At the European Molecular Biology Laboratory in Heidelberg, Germany, Peer Bork’s
research group has meticulously reconstructed a new tree of life – tracing the course of
evolution. Russ Hodge explains.
In the margins of one of Charles Darwin’s notebooks is a small, twig-like drawing –
unimpressive until you realise that it represents an enormous intellectual leap, a milestone in
human history. It is the first modern sketch of a tree of life, representing the fact that distinct
species had common ancestors. For a century, naturalists had collected facts about species,
naming them and grouping them according to their similarities. Darwin suddenly understood
that the similarities represented familial relationships.
Haeckel's Tree of Life
The German biologist Ernst Haeckel (1834 - 1919) was a noted scientific illustrator
and the first great popularizer of Darwin's Theory of Evolution. His "General
Morphology - founded on the the Descent Theory" traced the origin of all life to
Moneren, and first suggested that the ancestry of humans was among the Great
Apes. Note the position of Menschen ("men") at the very top of the tree, among the
Affen ("apes").
The first detailed evolutionary tree was published in 1866 in Haeckel's General Morphology of
Organisms. Haeckel organized all creatures, including man, into families, genera, and species on the
basis of progressive skeletonization. Rudolf Virchow applauded Haeckel's accomplishment:
"anthropology has become part of zoology." However, Haeckel's arrangement of organisms on an
ascending scale of development led to serious social and political misuse by Eugenicists and Nazis.
Two decades later, another tree was meticulously composed
by Ernst Haeckel, the great German naturalist and
embryologist and a fanatical admirer of Darwin. Haeckel’s
chart attempts to synthesize the plant and animal kingdoms
into a single genealogical record of life on Earth. He got a lot
of things right, but the tree goes back only so far. Once it
reached one-celled organisms, he was stuck – scientists were
only beginning to glimpse the amazing variety of such
species alive on Earth; they certainly didn’t know enough to
make a convincing phylogeny stretching back before the
divergence of plants and animals.
Since then, scientists have filled in branches and twigs,
climbed down the trunk, and pushed deeply into the roots,
drawing on the written record of evolution that is preserved
in DNA. Still, questions remain, particularly with regard to
the early history of life on Earth. Peer Bork’s group at the
Haeckel’s tree of life from
European Molecular Biology Laboratory in Heidelberg,
The Evolution of Man (1879)
Germany, has now finished the highest-resolution tree of
evolution that has yet been made. It may never be final –
millions of species surely remain to be found, and those we
know will continue to evolve. But it fills in many of the gaps,
and will help scientists sort out fragmentary clues of the
existence of new organisms. It also sheds light on the very
early history of life on Earth.
Early in Earth’s history, there existed an organism that would give rise to all the species
known today. In 1994, Christos Ouzounis and Nikos Kyrpides gave this shadowy creature a
name: LUCA, for the last universal common ancestor. Studies of DNA sequences taken from
plants, fungi, animals, bacteria, and another form of one-celled organism called Archaea
proved that it must have existed. But until recently, scientists could say very little else about
it.
“Two things have changed,” Peer says. “First is the immense amount of information we have
from DNA sequencing – over 350 organisms have been completely sequenced, spread across
the entire spectrum of life. This gives us a huge amount of data that can be compared to make
a good tree and also to answer some questions about LUCA. Certain key genes can be found
in all of them, and the chemical ‘spelling’ of these genes permits us to group them into
families and historical relationships.”
It also allows researchers to reconstruct hypothetical ancestors. A fundamental principle of
evolution, called the principle of common descent, states that if two organisms share features,
it is almost always because they inherited the characteristics from a common ancestor. So by
comparing existing species, scientists can obtain a picture of more ancient forms of life.
"Over the past few decades, scientists have realised there is an important exception to this
rule,” Peer says. “Bacteria can swap genes with each other, and sometimes they can even
steal a gene from a plant or an animal. Once that has happened, they pass the gene on to their
descendents. Such genes have a completely different profile to genes inherited the normal
way. It’s like finding a branch from a tree that grows crosswise and fuses into another
branch.”
Peer says that attempts have been made to find such genes and eliminate them when building
trees from DNA sequence data. But no one knew how often such events, called horizontal
gene transfer (HGT), happened, or had developed a convincing method for finding them.
“For a while, it was almost as if the amount of data was increasing the problem rather than
solving it,” Peer says. “There were big debates, and the numbers of classifications were
growing rather than reaching a consensus.” Part of the problem lay in the fact that the work
could only be done by computer in a highly automated way, due to the incredible amount of
genomic data that had to be sifted through.
