IB Biology · Theme A · A3.1

Diversity of Organisms

What makes a species — and why do genomes vary the way they do?

Guiding questions

What is a species?

What patterns are seen in the diversity of genomes within and between species?

Part one

What makes a species?

A3.1.1 – A3.1.5

A3.1.1

Variation is a defining feature of life

No two individuals are identical in all their traits.

The patterns of variation between organisms are complex, and they are the basis for naming and classifying organisms.
Some traits vary continuously: a whole range of values with intermediates, usually from many genes plus the environment, like human height.

Why it mattersThe pattern a trait follows is often the first clue to how many genes control it.

A histogram of the heights of 1000 adults in 5 cm classes from 150 to 200 cm: a bell-shaped spread with most people between 165 and 180 cm and every value possible. Label: many genes plus the environment

A bar chart of ABO blood groups in the UK: O 48%, A 38%, B 10% and AB 4%. Only four categories, no intermediates. Label: one gene with three alleles

A3.1.1

…and some traits fall into categories

The second recognisable pattern is discrete variation: a trait sorts cleanly into a small number of separate categories, with no intermediate values possible.

Discrete variation is usually controlled by one gene or a small number of genes, and is largely unaffected by environment.
Human ABO blood group is the standard example: every person is A, B, AB or O — never something in between, and never a continuous blend of two groups.

Why it mattersFew genes, sharp categories: discrete variation is usually the signature of one or two genes with a large effect, unlike continuous variation's many small contributors.

Two small brown pipistrelle bats hanging side by side under a wooden beam, looking almost identical: the common pipistrelle, Pipistrellus pipistrellus, which calls at about 45 kHz, and the soprano pipistrelle, Pipistrellus pygmaeus, which calls at about 55 kHz. They were recognised as two species only in the 1990s

A3.1.2

Species as groups with shared traits

The original idea of a species, used by Linnaeus, is a group of organisms with shared traits that can be observed.

This morphological concept groups organisms by body shape, structures and appearance.
It is still a practical first step, for example when classifying fossils or specimens in the field.

LimitationOrganisms that look almost identical can be separate species, like these two pipistrelle bats, which differ in their calls and their DNA.

A3.1.3

One name, recognised worldwide

In the binomial system, the first part of the name is the genus and the second distinguishes the species.

The genus has a capital letter and the species name is lower case: Panthera leo, the lion. Both are written in italics (underlined by hand).
Species in the same genus have similar traits: Felis catus and Felis silvestris are close relatives.
Sharing only the second word means nothing: Conus catus is a snail and Ameiurus catus a fish.

Why it mattersOne international name avoids the confusion of many local common names.

Four illustrations. Felis catus, the domestic cat, and Felis silvestris, the European wildcat, share the genus Felis and are close relatives. Conus catus, a cone snail, and Ameiurus catus, the white catfish, share only the second word, catus, and are not closely related

A horse (2n = 64) and a donkey (2n = 62) can mate; their hybrid, the mule, has 63 chromosomes and is sterile, so horses and donkeys are separate species

A3.1.4

The biological species concept

A species is a group of organisms that can breed and produce fertile offspring.

A horse and a donkey can mate, but their mule is sterile, so they are separate species.
Challenges: it cannot be tested on fossils, on organisms that reproduce asexually, or on populations that never meet; and some hybrids between species are fertile.

Competing definitionsBecause of these problems, other species concepts are also used, based on appearance, ecology or DNA.

A3.1.5

Where the boundary blurs

Speciation is the splitting of one species into two or more. It usually happens gradually, as populations become more and more different.

So whether two populations count as the same or different species can be an arbitrary decision.
In a ring species, each population interbreeds with its neighbours, but where the ring closes the two end populations rarely or never do.

Why it mattersThere is no single point in the ring where one species becomes two.

A ring species: a chain of salamander populations around California’s hot, dry Central Valley, coloured from blue to orange. Each interbreeds with its neighbours, but where the two ends of the ring meet in the south, the two forms live side by side and rarely or never interbreed

A fossil lineage drawn as a column of shapes from older rock at the bottom to younger rock at the top, changing gradually in size and colour from species A to species B. Dashed lines ask where the boundary between the species should be drawn

A3.1.5

Related, but reproductively isolated

A chronospecies is what the biological species concept (the BSC from the previous slides — the rule that a species can interbreed to produce fertile offspring) runs into when the same fuzzy boundary shows up along time instead of geography.

The earliest and latest members of one continuous fossil lineage are directly related — each descended from the last — yet they would almost certainly not have been able to produce fertile offspring together, had they ever coexisted.
The interbreeding test can never actually be applied across time — the two forms never coexist to be tested — so drawing a line between one named chronospecies and the next is unavoidably somewhat arbitrary.

