Applicant:  Valentin Amrhein, University of Basel

Co-applicants: Peter B. Pearman (University of the Basque Country), Eric Allen (University of Bern)

Start date: 1 November 2014

Duration: 36 months

Location of research: Switzerland

Support:  281,105 Swiss Franks

Expanded Abstract:

The diversity of functional traits in communities (i.e., functional diversity) is increasingly considered to be one of the most relevant components of biodiversity in the context of community ecology and conservation ecology. Here, we propose to examine functional diversity of vascular plant, butterfly and bird communities at a national scale, using data from the biodiversity monitoring program in Switzerland. Within this program, yearly landscape scale surveys have been undertaken since 2001, and the studied sites span an elevation gradient of more than 2'500 meters. The data provide unique opportunities to study patterns of functional diversity in different trophic levels and along a large elevation gradient. We will use contemporary approaches such as structural equation models to infer how the trophic links between plant, butterfly and bird communities change across space and times, and estimate a series of metrics for examining the functional structure of species communities in Swiss landscapes.

From a conservation point of view, landscape-scale studies are central because ecosystems are usually managed, and ecosystem services are delivered, at the landscape scale. Since manipulative experiments are hardly feasible at the landscape scale, inferring patterns from observational studies are necessary to understand relevant trait similarity patterns across landscapes. However, one of the greatest challenges when analysing ecological data of this type is the imperfect detection of species. We will thus study how biases resulting from imperfect detection could be accounted for in research on functional diversity. We will employ site-occupancy analyses using Bayesian posterior sampling to develop methods for estimating functional diversity by accounting for imperfect detection. We will use these methods to draw robust inference on patterns of functional diversity in subsequent analyses.

Combining a multitrophic perspective with an approach based on functional diversity has been suggested as the necessary next step to advance research on community ecology. This is further underpinned by the notion that many ecosystem services ultimately rely on interactions between plants and organisms belonging to other trophic levels. We propose analyses on elevational patterns and temporal trends in functional diversity that will be compared among plant, butterfly and bird communities. We will adopt conceptual frameworks from classic food web research and test predictions using measures of functional diversity. For example, we will test whether the links between trophic levels, quantified based on correlations in their functional diversity, change along a productivity gradient as predicted by a number of theoretical models. Furthermore, we will test whether functional redundancy, which could act to insure the maintenance of ecosystem functioning in the face of species loss caused by global change, varies with the environment and how the degree of redundancy varies between trophic levels. For example, it is currently unknown whether, within the same environments, communities from different trophic levels have similar (i.e., correlated) degrees of functional redundancy.
Overall, our proposed studies will provide a comparative synthesis of the patterns of functional diversity of three trophic levels across Swiss landscapes. The expected results will add to the understanding of the driving forces that structure ecological communities. Since we infer patterns of functional trait diversity, which is currently one of the most promising surrogate measures of community assembly and ecosystem services, the expected results will provide the possibility of mapping the delivery of ecosystem services at the national scale, which complies with the strategic goals of the Swiss biodiversity strategy to quantify ecosystem services across entire Switzerland.

Applicant: Peter B. Pearman (Swiss Federal Research Institute WSL)

Co-applicants: Nicolas Salamin (University of Lausanne), Christian Lexer (University of Freibourgh), Niklaus Zimmermann (Swiss Federal Research Institute), Felix Forest (Royal Botanic Gardens, Kew)

Start date: 1 October 2009

Duration: 44 months

Location of research: South Africa, Switzerland

Support: 964, 637 Swiss Franks

Expanded Abstract:

The species environmental niche consists of the biotic and abiotic conditions necessary for long-term persistence and the niche occupies a central place in the development of ecological theories of competition, limiting similarity, and character divergence.  We study interspecific variation in niche characteristics by adopting an evolutionary perspective.  Application of a toolkit used in the disciplines of systematics and evolutionary biology enables us to address how the environmental niche has changed in a family of plants during the diversification of a clade.  We focus on the Restionaceae, a monophyletic family of grass-like plants of which 340 of the 350 species are endemic to southern Africa.  This is a defensible choice because the relative climatic stability of this region during the Pleistocene suggests that these species distributions are currently at equilibrium with climate.  Under accelerating climate change, the capacity of these species for rapid niche evolution will contribute to determining their fate in a landscape where opportunities for successful dispersal to areas of favourable climate may be limited by intervening expanses of unsuitable habitat and the anthropogenic barriers of agriculture, transportation corridors and urbanization. 

