Ecophylogenetics redux

Abstract

Species’ evolutionary histories shape their present‐day ecologies, but the integration of phylogenetic approaches in ecology has had a contentious history. The field of ecophylogenetics promised to reveal the process of community assembly from simple indices of phylogenetic pairwise distances – communities shaped by environmental filtering were composed of closely related species, whereas communities shaped by competition were composed of less closely related species. However, the mapping of ecology onto phylogeny proved to be not so straightforward, and the field remains mired in controversy. Nonetheless, ecophylogenetic methods provided important advances across ecology. For example the phylogenetic distances between species is a strong predictor of pest and pathogen sharing, and can thus inform models of species invasion, coexistence and the disease dilution/amplification effect of biodiversity. The phylogenetic structure of communities may also provide information on niche space occupancy, helping interpret patterns of facilitation, succession and ecosystem functioning – with relevance for conservation and restoration – and the dynamics among species within foodwebs and metacommunities. I suggest leveraging advances in our understanding of the process of evolution on phylogenetic trees would allow the field to progress further, while maintaining the essence of the original vision that proved so seductive.

A roadmap towards predicting species interaction networks (across space and time)

“…However, functional-trait based proxies could enable better predictions of ecological interactions [34,[125][126][127]. Selection on functional traits could cause interactions to be conserved at some evolutionary scales, and therefore predictions of interaction could be informed by phylogenetic analyses [32,128,129]. Phylogenetic matching in bipartite networks is [130], even in the absence of strong selective pressure [131].…”

“…On broader taxonomic scales, we can infer interaction probability through the phylogenetic distance, assuming that functional traits themselves are conserved [129]. In this case, we can think of the probability that one species will interact with another as the distance between them in niche-space [93], and this can be modelled by simulating neutral expectations of trait variation on phylogenetic trees [128]. At the narrowest scales, we may be interested in predicting behavioural traits like foraging behaviour [34], and at this scale we may need to consider abundance's effect on the probability of an encounter [58].…”

A Roadmap Toward Predicting Species Interaction Networks (Across Space and Time)

“…However, functional-trait based proxies could enable better predictions of ecological interactions. Selection on functional traits could cause interactions to be conserved at some evolutionary scales, and therefore predictions of interaction could be informed by phylogenetic analyses (Davies 2021;Elmasri et al 2020;Gómez, Verdú, and Perfectti 2010). Phylogenetic matching in bipartite networks is consistent across scales (Poisot and Stouffer 2018), even in the absence of strong selective pressure (Coelho, Rodrigues, and Rangel 2017).…”

“…On broader taxonomic scales we can infer interaction probability through the phylogenetic distance, assuming that functional traits themselves are conserved (Gómez, Verdú, and Perfectti 2010). In this case, we can think of the probability that one species will interact with another as the distance between them in niche-space (Desjardins-Proulx et al 2017), and this can be modeled by simulating neutral expectations of trait variation on phylogenetic tree (Davies 2021). At the narrowest scales, we may be interested in predicting behavioral traits like foraging behavior (Bartomeus et al 2016), and at this scale we may need to consider abundance's effect on probability of an encounter (Wells and O'Hara 2013).…”

Towards a phylogenetic ecology of plant pests and pathogens

“…In what is now commonly referred to as Darwin's naturalization hypothesis, Darwin hypothesized that resource-use overlap, and thus competition with native species, would be lower if introduced species were more distant relatives. Both Darwin's naturalization hypothesis and the enemy release hypothesis predict similar ecophylogenetic patterns [74], such that additional information is needed to differentiate between them. However, because pests of non-native plants may over time invade the introduced range of the non-native plant, and pests of the native flora can evolve to use novel hosts (both commonly observed in intentionally introduced plants e.g.…”