1The idea in one paragraph

No two living things are identical, yet living things clearly fall into groups. A species is the name for those groups, and this subtopic is about how hard it is to draw their edges. Linnaeus drew them by looking; modern biologists usually draw them by asking who can breed with whom, and every definition breaks somewhere, because species are made by gradual splitting and a gradual process has no sharp line. Underneath the visible traits sits the genome: all the genetic information of an organism. Genomes are almost identical within a species, measurably different between species, and wildly different in size across life, in ways that do not follow how complex the organism looks. Reading chromosomes and sequencing genomes are how biologists now see all of this directly.

2Variation, and the first idea of a species

Look at any class photograph: height, eye colour, face shape. Variation between individuals is everywhere, and not only in humans. No two organisms of any species are identical in every trait; even identical twins differ slightly, because mutations arise in cell division and the environment leaves its mark. Variation is a defining feature of life. It also has patterns: similarities come in clusters, and every lion shares a set of traits no leopard has. Those clusters are the basis of naming and classifying organisms.

The oldest way to use them is the morphological species concept: a species is a group of organisms that share a distinct set of observable traits. This is how Carl Linnaeus worked in the eighteenth century. He had specimens, not DNA, so "looks the same in the ways that matter" was the only test available. Figure 1 sets it beside the concept that largely replaced it.

The morphological concept still does real work. A palaeontologist with a fossil, or a museum curator with a pinned beetle, has nothing else to go on. But it fails in two directions. Males and females of one species can look nothing alike: a male mallard duck is green-headed and a female is mottled brown. And two species can look almost identical, because looking alike is not the same as being able to interbreed.

3Naming: the binomial system

Common names are local: "robin" means one bird in Britain and a different, larger one in North America. Linnaeus fixed this with the binomial system: every species has a two-part Latin name, recognised in every language.

• The first part is the genus. A genus is a group of closely related species that share many traits.
• The second part is the species name. It distinguishes this species from the others in the same genus.
• The genus starts with a capital letter; the species name is all lower case.
• In print, the whole name is in italics. By hand, where italics are impossible, underline it.
• After first use, the genus may be shortened to its initial: Panthera leo, then P. leo.

Genus first, capital letter. Species second, lower case. Italic in print, underlined by hand: Panthera leo.

So Panthera leo (lion), Panthera pardus (leopard) and Panthera tigris (tiger) are three species in one genus, and the shared first word tells you at once that they are close relatives.

4The biological species concept, and where it strains

The definition you will use most is the biological species concept: a species is a group of organisms that can interbreed and produce fertile offspring. The last two words carry the weight. A horse and a donkey can mate and produce a mule, but a mule is sterile, so horses and donkeys stay separate species. The test is not "can they have young together?" but "can those young go on to breed?"

It is a better test than looks alone, because it goes to the heart of what a species is: a pool of genes that mixes within itself and not with others. But it has well-known challenges, and the guide expects you to know that they exist and that competing definitions exist too.

• Fossils cannot be tested. Nobody can check whether two extinct forms could have interbred.
• Populations that never meet cannot be tested. Two populations of frogs on different islands might be able to interbreed in principle, but they never do, and nobody may ever find out.
• Some separate species do produce fertile hybrids. Grey wolves and coyotes, for example, can interbreed and their hybrids are fertile, yet they are generally treated as different species.
• Some organisms do not interbreed at all. Species that reproduce only asexually have no interbreeding to test. HL students take this further in section 8.

Because of these gaps, competing definitions exist, such as an ecological concept (a species occupies its own niche) and a phylogenetic concept (the smallest group recognisable from shared ancestry in its DNA). Know that they exist; the details are not examined.

Why the line is sometimes arbitrary. New species form by speciation: one species splitting into two or more. This usually happens slowly. A population is divided, the two parts stop exchanging genes, and over many generations they become more and more different. At the start they are clearly one species. At the end they are clearly two. In the middle, where Figure 2 puts the question mark, they may still produce some hybrids, fewer of which are fertile, and whether you call them one species or two is a judgement, not a measurement.

The Ensatina salamanders of California are a real case: a chain of populations around the Central Valley, each interbreeding with its neighbours, whose two ends meet in the south and behave largely as separate species. One species or several? Biologists still disagree, and that is the point.

5Chromosome numbers and karyograms

Every species has a characteristic number of chromosomes, and the numbers vary widely. You need two examples and one rule.

• Humans have 46 chromosomes in each body cell. Chimpanzees have 48.
• Diploid cells almost always have an even number, because chromosomes come in homologous pairs: one of each pair came from the mother and one from the father. Humans have 23 pairs.

Other species run from a handful to hundreds: a fruit fly has 8, a pea plant 14, a dog 78. You do not need to learn those; they are here to show the range.

Karyotyping. A karyotype is the number and appearance of the chromosomes in a cell. A karyogram is the picture that displays them, sorted into pairs. To make one, cells that are dividing (white blood cells, or fetal cells, grown in a dish) are stopped in metaphase, when chromosomes are most condensed and easiest to see. The cells are burst on a slide, the chromosomes stained, photographed, and arranged.

Sorting uses three features, all shown in Figure 3.

1. Length. Pairs are numbered from the longest (1) to the shortest.
2. Centromere position. The centromere is the constriction that holds the chromosome together. It can be near the middle (metacentric), off-centre (submetacentric) or close to one end (acrocentric).
3. Banding pattern. Stains bind unevenly and leave a pattern of light and dark bands that is the same on both members of a pair and different on every other pair.

