A3.1 Diversity of organisms | IB DP Biology

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“What is a species?” sounds like a question with a textbook answer. It is not. There are several competing definitions, each works well for some organisms and badly for others, and the boundary between two populations and two species is often a judgement call. This topic is about living with that uncertainty — and about the tools, from karyograms to genome sequencing, that biologists use to describe diversity anyway.

🎯What you need to be able to do

Explain why variation is a defining feature of life and the basis for classification.
Distinguish the morphological species concept from the biological species concept, and outline the problems with each.
Write binomial names correctly and explain what each part tells you.
Explain why speciation makes it hard to tell populations from species.
State that chromosome numbers vary between species (humans 46, chimpanzees 48) and why diploid numbers are even.
Classify chromosomes in a karyogram, and evaluate the evidence that human chromosome 2 arose by fusion.
Describe the unity and diversity of genomes within and between species, compare genome sizes, and outline uses of whole genome sequencing.
AHL Explain why the biological species concept fails for asexual organisms and bacteria, why different chromosome numbers prevent fertile hybrids, how to build a dichotomous key, and how environmental DNA barcoding identifies species.

📚The biology

Variation as a defining feature of life

No two organisms are identical in all their traits — not even identical twins, whose fingerprints differ. Variation is everywhere, but it is not random chaos: organisms fall into groups that share many traits, and those groups fall into larger groups. These patterns of variation are what make it possible to name and classify organisms at all.

Species as groups with shared traits

The oldest species concept, used by Carl Linnaeus in the eighteenth century, is the morphological species concept: a species is a group of organisms that share a set of observable traits — body form, structure, appearance — that distinguish them from other groups. It is still how most museum specimens and fossils are classified, because appearance is often all there is to go on.

Its weakness is that appearance can mislead. Males and females of one species can look completely different; young stages can be unrecognizable as the same species as adults; and unrelated species can look alike.

The binomial system

Every species has a two-part scientific name, written in italics (or underlined when handwritten):

The first part is the genus, with an initial capital letter.
The second part identifies the species within the genus, all in lowercase.

For example, Homo sapiens (humans) and Panthera leo (lion). Species in the same genus, such as Panthera leo and Panthera tigris, share many traits because they are closely related. After its first use in a text, a name can be abbreviated: P. tigris. The system gives every species one internationally recognized name, avoiding the confusion of common names that differ between languages and regions.

The biological species concept

The biological species concept defines a species as a group of organisms that can interbreed and produce fertile offspring. It focuses on the thing that actually keeps species separate — whether genes can flow between them.

It has problems too:

It cannot be applied to fossils, whose breeding cannot be tested.
It is hard to test for populations that never meet in the wild; breeding in captivity does not show that they would breed naturally.
Some clearly distinct species do produce fertile hybrids occasionally (many plants, and some birds and mammals).
It does not work at all for organisms that do not reproduce sexually (see the AHL section below).

Because no single definition works for all organisms, several species concepts are in use, including ones based on DNA sequences and on evolutionary lineages. Which one a biologist uses depends on the organisms being studied.

Populations or species?

Speciation is the splitting of one species into two or more. It usually happens gradually: populations that stop interbreeding slowly accumulate differences over many generations. There is no single moment when one species becomes two. At any point during this process, two populations may be partly different, interbreed occasionally, or produce offspring of reduced fertility, and whether to call them one species or two is an arbitrary decision.

Chromosome numbers

Different species have different numbers of chromosomes. Humans have 46 chromosomes in each body cell; chimpanzees have 48. Chromosome numbers range from a handful to several hundred, and they are not related in any simple way to how complex the organism is.

In diploid cells, chromosomes come in homologous pairs, one of each pair inherited from each parent. That is why the diploid number is always even.

Karyotypes and karyograms

A karyotype is the number and type of chromosomes in a cell. A karyogram is an image of the chromosomes from a cell, photographed at metaphase of mitosis when they are most condensed, and arranged in homologous pairs in order of size. Chromosomes are classified by three features:

Length
Pairs are numbered from longest (1) to shortest. The sex chromosomes are placed at the end.

Centromere position
Central (arms equal), off-centre, or very near one end (one arm tiny).

Banding pattern
Staining produces a pattern of light and dark bands that is characteristic of each chromosome, so homologues can be matched.

Karyograms are used to deduce sex (XX or XY) and to detect chromosome abnormalities such as an extra chromosome 21 in Down syndrome (D2.1).

Human chromosome 2: a testable hypothesis

Humans have one pair of chromosomes fewer than chimpanzees, gorillas and orangutans. The hypothesis is that human chromosome 2 formed by the fusion of two separate chromosomes that are still separate in the other great apes (numbered 12 and 13 in older schemes; now usually called 2A and 2B). The evidence:

Banding patterns of human chromosome 2 match those of the two ape chromosomes placed end to end.
Telomere sequences, which are normally found only at the ends of chromosomes, occur in the middle of human chromosome 2, exactly where the fusion would have happened.
Human chromosome 2 has the remains of a second, inactive centromere in the position predicted by the fusion.
The gene sequences along chromosome 2 correspond, in order, to those along the two ape chromosomes.