Why it mattersRing species (space) and chronospecies (time) both show that close relatives don't always pass the interbreeding test — a real limitation of the biological species concept.

Quick check

A horse and a donkey can mate, and their mule offspring is healthy and strong. Under the biological species concept, are horses and donkeys the same species?

Yes — they can mate successfully

No — the mule is sterile, so no gene flow continues between them

Yes — mules can eventually reproduce with each other

It depends which parent is the mother

Correct answer: No, separate species. The BSC requires fertile offspring, not just successful mating — a sterile hybrid means no gene flow crosses the species boundary.

Part two

Chromosomes and genomes

A3.1.6 – A3.1.11

Photographs of six species with their diploid chromosome numbers: fruit fly, Drosophila melanogaster, 2n = 8; garden pea, Pisum sativum, 14; onion, Allium cepa, 16; maize, Zea mays, 20; horse, Equus caballus, 64; dog, Canis familiaris, 78. Every number is even, because chromosomes come in homologous pairs

A3.1.6

Chromosome numbers differ by species

Each species has a characteristic number of chromosomes, and the number varies widely between plant and animal species.

Diploid numbers include: fruit fly 8, garden pea 14, onion 16, maize 20, horse 64 and dog 78.
The diploid number is normally even, because chromosomes occur in homologous pairs, one of each pair from each parent.
Chromosome number does not follow size or complexity: some ferns have over a thousand chromosomes, and some ants have only two.

Know for the examThe guide's example: humans have 46 chromosomes and chimpanzees have 48.

A3.1.7

Reading a karyogram

A karyotype is a cell's full chromosome complement; a karyogram is the image made by photographing, cutting out and pairing those chromosomes.

Chromosomes are conventionally ordered by three criteria:
- Size (largest first)
- Centromere position
- Banding pattern
A karyogram also reveals biological sex directly: two X chromosomes for a female, one X and one Y for a male.
This is also how the chromosome 2 fusion hypothesis gets tested: a fused chromosome should show both original banding patterns joined end to end, with a leftover fusion site and often a second, non-functional centromere — exactly what human chromosome 2 shows.

Nature of scienceThis makes the fusion hypothesis genuinely testable — it predicts a banding and centromere pattern, a prediction that could have failed.

Photograph of an unsorted human male metaphase chromosome spread

Real chromosome spread

Courtesy: NHGRI

A3.1.7

From spread to karyogram

A karyogram arranges the chromosomes in homologous pairs, ordered by size, so that each one can be classified.

The 22 autosome pairs are numbered roughly from longest (1) to shortest (22); the sex chromosomes, X and Y, come last.
Each chromosome is matched with its partner by length, centromere position and banding pattern.
This karyogram has one X and one Y, so it is from a male. A female has two X chromosomes.

ClassifyMeasure the length, find the centromere, then match the dark and light bands.

A real human male karyogram with the 22 pairs of autosomes arranged in rows from pair 1, the largest, to pair 22, followed by the X and Y chromosomes, each numbered underneath. Each pair shows two chromosomes of matching length, centromere position and dark and light banding. Labels point to the centromere of a chromosome 1, a homologous pair (chromosome 6), the banding pattern on a chromosome 3, the printed pair number under pair 15, and the larger X and smaller Y chromosome at the end.

Karyogram: NHGRI, public domain (Wikimedia Commons)

Left, the genome drawn as a set of chromosomes, with one gene highlighted. Right, the base sequence of that gene, then two alleles of it from two individuals that differ at one base: a single-nucleotide polymorphism. A note says members of a species share most of their genome

A3.1.8

Gene, allele, genome

Members of the same species share, overwhelmingly, the same genes — individual diversity comes from different alleles of those genes.

Worth keeping distinct:
- Gene — a length of DNA that codes for a specific product
- Allele — one particular version of a gene
- Genome — an organism's entire DNA complement
Most of the genetic difference between two individuals of the same species is single-nucleotide polymorphisms (SNPs) — single-base differences scattered through the genome — rather than differences in which genes are present at all.

A3.1.9

The C-value paradox

Eukaryote genomes vary along two separate axes: overall size (total DNA) and base sequence (nucleotide order).

Genome size and gene number are only loosely related.
Some salamanders have genomes many times larger than the human genome without carrying proportionally more genes; the explanation is that much of a large genome is non-coding DNA — introns, repeats and regulatory regions that don't code for protein.
Sequence variation between species is also far larger than variation within a species, where members are typically distinguished only by SNPs.

