A couple of potential approaches to move forward questions about community phylogenetics are discussed below. The first is to consider the mechanisms behind the pattern-inference analyses and ask whether assumptions hold.
1) Phylogenies and traits - testing assumptions about proxy value
As you know, if you have read the introductory paragraph of many community phylogenetic papers, Charles Darwin was the first to highlight that two closely related species might have different interactions than two distantly related species. People have tested this hypothesis in many ways in various systems, with mixed results. The most important directions forward is to make explicit the assumptions behind such ideas and experimentally test them. I.e. Do phylogenetic distances/divergence between species capture trait and ultimately ecological divergence between species?
|From Kelly et al. 2015 Fig 1b.|
Recent findings have varied from “Stabilising niche differences were unrelated to phylogenetic distance, while species’ average fitness showed phylogenetic structure” (California grassland plants, Godoy et al. 2014); to, there is no signal in fitness or niche differences (algae species, Narwani et al. 2013); to, when species are sympatric, both stabilizing and fitness differences increase with phylogenetic distance (mediterranean annual plants; Germain et al. 2016). Given constraints, tradeoffs and convergence of strategies, it is really not surprising that the idea of simply inferring the importance of competition from patterns along a phylogenetic tree is not generally possible (Kraft et al. 2015; blogpost).
2) Phylogenies and the regional species pool
Really more interesting than testing for proxy value is to think about the mechanisms that tie evolution and community dynamics together. A key role for evolution in questions about community ecology is to ask what we can learn about the regional species pool—from which local communities are assembled. What information about the history of the lineages in a regional species pool informs the composition of local composition?
The character of the regional species pool is determined in part by the evolutionary history of the region, and this can in turn greatly constrain the evolutionary history of the community (Bartish et al. 2010). The abundance of past habitat types may alter the species pool, while certain communities may act as 'museums' harbouring particular clades. For example, Bartish et al. 2016 found that the lineages represented in different habitat types in a region differ in the evolutionary history they represent, with communities in dry habitats disproportionately including lineages from dry epochs and similar for wet habitats. Here, considering the phylogeny provides insight into the evolutionary component of an ecological idea like 'environmental filtering'.
Similarly, species pools are formed by both ecological processes (dispersal and constraints on dispersal) and evolutionary ones (extinctions, speciation in situ), and one suggestion is that appropriate null models for communities may need to consider both ecological and evolutionary processes (Pigot and Etienne, 2015).
Invasive species also should be considered in the context of evolution and ecology. Gallien et al. 2016 found that “currently invasive species belong to lineages that were particularly successful at colonizing new regions in the past.”
I think using phylogenies in this way is philosophically in line with ideas like Robert Ricklef's 'regional community' concept. The recognition is that a single time scale may be limiting in terms of understanding ecological communities.
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- Gerhold, Pille, et al. "Phylogenetic patterns are not proxies of community assembly mechanisms (they are far better)." Functional Ecology 29.5 (2015): 600-614.
- Schoener, Thomas W. "The controversy over interspecific competition: despite spirited criticism, competition continues to occupy a major domain in ecological thought." American Scientist 70.6 (1982): 586-595.
- Strong Jr, Donald R., Lee Ann Szyska, and Daniel S. Simberloff. "Test of community-wide character displacement against null hypotheses." Evolution(1979): 897-913.
- Kelly, Steven, Richard Grenyer, and Robert W. Scotland. "Phylogenetic trees do not reliably predict feature diversity." Diversity and distributions 20.5 (2014): 600-612.
- Godoy, Oscar, Nathan JB Kraft, and Jonathan M. Levine. "Phylogenetic relatedness and the determinants of competitive outcomes." Ecology Letters17.7 (2014): 836-844.
- Narwani, Anita, et al. "Experimental evidence that evolutionary relatedness does not affect the ecological mechanisms of coexistence in freshwater green algae." Ecology Letters 16.11 (2013): 1373-1381.
- Rachel M. Germain, Jason T. Weir, Benjamin Gilbert. Species coexistence: macroevolutionary relationships and the contingency of historical interactions. Proc. R. Soc. B 2016 283 20160047
- Nathan J. B. Kraft, Oscar Godoy, and Jonathan M. Levine. Plant functional traits and the multidimensional nature of species coexistence. 2015. PNAS.
- Bartish, Igor V., et al. "Species pools along contemporary environmental gradients represent different levels of diversification." Journal of Biogeography 37.12 (2010): 2317-2331.
- IV Bartish, WA Ozinga, MI Bartish, GW Wamelink, SM Hennekens. 2016. Different habitats within a region contain evolutionary heritage from different epochs depending on the abiotic environment. Global Ecology and Biogeography
- Pigot, Alex L., and Rampal S. Etienne. "A new dynamic null model for phylogenetic community structure." Ecology letters 18.2 (2015): 153-163.
- Gallien, L., Saladin, B., Boucher, F. C., Richardson, D. M. and Zimmermann, N. E. (2016), Does the legacy of historical biogeography shape current invasiveness in pines?. New Phytol, 209: 1096–1105.