discussionmentioning

confidence: 99%

Population genomic time series data of a natural population suggests adaptive tracking of environmental changes

Pfenninger

Foucault

2020

Preprint

Self Cite

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Population Genomic Time Series Data of a Natural Population Suggests Adaptive Tracking of Fluctuating Environmental Changes

Pfenninger

Foucault

2022

Integrative and Comparative Biology

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Natural populations are constantly exposed to fluctuating environmental changes that negatively affect their fitness in unpredictable ways. While theoretical models show the possibility of counteracting these environmental changes through rapid evolutionary adaptations, there have been few empirical studies demonstrating such adaptive tracking in natural populations. Here, we analysed environmental data, fitness-related phenotyping and genomic time-series data sampled over three years from a natural Chironomus riparius (Diptera, Insecta) population to address this question. We show that the population's environment varied significantly on the time scale of the sampling in many selectively relevant dimensions, independently of each other. Similarly, phenotypic fitness components evolved significantly on the same temporal scale (mean 0.32 Haldanes), likewise independent from each other. The allele frequencies of 367,446 SNPs across the genome showed evidence of positive selection. Using temporal correlation of spatially coherent allele frequency changes revealed 35,574 haplotypes with more than one selected SNP. The mean selection coefficient for these haplotypes was 0.30 (s.d. = 0.68). The frequency changes of these haplotypes clustered in 46 different temporal patterns, indicating concerted, independent evolution of many polygenic traits. Nine of these patterns were strongly correlated with measured environmental variables. Enrichment analysis of affected genes suggested the implication of a wide variety of biological processes. Thus, our results suggest overall that the natural population of C. riparius tracks environmental change through rapid polygenic adaptation in many independent dimensions. This is further evidence that natural selection is pervasive at the genomic level and that evolutionary and ecological time scales may not differ at all, at least in some organisms.

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Life on the edge: a new toolbox for population-level climate change vulnerability assessments

Barratt

Onstein

Pinsky

et al. 2023

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1. Global change is impacting biodiversity across all habitats on earth. New selection pressures from changing climatic conditions and other anthropogenic activities are creating heterogeneous ecological and evolutionary responses across many species' geographic ranges. Yet we currently lack standardised and reproducible tools to effectively predict the resulting patterns in species vulnerability to declines or range changes. 2. We developed an informatic toolbox that integrates ecological, environmental and genomic data and analyses (environmental dissimilarity, species distribution models, landscape connectivity, neutral and adaptive genetic diversity and genotype-environment associations) to estimate population vulnerability. In our toolbox, functions and data structures are coded in a standardised way so that it is applicable to any species or geographic region where appropriate data are available, for example individual or population sampling and genomic datasets (e.g. RAD-seq, ddRAD-seq, whole genome sequencing data) representing environmental variation across the species geographic range. 3. We apply our toolbox to a georeferenced genomic dataset for the East African spiny reed frog (Afrixalus fornasini) to predict population vulnerability, as well as demonstrating that range loss projections based on adaptive variation can be accurately reproduced using data for two European bat species (Myotis escalerai, and M. crypticus). 4. Our framework sets the stage for large scale, multi-species genomic datasets to be leveraged in a novel climate change vulnerability framework to quantify intraspecific differences in genetic diversity, local adaptation, range shifts and population vulnerability based on exposure, sensitivity, and range shift potential.

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On the use of population genomic time series for environmental monitoring

Cited by 4 publications

References 20 publications

Population genomic time series data of a natural population suggests adaptive tracking of environmental changes

Population genomic time series data of a natural population suggests adaptive tracking of environmental changes

Population Genomic Time Series Data of a Natural Population Suggests Adaptive Tracking of Fluctuating Environmental Changes

Life on the edge: a new toolbox for population-level climate change vulnerability assessments

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