Francesca Ciccarelli, a postdoc in Peer’s group, decided to tackle the problem of the tree
anew and find a solution to the problem of the HGTs. She started by combing the complete
genomes of 191 species for unique orthologues – genes in different species that had evolved
from a common ancestral gene. The task was difficult because it couldn’t be completely
automated. Francesca found 36 cases, five of which seemed to have been shuffled around
through HGTs and were thus discarded.
Eliminating these from the analysis, the scientists could now build a complete tree by
combining information from 31 genes. Peer was worried that some HGTs might have still
have slipped in – a single mistake could spoil the quality of the tree. So the scientists put the
computer to work doing some heavy lifting. The 31 genes were randomly divided into four
groups. Trees were systematically drawn over and over again, for all of the genes in each
group, with the exception of a single gene that was eliminated in each round. Then the results
were compared. If the branches of the trees changed from pass to pass, an HGT was likely to
be involved, and the gene was submitted to two more tests. In the end, the scientists found
seven more candidates for HGTs, which they eliminated from their analysis.
The remaining information was combined into a super-tree
which was compared once again to trees based on individual
genes in three different ways. “Any one of these methods on
its own might have left a tree with some mistakes,” Peer
says, “but by combining them, we’re confident that we have
an extremely accurate picture of the evolutionary history of
these molecules and the species.”
The new tree of life includes
all three domains of life:
Archaea, Bacteria and
The results clear up some old controversies, for example, a
debate about the very early evolution of animals. Some trees
in the past proposed that the vertebrates (which include
humans) split off from another branch which would remain
united for a while before splitting into separate branches
leading to worms and insects. The new version groups things
Eukaryota. There are so
many species that the tree
has to be drawn in a circle
differently: vertebrate and insect ancestors split off from the
worms together, and diverge from each other later.
The higher resolution of the tree is also important, Peer says, because of metagenomic studies
which are underway to sequence all the genes found in environments such as farm soil or
ocean water. His group has participated in several such projects. ”Most sequencing
approaches start with a given organism and work through its whole genome systematically,”
he says. “Metagenomics is sequencing a place – like a global positioning system coordinate.
In many cases we recover fragmentary traces of thousands of genes, and have no idea what
organism they come from. Often these molecules represent creatures that have never been
seen before.” The breadth and detail of the new tree will allow scientists to make much better
guesses about where such fragments fit in and what types of living beings they belong to.
Has the living world been fairly split up into major branches, limbs, and twigs, or have we
overemphasized the prominence of our own lineage? A close look at the new tree shows that
the latter seems to be the case. The eukaryotes, which include yeast, plants and animals such
as ourselves, are so visibly different from one another that scientists have pushed them apart
from each other on the tree. Genetically speaking, however, the species are often much more
closely related than many single-celled forms of life.
“Smaller genomes evolve faster,” Peer says. “There isn’t a single organism that has been
sequenced that is both evolving fast and has a large genome. It suggests that some of the
simplest species around have ended up that way because they have pruned things down.
Evolution isn’t always about acquiring complexity.”
The study also gives the scientists a closer look at LUCA. “One very big question has been
what the earliest bacteria were like when they split off from the Archaea. Bacteria are
grouped into two classes, called Gram-positive and Gram-negative, based on features of their
membranes. The new tree reveals that Gram-positive bacteria evolved first. And if you look
at their repertoire of genes, they seem to be suited to a very hot environment. The first
Archaea were discovered in hot ocean vents, and most of the species alive today are
thermophilic. It strongly suggests that LUCA was, too.”
Definition
Classification has been defined by Mayr as "The arrangement of entities in a hierarchical
series of nested classes, in which similar or related classes at one hierarchical level are
combined comprehensively into more inclusive classes at the next higher level." A class is
defined as "a collection of similar entities", where the similarity consists of the entities
having attributes or traits in common.[1]
What makes biological classification different from other classification systems (e.g.
classifying books in a library) is evolution: the similarity between organisms placed in the
same taxon is not arbitrary, but is instead a result of shared descent from their nearest
common ancestor. Accordingly, the important attributes or traits for biological classification
are 'homologous', i.e., inherited from common ancestors.[2] These must be separated from
traits that are analogous. Thus birds and bats both have the power of flight, but this similarity
is not used to classify them into a taxon (a "class"), because it is not inherited from a common
ancestor. In spite of all the other differences between them, the fact that bats and whales both
feed their young on milk is one of the features used to classify both of them as mammals,
since it was inherited from a common ancestor(s).
