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Cluster analysis of a regional-scale soil

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Article in Applied Geochemistry · June 2011

Impact Factor: 2.27 · DOI: 10.1016/j.apgeochem.2011.03.041

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 Applied Geochemistry 26 (2011) S105–S107

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Applied Geochemistry
journal homepage: www.elsevier.com/locate/apgeochem

Cluster analysis of a regional-scale soil geochemical dataset in northern California

Jean M. Morrison ⇑, Martin B. Goldhaber, Karl J. Ellefsen, Christopher T. Mills
US Geological Survey, Denver Federal Center, MS 964D, Denver, CO 80225, United States

a r t i c l e i n f o a b s t r a c t

Article history: A regional-scale soil geochemical study was conducted within a 22,000 km2 area in northern California
Available online 22 March 2011 including the Sierra Nevada, Sacramento Valley, and northern Coast Range. Over 1300 soil samples were
chemically analyzed for 42 elements. The distribution of distinct groups of elements demonstrates the
interplay of geologic, hydrologic, geomorphologic and anthropogenic factors; however, it is difficult to
fully appreciate the complexity of geochemical transport and weathering processes on a landscape-scale
in an area of very complex geology with such a large dataset containing more than 40 variables. To exam-
ine the data from a perspective of multi-element groupings, cluster analyses were applied to the dataset.
The analysis identified several groups of elements whose spatial patterns could be related to specific geo-
logic sources.
Published by Elsevier Ltd.

1. Introduction
The Sacramento Valley of northern California receives sediment
from three bordering mountain ranges: Sierra Nevada to the east,
Coast Range to the west and Klamath Mountains to the north.
The weathering and transport of sediment from these source areas
into the Sacramento Valley has resulted in distinct geochemical
spatial patterns that are revealed by mapping single elements in
surface soils (Goldhaber et al., 2009; Morrison et al., 2009). Gold-
haber et al. (2009) showed regional geochemical patterns con-
trolled by geologic and anthropogenic controls. Elements which
are abundant in silicic rocks (Ca, Na, Sr and rare earth elements)
were elevated in soils spatially associated with Tertiary volcanic
and Mesozoic plutonic rocks in the Sierra Nevada and those in
the eastern Sacramento Valley. Conversely, Cr and Ni are highly en-
riched in the ultramafic rocks of the Coast Range and the western
metamorphic belt located in the Sierra Nevada foothills. As a result,
soils throughout the Sacramento Valley are enriched in Cr and Ni,
but higher concentrations are found in the western Sacramento
Valley. This portion of the valley receives input from the Coast
Range, whereas eastern Sacramento Valley soils are diluted by
the silicic material from the Sierra Nevada (Morrison et al.,
2009). Another source of material to the western Sacramento
Valley is a thick sequence of marine sedimentary rocks, the Great
Valley Sequence, that lies between the Coast Range and western
Sacramento Valley (Morrison et al., 2009). Marine sedimentary
rocks are known to be elevated in Li and western valley soils typ-
ically have elevated concentrations of Li. Furthermore, overbank
⇑ Corresponding author. Tel.: +1 303 236 6366.
E-mail address: jmorrison@usgs.gov (J.M. Morrison).
and levee deposits along the Sacramento River are elevated in trace
elements characteristic of the massive sulfide mining region (Zn,
Cd, As and Cu) to the north in the Klamath Mountains (Goldhaber
et al., 2009).
This study sought to refine understanding of the regional distri-
bution of chemical elements in surface soils in this 20,000 km2
study area in northern California. Initial work examined the distri-
bution of single elements characteristic of specific rock types. It
was hypothesized that a more critical look at multiple-element
patterns using cluster analysis of this large dataset would provide
more detail about the geochemical controls on the Sacramento Val-
ley. Previous studies have shown that these types of clustering ap-
proaches can be useful tools in exploring relationships and
patterns in large geochemical datasets (Reimann et al., 2008;
Templ et al., 2008).
2. Methods
Using the R statistical software package, two types of cluster
analysis were used. First, hierarchical clustering was used to delin-
eate the relationships between elements. This type of clustering
shows which elements tend to have similar variations in concen-
trations. Second, non-hierarchical clustering was used to delineate
the relationships between samples to show which samples tend to
have similar concentrations.
Hierarchical clustering was done on the valley soil dataset,
which included 42-element ICP-MS analysis (following 4-acid
digestion) on 861 surface (upper 10–15 cm) samples. Non-hierar-
chical clustering, specifically, partition around medoids (PAM)
(Reimann et al., 2008), was then performed on the same dataset
and the number of clusters assigned was varied from 2 to 5. The

0883-2927/$ - see front matter Published by Elsevier Ltd.

doi:10.1016/j.apgeochem.2011.03.041
S106 J.M. Morrison et al. / Applied Geochemistry 26 (2011) S105–S107

log-transformed, standardised of the Sacramento River. In this case, soil samples from the source
40

areas in the Sierra Nevada were partitioned into 2–5 clusters. The
spatial trends apparent in the clusters were compared with the
35

mapped geologic units.

