You could plot the species with the largest SCBD along the river, as in Fig. 2.3.
# LCBD values
spe.beta$LCBD
# p-values
spe.beta$p.LCBD
# Holm correction
p.adjust(spe.beta$p.LCBD, "holm")
# Sites with significant Holm-corrected LCBD value
row.names(spe[which(p.adjust(spe.beta$p.LCBD, "holm") <= 0.05),])
# Plot the LCBD values on the river map
plot(spa,
asp = 1,
cex.axis = 0.8,
pch = 21,
col = "white",
bg = "brown",
cex = spe.beta$LCBD * 70,
main = "LCBD values",
xlab = "x coordinate (km)",
ylab = "y coordinate (km)"
)
lines(spa, col = "light blue")
text(85, 11, "***", cex = 1.2, col = "red")
text(80, 92, "***", cex = 1.2, col = "red")
We obtain SS Total ¼ 14.07 and BD Total ¼ 0.5025. These values differ slightly
from those of Legendre and De Cáceres (2013) because we used a different distance
coefficient. Five species have an SCBD higher than the mean SCBD: the brown trout
(Satr), Eurasian minnow (Phph), bleak (Alal), stone loach (Babl) and (to a
lesser extent) roach (Ruru). The (Hellinger-transformed) abundances of these
species vary the most among sites, which makes them interesting as ecological
indicators.
The largest LCBD values are concentrated in three zones around sites 1, 13 and
23 (Fig. 8.4). The permutation tests show that the LCBD values of sites 1 and 23 are
significant after a Holm correction for 29 simultaneous tests. Both sites stand out
because they harbour very few species, which makes them different from most of the
other sites. This point allows us to emphasize that sites having high LCBD values are
not automatically “special” in a good sense, e.g. by harbouring rare species or by
being exceptionally rich. Any departure from the overall species abundance pattern
increases the LCBD value. In the present example, site 1 was a pristine site at the
head of the river, harbouring a single species, the brown trout (Satr), whereas sites
23–25 suffered from urban pollution and were in need of rehabilitation.
8.4 Beta Diversity
387
# LCBD values
spe.beta$LCBD
# p-values
spe.beta$p.LCBD
# Holm correction
p.adjust(spe.beta$p.LCBD, "holm")
# Sites with significant Holm-corrected LCBD value
row.names(spe[which(p.adjust(spe.beta$p.LCBD, "holm") <= 0.05),])
# Plot the LCBD values on the river map
plot(spa,
asp = 1,
cex.axis = 0.8,
pch = 21,
col = "white",
bg = "brown",
cex = spe.beta$LCBD * 70,
main = "LCBD values",
xlab = "x coordinate (km)",
ylab = "y coordinate (km)"
)
lines(spa, col = "light blue")
text(85, 11, "***", cex = 1.2, col = "red")
text(80, 92, "***", cex = 1.2, col = "red")
We obtain SS Total ¼ 14.07 and BD Total ¼ 0.5025. These values differ slightly
from those of Legendre and De Cáceres (2013) because we used a different distance
coefficient. Five species have an SCBD higher than the mean SCBD: the brown trout
(Satr), Eurasian minnow (Phph), bleak (Alal), stone loach (Babl) and (to a
lesser extent) roach (Ruru). The (Hellinger-transformed) abundances of these
species vary the most among sites, which makes them interesting as ecological
indicators.
The largest LCBD values are concentrated in three zones around sites 1, 13 and
23 (Fig. 8.4). The permutation tests show that the LCBD values of sites 1 and 23 are
significant after a Holm correction for 29 simultaneous tests. Both sites stand out
because they harbour very few species, which makes them different from most of the
other sites. This point allows us to emphasize that sites having high LCBD values are
not automatically “special” in a good sense, e.g. by harbouring rare species or by
being exceptionally rich. Any departure from the overall species abundance pattern
increases the LCBD value. In the present example, site 1 was a pristine site at the
head of the river, harbouring a single species, the brown trout (Satr), whereas sites
23–25 suffered from urban pollution and were in need of rehabilitation.
8.4 Beta Diversity
387