Prospects & Overviews

Ancient biomolecules: Their origins,

fossilization, and role in revealing
the history of life
Derek E. G. Briggs
1)2)
and Roger E. Summons
3)
The discovery of traces of a blood meal in the abdomen
of a 50-million-year-old mosquito reminds us of the
insights that the chemistry of fossils can provide.
Ancient DNA is the best known fossil molecule. It is less
well known that new fossil targets and a growing
database of ancient gene sequences are paralleled by
discoveries on other classes of organic molecules.
New analytical tools, such as the synchrotron, reveal
traces of the original composition of arthropod cuticles
that are more than 400 my old. Pigments such as
melanin are readily fossilized, surviving virtually unal-
tered for 200 my. Other biomarkers provide evidence
of microbial processes in ancient sediments, and have
been used to reveal the presence of demosponges, for
example, more than 635 mya, long before their spicules
appear in the fossil record. Ancient biomolecules are a
powerful complement to fossil remains in revealing the
history of life.
Keywords:
.ancient DNA; biomarkers; fossil arthropods; fossil
preservation; melanin; molecular clock; molecular
taphonomy
Introduction
The common concept of fossilization is that of bones,
the larger the better. The notion that organic molecules
might survive for millions of years seems highly improb-
able, yet a recent report of traces of hemoglobin in a
50 million-year-old blood engorged mosquito [1] empha-
sizes that the unlikely happens. Indeed the preservation of
molecules provides complementary and often unique
evidence of the history of life. But just as organisms
undergo decay and degradation prior to fossilization and
are subsequently altered over millions of years by
processes acting on the rocks so too are their chemical
constituents modied by decay and diagenesis (changes in
composition during fossilization). The evidence for a blood
meal in the fossil mosquito included the presence of a
heme moiety together with a concentration of iron in the
abdomen, even though the hemoglobin molecule itself had
degraded.
Just as paleontologists hunt for more familiar fossils
(body fossils), the challenge for the molecular paleontolo-
gist is to discover chemical traces of ancient life (molecular
fossils or biological marker compounds biomarkers for
short) [2] either associated with fossil remains or isolated
within sedimentary rocks (Fig. 1). This search for ancient
biomolecules in rocks molecular paleontology began in
earnest in the 1960s with the recognition that organic
material in sedimentary rocks might yield information about
the history of life [2]. The term grew to embrace the use of
molecular data from living organisms to illuminate the
history of clades [3, 4], but that is not our primary focus here.
In some cases the origin of organic molecules in fossil
sedimentary sequences may not be immediately evident, and
the search is on for the parent organism. At the same time
we need to understand how and why the composition of
molecular fossils differs from their precursors (the science of
taphonomy applied to biomolecules). Only then can we
consider what kind of information such chemical fossils
might yield about the organism itself or the environment in
which it lived.
DOI 10.1002/bies.201400010
1)
Department of Geology and Geophysics, Yale University, New Haven, CT,
USA
2)
Yale Peabody Museum of Natural History, New Haven, CT, USA
3)
Department of Earth, Atmospheric and Planetary Sciences, Massachusetts
Institute of Technology, Cambridge, MA, USA
*Corresponding author:
Derek E. G. Briggs
E-mail: derek.briggs@yale.edu
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Ancient DNA is the most talked about
biomarker but it does not survive for
millions of years
The most celebrated chemical fossil is ancient DNA. Improved
techniques have resulted in a boost in interest particularly in
remains of humans and large extinct Pleistocene birds and
mammals [5]. The nuclear genome of the woolly mammothwas
the rst to be sequenced [6]; it was recovered from hair
preserved in permafrost. Ancient DNA from woolly mammoth
bone allowed the chimeric b/d globin gene to be sequenced [7].
