Taxonomy is the science of naming and classification of organisms based on their genetic (evolutionary) relationships. Taxonomy is very much a field of systematics in that it is based on phylogeny and comparisons between organisms and groups of organisms. It is the science of arranging living things into groups reflecting their relationships.

• Classification is the actual practice of placing animals into these groups.
• Nomenclature is the collection of rules and procedures of assigning names to the groups.

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Higher taxa

A taxon (pl. taxa) is a unit of classification of organisms Higher taxonomic categories (taxa) group species what evolutionary together, ideally according to relationships exist between species (just as human individuals group themselves into families, etc.)

Taxonomic categories, going from larger (most inclusive) to smaller include

1. Kingdom
2. Phylum
3. Subphylum
4. Superclass
5. Class
6. Subclass
7. Infraclass
8. Cohort
9. Superorder
10. Order
11. Suborder
12. Infraorder
13. Superfamily (-oidea)
14. Family (-idae)
15. Subfamily (-inae)
16. Tribe (in)
17. Subtribe (-ina)
18. Genus
19. Subgenus
20. Species
21. Subspecies

Artificial classification is based on one or a few easily observed characteristics, and is usually designed for a practical purpose with an emphasis on convenience and simplicity.

Linnaeus included all worm-like organisms in a single group, the Vermes. This included a wide range of animals, from simple nematode worms and earthworms to snakes. This was an artificial classification because it did not take account of important natural relationships, such as the fact that snakes have backbones and earthworms do not. Snakes have more in common with other vertebrates than with worms.

An example of an artificial classification of fish could be to group them as freshwater fish, brackish-water fish, and marine fish on the basis of their environment. This would be convenient for the purpose of investigating their mechanisms of osmoregulation. Similarly, all microscopic organisms are known as microorganisms a convenient group for the purposes of study but not a natural group.

Natural classification tries to use natural relationships between organisms. It considers more evidence than artificial classifications, including internal as well as external features.

It takes help from similarities of embryology, morphology, anatomy, physiology, biochemistry, cell structure and behavior are all relevant.

Most classifications in use today natural and phylogenetic.

Phylogenies: A typical goal of systematic (and paleontology) is the construction of phylogonies

A phylogeny of a description of the genealogical (i.e., blood, i.e., evolutionary) relationships between groups of organisms

A phylogeny thus can be a description of the macroevolutionary history of a species or of more than one species

A Phylogenetic classification is one based on evolutionary relationship. In such a systems organisms belonging to the same groups are believed to have a common ancestors. The phylogeny (evolutionary history) of a group can be shown by means of a ‘family tree’,

Phenetic Classification: Another way to classify organisms is to use a phenetic classification. This is an attempt to avoid the problem of establishing evolutionary relationships, which can be very difficult and very controversial, especially if there is little or no fossil evidence. The word ‘phenetic’ comes from the Greek phainomenon, ‘that which is seen’. This classification is based solely on observable characteristics (phenetic similarity) and all characters used are considered of equal importance.

All features of an organism can be considered, the more the better, and they do not necessarily have to be of evolutionary significance. Masses of data are collected and the degrees of similarities between different organisms are calculated, usually by computer because the calculations are extremely complex. The use of computers in taxonomy is known as numerical taxonomy. Phenetic classifications often resemble phylogenetic classifications, but they are notconstructed with this in view.

Cladogram: A cladogram is a graphical representation of a phylogeny

• Cladograms come in a variety of types; typical among all is an attempt to properly sort nodes, i.e., speciation events, such that descendant species are properly connected to their ancestral species, and species are grouped more closely to related species than they are to less-well related species

• As with the phylogeny it represents, the goal of a cladogram is to properly represent correct evolutionary relationships

Monophyletic taxon (clade): The goal of systematics is to define monophyletic taxa (also known as, clades). A monophyletic taxon is one that includes the common ancestor species as well as all descendant species.

“The ideal in systematics is for each taxon to be a monophyletic grouping, creating a classification that reflects the evolutionary history of organisms. Achieving this ideal is often easier said than done.”

Polyphyletic taxa: A polyphyletic taxon represents a mistake in classification. Essentially, a polyphyletic taxon is one that contains at least two descendant species but not all ancestor species. Such things happen when a species is inadvertently included in a clade that it doesn’t belong in.

