Studying rapid evolution in Berlin

This month, I took up a new postdoctoral position in Germany, as part of the Ecological Novelty group lead by Jonathan Jeschke at Freie Universität Berlin. I am thrilled to embark on a three-year project examining rapid evolution in novel ecosystems as part of the (much) larger Bridging in Biodiversity Science (BIBS) project. While I am still working on the particulars of the research project, the main idea will be to look for evidence of recent rapid evolution in plant and insect populations of urbanized and invaded areas of Berlin. Working with other teams from the BIBS project, I will examine the variation in phenotypic traits of native plants and herbivore insects along a gradient of urbanization. Using a reciprocal transplantation experiment, we aim to test for evidence of potential adaptation of populations exposed to urban abiotic conditions and novel biotic interactions. Understanding which plant and insect traits are under selection and whether an evolutionary response is occurring in these systems will give insight into future community dynamics and ecosystem services in a rapidly urbanizing world.

Impact of alien plants across spatial scales: at what minimum abundance does an invasive plant start having an impact?

Lately I have been digging further into an amazing vegetation dataset of Banks Peninsula (New Zealand), trying to understand at what minimum abundance alien species may start having an impact. This is a question to which we still have very few answers, since most impact studies to date have compared heavily invaded sites to uninvaded ones. This type of binary impact assessment has been very useful to detect impact size, but does not allow us to know at what abundance we need to start worrying about an invader. The little we do know suggests that relationships between invader abundance and impact are likely to be non-linear, with threshold effects which are invader-specific. This is especially important to understand invader impact at the landscape scale. For a given invader, the abundance threshold of impact will determine the spatial spread and the size of potential impact in the landscape.  Taking into account the differences in thresholds across alien species would provide a more accurate ranking of invader risks across a region, and could potentially provide better restoration targets for managers.

Last September, I presented some preliminary results at the EMAPi conference in Hawaii. You can find the talk here.

What’s the difference between an alien and a native plant across a landscape?

Impact studies in plant invasion ecology have consistently reported decreases in species richness associated with high abundances of invasive aliens, and interpreted it as a sign of negative impact of the alien. But how frequently do such correlative patterns occur across a landscape? Undoubtedly,  one could potentially detect similar patterns for some native plants as well. Do alien species show consistently different patterns from native species, or is the geographical origin of a species irrelevant compared to other factors such as growth forms?

In a study published this month in Journal of Ecology, we put this question to the test across a highly invaded landscape of New Zealand. We carried out the equivalent of 261 separate impact studies, examining correlations between species richness and the abundance of a given focal species across the landscape. We equally targeted native (146 species) and alien (115 species) plants, and compared how frequently we detect patterns suggestive of impact. We found that alien species showed indeed different patterns from natives, with more negative correlations with species richness compared to null models.

The observed number of significant positive (upward bars) and negative (downward bars) relationships was compared to expected frequencies according to null model 2, which randomly reassigns alien or native status to the total species pool. Significantly higher frequencies than expected are indicated (***P < 0.001, **P< 0.01, *P < 0.05)
Number of significant positive (upward) and negative (downward) correlations of alien and native focal species abundance with components of species richness across Banks Peninsula.

Importantly, we examined not only correlations with total species richness, but also with the native and alien components of richness. We show that these two components vary differently along gradients of invasion. Separately analysing relationship with alien and native components of richness can help distinguish between situations where aliens may be acting as the primary drivers in plant community changes or simply passengers. This is an essential first step in designing further experimental studies to determine the underlying ecological processes and potential ecosystem impacts of alien species.

Exploring the evolutionary history of leaf economics

fig5 Flores et al 2014
Model of LMA evolution according to a Ornstein–Uhlenbeck process with 5 phenotypic optima (from Flores et al. 2014, Fig. 5)

A new paper by Olivier Flores and collaborators came out in July in the open access journal Ecology & Evolution. It offers the first global phylogenetic comparative analysis of leaf mass per area (LMA) – one of the main leaf traits capturing the leaf economic spectrum –  across vascular plant species.

An evolutionary perspective on leaf economics: phylogenetics of leaf mass per area in vascular plants. Ecology and Evolution 2014; 4(14):27992811

This is a project I contributed to as part of my Master’s research with Eric Garnier and Olivier Flores. Olivier, then a post-doc in Eric’s lab, was in charge of the massive task of gathering, cleaning and matching both leaf trait data and phylogenetic data for over 5000 vascular plant species, and then analysing the phylgenetic signal across species. Such an ambitious project involved the contribution of an impressive list of co-authors and quite a large dose of hard work and perseverance from Olivier!

This study shows that during the diversification of vascular plants, strategies of resource acquisition and allocation captured by LMA appear to have been submitted to overall weak stabilizing selection, generating a low but existing signal of phylogenetic conservatism of LMA. This means that closely related plant species have a weak tendency to share similar leaf economics. Evolutionary models indicate that the rate of LMA evolution seems to have varied between lineages. In particular LMA diversification appears to have been strongly constrained and slowed down in lineages of woody plants, with the more recent evolution of herbs and grasses allowing for an increased diversification towards lower values of LMA, i.e. strategies of rapid resource acquisition.

