Phylogenetics in community ecology research

A. Narwani, B. Matthews, J. Fox and P. Venail

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During the last decade, the number of studies incorporating phylogenetic information into community ecology research exploded. As gene sequencing gets cheaper and the computational power to analyze these sequences improves, well defined and robust phylogenies for all types of organisms are becoming available. Thus, ecologists have now access to detailed information about the evolutionary relatedness among interacting species as well as the amount of phylogenetic diversity a community harbors.

Two fields of community ecology research have particularly benefited from the increased availability of phylogenetic information. These are community assembly and biodiversity-ecosystem functioning research. The former explores the processes and mechanisms by which species organize and interact with each other to establish local communities. The latter explores the influence biological diversity can have on the functioning of ecological systems in order to predict the consequences of its loss. In both cases, the amount of phylogenetic relatedness among different organisms has been considered as a substitute for their functional differentiation, which in principle is much more difficult to quantify.

Over the last few years Functional Ecology has published a series of papers illustrating how phylogenetic information can be incorporated into different aspects of community ecology research. This virtual issue on the incorporation of phylogenetics into community ecology research is composed of a series of nine papers published over the last two years that, in one way or another, link the amount of phylogenetic diversity of a given group of organisms to its assembly process or its functioning. Among these papers, four belong to an Extended Spotlight in Functional Ecology entitled: Using phylogenetics in community assembly and ecosystem functioning research (Narwani et al. 2015), which provides a critical evaluation of past work and a road-map for future research aiming to incorporate phylogenetics into community assembly or ecosystem functioning research.
The nine papers in virtual issue deal with three different aspects related to community phylogenetics research: phylogenetic signal, community assembly and ecosystem functioning.

Phylogenetic signal is a key concept in community phylogenetics. It is defined as the tendency for related species to be more similar to each other than to any other less related species randomly selected from a regional pool. Thus, the existence of a phylogenetic signal is central to the use of phylogenetic diversity as a proxy for ecological similarity. One example of phylogenetic signal can be found in the angiosperm plants of the subfamily Didymocarpoideae (Hao et al. 2015), in which the leaf concentrations of elements such as calcium, potassium and magnesium, among others, change progressively as species become less related. However, such a phylogenetic signal is absent within the Primulina genus. These findings show that the degree of the phylogenetic signal may depend on phylogenetic scale. The search for patterns of phylogenetic signal has very often led to several misconceptions and misleading interpretations such as the underlying causes that generate such a pattern (Münkemüller et al. 2015).

Community assembly is without doubt the field of community ecology that most actively incorporates phylogenetic information to understand the organization and structure of ecological communities. In a subtropical Chinese forest for instance, the phylogenetic dispersion of species was revealed to be less important than the environment and space in the distribution of five functional traits among 159 tree species, probably due to a lack of phylogenetic signal (Liu et al. 2013). Another study in a Chinese tropical forest explored the phylogenetic structure of tree assemblages (Yang et al. 2014), and found that the patterns of phylogenetic clustering or overdispersion depended on the size class of the trees and on the spatial scale considered. Similar shifts in the patterns of phylogenetic dispersion can be observed along a successional gradient, with early successional communities tending to be phylogenetically clustered or random and late successional communities being phylogenetically over-dispersed (Meiners et al. 2015). Such patterns of phylogenetic dispersion are very often used to determine the relative importance of stochastic, abiotic filtering and biotic filtering processes that drive community structure (Kraft et al. 2015). While informative and rather valuable, phylogenetic patterns may be poor descriptors of community assembly processes (Gerhold et al. 2015).

Finally, in the field of biodiversity and ecosystem functioning, measures of diversity other than species richness have been increasingly studied over the last few years. Phylogenetic diversity is one of the alternative facets of diversity that might – depending on the strength of the phylogenetic signal – be expected to have a higher impact on ecosystem functioning than the number of species. However, the topology of the phylogenetic tree used for establishing measures of relatedness among species may have a strong impact on the shape of the diversity-ecosystem functioning relationship (Cadotte 2015). Moreover, if the functional variation among species is not explained by their phylogenetic relatedness, it is possible that phylogenetic diversity has no influence on ecosystem functioning (Venail et al. 2015). 

Community phylogenetics is a relatively new area of research with lots of potential. While we expect the number of publications linking phylogenetic information to community structure and ecosystem functioning will keep increasing in the next few years, it is important to learn from past mistakes (Narwani et al. 2015) in order to make this field of research advance in the right direction. 

Image caption: Cedar Creek. Photo credited Jacob Miller

Untangling the influence of phylogeny, soil and climate on leaf element concentrations in a biodiversity hotspot
Zhuan Hao, Yuanwen Kuang and Ming Kang

Phylogenetic niche conservatism – common pitfalls and ways forward
Tamara Münkemüller, Florian C. Boucher,, Wilfried Thuiller andSébastien Lavergne

The environment and space, not phylogeny, determine trait dispersion in a subtropical forest
Xiaojuan Liu, Nathan G. Swenson, Jinlong Zhang and Keping Ma

Functional and phylogenetic assembly in a Chinese tropical tree community across size classes, spatial scales and habitats
Jie Yang, Guocheng Zhang, Xiuqin Ci, Nathan G. Swenson, Min Cao, Liqing Sha, Jie Li, Carol C. Baskin, J.W. Ferry Slik and Luxiang Lin

Is successional research nearing its climax? New approaches for understanding dynamic communities
Scott J. Meiners, Marc W. Cadotte, Jason D. Fridley, Steward T. A. Pickett and Lawrence R. Walker

Community assembly, coexistence and the environmental filtering metaphor
Nathan J. B. Kraft, Peter B. Adler, Oscar Godoy, Emily C. James, Steve Fuller and Jonathan M. Levine

Phylogenetic patterns are not proxies of community assembly mechanisms (they are far better)
Pille Gerhold, James F. Cahill Jr, Marten Winter, Igor V. Bartish and Andreas Prinzing

Phylogenetic diversity-ecosystem function relationships are insensitive to phylogenetic edge lengths
Marc W. Cadotte

Species richness, but not phylogenetic diversity, influences community biomass production and temporal stability in a re-examination of 16 grassland biodiversity studies
Patrick Venail, Kevin Gross, Todd H. Oakley, Anita Narwani, Eric Allan, Pedro Flombaum, Forest Isbell, Jasmin Joshi, Peter B. Reich, David Tilman, Jasper van Ruijven and Bradley J. Cardinale



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