Download Dissecting phylogenetic fuzzy weighting: theory and application in

Dissecting phylogenetic fuzzy weighting: theory and application in
metacommunity phylogenetics
Leandro D. S. Duarte1,*, Vanderlei J. Debastiani1, André V. L. Freitas2, Valério D.
Pillar1
1
Departamento de Ecologia, CP 15007, Universidade Federal do Rio Grande do Sul,
Porto Alegre, 91501-970, Brazil
2
Departamento de Biologia Animal, Instituto de Biologia, CP 6109, Universidade
Estadual de Campinas, Campinas, São Paulo, 13083-970, Brazil
Appendix S1. Matrix Q, phylogenetic pool and taxa sampling
Community ecologists often define their species sample based on a more or less
arbitrary spatial unit, which tends to be problem-delimited rather than evolutionarily
delimited. Thus, species samples analyzed in ecological studies do not necessarily
express the complete phylogenetic information of the clade under analysis.
Phylogenetic lineages containing a high number of species can be rare in some
metacommunities while are very common in others. Moreover, some branches of the
phylogenetic tree can be simply absent in some metacommunities. If we intend to
analyze phylogenetic patterns for a particular metacommunity, the most feasible
solution is to define the phylogenetic pool based on the species sampled across the
metacommunity. It logically implies that sampling species from a given biological
group (e.g. angiosperms, anurans, etc.) in two different metacommunities can render
different phylogenetic tree topologies, even though those metacommunities share
some species. How can sampling design affect matrix Q?
As we have seen in the main text, the SB value of a species will depend on the
frequency of ramifications between the tip node and the root of the tree. Further, CB
values between any pair of species will also depend on the topology of evolutionary
path of each species and on the phylogenetic distance between them. Thus, whenever
a sample-defined species pool, i.e. the set of species recorded in the metacommunity,
is used to compute SB and CB values, the matrix Q is valid only for that
metacommunity. Indeed, other phylogenetic metrics were already demonstrated to be
strongly dependent on the phylogenetic pool used to define it (Swenson et al. 2006).
The only way to compute the “true” SB (SBTRUE) and CB (CBTRUE) values for a taxa
sample is to extract those values directly from the complete phylogenetic tree for
those taxa. Otherwise, a species from a highly diversified lineage, which tend to show
a low SBTRUE value compared to other species from a less diversified clade, may
possibly show a high local self-belonging (SBLOCAL) if the clade to which it belongs is
locally rare. With sufficient sampling effort, a species with SBLOCAL >> SBTRUE might
possibly give some clue about the ecological mechanisms filtering the local
distribution of some lineages across the metacommunity. Therefore, in comparative
studies performed at the regional scale, a high SBLOCAL value can be also useful and
informative, even with the lack of the complete phylogenetic tree. In short, high
SBLOCAL values can tell us about the importance of a poorly represented lineage in a
given region (e.g., a conifer tree in a tropical forest), although the results cannot be
compared with those obtained from a region where such lineage is better represented
(e.g. comparing values from the above example with those obtained from a boreal
forest). In the same way, CB values among species will also vary according to the
phylogenetic tree used to compute Q where some nodes are pruned from the sampledefined phylogenetic tree.
Considering the dependency of self-belonging values on phylogenetic taxa
sampling, three possible situations can be found when we compute SB values:
1) Taxa sampling expresses the overall phylogenetic variability of the living
clades. In this case, the less diversified a lineage is, the higher the self-belonging of
the taxa within such lineage, and SBLOCAL ≅ SBTRUE. This means that poorly
diversified lineages are more "unique" than species from a very diversified clade. For
example, in a global assessment of mammalian diversity, monotremes will always
show a higher SB value when compared to any other mammalian lineage.
2) Taxa sampling captures the phylogenetic variability of a given lineage
across the metacommunity, but does not express the overall phylogenetic variability
of the living clades. This is a common situation, since local species pools recorded to
assess community assembly patterns often fail to capture the complete phylogenetic
variation in a given lineage. Thus, each taxon within a lineage with low local
phylogenetic representativeness will present a high self-belong value (SBLOCAL),
which does not necessarily represent its self-belonging (SBTRUE) when the global
representativeness of the clade is considered (SBLOCAL ≠ SBTRUE). For instance,
conifer trees of the Brazilian Atlantic Forest are represented by three species, which
means that in any local species pool these species will tend to show high SBLOCAL
values. On the other hand, angiosperm trees in boreal forests will likely show high
SBLOCAL values. A high SBLOCAL value can be useful and informative though. This
information tell us the local uniqueness of a given lineage, which can be a valuable
information to help understanding community assembly patterns and taking decisions
about conservation/management practices.
3) Taxa sampling neither capture the phylogenetic variability of a given lineage
across the metacommunity, nor express the overall phylogenetic variability of the
living clades. In this case the SB and CB values are merely an artifact, and should be
used with caution. Among the various reasons that lead to this situation we might
highlight biased and incomplete sampling and lack of phylogenetic data for many
biological groups.
Reference
Swenson, N.G., Enquist, B.J., Pither, J., Thompson, J. & Zimmerman, J.K. 2006. The
problem and promise of scale dependency in community phylogenetics.
Ecology 87: 2418–2424.