Supplementary material in Plant Ecology
Taxonomic, phylogenetic and functional diversities of ferns and lycophytes along
an elevational gradient depend on taxonomic scales
Takayuki Tanaka & Toshiyuki Sato (Shinshu University)
tanakanaka8150@gmail.com
Appendix 1
Fig. S1. The mean slopes of the last 10% of individual-based rarefaction curve as the
proxy for inventory incompleteness) in 100 m, 200 m, 300 m and 400 m intervals of
elevation. The values of a slope close to zero indicate saturation in the sampling,
whereas those close to one indicate high levels of incompleteness.
Fig. S1
Appendix 2
Table. S1. Fossil age constraints and associated lognormal distribution parameters used in BEAST
analysis.
clade
Stem/Crown
Offset
Mean (SD)
1
Leptosporangiate
Crown
282.0
3.63 (0.14)*1
2
Lygodium
Stem
167.7
3.92 (0.38)*2
3
Scaly Tree ferns
Stem
145.5
3.13 (0.55)*2
4
Marsileaceae
Stem
140.2
3.84 (0.36)*2
5
Polypods
Crown
121.0
3.78 (0.22)*1
6
Pteroids
Stem
93.5
4.24 (0.24)*2
7
Dennstaedtia/Microlepia
Stem
70.6
3.89 (0.24)*2
Stem
65.5
3.55 (0.28)*2
clade
8
Ceratopteris/Acrostichum
clade
9
Onoclea
Stem
55.8
3.09 (0.33)*2
10
Athyrioids
Stem
37.2
3.96 (0.18)*2
11
Polygrammoids
Stem
33.9
3.28 (0.23)*2
*1 We set the values of the mean in lognormal prior distribution parameters so that the median of the
lognormal distribution equals the mean molecular age listed in TABLE 1 in Pryer et al. (2004), and
set the values of standard deviation (SD) so that the 95% soft upper bound equals mean molecular
age plus 2SD listed in TABLE1 in Pryer et al. (2004).
*2 We set the values of the mean in lognormal prior distribution parameters so that the median of
lognormal distribution equals the best age listed in TABLE S3 in Schuettpelz and Pryer (2009) and
set the values of SD so that the 95% soft upper bound equals best age plus two times ten percent of
the best age listed in TABLE S3 in Schuettpelz and Pryer (2009).
Reference in Appendix 2
Pryer KM, Schuettpelz E, Wolf PG, Schneider H, Smith AR, Cranfill R (2004) Phylogeny and
evolution of ferns (monilophytes) with a focus on the early leptosporangiate divergences. Am J Bot
91: 1582-1598
Schuettpelz E, Pryer KM (2009) Evidence for a Cenozoic radiation of ferns in an
angiosperm-dominated canopy. PNAS 106: 11200-11205
Appendix 3
Fig. S3. Elevational pattern of (a) SES.RaoQ and (b) observed RaoQ in functional diversity without
frond dissection and reproductive type of ferns and lycophytes. In SES.RaoQ, trend lines were fitted
using linear and second-order polynomial regression analysis with statistical significance at the P <
0.05 level. In observed RaoQ, black circles indicate the value of RaoQ in observed species
assemblages, and grey circles indicate the mean value of RaoQ in the null assemblage. The dotted
lines indicate the 95% confidence interval of values obtained in the null assemblage. The dotted lines
and asterisk indicate the 95% confidence interval of values obtained in the null assemblage and
significant clustering or over-dispersion that deviated from the 95% confidence interval, respectively.
Fig. S3
Appendix 4
Fig. S4,1. Taxonomic diversity of lycophytes along an elevational gradient based on species richness
estimated using the method of linked individual-based rarefaction and extrapolation curves up to a
sample size of the elevation with maximum individuals. The error bars represent 95% unconditional
confidence intervals for estimated species richness. Trend line was fitted using simple ordinary least
squares regression with the quadratic terms of elevations (P = 0.0534).
Fig. S4,1
Fig. S4,2. Proportion of species richness of lycophytes to ferns and lycophytes along elevational
gradient.
Fig. S4,2