The reconstructed mammoth hemoglobin revealed amino acid
replacements that were shown experimentally to enhance the
release of oxygen at cold temperatures (compared to the Asian
Bacteria
Eukarya
Haptophytes
Ciliates
Animals
Fungi
Red algae
Foraminifera
Green
algae
Liverworts
Brown algae
archaeol
caldarchaeol
dinosterol
alkenones
Filamentous
anoxygenic
phototrophs
Purple sulfur
bacteria
Cyanobacteria
isorenieratene
chlorobactene
Green sulfur bacteria
2-methylbacteriohopanoids
Sulfate
reducers
sterols
bacteriochlorophylls e
diploptene
Flowering
plants
oleanoids
C n-alkane
29
isopropylcholesterol
Sponges
chlorophylls
abietic acid
O
HO
O
Methanogens
& methanotrophs
Halophiles
Hyperthermophiles
Marine
groups
crocetene
methanotrophs
chlorophyll a
HBIs
iso-C & C acids
15 17
bacteriohopanoids
ergosterol
brassicasterol
24-ethylsterols
N
N
N
N
HO
O
O
O
Mg
O
fatty acid glycerol esters
O
O
OH
O
O
OH
O
O
OH
Diatoms
Dinofagellates
C alkanol
28
10-methylhexa
-decanoyl
glycerol diester
Conifers
Aerobic
O
O
HO
O
O
O
O
HO
O
O
mid-chain methylalkanes
COOH
HO
HO
N
N
N
N
O
O
O
H3CO
O
Mg
HO
HO
OH OH
OH OH
HO
HO
HO
N
N
N
N
O
O
H
3
CO
O
Mg
O
HO
HO
3-methylbacteriohopanoids
OH OH
OH OH
okenone
O
O
crenarchaeol
O
O
O
O
OH
HO
PMIs
tetrahymanol
Archaea
OH OH
OH OH
Figure 1. A Tree of Life, based loosely on the nucleotide
sequences of small subunit ribosomal RNA, illustrating lifes three
domains and the lipids that are characteristic of the major groups of
organisms. Most eukaryotes, for example, utilize sterols and, in a few
cases such as diatoms, dinoagellates, and demosponges, particular
sterols are very specic to a taxonomic group. The membranes of
bacteria and simple eukaryotes are composed of lipids made up of
hydrocarbon chains that are linear or branched in straightforward
ways; these chains are mostly linked to glycerol via ester linkages.
Archaea, on the other hand, build equivalent structures using
isoprenoidal chains that are linked to glycerol with ether bonds.
Many of these lipids can be preserved in sedimentary rocks, and
some are major contributors to the hydrocarbons that make up fossil
fuels. Investigations have focused on how such organic molecules
are altered and preserved during fossilization, and how their chemis-
try relates to phylogeny, physiology, and environmental controls
(adapted from [2]).
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elephant). This remarkable result shows how ancient DNA can
even provide paleoenvironmental information. Ancient
DNA has also been recovered from coprolites, eggshell, and
feathers of the New Zealand moa, and used to explore its
species diversity [5]. The susceptibility of DNA to oxidation,
hydrolysis and the activity of bacterial enzymes [8], however,
means that lengthy sequences are not normally recovered from
materials much older than 60,000 years unless the DNA is
encapsulated in some way and protected from degradation.
Recent reports of human DNA isolated from bones have
pushed the record back (but see [9]). A more-or-less complete
Neanderthal sequence was obtained from a toe bone about
130,000 years old from the Altai Mountains in Siberia [10] and
the Sima de Los Huevos in northern Spain yielded an almost
complete mitochondrial genome of a Pleistocene hominin over
300,000 years old [11]. Evidence of the presence of DNA
has been reported from much older fossils, including late
Cretaceous dinosaur bone, where it occurs in very low
concentrations [12]. Although ever more sophisticated techni-
ques may allow such material to be tested in the future,
extending the reach of sequence data, the limits are presently
at hundreds of thousands rather than millions of years.
Fossil molecules vary in their preservation
potential
Ironically, perhaps, there tends to be an inverse relationship
between the amount of information encoded in ancient
molecules and their potential to become fossilized. Ancient
DNA carries the most phylogenetic/taxonomic information
among molecular remains of any extinct organism, yet nucleic
acids have the lowest preservation potential among fossil
biomolecules. At the other end of the spectrum, some of
the most robust molecules tend to be those biopolymers
that make up structural tissues cuticles in arthropods, for
example, and the lignied materials that support plants
but they are only specic to particular organisms at a very
general level. Even these molecules do not survive in pristine
condition over millions of years: the remains that we nd
as fossils are normally transformed to more recalcitrant
components through polymerization and loss of functional
groups, obscuring their original composition. But just as new
techniques are releasing more data from ancient DNA so too
are novel analytical methods allowing us to tease more
information out of older molecular materials.