We will develop models of niche evolution that serve both for understanding the evolution of extant species diversity and community structure, and for forecasting how diversity and community structure change, given projected climate change and the potential we identify for rapid niche evolution.  We will model characteristics of the ß-niche (habitat-specific, e.g. geology, fire frequency and vegetation type) and ?-niche (climatic), using field-acquired occurrence data for each species. New GIS data layers of fire frequency and geology will be developed.  The relationship between the fundamental and the estimated realized niche will be experimentally evaluated in multiple species.  We will compare in a greenhouse experiment the drought and flooding tolerances of species to their modelled precipitation requirements.  A transplant experiment in the field will help us determine whether species replacement along an elevation and rainfall gradient is driven primarily by fundamental niche requirements or by interspecific competition and, thus, the realized niche.  We will quantify the evolutionary lability of the environmental niche by modelling selected niche parameters over a completely-sampled species-level phylogeny.  This will indicate which parameters have constrained the evolution of the clade and which parameters are associated with differentiation and speciation.  However, working with species-level phylogenies and niche models has formerly entailed assumptions of constant evolutionary rates and equal inheritance of trait variance by new species.  These assumptions will be addressed in population-level analyses of species complexes to determine speciation modes and establish their impacts on the patterns of inheritance of niche variability.  Further studies will estimate using models of trait evolution the variation among clades in rates of niche change.

Using data on species distributions, chorological analyses and niche modeling we will determine current regional species pools.  These will further be stratified into habitat-specific species pools, using field observations, niche models and models of environmental filtering.  Then, using species traits and phylogenetic relationships, we will seek the determinants of community assembly (i.e., the combinations of species from the regional pool that can be combined into communities).  Using the model parameters developed to address the above questions, we will attempt to estimate the possible contribution of rapid evolution of species environmental niches to change in regional species pools and local communities that may accompany altered climate.  These analyses will provide a powerful tool with which to evaluate and predict the response to climate change by multiple, related species and how these changes could impact regional spatial patterns of diversity in the Restionaceae.

The SPEED project developes the tools necessary to address the effects of climate change and the evolutionary response of species to it.  We intend to develop means to convert knowledge on these changes into geographically-explicit patterns of species diversity in the Restionaceae.  We extend the potential impact of our work by including an integrated program for training three Ph.D. students in the evolutionary and ecological modeling techniques that we develop and use during this research.

Publications:

Lexer, C., R. Wüest, S. Mangili, M. Heuertz, K. N. Stölting, P. B. Pearman, F. Forest, N. Salamin, N. Zimmermann, and E. Bossolini. 2014. Genomics of the speciation continuum in an African plant biodiversity hotspot, I: Drivers of population divergence in Restio capensis (Restionaceae). Molecular Ecology 23:4373-4386.

Litsios, G., R. O. Wüest, A. Kostikova, F. Forest, C. Lexer, H. P. Linder, P. B. Pearman, N. E. Zimmermann and N. Salamin. 2014. Differential effect of fire-survival strategy on diversification among a replicated radiation on two continents. Evolution 68:453-465.

Perret, M., A. Chautems, A. O. De Araujo, and N. Salamin. 2013. Temporal and spatial origin of Gesneriaceae in the New World inferred from plastid DNA sequences. Botanical Journal of the Linnean Society 171:61-79.

Lexer, C., K. Stoelting, S. Mangili, F. Forest, E. Bossolini, P. B. Pearman, N. E. Zimmermann and N. Salamin. 2013. ‘Next generation' biogeography: towards understanding the drivers of species diversification and persistence. Journal of Biogeography 40:1013-1022.

D'Amen, M., N. E. Zimmermann, and P. B. Pearman. 2013. Conservation of phylogeographic lineages under climate change. Global Ecology and Biogeography 22:93-104.

Litsios, G., C. Sims, P. B. Pearman, R. O. Wüest, N. E. Zimmermann, and N. Salamin. 2012. Mutualism with sea anemones triggered the adaptive radiation of clownfish. BMC Evolutionary Biology 12:212.

Litsios, G. and N. Salamin. Effects of phylogenetic signal on ancestral state reconstruction. Systematic Biology 61:533-538.

Litsios, G., L. Pellissier, F. Forest, P. B. Pearman, N. E. Zimmermann, and N. Salamin. 2012. Trophic specialization influences the rate of environmental niche evolution in damselfishes (Pomacentridae). Proc. Royal Soc. B. 279:3662-3669.

Broennimann, O., M. Fitzpatrick, P. B. Pearman B. Petitpierre, L. Pellissier and A. Guisan. 2012.  Measuring ecological niche overlap from occurrence and spatial environmental data. Global Ecology and Biogeography 21: 481-497. 

Pearman, P. B., A. Guisan, and N. E. Zimmermann. 2011. Impacts of climate change on Swiss biodiversity: an indicator species approach. Biological Conservation 144:866-875.

Lexer, C. and K. N. Stölting. 2011. Tracing the recombination and colonization history of hybrid species in space and time. Molecular Ecology 20:3701-3704.

Pearman, P. B., M. D'Amen, C. Graham, W. Thuiller, and N. E. Zimmermann. 2010. Within-taxon niche structure: Niche conservatism, divergence and predicted effects of climate change. Ecography 33:990-1003. (Note: first two authors contributed equally to this paper.)

