A3.1 Diversity of organisms

An organism is an individual living thing: a bacterium, a fungus, a plant, an animal. One of the defining features of life is variation: no two individuals are identical in all their traits. Even identical twins differ in fingerprints and in some of the mutations their cells have picked up.

Variation is not random noise. It shows patterns:

• members of one species differ from each other only slightly, for example in height or eye colour;
• members of closely related species, such as humans and chimpanzees, share most traits but differ in some;
• distantly related organisms, such as humans and oak trees, or humans and E. coli, differ in almost every trait.

These nested levels of similarity are the basis for naming and classifying organisms: groups of similar individuals are named as species, similar species are grouped together, and so on (see A3.2 Classification and cladistics).

Species as groups with shared traits

From the 17th century onwards naturalists used the word species for a group of organisms with a characteristic set of shared traits. The Swedish botanist Carl Linnaeus (18th century) described and named thousands of species of plants and animals in this way, by their morphology: their outward form and inner structure. This is the morphological species concept: a species is a group of organisms that resemble each other closely and are clearly different from all other groups.

The morphological concept is practical, because it only needs observation, and it is still used to describe most new species and to identify fossils. But it relies on clear-cut differences between species, and these are not always present:

• Individuals of one species can look very different: males and females (sexual dimorphism), larvae and adults, or different breeds of dog.
• Different species can look almost identical (cryptic species), and are only told apart by their behaviour, their songs or their DNA.

These problems led to other ways of defining a species, below.

Every species has many common names, which vary between languages and regions: the bird called a robin in Britain is a different species from the American robin. To avoid confusion, scientists give each species a single scientific name using the binomial system popularized by Linnaeus. It is agreed internationally and used by biologists everywhere, a good example of scientific cooperation.

A binomial has two parts:

1. The genus name comes first and starts with a capital letter. A genus is a group of closely related species that share many similar traits.
2. The species name (the specific epithet) comes second and starts with a lower-case letter. It distinguishes this species from the others in the genus.

The whole name is printed in italics, or underlined when handwritten. After the first use, the genus can be shortened to its initial: E. coli for Escherichia coli.

Because species in the same genus are similar, a binomial carries information: Panthera leo and Panthera tigris are both big cats.

The biological species concept defines a species as a group of organisms that can interbreed and produce fertile offspring. Interbreeding keeps mixing the genes of the group (its gene pool), so its members stay similar. A group that does not interbreed with others is free to diverge and become more and more different.

Difficulties with the biological species concept

• Hybrids: some organisms that are clearly different species by morphology can still produce fertile offspring. Polar bears and grizzly bears occasionally interbreed in the wild and some of their hybrids are fertile.
• Untestable cases: interbreeding cannot be tested for extinct organisms known only from fossils, or for populations living far apart that never meet.
• Organisms that do not reproduce sexually: the concept cannot be applied to them at all (see the AHL section below).
• Degrees of fertility: crosses can be partly fertile, so there is no sharp yes-or-no answer.

Because of these problems, other species definitions are also used, for example ones based on morphology or on how closely the DNA of organisms is related (shared ancestry). Biologists have not agreed on a single definition, and the choice often depends on the group being studied.

Populations, species and gradual speciation

A population is a group of organisms of the same species living in the same area at the same time. Speciation is the splitting of one species into two or more. It usually happens when two populations stop interbreeding, for example because a mountain range or a stretch of sea separates them:

1. The populations live in different environments and change independently, so their traits gradually diverge.
2. Over many generations, differences in appearance, behaviour, chromosomes or breeding season build up.
3. Eventually the populations could not produce fertile offspring even if they met again: they have become separate species.

There is no single moment at which one species becomes two. Partway through, two populations may be partly different and partly able to interbreed, so deciding whether they are one species or two can be an arbitrary decision, and taxonomists often disagree. Speciation is covered fully in A4.1 Evolution and speciation.

