It is the job of a taxonomist to fit organisms into a hierarchical structure based on shared characteristics or ancestry. Historically this involved examining the anatomy and physiology of different groups to work out how they related to each other. Carl Linnaeus was a pioneer in this field from which we base many aspects of our taxonomy. The main levels of modern classification are: domain, kingdom, phylum, class, order, family, genus and species. Between these levels there are often sub-groups and super-groups.
The three domains of life are the Bacteria, Archaea and Eukarya which differ in their fundamental biochemistry and metabolism. The eukaryotes are more complex cells possessing organelles such as mitochondria and chloroplasts.
There are around six eukaryotic kingdoms including single cellular amoebas and multicellur animals, plants and fungi. Within the animals there are around 35 orders based on fundamental structure and embryonic development of which all but one are traditionally called invertebrates. These include cnidarians (jellyfish), arthropods, molluscs, platyhelminths (flat worms), annelids (round worms) and echinoderms (starfish and sea urchins).
One phylum, the Chordata, evolved the rudimentary spinal chord. A group of chordates, the Craniata, developed a skull but lacked a proper skeleton (as in hagfish) before the subphylum Vertebrata founded the vertebrae which would go on to be such a revolutionary adaptation. There are seven vertebrate classes: jawless fish, cartilaginous fish, bony fish, amphibians, reptiles, birds and mammals.
As explained elsewhere, there are over 27 orders of bird. Taking the Passeriformes as an example, the order is split into several families for example the Passeridae. The family, in turn, is split into genera (singular: genus) and genera contain species. Linnaeus' greatest legacy is probably the Latin binomial name which superseded the longer descriptions of prior naming systems. It was designed to be used universally in a relatively unbiased language without the confusion of local names in different dialects . The binomial name contains the genus (capitalised) and the species which are italicised for example Passer domesticus. When referring to species in the same genus (congenerics) in quick succession, thew genus name is often initialised e.g. P. montanus.
There are a few naming rules in taxonomy and within the birds. All animal families end 'idae' and tend to be based on a type species within that family e.g. the sparrowhawk, Accipiter nisus, is a member of the family Accipitridae. There is often a subfamily level between the family and genus which ends 'inae' e.g. Accipitrinae. At order level, most classes do not have naming (e.g. Rodentia, Primates, Carnivora) however bird orders end 'iformes' referring to the shape of the type species e.g. Accipitriformes. (When genus names end 'ius' or 'ia' this leads to families and orders containing double 'i's e.g. the Gavia within the order Gaviiformes). Finally when writing about different groups the formal name of the group is capitalised (the Corvidae) whilst informal names are not (corvids).
Taxonomy - Inductive Reasoning of the Past from the Present
In the days of Linnaeus, classification could be somewhat arbitrary as there was no a priori reason for organisms to be related in a certain way. However Darwin realised that all species where related but had evolved and diverged over time. This meant that there was a true relationship between organisms that reflected the way different groups had split over time. Taxonomists could now try to infer the evolutionary relationships of organisms from the morphology of living and fossil species. Darwin and others began to visually represent these relationships with dendrograms, trees of life.
When populations of a species become genetically divergent and reproductively isolated the species speciates into two daughter species. This means that all evolutionary relationships are based on a tree that continually splits into two. This adds an extra layer to classification so that given orders would have split more recently with one order than another. Large splits within classes become subclasses whilst multiple orders can be united in a superorder.
The ideal for a taxonomists is for groups of organisms to form clades. A clade is a group of organisms that contains the ancestor of the group as well as all of that ancestor's descendants. Such a group is said to be monophyletic. Birds are monophyletic because their common ancestor was a bird and all descends of that ancestor are birds. That sounds kind of obvious but there are many situations where that is not the case. A paraphyletic group contains the common ancestor but not all of that ancestor's descendant. Reptiles are paraphyletic because their ancestor was a reptile but birds are descended from reptiles and yet not included in the group. Paraphyletic groups are often called grades. Finally the worst situation is that a group is polyphyletic i.e. it doesn't even contain the common ancestor. Flightless birds are not descended from a flightless bird and have been grouped on a characteristic which they have all evolved independently. Nested evolutionary relationships are represented in cladograms. A good rule of thumb for whether a group is monophyletic is how many lines you cross when you encircle the group. If you only cross one line (just above the ancestor) the group is monophyletic whereas if you cross at least two the group is paraphyletic at best.
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| The evolutionary relationships of the primates showing monophyly, paraphyly and polyphyly |
The Rise of Phylogenetics
In the last 40 years, taxonomy based on morphology has been superseded by phylogenetics which uses differences in the DNA sequence to infer evolutionary relationships. It assumes that genes evolve at a predictable rate and that counting the relative differences in the same gene between species shows how much different groups have diverged from each other. Gene trees are built based on this hierarchical similarity. This was originally prone to some biases of gene choice and differential evolution in different lineages but now sequencing whole genomes is becoming so easy that we can build consensus trees based on all a species' genetic material. This should enable us to find the true relationships between organisms however with so much data and so many different models the field is still producing messy results. Thus when describing species in a taxonomic order one must still choose a phylogeny and these are being updated all the time. As my list of species is given in the order of the International Ornithologists' Union I shall use this consensus of experts as my taxonomy. Below is a cladogram of modern birds based on Kimball et al. (2013) and Yuri et al. (2013). Branches that split into more than two are called polytomies and result from unresolved relationships.
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