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At a Glance
Systematics/Systematic Biology:
Biological information organized
in a taxonomic or phylogenetic
manner.
Phylogeny: The natural,
evolutionary relationships
between groups of living things,
inferred using a variety of
techniques to establish the
relative importance of various
shared features (apomorphies and
plesiomorphies).
Taxonomy:The science of
organizing (= classifying)
living things into groups
reflecting their natural,
phylogenetic relationships. Such
groups are called taxa (sing.
taxon).
Nomenclature: The
assignment of correct names to
taxa.
Introduction
The systematic classification of
living, or once living, things –
which these days is encouraged
to be consistent with their
presumed evolutionary
relationships (“phylogeny”) – is
called taxonomy. Naming them, an
exacting pursuit in itself, is
called nomenclature. Systematics
is where taxonomy and
nomenclature meet; biological
reviews which organise their
material in a taxonomic or
phylogenetic manner are referred
to as “systematic.”
Phylogeny
Phylogeny is the true
evolutionary relationships
between groups of living things.
The adjective is phylogenetic
and the study of phylogeny is
phylogenetics.
It is intuitively obvious that
there exists a hierarchy of
phylogenetic relationships among
living things. Different kinds
of cat are clearly more similar
to one another than to any of
the various kinds of dog, and
vice versa. Moreover, cats and
dogs are clearly more similar to
each other than either is to a
frog, or a fish, or a housefly.
In fact, using intuition alone,
we can easily construct a
hierarchy of similarities among
these groups of animals, such as
that shown in fig. 1, with which
few would argue. Such an
illustration is called a
cladogram.
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Fig. 1: Intuitive relationships between some familiar animals. |
Unfortunately, when the broader
range of living things is
considered, intuition quickly
fails us. Is a sea snail more
like a crab, or a starfish?* To
answer questions like this,
organisms must be analysed in
great detail, and the
similarities carefully evaluated
to determine their phylogenetic
significance, if any. The
process is subjective, and
today's “truth” is always
provisional.
It might seem that the comparison
of gene sequences between taxa
can provide an objective measure
of similarity. Perhaps, one day,
it may be so. For the present,
unfortunately, genetic evidence
is as open to interpretation as
any other.
* The view today is that the
most fundamental division within
the bilateral animals is between
the protostomes and the
deuterostomes. Both sea snails
(which are types of mollusc) and
crabs (which are arthropods) are
protostomes, whereas starfish
(echinoderms) are deuterostomes.
Thus snails are more like crabs
than starfish.
Taxonomy
The science of organizing living
things into groups which reflect
their natural, phylogenetic
relationships, is called
taxonomy. The groups are called
taxa (sing. taxon, see below).
The division of familiar objects
into animal, vegetable and
mineral probably dates back to
prehistory, and it is
commonplace to hear the phrase
“animal kingdom” or “plant
kingdom.” Most students will be
aware, also, of the landmark
contribution made by the Swedish
naturalist, Carolus Linnaeus
(and variations on that
spelling) in the mid-1700s.
Today we still use a derived
form of the categories first
published by Linnaeus, although
much of the detail has changed.
For example, many single-celled
organisms – none of which were
known to Linnaeus – are regarded
as belonging to a kingdom of
their own, the Protista, which
stands alongside the Animalia
and Plantae. The fungi are no
longer considered plants; they
too have a kingdom to
themselves.
Most surprising, however, was the
discovery arising from genetic
studies that protists, plants,
animals and fungi, collectively
known as the Eucarya, are all
relatively similar to one
another, compared to the far
more fundamental differences
dividing them from two great
lineages of bacteria, the
Archaea and the Bacteria. These
three “domains” – the Archaea,
Bacteria and Eucarya – are now
considered the most fundamental
divisions of living things.
From highest (most inclusive) to lowest (most specific), the major formal
taxonomic units, or “ranks” are:
- Domain
(= Superkingdom)
- Kingdom
- Phylum (often called a
“Division” in botany)
- Class
- Order
- Family
- Genus
- Species
Intermediate divisions are often used, “subspecies” and “variety”
being very commonly employed at the lower end. |
| Taxonomic Units (or ranks) |
Taxon (pl. Taxa)
The published groups within each
of the divisions in the
phylogenetic hierarchy is known
as a taxon. Like the
relationships themselves, taxa
fall into a hierarchy.
The lowest level taxon in most
cases is the familiar species,
which one can informally think
of as a group of organisms which
are so closely related that they
can inter-breed freely. (This
concept obviously fails for
organisms which reproduce
asexually, and in other
circumstances also, but it is
sufficient for now.
Above the species level, grouping
together similar species, is the
genus (pl. genera). A familiar
example of a genus is Pinus, to
which several different but
related species of pine tree
belong. Above that again is the
family, and so on.
Identification
To identify an organism is to
determine which taxon it belongs
to. An “accurate” identification
is not only correct, but will
identify an organism with a
particular species.
However, it is not at all
unusual, in practice, that an
identification can only be made
to genus or even higher level.
There are many possible reasons.
Perhaps the organism being
identified is incomplete; some
part (e.g. a flower) which is
necessary for a completely
accurate identification is not
present. This problem is
particularly acute when it comes
to identifying fossils, which
are more commonly fragmentary
than not. In some cases, the
species may not have been
previously recognized, or even
if recognized, not formally
published.
