DP Biology HL A3.1 Diversity of Organisms

DP Biology HL A3.1 Diversity of Organisms - Full notes

RevisionPrep

DP Biology HL | A3.1 Diversity of Organisms

DP BIOLOGY · THEME A: UNITY AND DIVERSITY

A3.1

Diversity of Organisms

Full notes for HL · IB-style

Contents

1	Variation between organisms
2	What is a species?
3	Chromosome numbers and karyotypes
4	Genome size and whole genome sequencing
5	Diversity within and between species
6	The difficulties of the species concept (HL only)
7	Identifying species: dichotomous keys and DNA barcoding (HL only)
8	Variation between organisms
9	The species concept
10	Other species concepts
11	Binomial nomenclature
12	Chromosome number and karyotypes
13	Genome size and diversity
14	Dichotomous keys
15	Biodiversity: definitions and levels
16	Simpson's reciprocal index
17	Classification hierarchy (introduction)
18	Estimating the number of species
19	Using DNA to identify species
20	Mixed review: worked problems
21	Additional exam-style practice
22	Polyploidy and diversity
23	Ring species and gradual divergence
24	Practical: measuring variation
25	Common misconceptions and links
26	Exam-style question with markscheme
27	Check your understanding
28	Summary and topic map

These are full teaching notes. Read each section in order, try the Think about it question before you read on, and do every Quick check before moving to the next section.

Before you start

Rate yourself on each statement now, and again after you've worked through the notes. Shade R (not yet), A (getting there) or G (confident).

I can…	R	A	G
explain that variation exists between organisms and within species
distinguish the morphological and biological species concepts
explain the binomial system of naming species
explain chromosome numbers and diploid and haploid cells
interpret karyotypes and karyograms
compare genome sizes and explain whole genome sequencing
explain why there is variation within a species
explain difficulties in applying the species concept to asexual organisms and hybrids
construct and use dichotomous keys
explain DNA barcoding and environmental DNA

Sections marked HL only (Sections 6 and 7) are Additional Higher Level content. Every other section is common to SL and HL.

Guiding questions

What is a species, and how can we tell where one ends and another begins? What do chromosomes and genomes tell us about diversity?

How this topic is examined

A3.1 is examined through definitions (species concepts), data on chromosome numbers and genome sizes, and karyograms. Paper 2 questions often show a karyogram for you to interpret or a table of genome sizes to compare. At HL, dichotomous keys and DNA barcoding are common data-based questions.

Precise definitions (diploid, haploid, homologous, karyotype, genome) earn the marks.

Command term	What the examiner wants
State / Identify	a brief answer with no explanation needed
Outline	a brief account or summary
Describe	a detailed account, including trends or features, without reasons
Explain	a detailed account including causes, reasons or mechanisms
Distinguish / Compare and contrast	give the differences (and similarities), point by point
Calculate	a numerical answer with working and units
Deduce / Suggest	reach a conclusion from data; propose a reasonable explanation
Evaluate / Discuss	weigh strengths and limitations and reach a judgement

How to use these notes

Each section teaches one part of the syllabus in full. You'll see these boxes throughout; each has one job:

Box	What it's for
Think about it	a question to get you thinking before a section; the answer comes in the section
Key point	the one idea you must not forget
Common mistake	an error examiners see every year, and how to avoid it
In the real world	where the biology shows up outside the classroom
Try this	something quick you can do yourself to test the idea
Worked example	full solutions with IB-style marks (M1 method, A1 answer, R1 reasoning)
Quick check	short questions to test yourself at the end of each section

1 Variation between organisms

No two organisms are exactly alike.

Think about it

Siblings share the same parents, yet look different. Where does that variation come from?

Living organisms vary enormously. There are millions of species, from bacteria to blue whales, and within each species individuals differ in size, colour, behaviour and biochemistry. Biologists study this variation to classify organisms, to understand evolution and to conserve biodiversity.

Variation within a species comes from two sources. Genetic variation arises from mutations, which create new alleles, and from sexual reproduction, which shuffles alleles into new combinations through meiosis and random fertilization. Environmental variation arises from differences in diet, climate, disease and other conditions. Many characteristics, such as height, are influenced by both.

2 What is a species?

Two ways to decide whether organisms belong to the same species.

2.1 The morphological species concept

Historically, species were defined by their appearance: organisms that share a set of observable features (morphology) belong to the same species. Linnaeus classified thousands of species this way in the eighteenth century. The method is still widely used, especially for fossils and specimens. But it has problems: individuals of the same species can look very different (male and female birds, caterpillars and butterflies), and different species can look almost identical.

