Adaptation to Serpentine in the Sierra Bermeja

Adaptation to Serpentine in a Mediterranean Plant Community

Plants with populations on both serpentine and non-serpentine soils offer an opportunity to study the competing effects of selection and gene flow on adaptation and genomic variation, diversification and homogenization.

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Sierra Bermeja near Malaga in southern Spain has extensive areas of serpentine and other ultramaphic soils.

PI:   Peter B. Pearman

Collaborators: Noelia Hidalgo Triana, Andrés V. Pérez, Teresa Navarro de Águila, University of Malaga

Doctoral Student:  Pablo Arrufat

 

Serpentine soil presents a difficult edaphic environment for most plants for several reasons.  These soils have high concentrations of a variety of heavy metals, a low calcium to magnesium ratio, and tend to have low water content.  These environmental factors have been shown to drive local adaptation to soil in a variety of studies.  In the hills near Malaga, Spain, serpentine outcrops are common and interspersed with areas of non-serpentine soil.  Despite the selective pressure that surely exists for specialization to serpentine environments, a number of plant species have populations on both serpentine and non-serpentine soils, sometimes within sight of each other.  This suggests that there may be strong, contrasting selection among nearly adjacent populations.  This is of interest because adaptation to serpentine has been shown to entail costs, with serpentine genotypes being less able competitors when they occur in non-serpentine environments in reciprocal transplant experiments.

We are developing research that examines the interacting effects of selection and gene flow in several serpentine species, in order to get a broad picture of the response of populations in these communities.  Serpentine and other ultramafic and peridotitic soil is widely distributed in the Sierra Bermeja, not far from the southern Spanish city of Malaga.   We are curious whether gene flow is similar in populations of species that share this heterogeneous environment, and whether any barriers to gene flow are equally effective in the different species.  Some of the species have different subspecies that are typical of one soil or the other, while other species have no recognized morphological differences among populations on different soil types.   We are working with local botanists from Malaga, and we hope to systematically expand our preliminary collections once the pandemic has subsided.  We will then construct ddRADseq libraries at the UPV and contract their sequencing, then probe the data to determine the influences of both gene flow and selection across plant genomes. 

E. umbellatum population genomics

Population Genomics of a Widely-Distributed Perennial

This project seeks to understand historical demography, phylogeography and environmental adaptation in a widespread North American shrub.

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PI: Peter B. Pearman

Collaborators: J. Travis Colombus (California Botanical Garden, Claremont, California), Jean-Rémi Trotta and Tyler S. Alioto (Centro Nacional de Análisis Genómico, CNAG, Barcelona)

Start date: April 1, 2014

Duration: ongoing
Research location: Western North America


Support: ad-hoc and discretionary

While mobile animals and plants with substantial dispersal capabilities have the ability to move to follow the changing distributions of suitable climate, many species will have to adapt in situ if they are to persist in the face of climate change. While it is difficult to predict future adaptation, substantial information on the evolutionary history of species in relation to climate can be found by examining genomic variation, current geographic distribution, and morphological variation. This information can be used to inform us about how species potentially respond to the ongoing changing climate. Species with spatial distributions that span substantial environmental variation provide an opportunity to examine how adaptation contributes to maintaining both species breadth and geographic range. In this project we examine geographic variability in genomic variation that has been shaped by both selective and neutral processes, representing both adaptation and demographic history. These genetic patterns reflect distinct processes that are involved in population-level responses to a changing environment. By understanding the history and genomic basis of these responses, we will contribute to understanding how large-scale environmental change may affect future population distribution and adaptation.

Adaptation and evolutionary history in non-model organisms (lacking a reference genome) is increasingly possible through the use of techniques to construct genomic libraries that subsample the genome. We have chosen this approach to develop research on the demographic and evolutionary history of Eriogonum umbellatum (Polygonaceae), a small shrub with bright yellow flowers in western North America. The range of this species extends from the Sierra Nevada almost to the Rocky Mountains, and from the mountains in the southern Mojave Desert to the eastern slopes of the Cascade Range in central Oregon. E. umbellatum is adapted to a variety of arid, semi-arid, and mountainous environments, and occurs on well-drained serpentine and non-serpentine soils. Taxonomists have recognized substantial, though subtle, morphological variation in this species and have described 40 varieties. These varieties vary in the extent of their distribution and the range of environmental conditions they encounter. The high level of taxonomic, morphological, and environmental variation exhibited by the species suggests that rapid adaptive evolution of environmental tolerance characterizes this widely distributed species. Characterizing the genomic basis of this variation, at loci influenced by selection and at others dominated by processes of genetic drift and dispersal, will deepen our understanding of the processes that promote species cohesion or, alternatively, isolate populations and lead to adaptive speciation.

This investigation of population structure, evolutionary history, and environmental adaptation in E. umbellatum builds on previous collaborative work on evolution in Eriogonum and Polygonaceae. In the current work, we have used Genotyping-by-Sequencing to develop a sequenced GBS library and dataset with thousands of bi-allelic SNPs. We have also developed additional genomic resources, including a substantial collection of tissues from over 60 populations, a draft genome using both long-read and Illumina technology, an annotated transcriptome, and a custom bioinformatics pipeline. We are currently examining the diversity within E. umbellatum and some closely related congeners and other relatives in an effort to determine the species boundaries and monophyly of this taxon. Our SNP data encompass about 30 additional species in the genera Eriogonum and Chorizanthe. Our initial analyses indicate that species-level designation is needed for some taxa that are currently distinguished at the varietal level.

Once we know species boundaries, we will examine intraspecific structure and identify potential loci under environmental selection. This will serve as the basis for modeling genome-environment associations and, subsequently, the geographic displacement of suitable environmental conditions as climate change progresses. To do this, we will develop ddRADseq libraries at UPV. After sequencing, additional modeling will address the demographic and phylogeographic history of the species through the Neogene. We intend to identify clusters of populations that share a common demographic and evolutionary history. With this information, we will examine the environmental distribution of potentially adaptive loci using targeted sequencing methods.

Relevant Publications

Kostikova, A., N. Salamin and P. B. Pearman. 2014. The role of climatic tolerances and seed traits in reduced extinction rates of temperate Polygonaceae. Evolution 68:1856-1870.

Kostikova, A., G. Litsios, S. Burgy, L. Milani, P. B. Pearman, and N. Salamin. 2014. Scale-dependent adaptive evolution and morphological convergence to climate niche in the Californian eriogonoids (Polygonaceae). Journal of Biogeography 41:1326-1337.

Kostikova, A., G. Litsios, N. Salamin, and P. B. Pearman.  2013. Linking life history traits, ecology and niche breadth evolution in the North American eriogonoids (Polygonaceae). American Naturalist 182:760-774.

Last modification date: 09/02/2022