Are phylogenies resolved at the genus level appropriate for studies on phylogenetic structure of species assemblages?

Abstract

Phylogenies are essential to studies investigating the effect of evolutionary history on assembly of species in ecological communities and geographical and ecological patterns of phylogenetic structure of species assemblages. Because phylogenies well resolved at the species level are lacking for many major groups of organisms such as vascular plants, researchers often generate a species-level phylogenies using a phylogeny well resolved at the genus level as a backbone and attaching species to their respective genera in the phylogeny as polytomies or by using a megaphylogeny well resolved at the genus level as a backbone and adding additional species to the megaphylogeny as polytomies of their respective genera. However, whether the result of a study using species-level phylogenies generated in these ways is robust, compared to that based on phylogenies fully resolved at the species level, has not been assessed. Here, we use 1093 angiosperm tree assemblages (each in a 110 × 110 km quadrat) in North America as a model system to address this question, by examining six commonly used metrics of phylogenetic structure (phylogenetic diversity and phylogenetic relatedness) and six climate variables commonly used in ecology. Our results showed that (1) the scores of phylogenetic metrics derived from species-level phylogenies resolved at the genus level with species being attached to their respective genera as polytomies are very strongly or perfectly correlated to those derived from a phylogeny fully resolved at the species level (the mean of correlation coefficients is 0.973), and (2) the relationships between the scores of phylogenetic metrics and climate variables are consistent between the two sets of analyses based on the two types of phylogeny. Our study suggests that using species-level phylogenies resolved at the genus level with species being attached to their genera as polytomies is appropriate in studies exploring patterns of phylogenetic structure of species in ecological communities across geographical and ecological gradients.

Distinct Responses of Leaf Traits to Environment and Phylogeny Between Herbaceous and Woody Angiosperm Species in China

“…Second, we used a species-level phylogenetic tree of Chinese vascular plants that was based on a variety of molecular sequences ( Chen et al, 2016 ; Hu et al, 2020 ). Some studies have demonstrated that phylogenies representing different levels of phylogenetic resolution (i.e., family, genus, and species) may result in some bias in quantification of phylogenetic structure ( Molina-Venegas and Roquet, 2014 ; Qian and Jin, 2021 ). Further studies in developing phylogenies well resolved at the genus or species level with more species and gene markers will help for better understanding the geographical patterns of plant traits at the large scale ( Janssens et al, 2020 ).…”

Darwin’s preadaptation hypothesis and the phylogenetic structure of native and alien regional plant assemblages across North America

“…We pruned the megaphylogeny to generate a phylogenetic tree retaining only the angiosperm species present in North America. A recent study (Qian & Jin, 2021) shows that for the phylogenetic metrics used in our study (see below), values of a phylogenetic metric derived from a phylogenetic tree resolved only at the genus level are nearly perfectly correlated to those derived from a phylogenetic tree resolved fully at the species level (Pearson’s correlation coefficient ranges from .966 to 1.000), suggesting that patterns of phylogenetic structure measured with the phylogenetic metrics would be similar or identical regardless of whether a phylogenetic tree resolved at the species or genus level is used to calculate these phylogenetic metrics. Because the vast majority of the genera and a large number of species in our data were resolved in the phylogeny, the phylogenetic metrics (see below) derived from the phylogeny is considered to be robust (Qian & Jin, 2021).…”

Patterns of phylogenetic beta diversity measured at deep evolutionary histories across geographical and ecological spaces for angiosperms in China

“…Yue & Li, 2020; Zhang et al., 2020). Using a phylogeny generated in this way in a study of community phylogenetics is equivalent to using a phylogeny fully resolved at the species level in the study as long as all the families and at least most of the genera in the former are resolved (Qian & Jin, 2020). The phylogenetic tree used in the present study was also used in a recent study investigating geographical and ecological patterns of tip‐weighted phylogenetic beta diversity for angiosperms in China (Qian et al., 2020).…”