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The development of species: evolution and classification

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.


What does the rest of the hierarchy look like?

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

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


Determining evolutionary relationships

Before the era of molecular biology, species were organised based on their physical characteristics. This, however, has turned out to be somewhat incorrect, as many lineages converge to the same outcome after initially being separated. For example, there are different species of flying squirrel which live on different continents. Their last common ancestor was not a flying squirrel, and following separation onto different parts of the world, they continued evolving separately.

Due to similar niches in their environment, they happen to have both evolved their flying ability further down the line. This is called convergent evolution and it led scientists to assume these species must be closely related since they look similar. Similarly, archaea used to be lumped in with bacteria due to their apparent similarities, only to later be found to be separate altogether.

Molecular biology techniques such as genetic fingerprinting have enabled researchers to compare organisms and species on an unprecedented level with much more data and detail, to be able to ascertain their relatedness.

Any 2 given people share 99.9% of their DNA code. But the differences present in the remaining 0.01% of it are enough to enable reliable identification, with the exception of monozygotic twins. The DNA containing this is called variable number tandem repeats (VNTRs) because they are just sequences of DNA repeated many times.

Aside from genes, or coding DNA, there are non-coding regions which repeat themselves many times over in each individual, with some sequences contained within varying. This variability is less in closely related individuals. This is where the usefulness of genetic fingerprinting comes in. This covers medicine, criminology and biodiversity conservation among other things.


Technique

1. The sample DNA undergoes PCR then cleavage at multiple sites with restriction endonucleases

2. The resulting many small fragments are tagged using a radioactive molecule

3. They're separated using gel electrophoresis and viewed using a developed photographic film


Result



The bands exposed then undergo simple visual analysis by matching up the template DNA with other DNA that could be similar more or less, depending on situation. Above, the DNA found at a crime scene is compared with that of 3 suspects. The bands of suspect 2 are perfectly aligned with the crime scene DNA.

Different species may be compared in this way for the purpose of determining how closely they are related to one another. Another molecular biology technique which can be used to this end is enzyme comparison. Enzymes are the direct products of DNA sequences, so the similarity in amino acid sequence in the enzyme can be used to compare different species. Enzymes are proteins, so any protein could theoretically be used to test this, such as haemoglobin.




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).

In animals, the cytochrome c oxidase 1 enzyme in mitochondria is used for classification purposes. In plants, it is chloroplast genes. Both organelles are central to energy production and use, and entered eukaryotic cells a very long time ago.



This data helps build phylogenetic trees, such as those for hominids. Hominids are bipedal and include humans, and are a subgroup of hominoids, that also includes hylobatids and pongids. Conflicting evidence has been uncovered in the morphological and molecular studies carried out in this area. For example, mitochondrial DNA analysis has shown differences between Gorilla gorilla and Pongo pygmaeus that are not mirrored by difference in morphology in subspecies.


Human and plant adaptations

Adaptations can be behavioural, physiological and anatomical.

Behavioural adaptations of Homo sapiens include using various tools, as well as culture to establish social bonding.

Physiological adaptations include the production of melanin to determine skin pigmentation according to light exposure, and the production of lactase to digest lactose from cow milk where it is a major part of the diet.




Anatomical adaptations include walking upright i.e. bipedalism and brain size.

Plants that live in extreme conditions with regards to water, light and temperature show these types of adaptations too. "Behavioural" adaptations overlap with physiological ones e.g. photosynthesising during the day, closing stomata or rolling leaves. 

In terms of water availability, which correlates with light and temperature in terms of rate of transpiration, water loss and evaporation, the previously covered xerophytes and hydrophytes exhibit specific adaptations to their environemnt (see Transport systems in plants).

Shade tolerance refers to a plant's ability to cope with low light levels. Some plants shift their pigments from high light levels in summer to lower levels in winter (physiological adaptation). On a quicker basis, plants can rearrange their cell chloroplasts to respond to changing light levels.




