Phylogenetic Core Groups: a promising concept in search of a consistent methodological framework : Comment to ``A conceptual framework for the phylogenetically-constrained assembly of microbial communities''

Abstract

In this comment, we analyse the conceptual framework proposed by Aguirre de Cárcer (Microbiome 7:142, 2019), introducing the novel concept of Phylogenetic Core Groups (PCGs). This notion aims to complement the traditional classification in operational taxonomic units (OTUs), widely used in microbial ecology, to provide a more intrinsic taxonomical classification which avoids the use of pre-determined thresholds. However, to introduce this concept, the author frames his proposal in a wider theoretical framework based on a conceptualization of selection that we argue is a tautology. This blurs the subsequent formulation of an assembly principle for microbial communities, favouring that some contradictory examples introduced to support the framework appear aligned in their conclusions. And more importantly, under this framework and its derived methodology, it is not possible to infer PCGs from data in a consistent way. We reanalyse the proposal to identify its logical and methodological flaws and, through the analysis of synthetic scenarios, we propose a number of methodological refinements to contribute towards the determination of PCGs in a consistent way. We hope our analysis will promote the exploration of PCGs as a potentially valuable tool, helping to bridge the gap between environmental conditions and community composition in microbial ecology. Video Abstract.

Fig. 1

Analysis of synthetic scenarios. Two evolutionary histories (left column) of four species with traits, either appearing through duplication and divergent selection (case A), or also considering convergence and horizontal gene transfer (case B). The different scenarios take sampled niches (described by the traits which are needed to inhabit them) and, depending on the OTUs found and on the analysis of neutrality, the inferred PCGs and types of niches are shown. These scenarios are analysed in detail in the main text

Fig. 2

Summary of the proposed methodology. Starting from a regional pool of species (top), the immigration rate (turnover high or low) and the environmental filtering determine the species that can be observed. The environment may be homogeneous (coloured rectangles), heterogeneous (triangles), or may be shaped by continuous transformations due to strong feedbacks with the microbial activity (cyclic arrows). Sampling these environments, classifying the samples into classes, and performing neutrality tests will lead to a classification of environments into different types of niches