Results
Of
the 9,370 species (combined dataset of the three floras), 2,635 species
(28.1%) produced fleshy fruits. Temperate flora contained a lower
proportion of fleshy-fruited species (22.5%) than both tropical flora
(38.7%) and subtropical floras (32.6%; Fig. 2a, Table S1 in Supporting
Information). Woody species contained a higher proportion of
fleshy-fruited species (55.6%) than
herbaceous species (9.6%) (Fig. 2b, Table S1).
Phylogenetic
conservatism explained the vast majority of fruit type variation among
floras
(partial
R2lik = 79.5%), while climate region
and growth form explained little variation, with partial
R2lik values of 0.3% and 1.7%,
respectively (Table 2, Fig. 2c, d). To investigate the depth at which
this conservatism occurred within the phylogeny, we repeated the
logistic regression using a phylogeny in which nodes above the 0.67
threshold from the base of the phylogeny were collapsed (Fig. 1b). This
threshold corresponds roughly to the taxonomic level of families, so
this phylogeny removed phylogenetic information within families. The
phylogenetic conservatism occurred both towards the tips and towards the
base of the phylogenetic tree: when using the 0.67-threshold phylogeny,
the partial R2lik for phylogeny was
41.6%, implying that the phylogenetic information towards the base of
the phylogeny could explain roughly half as much variation as the full
phylogeny. Furthermore, the partial
R2lik values for plant growth form and
climate region were 25.1% and 3.9% (Table 2), implying that plant
growth explains more of the distribution of fruit type among species
when the explanatory information provided towards the tips of the
phylogeny is not available.
The low partial R2lik for growth form
can be better understood by considering the regression of growth form on
fruit type without the phylogeny or climate regions. In the model with
growth form alone (full model GF, Table 2), the
R2lik is 22.8% implying that growth
form explains a moderate amount of variation in fruit type. This is
expected, because 55.6% of the wood species had fleshy fruit, compared
to only 9.6% of the herbaceous species (Fig. 2b, Table S1). However, in
the model with growth form and phylogeny (full model GF+PHY, Table 2),
the partial R2lik for growth form is
1.5%. Therefore, when taking account of phylogeny, growth form gives
little additional information about fruit type. This suggests that the
apparent association between fruit type and growth form (Spearman rank
correlation = 0.503, Table S1, R2lik =
22.8%, Table 2) observed in this dataset cannot be distinguished from a
spurious effect of both fruit type and growth form being strongly
conserved phylogenetically. In contrast to growth form, the
R2lik for climate region remains low
even in the absence of phylogeny
(R2lik = 4.2%, full model CR, Table
2). This implies that phylogeny does not play a role in the poor
explanatory power of climate regions on fruit type.
To investigate lack of explanatory power of growth form and climate
region on fruit type in more detail, we investigated the phylogenetic
conservatism for each trait separately. Specifically, we performed
analyses with each trait as the dependent variable and no independent
variables. Both fruit type and plant growth form had very strong
phylogenetic signal (low values of α of the Ornstein-Uhlenbeck model of
evolution employed by phyloglm, Tung Ho and Ané 2014) and
R2lik values of 86.3% and 86.8%,
respectively, when the full phylogeny used (Table 3). When the
0.67-threshold phylogeny was used for the analyses, the
R2lik values decreased to 46.8% and
53.2%, respectively. This implies that phylogenetic conservatism
occurred both towards the base of the phylogeny (because the traits
R2lik values were high) and also
towards the tip (because the traits
R2lik values were not as high as for
the full phylogeny). The results for fruit type and plant growth form
contrast those for climate regions. For tropical, subtropical, and
temperate climate regions, the R2likvalues were 20.0%, 0%, and 12.2%, respectively. Furthermore, the
R2lik values of the three climate
regions computed for the 0.67-threshold phylogeny were similar to those
for the full phylogeny, implying that most of the information available
from the phylogeny occurred towards the base of the tree.
To obtain a more-complete picture of the pattern of phylogenetic
conservatism of the three traits, for each trait we computed the
R2lik across a range of threshold
phylogenies, from 1 (full phylogeny) down to 0.2 (only 20% phylogenetic
information near the basal was maintained) (Fig. 3). Both fruit type and
growth form show very strong phylogenetic conservatism, and as the
threshold above which nodes are collapsed increases, the values of
R2likincrease roughly linearly. This implies that the phylogenetic
information underlying the values of
R2lik are even distributed across the
phylogeny. In contrast, the values of
R2lik for tropical and temperate
climate regions stay roughly the same until the threshold drops below
0.8, implying that the phylogenetic relationships above this threshold
provide little information about whether species occur in the two
climate regions. The values of R2likonly drop substantially when they
are below the 0.8 threshold, implying that phylogenetic conservatism
occurs towards the base of the phylogeny. For the subtropical climate
region, R2lik is always close to zero,
implying that whether or not a species occurs in the subtropical climate
region is not explained by phylogeny.