Geoscience Reference
In-Depth Information
Gorilla
Gorilla
Human
Human
Chimpanzee
Chimpanzee
Bonobo
Bonobo
Orangutan
Orangutan
0
1 Unit
0
5
10 Ma
(a)
(b)
FIGURE 6.1
Taxonomic (a) and phylogenetic (b) trees are used to represent the hierarchy of relatedness
between organisms, in this case the great apes. A species-based analysis would treat humans, chimpanzees
and bonobos as equally different. A taxonomic tree allows for differences at the genus level, but the only effec-
tive difference is for comparisons involving chimpanzees and bonobos. The phylogenetic tree allows a more
refined measure of difference between each of the taxa, in this case millions of years of evolution since diver-
gence of each of the lineages. (Phylogenetic tree from Bininda-Emonds, O.R.P. et al.,
Nature
, 446, 507, 2007.)
and data collection become cheaper, individual organisms will increasingly be studied. However,
this will not change the basic approaches used.
Given the preceding conditions, the object data model is most commonly used in the analysis of
geolocated biological data. However, consistent with other object-based data, continuous fields can
be derived through processes such as smoothing, density estimation and interpolation.
6.2.1 t
axonoMieS
and
P
hylogenieS
A taxonomy is the familiar Linnaean system of classification where taxa are grouped into the hier-
archy of kingdom, phylum, class, order, family, genus and species (although other intermediate
and lower levels can be included) (see Figure 6.1). The concatenation of labels from different levels
results in a unique name for any taxon, although only genus and species are strictly needed for
identification (e.g.
Homo sapiens
for humans and
Brassica oleracea
for cabbage). A taxonomy is a
topological structure, in which distance between each level of the hierarchy does not represent a true
distance. In this sense, species within a genus are represented as being equally different from each
other, when in reality some will be more closely related than others.
A phylogeny is a more detailed representation of the relatedness between taxa than a taxonomy
(Figure 6.1). The branch lengths of a phylogeny can be interpreted as the rate of change of features
between organisms, such features typically being genes and/or morphological characteristics. By
means of appropriate calibration, one can derive a chronogram, enabling branch lengths to represent
time since divergence of the lineages within the tree.
The tree-based data structure makes a phylogeny an intuitive system to work with. A simple
interpretation of phylogenies can be derived by rephrasing Tobler's (1970) first law of geography
'That all species are related to all other species, but that phylogenetically close species are more
related than those phylogenetically further apart'. There is also no need for it to be displayed using
only two dimensions, with recent tools being developed to allow geographic visualisation of phylog-
enies on digital globes (Hill and Guralnick, 2010; Bielejec et al., 2011). Such approaches make for
an interesting addition to the visualisation tools already in use in GC (Gahegan, 2014).
Given its greater level of detail than a taxonomy, one would ideally use a phylogeny to represent
the relatedness between taxa in any analysis. However, the reality is that complete phylogenies are