Ancient organic molecules are not conned to recognizable
fossils they also occur in free and chemically bound forms in
sedimentary rocks. Much organic material in sedimentary rocks
is present as hydrocarbons; oil and gas exploration and
extraction rely to a degree on knowledge of both the source
organisms and pathways of preservation. Fossil molecules can
be categorized according to their preservation potential [13, 14]
and ranked in terms of decay resistance. This provides an
indication of the likelihood of their being preserved in the fossil
record or incorporated into fossil fuels. The categories, in
increasing order of decay resistance, are nucleic acids, proteins,
carbohydrates, lipids, and structural macromolecules (Table 1).
Higher preservation potential tends to be reected in a greater
maximum geologic age of preserved examples of the different
groups of molecules. Lengths of DNA suitable for sequencing
survive less than a million years whereas the carbon backbones
of some kinds of lipids, such as steroids, triterpenoids, and
carotenoid pigments, may be preserved as hydrocarbons for
billions of years. Likewise structural macromolecules, repre-
sented as organic-walled microfossils, account for most of the
Table 1. Distribution of major categories of biomolecules in organically preserved fossils through time (after [35])
Biomolecule
Source
organism
Archeological
record
Cenozoic record
<66 mya
Mesozoic-Paleozoic
record 66541 mya
Nucleic acids
DNA/RNA All organisms 10
5
10
6
yr. Physical
protection (such as
in bone) may enhance
preservation
None sequenced Reported in Cretaceous
dinosaur bone but too
fragmented to sequence
Proteins All organisms 10
3
10
6
yr in shell
and bones
Present in Oligocene
beetles
Reported in Carboniferous
scorpion (310 mya) and
Silurian eurypterid (417 mya)
Carbohydrates
Cellulose Vascular plants
and some fungi
Present Present in Eocene
Metasequoia
None
Chitin Arthropods
and fungi
Detected in Quaternary
beetles
Present in Oligocene
beetles
Reported in Carboniferous
scorpion (310 mya) and
Silurian eurypterid (417 mya)
Lipids All organisms Present Present, significant
proportion bound to
macromolecule
Present, significant proportion
bound to macromolecule
Structural macromolecules
Algaenan Algae Present Present, with greater
cross-linking
Present, with greater
cross-linking
Lignin Vascular plants Present Present in Eocene
Metasequoia
Diagenetically modified
Sporopollenin Vascular plants Present Present Diagenetically modified
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oldest fossils on the planet. But categorizing molecules in terms
of their resistance to decay is not straightforward. The protein
collagen, for example, decays readily, but may be protected
within bone [12, 15, 16] and is very resistant when cross-linked
in life to form a structural tissue such as that making up the
jaws of polychaete worms [17], which have an extensive fossil
record. Cross-linking processes also occur during the early
stages of fossilization and increase the preservation potential
of a diversity of organic fossils such as cephalopod jaws,
graptolites, microalgae, and the leaves and pollen of land
plants [18, 19].
The transformation of the organic components of living
organisms to molecules that are stable over geological
time is complex, and continues to be the subject of intense
investigation. Some biopolymers such as algaenans, which
occur in the cell walls of green algae, are highly aliphatic,
cross-linked compounds, and are probably preserved with
minimal alteration [20, 21]. Simple lipids are less resistant to
degradation but can be incorporated into macromolecular
structures in fossils or kerogen through various cross-linking
reactions to generate a similar aliphatic composition. Preser-
vation is particularly enhanced where sulfate is available in
aquatic environments. Sulde and polysulde generated by
the respiration activities of sulfate-reducing bacteria (SRBs) are
very effective at reducing labile functional groups and cross-
linking hydrocarbon chains [2224]. The rise of temperature
that occurs when sedimentary rocks are buried deeper in the
earths crust also promotes progressive loss of CO
2
, CH
4
, H
2
O,
N
2
, and other volatiles with the formation of fused carbon rings
(aromatization), and reductions in the proportion of H, O, and
N. As this process continues there is a progressive loss of
chemical structure: weaker bonds are cleaved and stronger
ones form, leading to an increasing concentration of carbon
and ultimately to graphite. Furthermore, internal structure
(within arthropod and plant cuticles, for example) is lost.