Determining whether similarities are homologous or analogous can be difficult. Thus until
recently, golden moles, found in South Africa, were placed in the same taxon (insectivores)
as Northern Hemisphere moles, on the basis of morphological and behavioural similarities.
However, molecular analysis has shown that they are not closely related, so that their
similarities must be due to convergent evolution and not to shared descent, and so should not
be used to place them in the same taxon.[3]
[edit] Taxonomic ranks
Main article: Taxonomic rank
A classification, as defined above, is necessarily hierarchical. In a biological classification,
rank is the level (the relative position) in a hierarchy. (Rarely, the term "taxonomic category"
is used instead of "rank".) There are seven main ranks defined by the international
nomenclature codes: kingdom, phylum/division, class, order, family, genus, species.
"Domain", a level above kingdom, has become popular in recent years, but has not been
accepted into the codes.
The most basic rank is that of species, the next higher is genus, and then family. Ranks are
somewhat arbitrary, but hope to encapsulate the diversity contained within a group — a
rough measure of the number of diversifications that the group has been through.[4]
The International Code of Zoological Nomenclature defines rank, in the nomenclatural sense,
as:
The level, for nomenclatural purposes, of a taxon in a taxonomic hierarchy (e.g. all families
are for nomenclatural purposes at the same rank, which lies between superfamily and
subfamily). The ranks of the family group, the genus group, and the species group at which
nominal taxa may be established are stated in Articles 10.3, 10.4, 35.1, 42.1 and 45.1.[5]
There are slightly different ranks for zoology and for botany, including subdivisions such as
tribe.
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d
e
Taxonomic ranks
[edit] Early systems
[edit] Ancient through medieval times
Aristotle, 384–322 BC.
Current systems of classifying forms of life descend from the thought presented by the Greek
philosopher Aristotle, who published in his metaphysical works the first known classification
of everything whatsoever, or "being". This is the scheme that gave such words as 'substance',
'species' and 'genus' and was retained in modified and less general form by Linnaeus.
Aristotle also studied animals and classified them according to method of reproduction, as did
Linnaeus later with plants. Aristotle's animal classification was eventually made obsolete by
additional knowledge and forgotten.
The philosophical classification is in brief as follows:[6] Primary substance is the individual
being; for example, Peter, Paul, etc. Secondary substance is a predicate that can properly or
characteristically be said of a class of primary substances; for example, man of Peter, Paul,
etc. The characteristic must not be merely in the individual; for example, being skilled in
grammar. Grammatical skill leaves most of Peter out and therefore is not characteristic of
him. Similarly man (all of mankind) is not in Peter; rather, he is in man.
Species is the secondary substance that is most proper to its individuals. The most
characteristic thing that can be said of Peter is that Peter is a man. An identity is being
postulated: "man" is equal to all its individuals and only those individuals. Members of a
species differ only in number but are totally the same type.
Genus is a secondary substance less characteristic of and more general than the species; for
example, man is an animal, but not all animals are men. It is clear that a genus contains
species. There is no limit to the number of Aristotelian genera that might be found to contain
the species. Aristotle does not structure the genera into phylum, class, etc., as the Linnaean
classification does.
The secondary substance that distinguishes one species from another within a genus is the
specific difference. Man can thus be comprehended as the sum of specific differences (the
"differentiae" of biology) in less and less general categories. This sum is the definition; for
example, man is an animate, sensate, rational substance. The most characteristic definition
contains the species and the next most general genus: man is a rational animal. Definition is
thus based on the unity problem: the species is but one yet has many differentiae.
The very top genera are the categories. There are ten: one of substance and nine of
"accidents", universals that must be "in" a substance. Substances exist by themselves;
accidents are only in them: quantity, quality, etc. There is no higher category, "being",
because of the following problem, which was only solved in the Middle Ages by Thomas
Aquinas: a specific difference is not characteristic of its genus. If man is a rational animal,
then rationality is not a property of animals. Substance therefore cannot be a kind of being
because it can have no specific difference, which would have to be non-being.
The problem of "being" occupied the attention of scholastics during the time of the Middle
Ages. The solution of St. Thomas, termed the analogy of being, established the field of
ontology, which received the better part of the publicity and also drew the line between
philosophy and experimental science. The latter rose in the Renaissance from practical
technique. Linnaeus, a classical scholar, combined the two on the threshold of the neoclassicist revival now called the Age of Enlightenment.
[edit] Renaissance through Age of Reason
Rhinoceros in Conrad Gesner's Historiae animalium, 1551
An important advance was made by the Swiss professor, Conrad von Gesner (1516–1565).
