Phylogenies vary in shape with regard to the rate of evolutionary change across a tree (influencing tree balance) and variation in the timing of branching events (affecting the distribution of node ages in trees), both of which may influence the structure of species interaction networks. Because ...
This term is applied to any kind ofphylogenetic tree, which is scaled or unscaled. This is the most common output generated from hierarchical clustering. The total number of the rooted and unrooted tree, which can be constructed using n taxa, can be calculated with the following formulas. ...
A morphology-based phylogeny illustrated that the oldest of our species occurred in the headwater and that specific phylogenetic distances from the root location in the tree were significantly related to the specific longitudinal occurrences in the Loire. Furthermore, traits such as oxygen consumption,...
2000). The small tree Amborella trichopoda that is endemic to New Caledonia is considered to be the sister group to all flowering plants (Soltis et al. 2002). It has very often been used as a proxy for the ancestral state of many phenotypic traits (e.g., Friedman and Ryerson 2009). ...
phytools(>=1.5-1)RoxygenNote7.2.3 Encoding UTF-8 NeedsCompilation no Author Carl Boettiger[aut,cre]Maintainer Carl Boettiger<***> Repository CRAN Date/Publication2023-10-0301:00:02UTC R topics documented:anoles (2)pmc (2)pmc_fit (3)simulate.gfit (4)tree (4)update.gfit (4)1...
From these 1000 trees, we calculated a maximum clade credibility tree using mean node heights with the software TreeAnnotator of the BEAST 2 package for use in subsequent analyses46. Functional traits and phylogenetic structure of waterbird communities Four functional traits were selected to calculate ...
the ML tree shows improved resolution and increased bootstrap support compared to the MP tree (Table3). The eurosids, asterids, and monocots are all resolved as monophyletic (Figure4). All plant families with multiple species present in the datasets are resolved as monophyletic with strong boot...
Tree traits and plant phylogeny reconstruction Corresponding to each sample, the basic traits of each tree were recorded in the field, including height, crown diameter and DBH. Mycorrhizal types of trees were assigned by experts’ knowledge and previous studies [45]. The species identification was ...
(version 3.3.6). Mantel analysis between GSCs and environmental factors was conducted using the function mantel of the vegan package (version 2.6–2). For GSCs, we calculated the weighted Unifrac distance between samples in conjunction with the phylogenetic tree; for environmental factors, we ...
A popular approach is to model the evolution of continuously varying traits as a Brownian diffusion process acting on a phylogenetic tree. However, standard Brownian diffusion is quite restrictive and may not accurately characterize certain trait evolutionary processes. Here, we relax one of the major...