Spectacular morphological features of organic remains may
survive, however, despite the loss of signicant chemical
information, when fossils are encapsulated in permineralizing
uids, for example, especially those rich in silica [2530], or
when they are converted to charcoal prior to burial [31, 32].
How does fossilization affect the
chemistry of arthropod cuticle?
Arthropods have been the most diverse and abundant
metazoans on earth since the Cambrian explosion. Few have
a biomineralized skeleton; the great majority of arthropod
cuticles are exclusively organic, made up of a chitinprotein
complex with, in terrestrial forms, an outer waxy layer. Yet
there is a signicant fossil record of cuticular remains, which
provide important evidence of the diversication of arthro-
pods during the Cambrian explosion [33] and of their
importance in early terrestrial ecosystems [34].
Arthropod cuticles can be used to illustrate the fossiliza-
tion of molecules [35]. Many of the chemical components of
cuticles are insoluble in normal solvents, which limits the
analytical techniques that can be applied to them. Pyrolysis-
GCMS (vaporizing material at very high temperatures
and passing it through a gas chromatograph coupled to a
mass spectrometer) of the cuticles of Pleistocene and even
Oligocene (25 mya) beetles generated spectra very similar to
those from living examples: signicant traces of chitin and
protein survive [36]. The search for older evidence of
molecular components is complicated by their chemical
transformation over time (the process of diagenesis) [37]. Few
if any molecules are completely stable on a geological time
scale, and their transformation is hastened by a number of
factors, particularly elevated temperatures and ionizing
radiation. Older samples of arthropod cuticle are dominated
by longer chain molecules (aliphatic or aromatic), indicating
modication of the cuticle composition by some kind of
polymerization process [38, 39]. A similar transformation
affects plant fossils [40]. Traces of cutin and lignocellulose in
young fossil leaves are absent in older ones, where spectra are
dominated by aliphatic or aromatic components.
Pyrolysis of untreated fossil material only detects some of
the molecules that constitute it. When chemical methods are
used to break down the material before it is subjected to
pyrolysis more information about composition and fossiliza-
tion is revealed. Older fossil arthropod cuticles contain a
signicant proportion of lipids, mainly C
16
and C
18
fatty acyl
moieties, indicating that fatty acids are a critical ingredient in
their transformation to hydrocarbons. This is conrmed by
removing fatty acids from cuticles by chemical means before
subjecting them to high temperatures in laboratory experi-
ments: no aliphatic components form and traces of chitin and
protein survive [41].
The synchrotron offers new methods to detect traces of the
original molecular constituents of even Paleozoic arthropod
cuticles traces that are invisible to other methods (Fig. 2).
Samples of cuticle of a Pennsylvanian scorpion (310 mya) and a
5 m
outer
inner
2 m
epoxy
eV
390 395 400 405 410 415 420
pure chitin
modern
scorpion cuticle
Carboniferous
scorpion cuticle
A)
C)
B)
Figure 2. Chemistry of living and Carboniferous scorpion cuticle
revealed in soft X-ray absorption images and XANES (X-ray absorp-
tion near edge structure) spectra generated with the Advanced Light
Source, Lawrence Berkeley Laboratory [42]. A, B: Modern and fossil
scorpion cuticle showing the distribution of nitrogen (enriched in
brighter bands). C: XANES spectra of nitrogen in the cuticle samples
compared with pure chitin. The peak at 403.6eV in the fossil sample
is interpreted as a nitro group formed through the oxidation of
primary amine, which could be derived from chitin and/or protein.
The inset photo is reproduced under the terms of a CC-BY-SA-3.0
license from Wikipedia (creator: Chris huh; http://en.wikipedia.org/
wiki/File:Asian_forest_scorpion_in_Khao_Yai_National_Park.JPG).