2.2 The biological species concept

The biological species concept defines a species as a group of organisms that can interbreed in nature to produce fertile offspring. Members of different species are reproductively isolated. Horses and donkeys can interbreed, but their offspring, mules, are sterile, so horses and donkeys are separate species.

This definition focuses on the process that keeps species distinct: gene flow within a species but not between species. But it cannot be applied to organisms that reproduce asexually or to extinct organisms known only from fossils, and some species do occasionally hybridize. These difficulties are discussed in Section 6.

2.3 The binomial system

Every species is given a two-part Latin name: the genus (written with a capital letter) and the species (lower case), both in italics when printed or underlined when handwritten. Humans are Homo sapiens; the tiger is Panthera tigris. The binomial system gives each species one internationally recognized name, avoiding confusion caused by local common names. After first use, the genus may be shortened: H. sapiens.

Common mistake

Writing 'homo Sapiens' or 'Homo Sapiens'. The genus has a capital letter; the species name never does.

Quick check

1. Define a species using the biological species concept.

2. Why are horses and donkeys separate species?

3. Write the scientific name of humans correctly.

Answers: 1. organisms that can interbreed to produce fertile offspring 2. their offspring (mules) are sterile 3. Homo sapiens (italic, capital H, lower-case s)

3 Chromosome numbers and karyotypes

Each species has a characteristic number of chromosomes.

A chromosome is a long DNA molecule with associated proteins. Each species has a characteristic number of chromosomes, and this number is one of its distinguishing features: humans have 46, chimpanzees 48, dogs 78, potatoes 48.

In most animals and plants, body cells are diploid (2n): they contain two sets of chromosomes, one inherited from each parent. The two chromosomes of each pair are homologous: they carry the same genes in the same positions, though possibly different alleles. Gametes are haploid (n): they contain one set. Fertilization of two haploid gametes restores the diploid number.

Chromosome number can differ between closely related species. Humans have 46 chromosomes while other great apes have 48: evidence suggests that two ape chromosomes fused to form human chromosome 2.

Organism	Diploid number (2n)	Haploid number (n)
Human (Homo sapiens)	46	23
Chimpanzee (Pan troglodytes)	48	24
Dog (Canis familiaris)	78	39
Rice (Oryza sativa)	24	12
Parascaris equorum (roundworm)	4	2

3.1 Karyotypes and karyograms

A karyotype is the number and appearance of the chromosomes in a cell. A karyogram is an image of the chromosomes arranged in homologous pairs, in order of decreasing size, with the sex chromosomes shown last. It is made by photographing chromosomes in dividing cells (when they are condensed) and arranging the images.

Karyograms are used to determine sex (XX in human females, XY in males) and to diagnose chromosomal abnormalities, such as Down syndrome, where there are three copies of chromosome 21 (trisomy 21), giving 47 chromosomes.

Figure 1. A karyogram arranges homologous chromosomes in pairs by size; sex chromosomes are placed last.

Quick check

1. Define diploid and haploid.

2. What are homologous chromosomes?

3. What abnormality causes Down syndrome?

Answers: 1. two sets / one set of chromosomes 2. a pair carrying the same genes in the same loci 3. trisomy 21

4 Genome size and whole genome sequencing

Bigger genomes don't always mean more complex organisms.

The genome is the whole of the genetic information of an organism: all of its DNA. Genome size is measured in base pairs (bp) or millions of base pairs (Mb).

Genome sizes vary enormously, from about 0.5 Mb in some bacteria to about 150 000 Mb in the plant Paris japonica. The human genome is about 3 200 Mb. Genome size does not correlate well with complexity: some plants and amphibians have genomes many times larger than ours, much of it non-coding, repeated DNA.

Whole genome sequencing determines the complete base sequence of an organism's DNA. The Human Genome Project (completed 2003) took 13 years and about $3 billion; today a human genome can be sequenced in a day for a few hundred dollars. Sequencing has many uses: comparing species to study evolution; identifying disease-causing mutations; personalized medicine; and conservation genetics.

Figure 2. Genome sizes on a logarithmic scale.

WORKED EXAMPLE 1 Comparing genomes

The human genome is about 3 200 Mb and contains about 20 000 protein-coding genes. The wheat genome is about 17 000 Mb with about 107 000 genes. Calculate how many times larger the wheat genome is and suggest why genome size is not a good measure of complexity.

Solution

17 000 ÷ 3 200 = 5.3 times largerA1

Much of a genome is non-coding or repeated DNAR1

Wheat is polyploid (six sets of chromosomes), which increases size without increasing complexityR1

Quick check

1. Define genome.

2. Give two uses of whole genome sequencing.

Answers: 1. all the genetic information of an organism 2. evolutionary comparison; medical diagnosis; personalized medicine; conservation

5 Diversity within and between species

Most genes are shared; small differences matter.