This is a testable hypothesis: it made predictions (telomeres in the middle, a vestigial centromere) that could have turned out false, and did not. That separates it from non-testable statements — claims that no possible observation could contradict.

The genome: unity within a species

The genome is all the genetic information of an organism — the entire base sequence of its DNA, including mitochondrial and chloroplast DNA. Members of one species share almost all of their genome: any two humans are about 99.9% identical in base sequence. The differences that exist are mostly single-nucleotide polymorphisms (SNPs), positions where a single base differs between individuals. SNPs give each person a unique genome and account for much of the variation within the species.

Diversity of eukaryote genomes

Genomes differ between species in two ways:

Size — the total amount of DNA, usually given in base pairs.
Base sequence — the order of bases, which determines the genes present.

The variation between species is much larger than the variation within a species. Humans and chimpanzees differ by a little over 1% of base sequence, far more than any two humans.

Comparing genome sizes

Genome sizes for thousands of species are available in online databases, and comparing them gives a surprising result: genome size is not a good predictor of complexity. The human genome is about 3.1 billion base pairs. Some amphibians, lungfish and flowering plants have far larger genomes: the Japanese canopy plant Paris japonica has about 149 billion base pairs. Much of the difference is due to non-coding DNA and repeated sequences, not to extra genes.

Whole genome sequencing

Sequencing a complete genome has become dramatically faster and cheaper. The first human genome took over a decade and billions of dollars across an international project; the cost of sequencing one human genome fell from around 100 million US dollars in 2001 to under a thousand by the early 2020s, and a genome can now be sequenced in a day or two.

Current use: evolutionary relationships
Comparing whole genomes of different species shows how closely related they are, when lineages diverged, and which genes were gained or lost. It has redrawn parts of the tree of life.

Potential future use: personalized medicine
A patient’s genome could show which drugs will work for them, what dose is safe, and which diseases they are at risk of, so treatment and screening can be tailored to the individual.

Where the biological species concept breaks down AHL

Asexually reproducing species never interbreed, so “can they produce fertile offspring together?” has no meaning. Every individual would be its own species. Many plants, fungi, protists and some animals reproduce entirely or mostly asexually.
Bacteria reproduce asexually, and they also exchange genes by horizontal gene transfer — taking up DNA from their surroundings or receiving plasmids from other cells, even of distantly related species. Genes move between what would otherwise be separate groups, so there is no clean boundary of gene flow for the concept to use.

For these organisms, species are defined by other means, typically similarity in DNA sequence.

Chromosome number as a shared trait AHL

Members of one species share the same chromosome number. When two closely related species with different numbers cross, their hybrid offspring inherit an odd set of chromosomes that cannot pair properly in meiosis. Without pairs, the hybrid cannot produce viable gametes, so it is usually infertile. The mule is the classic example: a horse (64 chromosomes) crossed with a donkey (62) gives a mule with 63 (A4.1). A difference in chromosome number is therefore an effective barrier between species.

Dichotomous keys AHL

A dichotomous key identifies an organism through a series of steps, each offering two alternatives about an observable feature. Each choice leads either to the next step or to a name. You are expected to have built one for local plants or animals.

To build a good key:

use features that are easy to see and do not change with age, season or sex;
make each pair of statements mutually exclusive (“leaves with toothed edges” / “leaves with smooth edges”), never vague (“large leaves”);
split the group roughly in half at each step, so the key is short;
number the steps and test the key on specimens someone else chooses.

Environmental DNA and barcodes AHL

Organisms constantly shed DNA into their surroundings in skin cells, mucus, faeces, pollen and gametes. This environmental DNA (eDNA) can be extracted from a sample of water, soil or even air. Short, standard gene regions that differ between species act as DNA barcodes — for animals, often part of the mitochondrial gene COI. The barcodes in a sample are amplified by PCR (D1.1), sequenced and compared with a reference database to list the species present.

eDNA barcoding lets the biodiversity of a habitat be surveyed rapidly, without seeing, catching or disturbing the organisms. It detects rare, shy, nocturnal and microscopic species that traditional surveys miss, and can detect invasive species early. Its limitations: it shows that DNA is present, not how many individuals there are or whether they are alive, and species not in the reference database cannot be named.

✏️Worked example

Genome sizes: Escherichia coli 4.6 × 10⁶ base pairs; Homo sapiens 3.1 × 10⁹ base pairs; Paris japonica 1.49 × 10¹¹ base pairs.
(a) Calculate how many times larger the human genome is than the E. coli genome, and how many times larger the Paris japonica genome is than the human genome.
(b) A student concludes that Paris japonica must be a more complex organism than a human. Evaluate this conclusion.
(c) Humans have 46 chromosomes and chimpanzees 48. State the haploid number of each species, and outline one piece of evidence that explains the difference.