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Silurian eurypterid (sea scorpion, 417 mya) were subjected to
X-ray absorption near edge structure spectromicroscopy
(XANES). XANES showed an aliphatic component, but revealed
that more than 50% of the cuticle consists of the original
chitinprotein complex: transformation of the cuticle to an
aliphatic composition is only partial. The aliphatic material that
formed during fossilization appears to have condensed onto a
chitin protein scaffold, obscuring these components to
pyrolysis. XANES spectroscopy revealed the carbon, nitrogen,
and oxygen content [42], which allowed the chitin protein
composition of the cuticle layers to be determined. The
association of degraded chitinprotein and aliphatic polymer
that formed during fossilization results in the long-term
stability and abundance of arthropod cuticles in the fossil
record. Apart from yielding new detailed information on
the chemistry of fossils, synchrotronmethods have the advantage
that they can showlayering in cuticle based on subtle differences
in composition. Such information has the potential to illuminate
the nature and afnities of organic fossils.
Melanin preserves evidence of the
original color of fossil animals
The recent discovery that fossil feathers can preserve the
morphology of the melanosomes within them provides a
method for reconstructing the plumage colors of feathered
dinosaurs and ancient birds [43, 44]. Comparing scanning
electron microscope images of the size, shape, packing, and
distribution of melanosomes in fossil feathers with those from
living birds allows pigment colors (white through gray, black,
brown, and red) to be reconstructed based on plots in
multidimensional space [44]. In some cases the packing of the
melanosomes (e.g. in thin surface lms) may also provide an
indication of structural effects such as iridescence [45]. The
morphological evidence for fossil melanosomes is compelling,
but when they were rst discovered in the early 1980s these
structures were interpreted as bacteria that had colonized
the feather surface [46]. The chemistry of melanin, which is
polymeric and highly cross-linked, indicates that it is likely to
have a high fossilization potential [47]. Thus a melanin
biomarker would provide a test of its presence.
Melanin occurs not only in feathers but in fungi,
cephalopod ink, and a diversity of vertebrate organs and
tissues including eyes and skin, and the brain, inner ear and
hair of mammals. Investigations of fossil melanosomes in
squid ink (162 and 195 mya) (Fig. 3) [47], and ichthyosaur skin
(190196 mya) [48], using a range of analytical techniques,
showed that melanin survives relatively intact in fossils at
least as old as Early Jurassic. Melanin has also been reported
in fossil turtle (55 mya) and mosasaur (86 mya) skin [48], and
in a sh eye (55 mya) [49], as well as in fossil feathers [50].
However, where the sedimentary sequence containing the
fossils has been subjected to elevated temperatures, the
melanin is transformed to a kerogen-like macromolecule and
the characteristic chemistry is blurred or lost altogether [51].
The morphology of the melanosomes/melanin granules,
however, appears largely unaffected by fossilization,
although maturation experiments show that their dimensions
may be altered [52]; this may not affect reconstructions of color
(e.g. [53]).
Biomarkers reveal the presence of
ancient microorganisms
A new approach to identifying the presence of organisms
in soils, sediments, and aquatic environments is by direct
sequencing of their nucleic acid contents, a method pioneered
by Willerslev and others in the early 2000s. It was initially
used to identify changes in the plants and animals present
in Holocene and Pleistocene sediments in permafrost
cores ranging from 20,000 to 400,000 years old [54]. The
method can be calibrated by comparing the oral diversity
revealed by DNA with that represented by pollen [55]. DNA
recovered from marine sediments has revealed dramatic
changes in the plankton communities following sea level
changes in the Black Sea that connected it to the Sea of
Mamara via the Bosporus about 10,000 years ago [56]. A
similar approach can be used to detect the presence of
organisms in seawater samples [57]. Genetic sequences can
be used to determine the diversity of bacteria and fungi in
soils. Most of the taxa detected in a recent investigation of
Quaternary cave deposits [58] are novel and apparently related
to extremophiles (maybe these are most likely to survive).
DNA does not survive long enough to identify the former
presence of bacteria in more ancient sediments, but other
kinds of molecular fossils are diagnostic of particular
microbial groups and the processes they use to extract carbon
and energy. The microbes themselves bacteria, archaea, and
protists are only preserved in exceptional circumstances.