The number of chromosomes in the nucleus is a characteristic feature of a species, and it varies widely between species. Some species have a few large chromosomes; others have many small ones.

• Humans have 46 chromosomes in each body cell.
• Chimpanzees have 48, as do our other closest relatives, gorillas and orangutans.

These are the only two numbers you need to learn. The comparison chart in the genome-size section below (switch it to Chromosome number) shows how wide the range is, from 2 in an Australian ant to 78 in dogs and chickens, and that the number has nothing to do with how complex an organism is.

Why diploid numbers are even

Most plant and animal cells are diploid: their nucleus holds two sets of chromosomes, one inherited from each parent. The chromosomes therefore come in homologous pairs with the same genes in the same order, and the diploid number (2n) is even. Human gametes are haploid, with one set of 23 (n = 23); fertilization restores 46. See D2.1 Cell and nuclear division for how meiosis halves the number.

The difference between 46 and 48 in humans and chimpanzees raises a question: what happened to one pair? The next section shows how karyograms answer it.

A karyotype is the number and type of chromosomes in a cell or organism. A karyogram is an image in which those chromosomes are arranged in homologous pairs, conventionally in order of decreasing length.

To make one, cells are grown in culture and stopped in metaphase of mitosis, when the chromosomes are most condensed. They are stained and photographed, and a cell in which no chromosomes overlap is chosen. The image of each chromosome is then sorted into its pair, today usually with software. Three features identify each chromosome:

• Length: human chromosome 1 is the longest, about five times the length of chromosome 21, the shortest. Pairs are numbered roughly by size.
• Centromere position: the centromere is the constriction where the sister chromatids are held together. Its position is fixed for each type: near the middle (metacentric), off-centre (submetacentric) or close to one end (acrocentric).
• Banding pattern: stains such as Giemsa produce a pattern of dark and light bands that is the same on both homologues and different for every type of chromosome.

The 23rd pair is the sex chromosomes. A female has two X chromosomes; a male has one X and a much smaller Y. Karyograms are used to find the sex of an individual and to detect chromosome abnormalities. One of the three people in the sorter has three copies of chromosome 21 (trisomy 21), the cause of Down syndrome; their karyotype is written 47,XY,+21.

Evidence that human chromosome 2 formed by fusion

Hypothesis: the common ancestor of humans and chimpanzees had 48 chromosomes, and in the human lineage two of them fused end to end to form chromosome 2. The two ancestral chromosomes correspond to chimpanzee chromosomes 2A and 2B (numbered 12 and 13 in older karyograms).

The hypothesis makes predictions that could have turned out to be false:

1. Banding: the banding of human chromosome 2 should match two ape chromosomes placed end to end. It does.
2. Telomeres in the middle: chromosomes normally carry telomeres, repeats of the sequence TTAGGG, only at their ends. If two ends fused, telomere repeats should be found inside chromosome 2. Sequencing found them in the long arm (band 2q13), arranged head to head, exactly as a fusion of two chromosome tips would leave them.
3. A second centromere: each ancestral chromosome had a centromere, so human 2 should carry the remains of a second one. There is an inactive centromere in 2q21, in the position matching the centromere of chimpanzee 2B.

The genome is all the genetic information of an organism: the complete base sequence of all its DNA. In humans it is the DNA of the nuclear chromosomes (one set of 23 holds about 3.1 billion base pairs) plus the small circular DNA of the mitochondria.

Unity within a species

Members of a species have almost all the same genes, in the same order, on the same chromosomes (apart from small structural variants). This shared organization is what allows homologous chromosomes to pair up and exchange sections during meiosis without genes being lost or duplicated. Any two humans have the same base at roughly 99.9% of positions in their genomes.

Diversity within a species: SNPs

Most of the differences that remain are single-nucleotide polymorphisms (SNPs): positions where one base varies between individuals, for example an A in some people and a C in others. A variant is usually counted as a SNP when the less common base is carried by at least 1% of the population. Different versions of a gene (alleles) usually differ by one or a few SNPs.