Two bar charts. Genome size in billions of base pairs: fruit fly 0.14, human 3.1, axolotl 32. Protein-coding genes in thousands: fruit fly 14, human 20, axolotl 23. The axolotl genome is about ten times ours, with a similar number of genes

Horizontal bars on a log scale of genome sizes from databases: E. coli 4.6 million base pairs, baker’s yeast 12 million, Arabidopsis 135 million, fruit fly 140 million, human 3.1 billion, bread wheat 16 billion, axolotl 32 billion and the fork fern Tmesipteris 160 billion

A3.1.10 · Skill

Comparing genome sizes

Genome size is the total amount of DNA, in base pairs: millions (Mb) or billions (Gb).

Look up genome sizes for different groups in a database such as NCBI Genome, the Animal Genome Size Database or Kew’s Plant DNA C-values database.
Compare size with complexity: the human genome is 3.1 billion base pairs, but wheat, salamanders and some ferns have far larger ones.

ConclusionGenome size is not a good guide to how complex an organism is: much of a large genome is non-coding DNA.

A3.1.11

Uses of whole genome sequencing

Whole genome sequencing reads an organism’s entire DNA base sequence.

It is getting much faster and cheaper: the first human genome took 13 years; now one costs a few hundred dollars and takes about a day.
Now: research into evolutionary relationships, by comparing whole genomes; also tracing disease outbreaks.
In future: personalized medicine, choosing treatments to suit a person’s genome.

Why it mattersThe more similar two genomes are, the more recently the species shared an ancestor.

A line graph on a log scale of the approximate cost of sequencing one human genome: about 100 million dollars in 2001, 10 million in 2007, 10 000 in 2011, 1250 in 2015 and 500 in 2022. A panel of uses: now, comparing genomes to work out evolutionary relationships and tracing outbreaks; in future, personalized medicine. The first genome took 13 years; now it takes about a day

Key vocabulary — species and genomes

Worth being able to define in a single sentence each

Species

Under the biological species concept, a group able to interbreed and produce fertile offspring.

Binomial name

A two-part scientific name (genus + species epithet) unique to one species.

Karyotype / karyogram

A cell's chromosome complement / the ordered image of its chromosomes.

Gene / allele / genome

A DNA sequence coding for a product / one version of a gene / an organism's entire DNA.

SNP

Single-nucleotide polymorphism — a one-base difference in DNA sequence between individuals.

Non-coding DNA

DNA that doesn't code for protein, including introns and repeated sequences.

Part three · HL only

Species boundaries and modern tools

A3.1.12 – A3.1.15

Two panels. Asexual reproduction: one bacterium divides again and again, so offspring come from one parent without mating and there is no interbreeding to test. Horizontal gene transfer: a donor bacterium passes a plasmid through a pilus to a recipient that is not its offspring

A3.1.12 · HL

When the BSC breaks down

The biological species concept (BSC) defines a species as a group of organisms that can interbreed to produce fertile offspring. It is built entirely around interbreeding, so it breaks down for organisms that don't reproduce sexually at all.
Asexually reproducing organisms (many bacteria, some plants and invertebrates) produce offspring without mating, so there's no interbreeding test to apply.
Species boundaries in these groups have to be drawn on other grounds instead, such as morphological or genetic similarity.

A3.1.12 · HL

Bacteria break the rule twice over

Bacteria present a further complication on top of asexual reproduction: genes don't only pass from parent to offspring.

Horizontal gene transfer moves DNA directly between bacterial cells that aren't parent and offspring — even between quite distantly related bacteria.
This blurs the clean genetic lineages that species boundaries usually rely on, since a bacterium's genome can be a patchwork acquired from multiple sources rather than inherited along one line of descent.

Why it mattersBetween no interbreeding test and genes moving sideways across lineages, bacterial "species" end up defined by convention — shared traits and genome similarity — rather than by the BSC.

A 3D render of two rod-shaped bacteria joined by a pilus. The donor cell, for example E. coli, holds its chromosome and a plasmid with an antibiotic-resistance gene; a strand of DNA passes along the pilus, and the recipient cell, which can be another species, now holds a new copy of the plasmid

A3.1.13 · HL

Chromosome number as a species trait

Diploid chromosome number is normally constant across a species, and this connects directly to the BSC's fertile-offspring test: cross-breeding between closely related species is unlikely to produce fertile offspring if their chromosome numbers differ.
During meiosis, homologous chromosomes must pair up — if a hybrid inherits mismatched chromosome sets, pairing fails, meiosis can't produce viable gametes, and the hybrid is sterile, the same underlying reason the horse × donkey mule can't reproduce.
This makes a consistent chromosome-number difference a useful extra trait: two similar-looking organisms that consistently differ in diploid number are very likely separate species.