Plants like the snow saxifrage can survive in extreme cold environments. They have small leaves (anatomical adaptation), grow close to the ground to avoid the impact of wind and ice, and can carry out photosynthesis at a lower temperature.

Practical experiments can be carried out into the adaptations of plants to environmental factors.


Competing theories: language

Competing theories exist in many fields that are yet to establish a single accepted theory e.g. due to a lack of sufficient evidence, or conflicting evidence. The evolution of language is one of these fields.

Evidence is hard to compile due to the nature of spoken language not leaving traces. There are many hypotheses on how language might have evolved in humans.

One of them is the mother tongue hypothesis. It states that language evolved as a way for parents and offspring to manifest their relatedness. Language was a means to connect kin as opposed to non-kin, and so evolved through networks of relatedness.

A competing hypothesis is the gossip hypothesis. It argues that gossip serves a function similar to that of grooming in other primates. This functions is a mutually beneficial expression of trust and alliance. As physical grooming became impractical for increasing groups of people, verbal "grooming" via language i.e. gossiping, evolved as a more efficient way of maintaining relationship.


Natural selection

Here is an all-time classic example. The most frequent initial moth colour in a population landing on tree trunks was dark, to match that of the tree trunks. Few moths could get away with being light-coloured. Once the tree trunks were painted white, the former moths became very apparent to predators, and so the light-coloured moths evaded predation much better and survived to reproduce. Essentially, the tables had turned!


This resulted in the allele for light colour to spread and become the most frequent compared to that for dark colour. The latter sharply dropped in frequency and became the minority.




This is an example of directional selection. It tends towards an extreme, either the light-coloured or the dark-coloured, depending on scenario. 

Selection can also tend towards a "happy medium" and avoid either extreme. This is stabilising selection. If really small lions don't survive long, but really large lions can't supply themselves enough food, then the average lions are selected for and achieve the highest frequency.




Directional selection also takes place when antibiotics are used against bacteria. The adaptive pressure favours bacteria that have the antibiotic resistance gene and can survive the hostile environment.

On the other hand, a scenario such as human birth weight showcases stabilising selection. The average weight is large enough to keep the newborn healthy and increasingly able to survive independently, but small enough to enable the actual birth.

Natural selection therefore results in species increasingly and consistently adapted to their environment via anatomical, physiological or behavioural changes.

The train of thought leading to natural selection includes these key points:

1. Individuals within a population exhibit variety of phenotypical traits caused by both their alleles and the environment.


Primarily the source of this variation is mutation. Secondarily it is meiosis and the random fertilisation of gametes in the case of sexual reproduction.

2. The balance of survival and reproduction is affected by factors including predationdisease and competition. Some appearances and behaviour can attract more predators while others such as camouflage can avert them.

Disease can impede survival and reproduction, while competition enables hidden traits that might have gone unnoticed or been "neutral" before to come in handy when unforeseen selection pressures arise. If the positive outcome of such competition, such as resources needed for survival, are limited relative to the population seeking them, then competition acts further to select certain traits.


3. Any favourable traits controlled by alelles will end up in more offspring, thereby shifting the alelle frequency and over time, the entire gene pool of a population or species.


Types of selection

We looked at stabilising and directional selection previously.

There is a third type called disruptive selection. Instead of shifting the traits towards an end, or towards a middle ground, disruptive selection splits the pool down the middle, where both extremes of a trait are favourable, but not a middle value.



An example of this is an original population of purple individuals which stand out quite a lot amongst red and blue flowers in a field. They will end up shifting towards either red or blue, but not staying purple as this attracts predators.
Little devil bats. Birds? Anyway.


Biodiversity

Species diversity is the diversity of species in a community. Put simply, how many different species are there in a community? 5 or 5,000? W
hich has the higher diversity? Not rocket science I hope.


^That's some rocket science, I don't really know what it is, but I don't wish to find out, and neither do you. Just a little motivator to not complain about biology.

