Geoscience Reference
In-Depth Information
6.2.3 P
henotyPeS
, t
raitS
and
P
henology
The genotype is the genetic structure of an organism (its genome), but this is merely the starting
point for its structure and shape. The phenotype is the expression of an organism's genotype given
the environment in which it occurs, for example, climate, available resources and competition from
other organisms. Examples include fruit length and size, growth forms and height (Moles et al.,
2007, 2009).
Given the variability of environments, there is often considerable temporal variation. Phenological
variations are the response of the organism to seasonal and/or other temporal fluctuations, for
example, the time of flowering. Climate change effects on phenology are an area of active research
(e.g. Visser and Both, 2005).
6.2.4 d
ata
e
xPloSion
GC practitioners have for many years recognised the fact that we are in the midst of a spatial data
explosion (Openshaw, 1999). Earth observation systems constantly deliver terabytes of satellite imag-
ery from orbit; millions of geocoded/geolocated LiDAR data points can be captured in minutes via low
flying aircraft; and a bewildering array of different tracking technologies can be employed to record
the locational whereabouts of individuals, for example, use of platform transmitter terminal (PTT) or
radio-frequency identification (RFID) tagging, CCTV cameras or mobile devices. However, the bio-
sciences have also experienced a similar explosion in data over the same time period, partly because
both the geosciences and biosciences have been supported by similar underlying technological devel-
opments such as increases in computer power and data storage capacity. Much of this biological data
is not geolocated, but it can be linked to geolocated observations of biological entities.
In terms of available specimen data, there is an ever-increasing availability of geolocated records.
Two examples are the Atlas of Living Australia (http://www.ala.org.au/), a database containing
more than 40,000,000 specimens for Australia (as of January 2014), and the Global Biodiversity
Information Fund (GBIF; http://www.gbif.org) which maintains a global extent database of more
than 370,000,000 indexed records with coordinates (http://data.gbif.org/welcome.htm). This number
is far from a complete census. Many areas, marine environments in particular, are poorly sampled
for most taxonomic groups. Even well-sampled areas can still be poorly sampled for many groups
(Newbold, 2010). For example, large trees are easy to identify, but small herbs and fungi are not.
Many such geolocated data are derived from museum records, all of which have location infor-
mation at some level of detail, ranging from GPS-derived coordinates to statements such as
Terra
Australis
or
Nova Hollandia
. Others are derived from opportunistic sightings such as those recorded
in bird watcher databases. Following an assessment of museum-derived data for taxonomic and geo-
graphic accuracy, it is not unusual for 40% of the original records to be discarded prior to analysis
(Kooyman et al., 2012).
For descriptions and relationships among these data, the
Encyclopedia of Life
(http://eol.org/)
has close to one million pages containing species information, plus millions of pages compris-
ing only a name that are still waiting to be completed (http://eol.org/collections/34). The Tree of
Life (Maddison and Schulz, 2007; http://tolweb.org) already contains more than 10,000 pages with
phylogenetic information for extant and extinct biotic groups. The Catalogue of Life is attempting
to be a comprehensive catalogue of species and for the 2011 edition had 1,347,224 species listed
(Bisby et al., 2011). These archives represent small steps on what is a very long road.
Researchers in phylogenetics are encouraged, and for publication in some journals, required
to submit phylogenies to TreeBASE, a public repository of phylogenies (http://www.treebase.org/
treebase-web/home.html). At the time of writing, TreeBASE contained 8,462 trees comprising a
total of 465,762 distinct taxon labels mapping to approximately 82,043 distinct taxa. For genetic
data from which many phylogenies are derived, GenBank (Benson et al., 2012) is a standard data-
base. Release 185 of GenBank contained more than 340 billion base pairs (Benson et al., 2012).