Gesner's work was a critical compilation of life known at the time.
The exploration of parts of the New World by Europeans produced large numbers of new
plants and animals that needed descriptions and classification. The old systems made it
difficult to study and locate all these new specimens within a collection and often the same
plants or animals were given different names simply because there were too many species to
keep track of. A system was needed that could group these specimens together so they could
be found; the binomial system was developed based on morphology with groups having
similar appearances. In the latter part of the 16th century and the beginning of the 17th,
careful study of animals commenced, which, directed first to familiar kinds, was gradually
extended until it formed a sufficient body of knowledge to serve as an anatomical basis for
classification. Advances in using this knowledge to classify living beings bear a debt to the
research of medical anatomists, such as Fabricius (1537–1619), Petrus Severinus (1580–
1656), William Harvey (1578–1657), and Edward Tyson (1649–1708). Advances in
classification due to the work of entomologists and the first microscopists is due to the
research of people like Marcello Malpighi (1628–1694), Jan Swammerdam (1637–1680), and
Robert Hooke (1635–1702). Lord Monboddo (1714–1799) was one of the early abstract
thinkers whose works illustrate knowledge of species relationships and who foreshadowed
the theory of evolution.[7]
[edit] Early methodists
Since late in the 15th century, a number of authors had become concerned with what they
called methodus, (method). By method authors mean an arrangement of minerals, plants, and
animals according to the principles of logical division. The term Methodists was coined by
Carolus Linnaeus in his Bibliotheca Botanica to denote the authors who care about the
principles of classification (in contrast to the mere collectors who are concerned primarily
with the description of plants paying little or no attention to their arrangement into genera,
etc.). Important early Methodists were Italian philosopher, physician, and botanist Andrea
Caesalpino, English naturalist John Ray, German physician and botanist Augustus Quirinus
Rivinus, and French physician, botanist, and traveller Joseph Pitton de Tournefort.
Andrea Caesalpino (1519–1603) in his De plantis libri XVI (1583) proposed the first
methodical arrangement of plants. On the basis of the structure of trunk and fructification he
divided plants into fifteen "higher genera".
John Ray (1627–1705) was an English naturalist who published important works on plants,
animals, and natural theology. The approach he took to the classification of plants in his
Historia Plantarum was an important step towards modern taxonomy. Ray rejected the system
of dichotomous division by which species were classified according to a pre-conceived,
either/or type system, and instead classified plants according to similarities and differences
that emerged from observation.
Both Caesalpino and Ray used traditional plant names and thus, the name of a plant did not
reflect its taxonomic position (e.g. even though the apple and the peach belonged to different
"higher genera" of John Ray's methodus, both retained their traditional names Malus and
Malus Persica respectively). A further step was taken by Rivinus and Pitton de Tournefort
who made genus a distinct rank within taxonomic hierarchy and introduced the practice of
naming the plants according to their genera.
Augustus Quirinus Rivinus (1652–1723), in his classification of plants based on the
characters of the flower, introduced the category of order (corresponding to the "higher"
genera of John Ray and Andrea Caesalpino). He was the first to abolish the ancient division
of plants into herbs and trees and insisted that the true method of division should be based on
the parts of the fructification alone. Rivinus extensively used dichotomous keys to define
both orders and genera. His method of naming plant species resembled that of Joseph Pitton
de Tournefort. The names of all plants belonging to the same genus should begin with the
same word (generic name). In the genera containing more than one species the first species
was named with generic name only, while the second, etc. were named with a combination of
the generic name and a modifier (differentia specifica).
Joseph Pitton de Tournefort (1656–1708) introduced an even more sophisticated hierarchy of
class, section, genus, and species. He was the first to use consistently the uniformly
composed species names that consisted of a generic name and a many-worded diagnostic
phrase differentia specifica. Unlike Rivinus, he used differentiae with all species of polytypic
genera.
[edit] Linnaean taxonomy
Main article: Linnaean taxonomy
Carolus Linnaeus
Carolus Linnaeus' great work, the Systema Naturæ (1st ed. 1735), ran through twelve editions
during his lifetime. In this work, nature was divided into three kingdoms: mineral, vegetable
and animal. Linnaeus used five ranks: class, order, genus, species, and variety.
He abandoned long descriptive names of classes and orders still used by his immediate
predecessors (Rivinus and Pitton de Tournefort) and replaced them with single-word names,
provided genera with detailed diagnoses (characteres naturales), and combined numerous
varieties into their species, thus saving botany from the chaos of new forms produced by
horticulturalists.