Their membranes are composed of lipids, including fatty
acids, hydrocarbons, alcohols, chlorophyll, and carotenoid
pigments and diverse glycerol esters and glycerol ethers. The
hydrocarbon chains of these membrane lipids have a high
preservation potential. Their chemistry is often diagnostic of
a particular group [59, 60] (Fig. 1), particularly when the
isotopic composition of their carbon, hydrogen, and some-
times nitrogen is taken into account [61, 62]. The structure of
microbial lipids may also vary with the temperature that
prevails as they grow [6366]. The distributions of C
37
long-
chain ketones produced by haptophyte algae, and isoprenoi-
dal tetraether lipids produced by archaea often showexcellent
correlation with sea surface temperatures [67, 68]. Isotopes
are particularly useful for characterizing sources of C and N
and their assimilation pathways in the individual molecules
of autotrophs (e.g. [61, 69]). Molecular-level H-isotopes
in bacterial lipids reect aspects of physiology and bio-
synthesis [70] and those in plants reveal information about
physiology and paleohydrology [71, 72]. Records of history and
behavior are recorded, for example, in isotopic data preserved
in tree ring cellulose (C and H) and the collagen in growth
rings of shark vertebrae (C and N) [73, 74].
Two classes of polycyclic lipids, sterols and hopanoids,
are diagnostic for eukaryotes and bacteria respectively.
Both are derived from squalene via pathways that diverged
once molecular oxygen became available for respiration and
biosynthesis more than 2.4 billion years ago [7578]. Related
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biosynthetic pathways evolved further with the radiation of
vascular plants [79, 80]. Until recently the identication of the
origin of such triterpenoid lipids in sediments was a
painstaking process based largely on phytochemical surveys
and, as necessary, analyses of likely source organisms in
culture collections [80, 81]. Targeted identication of key
genes involved in the synthesis of the lipids, and the use of
genomic tools to query both cultures and environmental
samples for genes of interest, are allowing our knowledge of
the biosynthetic pathways and physiological properties of
lipids diagnostic of particular organisms to be rened [8287].
While genetic data are only available from young sediments
this approach may also improve our ability to identify the
source of biomarkers in older rocks.
Molecules are critical to interpreting the
early history of life on Earth
The application of molecular data in paleontology extends
beyond the information gleaned directly from molecular
fossils themselves. Molecular phylogenies can be used
to estimate the timing of evolutionary transitions. Once
particular diversication events are tied to the geologic time
scale based on rst appearances in the fossil record, the age of
other branching events can be estimated using molecular
distances. Most of the major animal phyla originated during
the Cambrian explosion, and molecular estimates of times
of origin are compatible with the evidence of the fossil
record [88, 89]. Molecular clock estimates of the origin
of sponges, however, indicate a Cryogenian appearance,
>650 mya [4, 90, 91] even though there is no known fossil
record of siliceous spicules to support this early origin [92].
Molecular fossils, as well as spicules or other body
fossils, can provide important evidence of rst appearances,
particularly where fossilization generates a signature molecule
(i.e. a specic biomarker). Such biomarkers are important
Modern Sepia ink
Jurassic ink thermally immature
Jurassic ink thermally mature
A)
D)
E)
F)
C) B)
30 20 10 40 50
3
3
3
2
2
2
1
1
1
4
4
5
5
6
6
7
7
8
8
8
9
9
10
10
10
12
12
11
11
C -C steranes
13
13
14
14
15
cholestadienes
a
b
c, d
c, d
e, f
1.4 cm
1 m
27 29
n-alkanes
1-15: Discrete carbon-, nitrogen- and oxygen-containing
pyrolysis products of melanin
a-f: Sulfur-containing molecules formed from
melanin during fossilization
Figure 3. Chemistry of living and fossil cephalopod ink showing the
effect of increasing thermal maturity during fossilization [47, 51].
A: The cuttlesh Sepia (photo reproduced under the terms of a CC-
BY-SA-3.0 license from Wikipedia; creator: Hans Hillewaert; http://
commons.wikimedia.org/wiki/File:Sepia_ofcinalis_%28aquarium%29.
jpg). B: Ink sac from the Jurassic of Holzmaden, Germany, with SEM
image of melanin granules. C: The belemnite Passaloteuthis from
Holzmaden, showing the ink sac and tentacles (photo reproduced
under the terms of a CC-BY-SA-3.0 license from Wikipedia; creator:
Ghedoghedo; http://commons.wikimedia.org/wiki/File:Passaloteu-
this_bisulcata.JPG). DF: Pyrolysis traces of ink from living Sepia (D),
and from fossil squids from the Jurassic of Lyme Regis, UK (E) and
Holzmaden (F from specimen in B). The Lyme Regis example
shows the peaks characteristic of living Sepia ink whereas the more
thermally mature Holzmaden ink differs signicantly, particularly in the
presence of longer chain aliphatic components.
