ECR feature: Rafael M. Venegas on phylogenetic community structure

Rafael Venegas is an ecologist with a passion for plants. He is currently a postdoc at the University of Alcalá. He uses phylogenetic methods to address questions in macroecology and biogeography to ultimately understand what shapes biodiversity and ecosystem services. In his recent paper with the Journal of Biogeography, he extends theory on phylogenetic community structure through specific consideration of phylogeny branching patterns. Rafael shares how insights on community assembly can be gained from this new analytical framework.

Rafael Molina Venegas. PhD and current postdoctoral researcher at the University of Alcalá (Madrid, Spain), posing in front of a pine forest (Pinus pinea) in the surroundings of Doñana National Park (southwestern Iberian Peninsula) 

Links: Personal page

Institution: University of Alcalá (Madrid, Spain)

Academic life stage: Postdoc

Research interests: Phylogenetics, macroecology, biogeography, plant biodiversity, ecosystem services.

Current study system: I’ve been working on Mt. Kilimanjaro flora for two years. Kilimanjaro is the highest single free-standing volcanic massif in the world, and includes lush jungles, cloud forests and cold and fire-adapted bushlands and scrublands that spread until the glacier’s domain at 4500 m. This montane vegetation stands in splendid isolation above the surrounding plains, where savanna woodlands and agricultural fields dominate the landscape. The geographical isolation of Kilimanjaro makes its people highly dependent on natural resources (the so-called ecosystem services), creating an interesting socio-ecological context that inspired me to design the project I’m currently leading. This project aims to explore connections between ethnobotanical knowledge (in my opinion one of the most palpable proofs of the reality of ecosystem services) and global plant biodiversity from an evolutionary perspective.

The truth is that phylogenies have always been in the background of my research agenda, including the development and refinement of phylogenetic methods for the study of biodiversity. Indeed, some of my ongoing collaborations concern spatial phylogenetics with a focus on the endemic flora of the Iberian Peninsula (~1975 species and subspecies, 27% of the vascular flora of the region), an outstanding plant biodiversity hotspot in the western Mediterranean. I am particularly interested in evaluating the role that soil conditions have played in the diversification and maintenance of this flora.

(left) Rafael, exploring the forests in the foothills of Mt Kilimanjaro. (right) A chamaephyte community studied by Rafael in the Iberian Peninsula, a hotspot for plant biodiversity in Europe. Amidst the Quercus oaks, purple lavenders (Lavandula pedunculata) and white-flowered gum rockroses (Cistus ladanifer) bloom in the Mediterranean sunshine.

Recent paper in Journal of Biogeography: Molina-Venegas, R., Fischer, M. & Hemp, A. (2019) Disentangling the fundamental branching patterns of phylogenetic divergence to refine eco‐phylogenetic analyses. Journal of Biogeography, 46, 2722-2734.

Motivation for the paper: My first steps in science took me to the field of eco-phylogenetics, which aims to infer community assembly mechanisms by means of the footprint they left on the phylogenetic structure of communities. For example, little phylogenetic divergence (i.e. clustering) may indicate community structure is shaped by environmental filtering, which is a major mechanism in harsh habitats such as Mediterranean saline soils, where closely-related salt-adapted lineages predominate (e.g. Tamaricaceae, Frankeniaceae, Amaranthaceae). However, classical indices of phylogenetic divergence disregard much of the biological information encoded in the phylogenies, because they are simply “blind” to the exact branching pattern of phylogenies. This is problematic because it precludes understanding of how ecological processes affect evolutionary relationships within communities. The prospect of overcoming this methodological shortcoming was the main motivation to work on this paper.

Key methodologies: In this paper, we show that phylogenetic divergence can be driven by different branching patterns that arise from specific ecological processes and propose a method to identify their signature in communities. Let’s picture two communities that experience different assembly processes (see schematic figure below), namely, competitive exclusion between close-relatives due to resource depletion (as predicted by limiting similarity theory, top community) and facilitation by a distant-relative nursery plant that mitigates the harshness of environmental conditions. Both mechanisms lead to increased phylogenetic divergence (more overdispersion), but the underlying branching pattern of such divergences (community phylogenies to the right) are markedly different. Still, the new communities may show similar phylogenetic divergence values, and therefore one may erroneously conclude that the same mechanism is at stake if the underlying branching patterns are ignored. Our method provides a handle to integrate both sources of information (i.e. phylogenetic divergence and the underlying branching patterns) using simple statistical tests.