Linnaeus is best known for his introduction of the method still used to formulate the scientific
name of every species. Before Linnaeus, long many-worded names (composed of a generic
name and a differentia specifica) had been used, but as these names gave a description of the
species, they were not fixed. In his Philosophia Botanica (1751) Linnaeus took every effort
to improve the composition and reduce the length of the many-worded names by abolishing
unnecessary rhetorics, introducing new descriptive terms and defining their meaning with an
unprecedented precision. In the late 1740s Linnaeus began to use a parallel system of naming
species with nomina trivialia. Nomen triviale, a trivial name, was a single- or two-word
epithet placed on the margin of the page next to the many-worded "scientific" name. The only
rules Linnaeus applied to them was that the trivial names should be short, unique within a
given genus, and that they should not be changed. Linnaeus consistently applied nomina
trivialia to the species of plants in Species Plantarum (1st edn. 1753) and to the species of
animals in the 10th edition of Systema Naturæ (1758).
By consistently using these specific epithets, Linnaeus separated nomenclature from
description. Even though the parallel use of nomina trivialia and many-worded descriptive
names continued until late in the eighteenth century, it was gradually replaced by the practice
of using shorter proper names consisting of the generic name and the trivial name of the
species. In the nineteenth century, this new practice was codified in the first Rules and Laws
of Nomenclature, and the 1st edn. of Species Plantarum and the 10th edn. of Systema
Naturae were chosen as starting points for the Botanical and Zoological Nomenclature
respectively. This convention for naming species is referred to as binomial nomenclature.
Today, nomenclature is regulated by Nomenclature Codes, which allows names divided into
taxonomic ranks.
[edit] Modern system
Main articles: Evolutionary taxonomy and Phylogenetic nomenclature
Evolution of the vertebrates at class level, width of spindles indicating number of families.
Spindle diagrams are typical for Evolutionary taxonomy
The same relationship, expressed as a cladogram typical for cladistics
Whereas Linnaeus classified for ease of identification, the idea of the Linnaean taxonomy as
translating into a sort of dendrogram of the Animal- and Plant Kingdoms was formulated
toward the end of the 18th century, well before the On the Origin of Species was published.
Among early works exploring the idea of a transmutation of species was Erasmus Darwin's
1796 Zoönomia and Jean-Baptiste Lamarck's Philosophie Zoologique of 1809. The idea was
popularised in the Anglophone world by the speculative, but widely read Vestiges of the
Natural History of Creation, published anonymously by Robert Chambers in 1844.[8]
With Darwin's theory, a general acceptance that classification should reflect the Darwinian
principle of common descent quickly appeared. Tree of Life representations became popular
in scientific works, with known fossil groups incorporated. One of the first modern groups
tied to fossil ancestors were birds. Using the then newly discovered fossils of Archaeopteryx
and Hesperornis, Thomas Henry Huxley pronounced that they had evolved from dinosaurs, a
group formally named by Richard Owen in 1842.[9] The resulting description, that of
dinosaurs "giving rise to" or being "the ancestors of" birds, is the essential hallmark of
evolutionary taxonomic thinking. As more and more fossil groups were found and recognized
in the late 19th and early 20th century, palaeontologists worked to understand the history of
animals through the ages by linking together known groups[10] With the modern evolutionary
synthesis of the early 1940s, an essentially modern understanding of evolution of the major
groups was in place. The evolutionary taxonomy being based on Linnaean taxonomic ranks,
the two terms are largely interchangeable in modern use.
Since the 1960s a trend called cladistic taxonomy (or cladistics or cladism) has emerged,
arranging taxa in a hierarchical evolutionary tree, ignoring ranks. If a taxon includes all the
descendants of some ancestral form, it is called monophyletic. Groups that have descendant
groups removed from them (e.g. dinosaurs, with birds as offspring group) are termed
paraphyletic, while groups representing more than one branch from the tree of life are called
polyphyletic. A formal code of nomenclature, the International Code of Phylogenetic
Nomenclature, or PhyloCode for short, is currently under development, intended to deal with
names of clades. Linnaean ranks will be optional under the PhyloCode, which is intended to
coexist with the current, rank-based codes.
[edit] Kingdoms and domains
Main article: Kingdom (biology)
From well before Linnaeus, plants and animals were considered separate Kingdoms.
Linnaeus used this as the top rank, dividing the physical world into the plant, animal and
mineral kingdoms. As advances in microscopy made classification of microorganisms
possible, the number of kingdoms increased, five and six-kingdom systems being the most
common.