Salamin, N., R. O. Wüest, S. Lavergne, W. Thuiller and P. B. Pearman. 2010. Assessing rapid evolution in a changing environment. Trends in Ecology and Evolution 25:692-698.
 

Applicant: Peter B. Pearman (Swiss Federal Research Institute WSL)

Co-applicant: Nicolas Salamin (University of Lausanne)

Start date: 1 June 2009

Duration: 41 months

Location of research: California, USA and Switzerland

Support: 240,833 Swiss Franks

Expanded Abstract: 

Ecologists seek to understand the factors that lead some exotic plant species to become ecologically dominant and widespread. This attention is justified because these invasive species can alter community composition, impact ecosystem function, affect species' evolutionary trajectories, and lead to species extinctions. Despite these impacts, finding characteristics that are consistently shared by invasive species is difficult. The climatic niche of plants (the climatic conditions under which population growth is positive) potentially facilitates plant invasions. Some groups of invasive plants have native ranges that span large latitudinal gradients.  Other invasive species have experienced shifts of climatic niche during the invasion process.  Niche shifts, both recent and deep in species evolutionary history, likely influence whether immigrant species become established, naturalized and, subsequently, invasive. The evolutionary dynamics of the climatic niche, per se, have seen very little work and there is substantial disagreement over the occurrence, magnitude and rate of climatic niche shifts. These evolutionary niche dynamics are the focus of this proposal.

The main goal of this project is to understand the influence of evolutionary history, especially the history of shifts of the climatic niche, on the invasiveness of exotic species.  Studying the evolutionary history of niche dynamics is not specific to invasive species. Invasive species are a convenient set of model systems (i.e. genera) in which the literature suggests that it is likely that evolution of the climatic niche influences the presence of a detectable ecological quality: invasiveness. Without the criterion of presence of invasives, we could have selected genera at random or used other criteria that would not likely lead the research to have similarly broad interest. In this research we: (a) use a bioinformatics approach to obtain existing data on species distribution and molecular variation within genera that contain invasive species; (b) modify and use existing software to test the degree to which alternative evolutionary models suffice in describing phylogenetic patterns of niche evolution within these genera; (c) test for evolutionary and historical correlates of niche shift and invasiveness by drawing on information from phylogenetic reconstructions, functional traits, and climatic niche characteristics of species.

The first part of the work focuses on collection of (a) ecological, occurrence, and climate data that describe the distribution-climate relationships of species, (b) data on species functional traits, and (c) existing sequence data for phylogeny reconstructions.  We extract species distribution data from online databases and a wide array of other data sources, including the primary literature. We obtain molecular data directly from GenBank.  Additionally, plant tissue for additional sequencing will be collected at national herbaria and botanical gardens.  We model and quantify niche optima and limits using species distribution models and we construct phylogenetic trees of species.  We model the evolution of the climatic niche using existing open-source software, examining potential effects of both selection and random evolution on niche variability. We produce a supertree of the genera and, using both niche and functional trait data, develop general linear models to examine the relationship of these variables to establishment and invasion by exotic species.  Finally, we expand existing software to examine how heterogeneous selection among subclades affects the likelihood of niche shifts and species invasiveness. 

Beyond the importance of understanding the factors that contribute to species invasiveness, this research will contribute to understanding how niche shifts contribute to evolution within genera and affect species distributions. By using genera that include invasive species in Switzerland and elsewhere, the project will contribute to efforts to identify potentially invasive species before they become introduced.  We will gain better understanding of the role of selection and random evolution in niche shifts of invasive species, closely related species, and their ancestors. By helping us to understand the evolutionary history of niche shifts, this research will improve confidence in the use of species distribution models to predict the potential distributions of invasive species.  Finally, understanding evolutionary processes that enable species to expand into new environments may help to predict more accurately the impacts of climate change on plant biodiversity.

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.

D'Amen, M., N. E. Zimmermann, and P. B. Pearman. 2013. Conservation of phylogeographic lineages under climate change. Global Ecology and Biogeography 22:93-104.

Broennimann, O., M. Fitzpatrick, P. B. Pearman B. Petitpierre, L. Pellissier and A. Guisan. 2012.  Measuring ecological niche overlap from occurrence and spatial environmental data. Global Ecology and Biogeography 21: 481-497. 

Engler, R. and 19 additional authors.  2011. 21st century climate change threatens mountain flora unequally across Europe. Global Change Biology 17:2330-2341.

Pearman, P. B., A. Guisan, and N. E. Zimmermann. 2011. Impacts of climate change on Swiss biodiversity: an indicator species approach. Biological Conservation 144:866-875.

Pearman, P. B., M. D'Amen, C. Graham, W. Thuiller, and N. E. Zimmermann. 2010. Within-taxon niche structure: Niche conservatism, divergence and predicted effects of climate change. Ecography 33:990-1003.

Salamin, N., R. O. Wüest, S. Lavergne, W. Thuiller and P. B. Pearman. 2010. Assessing rapid evolution in a changing environment. Trends in Ecology and Evolution 25:692-698.