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where body fossils are not preserved due, for example, to small
size or the lack of a biomineralized skeleton. However, the
search for the earliest biomarkers must take account of the risk
of the migration of soluble organic components (bitumen)
through sedimentary rocks, mobilization that can sometimes
introduce younger contaminants into older rocks. When the
biology, chemistry, and sedimentary geology are well under-
stood, and such contamination can be discounted, the
distribution of biomarkers in ancient sediments can be
informative about the evolutionary history of taxa, including
plankton in the oceans [9398].
Where body fossils are rare in Precambrian rocks, any
evidence for the presence of animal groups is critical. A fossil
molecular marker diagnostic for demosponges, 24-isopropyl-
cholestane, occurs in marine sequences 630540 million
years old in Oman, Siberia, and elsewhere (Fig. 4). This
biomarker is very rare or absent in samples younger than
Cambrian in age [99, 100] probably because the biomass of
sponges is no longer sufcient except in unusual circum-
stances [101]. Research associated with oil and gas exploration
has revealed how sterols are transformed to steranes in
sedimentary rocks and, during deep burial, to mixtures of
steroisomers [102104]. Such an approach allows the precur-
sor of the biomarker 24-isopropylcholestane to be identied as
a sterol characteristic of demosponges [99]. Contrary to some
views [105], an algal source cannot account for the high 24-
iso/24-n-propylcholestane ratios observed in Neoproterozoic-
Cambrian rocks and oils, although a trace of 24-isopropyl-
cholesterol is present with 24-n-propylcholesterol in some
pelagophyte algae [106]. The signicance of this discovery is
twofold: the chemical fossil indicates a 200 my gap in the
PreCambrian fossil record, dubbed missing glass [92] and, in
this case, the chemical fossil may have fossilization potential
in situations where body fossils do not survive.
Conclusions and outlook
Molecular fossils allow us to address a range of questions:
the identity and relationships of extinct organisms, the
biodiversity represented in ancient soils and sediments, the
contribution of different organisms to sedimentary organic
matter and fossil fuels, the environmental conditions that
prevailed in the water column and sediments in the past, and
the thermal history of sedimentary sequences. The analytical
limitations of such investigations are continually being pushed
back by the development of more sophisticated approaches
with ever greater resolution: methods for sequencing ancient
DNA, and the imaging and analytical precision offered by
synchrotron methods are just two examples. As analytical
methods advance, so too does our understanding of the
chemical pathways involved in the formation of molecular
fossils, and the conditions required for their preservation. The
preservation of traces of blood in a fossil mosquito was
unexpected [1]. So too was the recent discovery of biomarkers
characteristic of phytoplankton, green sulfur bacteria, and
sulfate-reducing bacteria in a 380mya concretion from the
Devonian Gogo Formation in Western Australia that contained
mineralized muscle tissue of a possible crustacean [107].
Exceptionally preserved fossils in deposits that have not
undergone deep burial and consequent thermal maturation
may provide a rich, hitherto underexploited, source of
chemical clues to the life of the past. Where modern methods
meet ancient molecules the possibilities are extraordinary.
Acknowledgments
We thank Jane Hall for assistance with manuscript prepara-
tion and gures. We acknowledge the NASA Astrobiology
Institute (NNA13AA90A) Foundations of Complex Life,
Evolution, Preservation, and Detection on Earth and
Beyond. R.E.S. acknowledges additional support from NSF
OISE-1048974.
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Marinoan glaciation (635 million years ago)
Sturtian glaciation (713 million years ago)
Continuous record of Porifera
from >635 to <541 million years ago
635
713
541
Millions
of years
South Oman Salt Basin Fossilization of 24-isopropylcholesterol
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System Lithology
Basement
Shale Evaporite
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approx
500m
20
24
17
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HO
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A) B)
Figure 4. A: Stratigraphy of the South Oman
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