What is a population? A population is all the individual organisms found in a given habitat, of one species. So you could talk about a population of wolves in the woods. If you want to talk about the wolves and rabbits in the woods, then you'd be referring to a community. A community is made up of the various populations in a habitat. So the summation of all the living things in a given area is called a community. What then is an ecosystem?

An ecosystem comprises the community of living organisms in a habitat, together with all the non-living components such as water, soil, temperature, etc. called abiotic factors.

Why are different organisms of different species able to coexist in the same habitat? How come they don't directly compete with one another and drive others out? Have a watch...


So that's the last and loveliest new term: niche. It rhymes with quiche. A niche is the interaction, or way of life, of a species, population or individual in relation to all others within an ecosystem. It's how it behaves, what it eats, how it reproduces, where it sleeps, etc.; a species' niche is determined by both biotic factors (such as competition and predation) and abiotic factors.

Species richness is defined by the number of different species in a habitat. However, in order to have biodiversity, the relative abundance of each species is also key. The more species, the higher the diversity. What if there are two separate communities like this:

Community #1 has 150 individuals per each of 20 different species (3000 individuals in total)
Community #2 has 10 individuals per each of 19 species, and 2990 individuals of the last species (3000 individuals in total)

It doesn't take a complex formula to figure out that community #1 is far more diverse compared to community #2, despite them having the same number of species and individuals. The distribution of individuals to species is important in determining a community's diversity.

Now for a little talk about deforestation and agriculture. Deforestation is the removal of trees in forests. and agriculture is the cultivation of useful plants to people which are often carefully selected for, and occupy a large area by themselves (like corn).

It's not hard to figure out the impact both have on species diversity. Deforestation practically removes many, whole trees, and with them goes the shelter and food source of many other organisms. A great reduction in species diversity can be expected as a result.

Agriculture by humans results in a single dominant species which occupies vast land at the expense of others. Humans actively remove other species by the use of pesticides, insecticides and (indirectly) fertilisers. This, too, will lead to a great decrease in species diversity.

Other factors affecting species diversity include the degree of isolation, for example as seen on islands. The ability of individuals of certain species to move between different habitats can affect the biodiversity of different areas. When an area that is smaller harbours niches that can only cater to animals that can fly, or those that can eat fruit, the resulting community of populations of different species would not be as diverse as a larger, better connected area with more niches.




Alongside species diversity, other levels of diversity can be measured including genetic diversity at the level of different alleles, and ecosystem diversity at the level of different ecosystems in an area.

In the wild, each species may exist as one population or multiple populations. Different populations correspond to defined areas - habitats.

The sum of all present alleles for a given gene in a given population is known as the gene pool.

This is essentially a way of thinking about all the individuals in a population contributing their alleles towards the overall allele frequency. The extent of different alleles present gives the genetic diversity of a population.




The allele frequency in a population's gene pool can change as a result of selection. The effectors of selection can be varied, yet the outcome is similar: advantageous or preferred alleles and the traits associated with them increase in frequency, while detrimental or disfavoured alleles and the traits associated with them decrease in frequency.

On the Earth as a whole, ecological diversity is overarching and includes within it both species diversity and genetic diversity.




It can be assessed in different ways, including geographically by ecosystem features e.g. deserts, oceans, forests, as well as biologically e.g. through the number of trophic levels in an ecosystem.


Measuring biodiversity

Measuring biodiversity in a population involves obtaining the percentage of genes in the genome that have variants i.e. alleles. This is equivalent to the percentage of genes in the genome that vary.

proportion of polymorphic genes = number of polymorphic genes / total number of genes

So, a population which has 37% of its genes as polymorphic (have more than one allele) is more genetically diverse than a population which has 28% of its genes as polymorphic.



The remaining 63% of genes are not polymorphic and only have one allele. This means the gene product is the same amongst all individuals in the population. The second population has 72% of its genes without variants i.e. not polymorphic. The diagram examples are simplified. Populations will have thousands of genes not just 2!

Ok byeeeeee


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