Domains are a relatively new grouping. The three-domain system was first proposed in 1990,
but not generally accepted until later. One main characteristic of the three-domain method is
the separation of Archaea and Bacteria, previously grouped into the single kingdom Bacteria
(a kingdom also sometimes called Monera). Consequently, the three domains of life are
conceptualized as Archaea, Bacteria, and Eukaryota (comprising the nuclei-bearing
eukaryotes).[11] A small minority of scientists add Archaea as a sixth kingdom, but do not
accept the domain method.
Thomas Cavalier-Smith, who has published extensively on the classification of protists, has
recently proposed that the Neomura, the clade that groups together the Archaea and Eukarya,
would have evolved from Bacteria, more precisely from Actinobacteria. His classification of
2004 treats the archaebacteria as part of a subkingdom of the Kingdom Bacteria, i.e. he
rejects the three-domain system entirely.[12]
Woese CavalierHaeckel
Whittake
Linnaeus
Copeland
et al.
Smith
1866[14] Chatton
r
Woese et al.
[17][18]
[22] 2004[12]
1735[13]
1938
1990
3
1925[15][16]
1969[19]
1977[20][21]
2
4
3
6
kingdom 2 empires
5
6 kingdoms
kingdoms
kingdoms
domain kingdom
s
kingdoms
s
s
Eubacteria
Bacteria
Prokaryot
Monera Monera
Bacteria
Archaebacteri
a
Archaea
a
(not
Protista
treated)
Protozoa
Protoctist
Protista
Protista
Chromist
a
a
Eukaryota Plantae
Plantae
Plantae
Eukarya Plantae
Vegetabili
Plantae
Protoctist
a
Fungi
Fungi
Fungi
a
Animalia Animalia
Animalia Animalia Animalia
Animalia
[edit] Authorities (author citation)
An "authority" may be placed after a scientific name. The authority is the name of the
scientist who first validly published the name. For example, in 1758 Linnaeus gave the Asian
elephant the scientific name Elephas maximus, so the name is sometimes written as "Elephas
maximus Linnaeus, 1758". The names of authors are frequently abbreviated: the abbreviation
"L." is universally accepted for Linnaeus, and in botany there is a regulated list of standard
abbreviations (see list of botanists by author abbreviation). The system for assigning
authorities differs slightly between botany and zoology. However, it is standard that if a
species' name or placement has been changed since the original description, the original
authority's name is placed in parentheses.
[edit] Globally unique identifiers for names
There is a movement within the biodiversity informatics community to provide globally
unique identifiers in the form of Life Science Identifiers (LSID) for all biological names. This
would allow authors to cite names unambiguously in electronic media and reduce the
significance of errors in the spelling of names or the abbreviation of authority names. Three
large nomenclatural databases (referred to as nomenclators) have already begun this process,
these are Index Fungorum, International Plant Names Index and ZooBank. Other databases,
that publish taxonomic rather than nomenclatural data, have also started using LSIDs to
identify taxa. The key example of this is Catalogue of Life. In the next step in integration,
these taxonomic databases will include references to the nomenclatural databases using
LSIDs.
The system that we still use today for giving scientific names to plants and animals has
many founders, from the Greek philosopher Aristotle to the Swedish physician and botanist
Carolus Linnaeus.
Taxonomy is the study
of scientific
classification, in
particular the
classification of living
organisms according to
their natural
relationships.
Taxonomy's first father
was the philosopher
Aristotle (384-322
BC), sometimes called
the "father of science."
It was Aristotle who first introduced the two key concepts of
taxonomy as we practice it today: classification of oranisms by type and binomial definition.
Aristotle was the first to attempt to classify all the kinds of animals in his History of
Animals (Historia Animalium in Latin). He grouped the types of creatures according to their
similarities: animals with blood and animals without blood, animals that live on water and
animals that live on land. Aristotle's view of life was hierarchical. He assumed that creatures
could be grouped in order from lowest to highest, with the human species being the highest.
Subsequent commentators on Aristotle interpreted this as a "ladder of nature" (scala naturae)
or a "Great Chain of Being," but these were not Aristotle's terms. His system of classification
was not evolutionary, and the various species on the ladder had no specific genetic
relationship to each other. Aristotle regarded the essence of species as fixed and unchanging,
and this view persisted for the next two thousand years.
His other innovation was binomial definition. "Binomial" means "two names," and according
to this system each kind of organism can be defined by the two names of its "genus and
difference." The word "genus" comes from the Greek root for "birth," and among its
meanings are "family" and "race." Aristotle's notion of definition was to place every object in
a family and then to differentiate it from the other members of that family by some unique
characteristic. He defined humans, for example, as the "rational animal." This, according to
Aristotelian thought, defines the essence of what it is to be human, as opposed to such
pseudo-definitions as "featherless biped."