In a human karyogram, pairs 1 to 22 are the autosomes, and the last pair is the sex chromosomes: XX in a female, XY in a male. A karyogram can therefore show sex, and it shows whole-chromosome changes, such as an extra copy of one chromosome.

Human chromosome 2: a hypothesis you can test. If humans and chimpanzees share a recent common ancestor, why do we have one pair of chromosomes fewer? The fusion hypothesis says that two chromosomes that are still separate in the other great apes joined end to end in the human lineage, forming human chromosome 2. In chimpanzees those two are now called 2A and 2B; older numbering called them 12 and 13, which is the wording the guide uses.

A good hypothesis makes predictions that could turn out false. This one makes several, and Figure 4 marks them.

Evaluating it. The evidence is strong because it is independent: counts, microscope banding and DNA sequence all point the same way, and the telomere result was a prediction that could have failed. The weaknesses are small. Nobody saw the fusion, so it is an inference, and the telomere repeats at the fusion site are shorter and more degraded than at a real chromosome tip, although decay by mutation is what an ancient fusion predicts. The alternative, that the ancestor had 46 and the ape lineages split a chromosome, needs more events and does not explain telomere sequence in the middle of human chromosome 2.

Testable and non-testable. "Human chromosome 2 formed by fusion of two ancestral chromosomes" is a testable hypothesis: it predicts things you can look for, and could be shown false if they are missing. "The fusion was the most important event in human history" is not testable: no observation could confirm or refute it, because it is a value judgement. Science deals only in the first kind. A Paper 1B or Paper 2 question may give you a list of statements and ask which could be tested.

6Genomes: unity within a species, diversity between them

The genome is all the genetic information of an organism: every base of its DNA, genes and the stretches between them.

Unity within a species. Two members of a species share almost all of their genome. Two unrelated humans are roughly 99.9% identical base for base. Most of the differences are single-nucleotide polymorphisms (SNPs): positions where one person has one base and another person has a different one, as in Figure 5.

0.1% sounds tiny, but the human genome is about 3,100 million base pairs long, and 0.1% of that is about 3 million differences. That is enough to make every person genetically unique (identical twins aside) and to power DNA fingerprinting, ancestry testing and medical research.

Diversity between species. Genomes of different species vary in two ways.

• Base sequence. Variation between species is much larger than variation within one. Human and chimpanzee genomes are close to 99% identical when single bases are compared in the parts that line up, which is still around ten times the within-human difference. Between a human and a mouse, the difference is far bigger again.
• Genome size, the total amount of DNA. This varies enormously, as the next part shows.

Genome size and complexity. The guide wants you to take genome sizes from a database, such as the NCBI Genome database or the Plant DNA C-values Database, and compare them with complexity. Sizes are given in megabase pairs (Mb), millions of base pairs, or as picograms of DNA per nucleus. Compare like with like: one unit, and the haploid genome (one set) each time. Figure 6 plots rounded values.

Notice the axis first. It is logarithmic: each gridline is ten times the one before, because the values span more than 30,000-fold. On a normal axis every bar but the last would be invisible.

Now read it. Prokaryotes such as E. coli have small genomes, and among the simplest eukaryotes, such as yeast, genomes are small too. So at the broadest scale, bigger genomes go with more complex life. But inside the eukaryotes the pattern collapses.

A nematode worm made of about a thousand body cells has roughly as many protein-coding genes as a human, about 20,000 each. The conclusion to write: genome size does not reliably reflect complexity. Much of a large genome is non-coding DNA, especially repeated sequences that have copied themselves over evolutionary time, and some plants carry several whole sets of chromosomes (bread wheat carries six). Size tells you how much DNA there is, not how much it does.

7Whole genome sequencing

Whole genome sequencing reads the entire base sequence of an organism's genome. The Human Genome Project took about thirteen years and a few billion US dollars, finishing in 2003; today a human genome can be sequenced in about a day for a few hundred dollars. That rising speed and falling cost is what turned sequencing from a one-off project into a routine tool.

Current uses.

• Research into evolutionary relationships. Comparing whole genomes shows how closely species are related and when lineages split. Sequencing Neanderthal DNA from fossil bone showed that most people with non-African ancestry carry a small percentage of Neanderthal DNA, so the two groups interbred.
• Tracking pathogens. Sequencing a virus or bacterium from many patients shows how an outbreak is spreading and when a new variant appears, as happened throughout the COVID-19 pandemic.
• Diagnosing rare genetic disease, especially in newborns, where finding the mutation quickly can change treatment.

Potential future uses. The one the guide names is personalised medicine: choosing a drug and a dose to fit the patient's genome. Some people carry variants of liver enzyme genes that make them process certain drugs too slowly or too fast; sequencing first would avoid the harm or the wasted treatment. Wider screening could also predict the risk of diseases years ahead. Each of these raises questions of privacy and of who may see the data, which is fair material for a "discuss" question.

11Linking questions

What might cause a species to persist or go extinct? Variation is the raw material. A species with many alleles is more likely to contain individuals that survive a new disease or a changed climate (D4.1); a species reduced to a few near-identical individuals has little for selection to act on. A4.2 takes up the human causes of extinction.

How do species show both continuous and discontinuous variation? Height varies continuously, because many genes and the environment contribute; blood group and chromosome number vary discontinuously, in categories. Species are discontinuous clusters, yet section 4 showed that the divide between them forms continuously.