Similarity in LMA as a function of divergence time.
Similarity in LMA among vascular plants as a function of divergence time. (A) the complete species set (n = 5401), and (B) the herbaceous (squares, n = 2417) and woody (triangles, n = 2564) growth forms. Filled (resp. open) symbols indicate (non-)significant correlations (]level: 0.05). Dotted lines represent linear fits (Brownian Motion model, BM); dashed lines represent exponential fits (Ornstein–Uhlenbeck model, OU). Arrows indicate major evolutionary nodes. (from Flores et al. 2014)

Assessing the reliability of the point-intercept method in diverse grasslands

A new paper by Karim Barkaoui, Marie-Laure Navas and myself has just come out in Folia Geobotanica:

Barkaoui, K., Bernard-Verdier, M., & Navas, M.-L. (2013). Questioning the Reliability of the Point Intercept Method for Assessing Community Functional Structure in Low-Productive and Highly Diverse Mediterranean Grasslands. Folia Geobotanica, doi:10.1007/s12224-013-9172-2
Prediction of aboveground biomass by the Point-Intercept method (PIM) of vegetation survey in a diverse grassland commuity
Prediction of aboveground biomass by the Point-Intercept method (PIM) of vegetation survey in a diverse grassland commuity

In this paper, we tested the accuracy of the point-intercept method for measuring species relative abundances in plant communities and calculating functional diversity indices.

This method of botanical survey was first introduced 80 years ago by Levy & Madden (1933) and is still commonly used in community ecology with the advantages of being non-destructive and somewhat less subjective than other visual methods.

It consists in systematically introducing a fine pin vertically in the vegetation layer along a regular grid (e.g. a quadrat), and counting the number of contacts of the pin with live plant organs at each point of the grid. The number of contacts per species is used as a proxy for above-ground biomass.

One of our expectations was that, in functionally diverse communities composed of very different growth forms (e.g. tussock grasses mixed with small shrubs), the method would be biased by over- or under-representing certain plant architectures. We show that, despite a slight bias for different growth forms, the method gives consistently accurate predictions of species relative biomass in highly diverse Mediterranean rangeland communities. Moreover, we show that growth form biases can easily and accurately be accounted for by simple calibrations, allowing for an accurate prediction of absolute biomass in these grasslands.

All in all, a reliable method, highly recommended and not as time-consuming as it might seem!

sharing a few Rcodes…

Not being an especially hardcore R programmer, I did not think at first that the simple Rcodes I wrote during my PhD would be of interest to anyone but me. I did wonder if I should include my codes as supplementary information in my papers, but, facing the rush of final deadlines and the fact that, fundamentally, the methods I was using were not entirely new, I abandoned the idea.

In the past year, however, a number of people, mostly students, have asked me if they could have a look at my R codes. I suspect they were mostly looking for some coding ‘inspiration’ (i.e. to have a basis on which to build their own code), but I also realized that they were interested because it is often the best (only?) way to really grasp what the authors have done. After all, most of my R-coding know-how has been acquired from delving into the well-polished codes of experienced mentors (thanks Olivier!), and making them mine.

So here is a new page with a collection of a few R functions, mostly dealing with analyzing functional and phylogenetic community structure to detect community assembly patterns.  These are all modest and certainly imperfect codes, so please do not hesitate to send me useful feedback! I will be adding new ones along the way, as well as links to other interesting R code sources.

Post-doctoral project on plant invasions in NZ

Akaroa Harbour entrance, Canterbury, New Zealand
I am very excited to start working in July 2013 on a new post-doctoral project on plant invasions and their impact on community structure in New Zealand’s Banks Peninsula. I will be joining Philip Hulme for one year at the Bio-Protection Research Center in Lincoln University, NZ, and hopefully will get the chance to discover NZ’s amazingly diverse nature as well as the kiwi lifestyle…

Functional and Phylogenetic diversity capture different aspects of community structure

“Partitioning phylogenetic and functional diversity into alpha and beta components along an environmental gradient in a Mediterranean rangeland” by Bernard-Verdier M., Flores O., Navas M.-L. and Garnier E.

Phylogenetic and functional diversity in grasslands along a  soil depth gradient (Bernard-Verdier et al., 2013, JVS)
Phylogenetic and functional diversity in grasslands along a soil depth gradient (Bernard-Verdier et al., 2013, JVS)

This paper, now in early view, is part of a special feature on Functional Diversity edited by Norman Mason and Francesco De Bello, which will be published in a single issue of JVS very soon.

In this paper, we show that phylogenetic and functional diversity both capture very different facets of community structure in a Mediteranean rangeland. Phylogenetic diversity was not a proxy for functional diversity either at the alpha (within communities) or the beta (among communities) scale. However, phylogenetic patterns did reveal some complementary information not captured by the set of functional traits under study. An important methodological message of this paper was to highlight the need to take into account (and remove) the effect of species abundance evenness within communities in order to properly compare patterns of functional and phylogenetic diversity.

New paper in Journal of Ecology

A new paper is now out in Journal of Ecology (100:6) :

Community assembly along a soil depth gradient: contrasting patterns of plant trait convergence and divergence in a Mediterranean rangeland

Maud Bernard-Verdier, Marie-Laure Navas, Mark Vellend, Cyrille Violle, Adeline Fayolle and Eric Garnier

This study highlights how the combination of abundance data with multiple plant traits capturing different functional dimensions may be critical to the detection of the complex functional responses of plant communities to environmental gradients. By contradicting and refining a number of widespread hypotheses from the literature, this study takes us further towards a general understanding of plant community assembly.