Phylogenetic
signal
Phylogenetic signal was tested using two methods: the ’aotf’ function in
Phylocom 4.2 (Webb et al. , 2011) for the quantitative traits
(maximum diameter, maximum height and relative coverage), and
calculating the traitNRI for the qualitative traits (Gastauer et
al. , 2017), except for Selaginella convoluta , which was not
considered in the tests of the phylogenetic signal so as not to create
bias caused by imbalanced phylogenetic trees because of the large
phylogenetic distance (566 myr) between this only pteridophyte species
and all the others (see (Duchêne et al. , 2015; Holman, 2005). For
the endozoochory trait, maximum diameter and maximum height only the
species of the woody component were considered (n=87). For the relative
coverage trait (RC) only the species of the non-woody component were
considered.
The ’aotf’ module compares the variance rank of the observed mean
variance of the trait of interest across all nodes from a null generated
distribution of 9999 random repeats to trait values through phylogeny
(Webb et al. , 2011).
In order to evaluate trait conservatism, the significance of the
variance of the independent contrasts was analyzed. 9999 randomizations
were made and the trait was considered conserved if the variation of
contrasts observed was less than 2.5% of the randomizations. TraitNRI
and traitNTI were used to assert that all species possessing a given
qualitative trait are more related to each other than expected by
chance. The traitNRI was calculated for the phylogenetic structure of
the community formed by the species with each trait, in order to emulate
the phylogenetic signal of these traits. One thousand randomizations
were performed and evaluated through null model. If traitNRIs or
traitNTIs were lower than – 1.96 or higher than 1.96
(p<0.05), they were considered significant (Gastauer et
al. , 2017).