Convergent evolution (analogy)

Polyphyletic taxa occur as a consequence of mistaking analogies for homologies

Analogies are two structures that superficially resemble each other, i.e., which appear (at the very least at first glance) to be homologous but are not Analogies result from convergent evolution: the two species do similar things in similar environments so consequently evolve similar structures to perform these similar functions

The key difference between an analogy and a homology are two-fold:

• The common ancestor between the two species will have lacked the common structure

• The development of the structure will differ-more generally, homologies predict other homologies between two species whereas anaologies give rise to much less predictive power about the existence of additional homologies between two species

Paraphyletic taxa: A paraphyletic taxon is also a mistake, but a legitimately made one (unlike a polyphyletic taxon). Like a polyphyletic taxon, paraphyletic taxon does not represent a clade. However, paraphyletic taxa are not clades for a reason and that reason has to do with evolutionary innovation.

• Typically, paraphyletic taxa are ones which include phenotypically similar descendant taxa, but exclude phenotypically dissimilar taxa

• For example, reptiles form a paraphyletic taxon if mammals and birds are not included among the reptiles. Lizards are paraphyletic if you don’t include snakes (which are derived from lizards)

• Similarly, the apes form a paraphyletic taxon if humans are not included among the apes

Cladistics

1. Cladistics is a technique by which organisms are assigned to different (monophyletic) taxa
2. Cladistics works by identifying homologies and grouping together organisms such that within taxa individuals share more homologies than they do with individuals found in different taxa
3. Cladistics also rejects the inclusion of similarities

• That are the result convergent evolution (i.e.,analogies)
• That are homologies but that are shared with other taxa
• Note, that this is not to say that it is necessarily easy to distinguish analogies from homologies

4.Cladistic techniques are not able to judge evolutionary divergence in terms of the time between nodes (speciation events); time information instead is derived from the fossil record

5.”Cladistic analysis has become synonymous with phylogenetic analysis. A clade (Gr. Clados, “branch”) is an evolutionary branch. Cladistic analysis classifies organisms according to the order in time that branches arose along a dichotomous phylogenetic tree. Each branch point in a tree is defined by novel homologies unique to various species on that branch. Because it views the extent of divergence among organisms as uninformative in assessing evolutionary relationships, cladistic analysis considers only homologies in developing hypotheses about classification and phylogony.”

Shared derived characters

A cladist derives phylogonies from shared derived characters (a.k.a., synapomorphies), those homologies that are unique to individual taxa (possessed by all members of a given clade)

For example, in cladistics the fact that bats have wings would not include bats in a taxa including birds on the basis of both having wings (birds and bats both have wings as a consequence of convergent evolution, and a bat-bird taxon, were such a taxon to exist, would be a good example of a polyphyletic taxon since it would exclude the non-winged common ancestor to both the birds and the bats)

In general, the existence of homologies predicts the existence of additional homologies, and cladistics uses these correlations to define taxa

Shared primitive characters

• Not all shared characters are shared derived characters

• For example, a cladist would not use the fact that both dogs and bears have hair as a means of classifying both dogs and bears as carnivores, since the ancestor of the ancestral carnivore, a mammal, also had hair

• However, a cladist would use the fact that dogs and bears both have hair to include both among the mammals

• That is, hair cannot be employed to distinguish mammals because hair is a shared by all mammals, i.e., it is a shared primitive character when comparing among mammals, but a shared derived character when grouping mammals as distinct from other lineages

Molecular systematics

• In the past two decades, molecular systematics has come to dominate the study of evolutionary relations (which is not to say that molecular systematics has supplanted other approaches, it instead serves as an increasingly important tool)
• Molecular systematics seeks out homologies, like cladistics, though it is more difficult to distinguish analogies from homologies (that is, two nucleotides in a gene sequence could be identical because they have always been identical, i.e., since common ancestry, or due to divergence followed by mutation back to the same nucleotide)

• “One advantage of this molecular tool of systematics is that it is objective and quantitative. A second advantage is that it can be used to assess relationships between groups of organisms that are so physiologically distant that they share very few morphological similarities… [Third] molecular comparisons go right to the heart of evolutionary relationships.”