In such cases, a relationship to
a similar species which has been
described might be indicated
with an aff. indicating
“;affinity to,” or the
less confident cf.
meaning “compare with.”
Nomenclature
In order to communicate
biological information, it is
essential to have universally
understood “name tags” for the
biological entities we are
referring to. This labeling is
theoretically possible by means
of formulas or letters, though
they are not euphonious and
would be mnemonically difficult
for most people. Instead,
Latinized names are employed.
“The purpose of formal
nomenclature is to provide a
precise, simple, and stable
system of unique names used by
scientists in all countries. The
system must allow for reasonable
expansion and refinement to
accommodate increasing
knowledge. In other words, the
stability must not become a
straitjacket” (Traverse 1996, p.
13).
Homonyms and Synonyms
Homonyms are identical
names for two different taxa.
Synonyms are different
names for the same taxon.
Neither can be tolerated in a
rational nomenclature. As a
general rule, when these
situations arise it is the first
name to be published which is
retained. However, the correct
outcome is not always obvious
because the distinction between
taxa is often quite subjective.
In fact, there are colloquial
terms in common usage for
scientists to tend to create
inclusive taxa, with quite broad
accommodation for variety (they
are called “lumpers”) as
opposed to those who subdivide
very finely, creating taxa which
accommodate very little
variation at all (“splitters”).
And, in fact, there is no
“right” answer: man classifies;
nature does not.
Cladistics
As we have seen, phylogeny is
the evolutionary relationships
among organisms. The patterns of
lineage branching produced by
the true evolutionary history of
the organisms being considered
comprise a hierarchy, for which
the common metaphor is a tree.
We often hear reference to a
family tree, or even a branch of
a family tree, in our daily
lives.
A branch on such a tree is
defined by context: we may be
referring to a single twig which
has no dependent parts, or to
quite a large branch which has
many smaller branchlets or twigs
depending from it. In either
case, such a branch is called a
“clade.”
“Cladistics” is the word
we give to the study of clades,
and it is not substantively
different from phylogenetics
- the study of phylogeny. If
there is any useful difference
at all, it is a matter of
emphasis: whether upon lineages
(cladistics) or
relationships (phylogenetics).
Outgroup
We have seen above that a clade
is a branch on a tree of
descent. Anything occurring
outside that branch, further
towards the root of the tree, is
an outgroup.
The distinction is more than
simply contextual: For example,
in order to calculate the
similarity of genome sequences,
it is essential to include
within the study one or,
preferably, several taxa that
lie outside the group in which
we are trying to detect
relationships. If we are
interested in determining the
relationships of tigers, we
would use close relatives of
tigers as our outgroups.
Outgroup comparison is
the way we determine how
widespread a particular feature
may be, whether it is found only
within the group (apomorphies)
of interest, or beyond that
group.
Monophyly (Monophyletic
Group)
A monophyletic group is one
which includes an ancestral
species and all its descendants.
It is a complete clade.
As we have seen, a monophyletic
group can be extremely large and
inclusive – for example, most
people today would agree the
legions of different kinds of
insects comprise a monophyletic
group – or quite small and
exclusive – ex: the
enigmatic sea spiders (class Pycnogonida)
Paraphyly (Paraphyletic
Group)
A paraphyletic group is a clade
lacking some of the descendant
species.
Today there is a movement away
from applying formal names to
groups which are known to be
paraphyletic, although some of
the old taxa are still very
useful even though they are now
believed to be paraphyletic.
Perhaps the best example is the
reptiles. Because both mammals
and birds evolved from reptilian
ancestors, but are not included
in the class Reptilia, the
latter is clearly paraphyletic
and a cladistic purist might
prefer not to use the name.
However, the meaning and scope
of the reptile class is still a
very well understood and useful
concept.
What is more, if we were to
blindly enforce “Russian doll
nomenclature” in this fashion,
it seems unlikely the existing
hierarchy of taxonomic ranks
will cope.
Polyphyly (Polyphyletic
Group)
A polyphyletic taxon is an
“unnatural” assemblage of two or
more clades, united by some
characteristic which is not a
primitive feature (plesiomorphy).
Groupings which are thought to
be polyphyletic truly are
avoided by taxonomists, which is
one reason there are not too
many familiar real examples. An
artificial example is “warm
blooded animals,” a group which
includes both mammals and birds.
However, both these groups
arose, at different times, from
cold-blooded (reptilian) stock:
their warm-bloodedness is not an
apomorphy, but it evolved
separately, and is different in
detail.
Again, however, all is not plain
and simple. Some taxa, even
those with a long history of
study such as the arthropods,
are still subject to on-going
controversy. Although most
researchers are of the view that
the Arthropoda are a "good"
monophyletic clade, there remain
a few who argue that the
arthropod characteristics were
arrived at separately by more
than one lineage, and thus the
group is polyphyletic. They are
in a small minority, but some
small doubt remains.
References
Nielsen, Claus 2000 Animal
Evolution. Second Edition. 563
pp. Oxford University Press.
Traverse, A. 1996: Nomenclature
and Taxonomy: Systematics. In
Jansonius, J.; McGregor, D.C.
(eds.) 1996: Palynology:
Principles and Applications.
American Association of
Stratigraphic Palynologists
Foundation, v. 1: 11-28.
Tudge, Colin 2000: The Variety
of Life. Oxford.
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