(a) Divide the larger genome by the smaller:

\[ \frac{3.1 \times 10^{9}}{4.6 \times 10^{6}} = 670 \qquad \frac{1.49 \times 10^{11}}{3.1 \times 10^{9}} = 48 \]

The human genome is about 670 times larger than that of E. coli; the Paris japonica genome is about 48 times larger than the human genome.

(b) The conclusion is not supported. Genome size is the total amount of DNA, not the number of genes or the amount of information that is used. A large proportion of many eukaryote genomes is non-coding and repetitive DNA, and some plants have duplicated their whole genome several times (polyploidy). Across many species, genome size does not correlate with complexity — humans are, by most measures, more complex than a plant, yet have a much smaller genome. Three species are also far too few to support any general conclusion; a database of many species within each group would be needed.

(c) Haploid numbers: human 23, chimpanzee 24. Evidence: human chromosome 2 contains telomere sequences in its middle and a second, inactive centromere, and its banding pattern matches two separate chimpanzee chromosomes placed end to end — indicating that two ancestral chromosomes fused in the human lineage.

Check it. With standard form, divide the numbers and subtract the powers separately: 3.1 ÷ 4.6 ≈ 0.67 and 10⁹⁻⁶ = 10³, giving 0.67 × 10³ = 670. For the second ratio, 1.49 ÷ 3.1 ≈ 0.48 and 10¹¹⁻⁹ = 10², giving 48. Any answer in the millions means the powers were multiplied instead.

Confusing genome size with gene number. Examiners ask about genome size precisely because the intuitive answer — bigger genome, more complex organism — is wrong. Genome size is measured in base pairs of DNA, and most of the variation in size is in DNA that does not code for proteins.

📝Practise

Work through these on paper, then reveal the answer. Questions 5 and 6 are AHL.

1. The scientific name of the domestic dog is written by a student as “canis Familiaris”. Identify two errors and state what each part of the name tells you.

Errors: the genus name should have a capital letter (Canis) and the species name should be lowercase (familiaris); the name should also be italicized (or underlined when handwritten). Correct: Canis familiaris. The first part, Canis, is the genus, shared with closely related species such as the wolf; the second part identifies the species within that genus.

2. Outline two difficulties in applying the biological species concept.

Any two of: it cannot be applied to fossils, since breeding cannot be observed; populations that are geographically separated cannot be tested for interbreeding in the wild; some distinct species produce fertile hybrids; it cannot be applied to asexually reproducing organisms, which do not interbreed at all; during gradual speciation populations may partly interbreed, so the boundary is arbitrary.

3. State three features used to arrange chromosomes into pairs in a karyogram.

(1) Length of the chromosome — pairs are numbered from longest to shortest. (2) Position of the centromere. (3) Banding pattern after staining.

4. Explain what is meant by a single-nucleotide polymorphism, and why genomes of individuals in the same species are similar but not identical.

A single-nucleotide polymorphism (SNP) is a position in the genome where the base differs between individuals of a species — for example some people have A and others G at that position. Members of a species share almost all of their base sequence because they share the same genes, inherited from common ancestors, in the same arrangement. But mutations have produced SNPs and other small differences throughout the genome, and sexual reproduction reshuffles them, so each individual has a unique combination.

5. AHL Explain why the biological species concept is particularly difficult to apply to bacteria.

Bacteria reproduce asexually by binary fission, so they do not interbreed, and “producing fertile offspring together” cannot be used to group them. In addition, bacteria exchange genes by horizontal gene transfer (for example transfer of plasmids, or uptake of DNA from the environment), and this can happen between different species. Genes therefore flow between groups that would otherwise be distinct, so there are no clear reproductive boundaries for the concept to rely on.

6. AHL Suggest two advantages and one limitation of using environmental DNA barcoding to survey the fish in a river.

Advantages (any two): it is rapid, since one water sample can reveal many species at once; it does not require catching or disturbing the fish; it can detect rare, elusive or nocturnal species that netting or observation would miss; it can give early warning of an invasive species. Limitation (any one): it does not show how many fish are present or their sizes; DNA may come from dead fish or have been carried downstream from elsewhere; species not in the reference database cannot be identified; contamination can give false positives.

🔗Go deeper — other people’s work

These are external resources, not mine. If one stops working, tell me and everything above it on this page still stands.

NCBI Genome database and the Animal Genome Size Database — real genome sizes across taxonomic groups, for the database skill in this topic.
National Human Genome Research Institute — the Cost of sequencing a human genome page, with the data behind the fall in cost.
Barcode of Life Data System (BOLD) — the reference library used to identify species from DNA barcodes.