The empires of life

Living individuals all belong to naturally isolated units
called species. Ideally, these species are freely interbreeding
populations that share a common ecological
niche. Even those lowly organisms that disdain sexual
reproduction (such as the silicoflagellates) or do not
have the organization for it (such as the cyanobacteria),
occur in discrete morphological and ecological
species. Obviously it is impossible to prove that a population
of microfossils was freely interbreeding but, if
specimens are sufficiently plentiful, it is possible to
recognize both morphological and ecological discontinuities.
These can serve as the basis for distinguishing
one fossil species from another.
Whereas the species is a functioning unit, the higher
taxonomic categories in the hierarchical system of
classification are mere abstractions, implying varying
degrees of shared ancestry. All species are placed within
a genus that contains one or more closely related
species. These will differ from other species in neighbouring
genera by a distinct morphological, ecological
or biochemical gap. Genera (plural of genus) tend to
be more widely distributed in time and space than do
species, so they are not greatly valued for stratigraphical
correlation. They are, however, of considerable value
in palaeoecological and palaeogeographical studies.
The successively higher categories of family, order and
class (often with intervening sub- or super-categories)
should each contain clusters of taxa with similar grades
of body organization and a common ancestor. They
are of relatively little value in biostratigraphy and
palaeoenvironmental studies. In ‘animals’ the phylum
taxon is defined on the basis of major structural differences,
whereas in ‘plants’ the corresponding division
has been defined largely on structure, life history and
photosynthetic pigments.
An even higher category is the kingdom. In the
nineteenth century it was usual to recognize only
the two kingdoms: Plantae and Animalia. Plants were
considered to be mainly non-motile, feeding by
photosynthesis. Animals were considered to be motile,
feeding by ingestion of pre-formed organic matter.
Although these distinctions are evident amongst
macroscopic organisms living on land, the largely
aqueous world of microscopic life abounds with
organisms that appear to straddle the plant–animal
boundary. The classification shown in Box 1.1 overcomes
these anomalies by recognizing seven kingdoms:
the Eubacteria, Archaebacteria, Protozoa, Plantae,
Animalia, Fungi and Chromista.
The highest category is the empire. The Bacteria are single celled but they lack a nucleus, cell vacuoles and organelles. This primitive prokaryotic condition, in which proper sexual
reproduction is unknown, is characteristic of such
forms as cyanobacteria. The empire is currently
divided into two kingdoms, the Archaebacteria and
the Eubacteria. The other five kingdoms are eukaryotic.
That is their cells have a nucleus, vacuoles and
other organelles and are capable of properly coordinated
cell division and sexual reproduction. Attempts
to divide unicellular eukaryotic organisms, often
called protists, into plants or animals based on feeding
style were abandoned when it was recognized that
dinoflagellates, euglenoids and heterokonts have
members that are both photosynthetic and heterotrophic,
feeding by engulfing. Since the 1970s both
ultrastructural analysis under the scanning electron
microscope and molecular sequences have been used
to elucidate protistan phylogenies and develop a largescale
classification. The new classification of Cavalier-
Smith (1981, 1987a, 1987b, 2002) has put forward two
new categories: the predominantly photosynthetic kingdom
Chromista (brown algae, diatoms and their various
relatives) and the primitive superkingdom Archezoa
(which lack mitochondria (amitochondrial)). He has
also proposed an ultrastructurally based redefinition
of the kingdom Plantae which requires the exclusion
of many aerobic protists that feed by ingestion
(phagotropy). The kingdom Protozoa is now considered
to contain as many as 18 phlya (Cavalier-Smith
1993, 2002) and their classification and phylogenetic
relationships, which is in a state of flux, is largely based
upon cell ultrastructure and increasingly sophisticated
analyses of new molecular sequences. The kingdom
Protozoa includes two subkingdoms, the Gymnomyxa
and Corticata. Members of the Gymnomyxa have a
‘soft’ cell wall often with pseudopodia or axopodia
(e.g. foraminifera). The Corticata are ancestorally
biciliate (e.g. dinoflagellates).
Members of the superkingdom Archezoa differ from
most Protozoa in having ribosomes, the RNA-protein
structures on which messenger RNA is ‘read’ during
protein synthesis, found in all other eukaryotes, and
they also lack certain other organelles (e.g. mitochondria,
Golgi bodies). The Archezoa comprise three phyla:
the Archamoebae, Metamonada and Microsporidia.
There is reasonable rDNA phylogenetic evidence to
suggest that the latter two represent surviving relics of
a very early stage in eukaryote evolution. The evolution
of the eukayotes can thus be divided into two
major phases. The origin of the eukaryote cell (the
first archezoan) is marked by the appearance of the
membrane-bounded organelles, cytoskeleton, a threedimensional
network of fibrous proteins that give
order and structure in the cytoplasm, nucleus and cilia
with a 9+2 structure. This was apparently followed
by the symbiotic origin of mitochondria and
peroxisomes (Margulis 1981; Cavalier-Smith 1987c)
to produce the first aerobically respiring protozoan.
The change in their ribosomes may have occurred
somewhat later in their evolution.
The kingdom Chromista is a predominantly photosynthetic
category in which the chromoplasts are
located in the endoplasmic reticulum but separated
by a unique smooth membrane, thought to be a relic
of the cell membrane of the photosynthetic eukaryotic
symbiont that was ‘engulfed’ by the protozoan
host, leading to the emergence of the Chromista
(Cavalier-Smith 1981, 1987c). The Chromista contains
a number of important microfossil groups
such as the silicoflagellates, diatoms and calcareous
nannoplankton.
The kingdon Plantae is taken to comprise two subkingdoms.
The subkingdom Viriplantae includes the green plants including the green algae (Chlorophyta),
the Charophyta and the ‘land plants’ or the Embryophyta.
The subkingdom Biliphyta includes the red algae
(Rhodophyta) and the Glaucophyta. It is not yet clear
whether these two subkingdoms are correctly placed
together in a single kingdom or should be separate
kingdoms. The Viriplantae have starch-containing
chloroplasts and contain chlorophylls a and b. The
Biliphyta have similar chloroplasts but there is a total
absence of phagotrophy in this group.
The kingdom Fungi comprises heterotrophic
eukaryotes that feed by the adsorption of pre-formed
organic matter. They are rarely preserved in the fossil
record and have received little study as fossils and are
not considered further in this book.
The kingdom Animalia comprises multicellular
invertebrate and vertebrate animals that feed by the
ingestion of pre-formed organic matter, either alive or
dead. Invertebrates that are microscopic when fully
grown, for example the ostracods, are considered as
microfossils, but we are obliged to leave aside the
microscopic remains of larger animals (such as sponge
spicules, echinoderm ossicles and juvenile individuals).