Here positions 4 and 7 are SNPs; the rest are identical. Over 100 million SNP positions are known in humans, but a typical person differs from the human reference genome at only about 4–5 million of its 3.1 billion positions.

Diversity between species

Genomes of different species differ in two ways:

• Size, the total amount of DNA, which varies enormously among eukaryotes. Genes can be duplicated or deleted, whole chromosome sets can be added (polyploidy), and the amount of non-coding DNA varies greatly.
• Base sequence: once two species have separated, differences build up independently in each. Human and chimpanzee genomes differ at about 1.2% of aligned bases, and distantly related species differ far more. Genes with vital functions, such as the gene for cytochrome c used in respiration, change slowly and stay recognizably similar even between very distant species.

Two members of different species differ far more in their DNA than two members of the same species.

Genome size is the total amount of DNA in one set of chromosomes (a haploid genome). It is given either as a number of base pairs, in megabase pairs (1 Mb = 10⁶ bp) or gigabase pairs (1 Gb = 10⁹ bp), or as a mass of DNA in picograms, the C-value (1 pg is about 978 Mb). For prokaryotes, the figure is the DNA content of one cell.

Using a database

Genome sizes for thousands of species are held in free online databases, for example the NCBI Genome database (sequenced genomes of all groups), the Kew Plant DNA C-values Database and the Animal Genome Size Database. To compare genome size with complexity:

1. Choose species from different taxonomic groups (bacteria, fungi, plants, invertebrates, vertebrates).
2. Look up each genome size and convert to the same unit.
3. Plot the values on a log scale, because they span more than five orders of magnitude.
4. Compare with a measure of complexity, such as the number of cell types.

Does genome size follow complexity?

Only very loosely. Prokaryotes have the smallest genomes, and single-celled eukaryotes such as yeast have smaller genomes than most multicellular ones. But among eukaryotes there is no simple relationship:

• An onion has about five times as much DNA as a human, and the plant Paris japonica almost 50 times as much.
• Among animals, the axolotl (a salamander) has about ten times as much DNA as a human and the marbled lungfish about 40 times, while the pufferfish has about one-eighth.
• Much of a large genome is non-coding DNA, especially repeated sequences, rather than extra genes. The human genome has only about 20,000 protein-coding genes.

Whole-genome sequencing means working out the base sequence of an organism’s entire genome. The first genome of a free-living organism, the bacterium Haemophilus influenzae, was sequenced in 1995. The Human Genome Project took 13 years (1990–2003) and cost about US$3 billion.

Faster and cheaper

Sequencing technology has improved dramatically. Machines now read millions of DNA fragments in parallel, so a human genome can be sequenced in a day or two for a few hundred US dollars. As a result, the number of species with a sequenced genome is rising very rapidly, and millions of individual human genomes have been sequenced. The Earth BioGenome Project aims to sequence every known species of eukaryote.

Current use: evolutionary relationships

Comparing the base sequences of whole genomes shows how closely species are related: the more differences, the longer ago they shared a common ancestor. Genome comparisons have confirmed that chimpanzees and bonobos are our closest living relatives, revealed the chromosome 2 fusion, shown that some Neanderthal DNA is present in most modern humans, and are redrawing the classification of many groups (A3.2 Classification and cladistics).

Potential future use: personalized medicine

If a patient’s genome is known, treatment could be matched to it:

• predicting a person’s risk of particular diseases from the alleles they carry, so that screening or prevention can start early;
• choosing drugs and doses that suit the person’s genes. Some people carry variants of a liver enzyme gene (CYP2C19) that stop them activating the anti-clotting drug clopidogrel, so another drug works better for them;
• sequencing the genome of a person’s cancer cells to choose a drug that targets the mutations driving that tumour.

Personalized medicine raises questions about the privacy of genetic data and about who can afford it.