But what Aristotle did not do was methodically use binomial definition in his system of
biological classification. This innovation had to await the development of modern science
after the Rennaissance.
Aristotle's influence was profound and long-lasting. Much of his work has not survived to the
present day, so that we don't know the details of his study of plants, but his student
Theophrastus (372-287 BC) continued it, becoming known as the "father of botany." He is
believed to have planted the first botanical garden on the grounds of Aristotle's Lyceum.
Most of the text of his two botanical works, On Plants (De Historia Plantarum) and The
Causes of Plants (De Causis Plantarum) still exists, although only in Latin translations. The
first describes the anatomy of plants and classifies them into trees, shrubs, herbaceous
perennials, and herbs. The second work discusses their propagation and growth and served in
part as a practical guide to farmers and gardeners. However, he introduced no new principles
of classification.
After Aristotle, there was little innovation in the fields of the biological sciences until the
16th century AD. At this time, voyages of exploration were beginning to discover plants and
animals new to Europeans, which excited the interest of natural philosophers, as scientists
were then called. There was great interest in naming these new species and fitting them into
the existing classifications, and this in turn led to new systems of classification. Many of the
botanists of this period were also physicians, who were interested in the use of plants for
producing medicines.
Andrea Cesalpino (1519-1603) was an Italian physician who
created one of the first new systems of classifying plants since
the time of Aristotle. He was a professor of materia medica,
the study of the preparation of medicines from plants, at the
University of Pisa, and was also in charge of the university's
botanical garden. There, he wrote a series of works titled On
Plants (De Plantis), detailing his system of classification.
While his work was in large
part based on the work of
Aristotle and his successors,
his innovation in basing his
system of classifying plants on the basis of the structure of
their fruits and seeds influenced subsequent scientists such as
Linnaeus.
One botanist who was influenced by Cesalpino was Gaspard
Bauhin (1560-1620), a Swiss physician and anatomist. In his
1623 Illustrated Exposition of Plants (Pinax Theatri
Botanica), he described about six thousand species and gave
them names based on their "natural affinities," grouping them
into genus and species. He was thus the first scientist to use
binomial nomenclature in classification of species,
anticipating the work of Linnaeus.
By the time Carl (Carolus) Linnaeus (1707-1778) was born, there were many systems of
botanical classification in use, with new plants constantly being discovered and named. This,
in fact, was the problem — there were too many inconsistent systems, and the same plant
might have several different scientific names, according to different methods of
classification.
During his childhood, Linnaeus was so fond of collecting plants that he was known as "the
little botanist." He later became a physician, as so many other early taxonomists did, but
returned to botany as his primary study.
He published his most innovative work as a young man in 1735. The System of Nature
(Systema Naturae) is notable for an overall framework of classification that organized all
plants and animals from the level of kingdoms all the way down to species. The full subtitle
of its tenth edition was: System of nature through the three kingdoms of nature, according to
classes, orders, genera and species, with characteristics, differences, synonyms, places. This
system of classification, although greatly modified, is essentially the one we use today.
Linnaeus followed this work with
The Genera of Plants and The
Species of Plants, setting out a
system of plant classification based
on the structure of flower parts, in
which he was influenced by
Cesalpino. This method, in which
plants were grouped together
according to the number of stamens
in their flowers, for example, was
not accurate, but it was easy to use
and thus readily adapted by
scientists who were continually
discovering more new varieties of
plants. Linnaeus himself undertook
much work in the field, and he was
even more influential through his
students, whom he sent around the
world to gather specimens.
His major works went through a
great deal of revision in his lifetime,
eliminating errors and coming closer
to the system that was eventually
adopted by taxonomists worldwide.
His methods of classifying plants
have been completely superseded by
a deeper scientific understanding.
Originally, Linnaeus had only used
binomial nomenclature to classify
plants, but he later extended this
system to include animals and even
minerals. There were also errors,
subsequently corrected. At first, for example, he had placed the whales among the fishes, but
later moved them into the mammals. He was also the first taxonomist to place humans among
the primates (or Anthropomorpha) and to give them the binomen Homo sapiens.
If Linnaeus is now considered the father of taxonomy, his success rested on the work of his
predecessors. He was the first, in his System of Nature, to combine a hierarchical system of
classification from kingdom to species with the method of binomial nomenclature, using it
consistently to identify every species of both plants and animals then known to him.