30
Height

Cd
Ti
Mn
25

S
Bi

Mo
Na

Pb
Sn
3. Results and discussion

P
Cu
Zn
20

Al
Sb
As

Ba
K
Be
Mg
In

U
Tl
Rb
Hierarchical clustering of the Sacramento Valley soils showed
15

Li
Cs

Nb
element associations that could be interpreted in terms of source
Co
Sc

Th
Ca
Sr
10

Y
Ga
Ni
Cr

rock types. This is shown as a dendrogram in Fig. 1.Elements typ-

V
Fe

Ce
La
Fig. 1. Dendrogram showing results of hierarchical clustering of log-transformed
standardized data.
results were analyzed in the context of existing geochemical
knowledge based on spatial trends of the clusters and their corre-
lation to mapped geologic units.
Non-hierarchical clustering was also used to more closely
examine the spatial patterns observed within the complex geology
of the Sierra Nevada and the relationship with valley alluvium east
ically abundant in silicic rocks such as Ca, Na and Sr, are closely
associated in the dendrogram and distinctly separated from ele-
ments common in rock types of different chemical compositions.
Elements typically associated with ultramafic rocks (Cr, Ni, Mg)
were closely associated in the dendrogam. Also closely related,
but to a lesser extent, are Fe and V. These elements are commonly
enriched in ultramafic rocks, but are less specific to ultramafic
rocks than Cr and Ni. Copper and Zn, two of the elements that occur
in massive sulfide deposits in the Klamath Mountains at the north-
ern end of the Sacramento Valley, are also closely related on the
dendrogram. However, they are not strongly associated with Cd

Fig. 2. Map showing non-hierarchical clustering (PAM) results for two clusters and relative distribution of elements characteristic of rock types. The Sacramento River is
shown by the bold line running north to south.

Fig. 3. Map showing non-hierarchical clustering (PAM) results for three clusters and relative distribution of elements characteristic of rock types. The Sacramento River is
shown by the bold line running north to south.
 J.M. Morrison et al. / Applied Geochemistry 26 (2011) S105–S107
and As, two other elements that are thought to be elevated as a re-
sult of mining in the Klamath Mountains.
When non-hierarchical clustering of the Sacramento Valley
soils was performed with two clusters, a relatively distinct pattern
emerged splitting the valley samples into an eastern cluster and
western cluster with the Sacramento River as the approximate
dividing line (Fig. 2). Relative abundances of a select number of
elements show that soils in the western cluster are higher in ele-
ments associated with ultramafic rocks (Cr, Ni and Mg) and soils
in the eastern cluster are relatively higher in elements associated
with silicic rocks (Ca, Sr). This result agrees with a similar spatial
pattern observed in single element comparisons done in previous
studies (Goldhaber et al., 2009; Morrison et al., 2009). However,
the two cluster map also reveals that the southwestern portion
of the study area is characterized by the more silicic association
of the eastern valley. This feature was not previously recognized
in the earlier reports. Comparison with the geologic maps shows
that this southwestern area has silicic Tertiary volcanic rocks in
its headwaters.
When three clusters are used, an additional cluster emerges
along two drainages in the eastern part of the study area. This third
cluster is characterized by elevated Sr, U and Th (Fig. 3). The
southernmost of these two groups is along the drainage of the
Mokelumne River. Both aeroradiometric maps of this area (Hill
et al., 2009) and stream sediment geochemistry (Morrison et al.,
2008) show elevated U content in this area. It is hypothesized that
one or more plutons in the Sierra Nevada are enriched in this suite
of elements and this cluster is showing a dominant transport path
of this source material to the valley.
Results from four and five clusters (not shown) indicated fur-
ther geochemical distinction between western valley soils and
overbank deposits bordering the Sacramento River as described
by Goldhaber et al. (2009). However, further analysis is needed
to determine if the increased number of clusters is actually identi-
fying a geochemically distinct group or if it is responding to noise
within the data.
S107
When non-hierarchical clustering was applied to Sierra Nevada
source soils, the clusters show some relationship to the mapped
geologic units including metamorphic rocks, Tertiary volcanics,
and Mesozoic granite (data not shown). However, these results
are preliminary and the analysis must be refined to clarify the
relationships.
4. Conclusions
The use of cluster analysis helped refine understanding of the
evolution of valley alluvium from the perspective of parent mate-
rial. Results showed that using cluster analysis is beneficial in fur-
thering ability to discern related groups of elements resulting from
a variety of parent materials and understanding their transport and
distribution throughout the Sacramento Valley. As Templ et al.
(2008) and Reimann et al. (2008) suggest, cluster analysis is a use-
ful exploration tool but must be accompanied by geochemical intu-
ition and knowledge of the geologic controls of a particular region.
References
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