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Taxonomy

Species and their classification

Taxonomy refers to the classification of living things by giving unique names to each species, and creating a hierarchy based on evolutionary descent. This is a challenging task, as most species that have ever lived on this planet are now extinct, and many more alive today have yet to be discovered and classified.


In order to achieve the above, though, we need a definition for both species and hierarchy. In the old days, a species was known as a collection of individuals similar enough in resemblance to be put in the same box. This was purely based on physical features. Today we know that similar physical characteristics on their own aren't enough to define a species.


species is defined in terms of observable physical features as well as the ability to produce fertile offspring.


This is Hercules, the liger. Hercules has a lion father and a tiger mother. Does that mean tigers and lions are really one species? This is one example of the issues surrounding both the definition of species, and taxonomy generally.

What is a hierarchy? A hierarchy, put simply, is a system of classification comprised of small groups contained within larger groups contained within larger groups, and so forth, where there is no overlap.


The above diagram is a phylogenetic tree. It is a representation of various species in terms of their genetic relatedness. Each "crossroads" is a different ancestor. From this diagram it is easy to see that humans are more closely related to whales than to birds, or indeed any other species represented.

The species with a red circle beneath are extinct. If a phylogenetic tree was made with all species that have ever lived up to today, the vast majority would be extinct. 

Aside from simple observable features and their similarity, advances in immunology and genome sequencing can add to the information required to create, maintain and update the tree of life according to new findings. Different organisms' genes, proteins and physiologies can be compared to see how closely related they are.

The names above are used for convenience, yet the scientifically correct way of classifying organisms is by giving them a two-word (binomial) name. These names are in Latin or Greek.

Let's take Homo sapiens for example (us!):

1. It's written in italics as all species names should be, by convention.

2. It's made up of two words: Homo and sapiens.

3. Homo denotes the genus to which the species belongs to. A genus is the group higher than species. For example, Homo erectus and Homo neanderthalensis are part of the same genus as Homo sapiens (both now extinct). That genus is called Homo... getting the hang of it?

4. Sapiens denotes the species itself, and is the smallest group in the hierarchy.

Nomenclature refers to the naming of species using the binomial system, while systematics refers to placing species together based on their similarities and differences.


What does the rest of the hierarchy look like?

Kingdom, Phylum, Class, Order, Family, Genus, Species (fearing you can't possibly remember this sequence?)

Kinky, Policemen, Can, Often, Find, Gay, Sex. You're more than welcome.

The genus is a group of similar and closely related species, while the family is a group of apparently related genera, and so on.

The phylum is a group of organisms that are constructed on a similar body plan e.g. animal, plant, bacteria.

The kingdom is the largest all-encompassing group, containing all other subgroups.

Comparison points for organising organisms into these different groups in the hierarchy include morphological and anatomical features, cell structure i.e. eukaryote or prokaryote, and biochemistry. Closely related organisms have identical or very similar key proteins and genes.

While morphology may be misleading e.g. due to convergent evolution where otherwise unrelated species end up looking similar, biochemical analysis of DNA or proteins is much more robust. It can trace back the evolution of different species relative to each other by using very basic, fundamental features of how the organism is alive. These properties are more reliable and less susceptible to convergence.


Determining evolutionary relationships between species

In the era of molecular biology, we no longer have to rely on superficial visual cues only in order to classify species. We can look at and compare their DNAproteins, etc. A common method of visualising these differences is gel electrophoresis which involves loading small volumes of samples on a gel and running a current across it in order to separate the samples by size.

Since the gel has a microscopic matrix inside that provides resistance against sample movement through it, the larger molecules move more slowly while the smaller fragments can move more quickly.



The positive charge is at the bottom of the tank, while the samples are loaded at the top. This way, they will move downwards towards the bottom of the gel because they have a negative charge as molecules. The current is run across the gel for around 30-60 minutes (ensuring the samples don't run too long and hence run off the gel into the buffer solution! if that happens they are lost) after which the sample's progression on the gel can be visualised by using a stain solution or pre-existing coloured label visible under UV light.

The protein or DNA samples for example can come from the different species' muscle or some other tissue source. DNA samples can be replicated in the lab using specific primers (in PCR) to make certain genes or sections of DNA that are to be compared and looked at on a gel. Alternatively, all present proteins in a sample can be investigated by running the whole sample on a gel and comparing the differences.




The bands on the gel might look something like this. Based on the height on the gel of the different bands (which represent different proteins in the sample), we can see that all species have the band at the top. This is a protein of the same size that they all share.

The second largest protein (the second highest band on the gel) belongs to Species Y and is unique to it, not being shared by the other species. Same for the third one down of Species Z. Looking at all the bands for each species, we can see that Species A and Species Z share the most bands in common (3), so we assume from this data that based on their proteins, Species A and Species Z are the most closely related compared to any other species combination here (A, X, Y, Z).

With advancing technology, scientists no longer have to rely on capturing animals or gathering data manually in the field. Bioinformatics enables the analysis of a whole genome from a computer. Once the initial DNA sequencing has taken place, a lot of research can be conducted just from that data. For example, the DNAmRNA or amino acid sequence between two individuals or species can be compared.




From this short sequence of amino acids in the haemoglobin of these different species we can infer several things. Let's do humans and chimps first! How many differences are there? Lys, Glu, His, Iso and... Lys, Glu, His, Iso. Right. Absolutely no difference. Humans and gorillas have one difference, zebras and horses have one difference and zebras and humans have 3 differences!

We can infer a lot of different information from this table, and it's just a very small sequence in just one protein looking at just five different species. The potential of investigating diversity with molecular biology tools is astounding.




DNA can be studied similarly, and a lot of creativity can be employed to come up with ways to twist and turn heaps of genetic data in such a way that interesting information can be pulled out. In this example, it's a fairly straightforward, run of the mill comparison between the DNA sequence itself of a mouse gene versus a fly gene.

We can see that the sequence itself is 76.66% identical, while the protein product resulting from the exons only, is actually identical in its entirety at 100% between the two sequences (highlighted in green).

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