Hypothetical plant communities experiencing different ecological processes, namely competitive exclusion between close-relatives (top) and facilitation (bottom). In the top-left community, resources are abundant and competition does not occur. When resources are scarce (top-right), competitive exclusion between close relatives comes into play and phylogenetic divergence increases. In the bottom-left, a community of species with narrow thermal niches thrive at an ambient temperature of 25ºC. A temperature increase of 5ºC (bottom-right) could lead to the collapse of the community, but the species can still persist under the canopy of a distantly-related facilitating species that provides microclimatic amelioration and augments phylogenetic divergence in the community.

Unexpected challenges: This research was not planned at all by the time I got involved in the Kili Research Unit, a multidisciplinary project that revolved around Mount Kilimanjaro biodiversity and ecosystem services. Dr. Markus Fischer, my postdoc advisor at the time, and Dr. Andreas Hemp, a botanist with more that 30 years of experience in the flora of East Africa, were interested in studying plant community assembly at Mount Kilimanjaro using phylogenetic information. However, I had a hunch that the tools available were insufficient for the project, so the opportunity presented itself allowing me to incorporate new ideas and concepts into existing theory. Through this I really had to put my statistics and programming skills to the test.

Major results and contribution to the field: Community phylogenetics is a young but controversial discipline, likely because too much has been demanded of both the original conceptual framework and classical descriptors of phylogenetic structure. In think our approach may contribute to mitigate this controversy by providing ecologists a handle to analyse phylogenetic divergence in the light of the underlying branching patterns, which is critical if we are to avoid spurious interpretations of phylogenetic information. I don’t mean by that our method is the ultimate solution, as the community phylogenetic discipline is not without methodological shortcomings that need addressing (see Cadotte et al. 2017, Ecological Monographs, 87, 535-551 for an excellent review), yet it represents one step forward in the field. To make the method more accessible to the community, we implemented it in R language and provided the code in full as a user-friendly function in the Supplementary of the article.

What are the next steps? There are still lots of interesting questions in community phylogenetics. For example, testing whether clades that are overrepresented in communities show different modes of trait evolution seems a promising avenue for future research (see Pearse et al 2019, Global Ecology and Biogeography, 28, 1499-1511 for a recent paper). Phylogenies are not magic wands that will unravel assembly mechanisms by means of few phylogenetic metrics, but just an important, exciting and necessary tool for understanding how biodiversity is generated and maintained. After all, elephants will never fly and butterflies will not eat lions because lineages are functionally constrained, meaning that evolutionary history matters. A new generation of eco-phylogenetic methods is coming up, and re-analyzing previous datasets with new available tools might unravel biological information that remains encoded in the phylogenies.       

If you could study any organism on Earth, what would it be and why? I would love to delve into the flora of the Wallacea Islands (particularly Sulawesi and Moluccas) and New Guinea”. On the one hand, this region combines multiple biogeographically interesting factors such as tropicality, isolation (islands) and sharp environmental gradients (mountains), which make the region extraordinarily appealing to me. On the other hand, these islands awaken the sense of adventure that many biogeographers carry inside of us. Even today, there is a continuous dripping of new species of birds, small mammals and plants reported from New Guinea! I have already visited the region once, specifically the Wakatobi archipelago in southeast Sulawesi (mostly a diving trip, so that time was more about coral reefs, likely my favourite animal taxa), and I am determined to come back.

Any other little gems you would like to share? I love teaching. I have taught General Ecology and Botany in bachelor’s degree and phylogenetic methods in postgraduate courses so far, which complements my facet as a researcher. After all, today’s students will be tomorrow’s researchers, the reason why I consider teaching a fundamental duty of scientists. At this point, I have to make a confession; plants are my true motivation in science, and I could not imagine being an ecologist without a focus on plants. And guess what? This is simply because I had good botany teachers during my time as an undergraduate student.

Published by jbiogeography

Contributing to the growth and societal relevance of the discipline of biogeography through dissemination of biogeographical research.

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