While he continued throughout his lifetime to revise and expand this great work, so his
successors have continued to revise the principles of taxonomy, now according to genetic
principles, informed by the analysis of DNA. So it always is with science: we stand on the
shoulders of our predecessors, always reaching higher.
Georges Cuvier was one of the most influential figures in science during the early nineteenth
century. A self-appointed referee of proper science from his stronghold in the elite Académie
des Sciences, Cuvier was as successful in creating his own image as a great man of science as
he was in the many areas of science he studied.
Cuvier was born on 23 August 1769, at Montbéliard, a French-speaking community in the
Jura Mountains then rule by the Duke of Württemberg. Cuvier went to school at the
Carolinian Academy in Stuttgart from 1784 to 1788. He was then a tutor for a noble family in
Normandy. Here he first began to establish a reputation as a naturalist. In 1795 Geoffroy
Saint-Hilaire invited Cuvier to come to Paris. Cuvier was first appointed an assistant and later
a professor of animal anatomy at the post-French revolution Musée National d'Histoire
Naturelle. When Napoleon came to power Cuvier was appointed to several government
positions, including State Councillor and Inspector-General of public education. After the
restoration of the monarchy Cuvier still managed to preserve his status. In 1831 he was made
Baron and a Peer of France. Cuvier had a deep abhorrence against a popularization or
democratization of scientific knowledge.
Statue of Cuvier on the rear wall of the Royal Academy, London [Click on image for larger
picture]
Cuvier's scientific achievements are difficult to overestimate. It was widely recounted that he
could reconstruct a skeleton based on a single bone. His work is considered the foundation of
vertebrate palaeontology. Cuvier expanded Linneaun taxonomy by grouping classes into
phyla. Cuvier arranged both fossils and living species in this taxonomy. Cuvier convinced his
contemporaries that extinction was a fact- what had been a controversial speculation before.
Cuvier strongly opposed Geoffroy's theory that all organisms were based on a basic plan or
archetype and that they blended gradually one into another. Cuvier argued instead that life
was divided into four distinct embranchements (life-vertebrates, molluscs, articulates (insects
& crustaceans), and radiates). For Cuvier, it was function- not hypothetical relationships, that
should form the basis of classification. This issue, which obviously could support or
contradict a theory of evolution, was part of the famous Cuvier/Geoffroy debate in 1830. The
debate has often been interpreted in the retrospect of a post-Darwin age as a debate over
evolution. However the debate mostly revolved around the number of archetypes necessary to
categorize all organisms. In his Essay on the Theory of the Earth (1813) Cuvier proposed that
new species were created after periodic catastrophic floods. His study of the Paris basin with
Alexandre Brongniart established the basic principles of biostratigraphy.
Cuvier was a strong opponent of his colleague Lamarck's theory of evolution. (See Cuvier's
Elegy of Lamarck) Cuvier believed there was no evidence for the evolution of organic forms
but rather evidence for successive creations after catastrophic extinction events. Some of
Cuvier's most influential followers were Louis Agassiz on the continent and in America, and
Richard Owen in Britain.
Term
Node-based definition
Monophyly A clade, a monophyletic taxon, is a
Character-based definition
A clade is characterized by one or more
taxon which includes all descendants apomorphies: derived character states present in
of an inferred ancestor.
the first member of the taxon, inherited by its
descendants (unless secondarily lost), and not
inherited by any other taxa.
Paraphyly A paraphyletic assemblage is one
A paraphyletic assemblage is characterized by one
which is constructed by taking a
or more plesiomorphies: character states
clade and removing one or more
inherited from ancestors but not present in all of
smaller clades.[28] (Removing one
their descendants. As a consequence, a
clade produces a singly paraphyletic paraphyletic assemblage is truncated, in that it
assemblage, removing two a doubly excludes one or more clades from an otherwise
paraphylectic assemblage, and so
monophyletic taxon. An alternative name is
on.)[29]
evolutionary grade, referring to an ancestral
character state within the group. While
paraphyletic assemblages are popular among
paleontologists and evolutionary taxonomists,
cladists do not recognize paraphyletic
assemblages as having any formal information
content – they are merely parts of clades.
Polyphyly A polyphyletic assemblage is one
A polyphyletic assemblage is characterized by one
which is neither monophyletic nor
or more homoplasies: character states which have
paraphyletic.
converged or reverted so as to be the same but
which have not been inherited from a common
ancestor. No systematist recognizes polyphyletic
assemblages as taxonomically meaningful entities,
although ecologists sometimes consider them
meaningful labels for functional participants in
ecological communities (e. g., primary producers,
detritivores, etc.).