A horse (2n = 64, gametes n = 32) and a donkey (2n = 62, gametes n = 31) produce a mule with 63 chromosomes. Its two sets of chromosomes do not match and one chromosome has no partner, so pairing fails at meiosis and the mule is sterile

Images of four leaves numbered 1 to 4: an oak leaf with rounded lobes, a beech leaf with a wavy edge, a horse chestnut leaf with leaflets spreading from one point, and an ash leaf with leaflets in pairs along a stalk. Below, a dichotomous key: 1a leaf divided into leaflets, go to 2; 1b leaf in one piece, go to 3; 2a leaflets spread from one point, horse chestnut; 2b leaflets in pairs along a stalk, ash; 3a edge with deep rounded lobes, oak; 3b edge smooth or wavy, beech

A3.1.14 · HL · Skill

Building a dichotomous key

A dichotomous key identifies an organism through steps that each offer two contrasting choices, based on features you can see.

Work with real local species: collect leaves, or photograph animals, and list the features that differ.
Choose features that are easy to observe and that split the group roughly in half at each step.
Test the key on someone else, and improve any step that gives the wrong answer.

ExampleFour common trees, keyed out from their leaves.

A3.1.15 · HL

Species detection from environmental DNA

Environmental DNA (eDNA) is genetic material shed by organisms into their surroundings, recoverable directly from soil, water or air without ever seeing the organism itself.

DNA barcoding compares a short, standardised region of that recovered DNA against a reference database of known sequences to identify which species are present in a sample.

Why it mattersMakes it possible to detect rare, elusive or cryptic species — and survey whole communities at once — far more easily than direct observation, a fast-growing tool in ecological monitoring.

Five steps of environmental DNA barcoding: collect a water or soil sample, extract the DNA, copy a short barcode region such as the COI gene by PCR, sequence it, and match each sequence to a reference database. The result is a list of species present, such as brown trout, European eel and great crested newt, without catching them

Key vocabulary — HL

Worth being able to define in a single sentence each

Horizontal gene transfer

Movement of DNA directly between cells that aren't parent and offspring, common in bacteria.

Dichotomous key

An identification tool built from a series of two-choice steps based on observable features.

Environmental DNA (eDNA)

Genetic material shed into the environment and recoverable without capturing the organism.

DNA barcoding

Comparing a short standardised DNA region against a reference database to identify species.

Quick check · HL

Two bacterial species swap genes directly through horizontal gene transfer rather than through reproduction. Why does this make the biological species concept hard to apply to bacteria?

Bacteria don't have DNA

It blurs the clean genetic lineages species boundaries rely on, and bacteria don't interbreed to test anyway

Bacteria can only reproduce sexually

The BSC only applies to plants

Correct answer: it blurs lineages and removes the interbreeding test. The BSC is built around interbreeding to produce fertile offspring — asexual bacteria never do this, and horizontal gene transfer moves DNA between unrelated cells, so species boundaries have to be drawn on other grounds.

Where this shows up again

A3.2 · Classification and cladistics

How are individual species grouped into larger categories such as genus, family and higher taxa?

A4.1 / D1.3 · Evolution and speciation / Mutation and gene editing

How does variation within a species provide the raw material for natural selection and the formation of new species?

D1.3 / A1.2 · Mutation and gene editing / Nucleic acids

What is the molecular origin of the mutations that create variation between and within species?

A1.2 / A3.2 · Nucleic acids / Classification and cladistics

How does comparing DNA base sequences help resolve cases where the biological species concept is hard to apply?

A3.1 Diversity of Organisms — one-page recap

Screenshot this slide to revise from

Species concepts

Morphological: grouped by appearance — look-alikes can still differ genetically.
Biological (BSC): interbreed to produce fertile offspring — horse × donkey mule is sterile.

Fuzzy boundaries

Ring species: every neighbour interbreeds except where the ring closes.
Chronospecies: fossil lineage split into species is unavoidably arbitrary.

Chromosomes

Number varies by species: human 46, chimp 48, always even.
Human chr 2 = ancestral ape chromosomes 12 + 13, fused.

Genomes

Gene / allele / genome / SNP — one product, one version, all DNA, one-base difference.
C-value paradox: genome size and gene number are only loosely related.

HL · Species boundaries

Asexual organisms: no interbreeding, so no BSC test.
Bacteria: horizontal gene transfer blurs lineages further.

HL · Modern tools

Chromosome number as extra evidence for a species split.
Dichotomous keys and eDNA barcoding identify species by feature or by trace DNA.

Next step

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A species isn't a fixed box — it's wherever fertile gene flow actually stops.

Next: how do we group species themselves into genus, family, and the rest of the tree of life?

A3.1 Diversity of Organisms · BioCentral IB