Individuals of the same species share the same genes in the same positions, but they may carry different alleles (versions of a gene). Any two humans share about 99.9% of their DNA sequence; the remaining differences, mostly single nucleotide polymorphisms (SNPs), account for much of human genetic variation.

Comparing genomes between species shows how closely related they are. Humans and chimpanzees differ in only about 1.2% of their DNA sequence. Such comparisons are the basis of modern classification (A3.2).

6 The difficulties of the species concept (HL only)

Real organisms don't always fit neatly into species.

HL only

This section is Additional Higher Level content. SL students do not need it.

Asexual reproduction. Many bacteria, some plants and some animals reproduce asexually, so the biological species concept cannot be applied. Bacteria also exchange genes by horizontal gene transfer, blurring boundaries further.

Hybridization. Some species interbreed in nature and occasionally produce fertile hybrids, for example certain oak species and some wolves and coyotes.

Ring species and gradual divergence. Populations may diverge gradually, so there is no clear point at which they become separate species. When populations are geographically separated, it is impossible to test whether they could interbreed.

Extinct organisms. Fossils cannot be tested for interbreeding, so palaeontologists use the morphological concept.

Because of these problems, biologists use several species concepts and increasingly rely on DNA evidence to decide whether populations are distinct species.

7 Identifying species: dichotomous keys and DNA barcoding (HL only)

Two tools for naming the organism in front of you.

HL only

This section is Additional Higher Level content. SL students do not need it.

A dichotomous key identifies an organism through a series of steps, each with two contrasting descriptions (couplets). The user chooses the description that fits and follows it to the next step until a name is reached. Good keys use clear, observable features that do not vary within a species (such as number of legs, not colour or size).

Step	Description	Go to
1a	has jointed legs	2
1b	no jointed legs	earthworm
2a	six legs	3
2b	eight legs	spider
3a	has wings	housefly
3b	no wings	ant (worker)

DNA barcoding identifies species using a short, standard DNA sequence that varies between species but little within a species. In animals the barcode region is usually part of the mitochondrial gene COI (cytochrome c oxidase I); in plants, chloroplast genes are used. The sequence is compared with a reference database.

Environmental DNA (eDNA) consists of traces of DNA shed by organisms into water, soil or air. By sampling a river and sequencing the DNA it contains, scientists can detect which species live there without seeing or catching them. eDNA is used to monitor rare and invasive species and biodiversity.

In the real world

DNA barcoding has revealed seafood fraud: studies have found that about a fifth of fish sold in restaurants and shops worldwide was a different species from the one on the label.

Quick check

1. Why should keys avoid colour as a feature?

2. Which gene is used for animal DNA barcoding?

3. What is eDNA?

Answers: 1. colour varies within species 2. mitochondrial COI 3. DNA shed into the environment, used to detect species

8 Variation between organisms

Continuous and discrete.

Organisms of the same species vary. Continuous variation (height, mass) shows a range of values, usually controlled by many genes and the environment. Discrete variation (blood group) falls into distinct categories, usually controlled by one or a few genes.

WORKED EXAMPLE 2 Classifying variation (standard)

Classify: human height, ABO blood group, leaf length, eye colour.

Solution

Continuous: height, leaf lengthA1

Discrete: blood group (eye colour is often treated as discrete but is polygenic)A1

Quick check

1. Sketch the typical distribution for continuous variation.

Answers: 1. bell-shaped (normal) distribution

9 The species concept

Defining a species.

The biological species concept: a group of organisms that can interbreed to produce fertile offspring. Problems: it cannot be applied to asexually reproducing organisms, fossils, or populations that are geographically separated; hybrids (such as mules) are infertile.

WORKED EXAMPLE 3 Mule (standard)

Explain why horses and donkeys are different species although they can mate.

Solution

Their offspring (mules) are infertileR1

Quick check

1. Give two limitations of the biological species concept.

Answers: 1. cannot apply to asexual organisms or fossils

10 Other species concepts

Morphological and phylogenetic.

The morphological species concept groups organisms by shared structural features; it applies to fossils but can be misled by variation within species or similarity between species. The phylogenetic species concept uses DNA sequences and evolutionary relationships.

Concept	Based on	Strength	Weakness
biological	interbreeding	tests reproductive isolation	not for asexual organisms or fossils
morphological	shared structure	usable for fossils	variation and convergence mislead
phylogenetic	DNA and ancestry	objective, for all organisms	requires sequencing; where to draw lines

11 Binomial nomenclature

Genus and species.

Every species has a two-part Latin name: the genus (capitalized) followed by the specific name (lowercase), written in italics (or underlined when handwritten), e.g. Homo sapiens. After first use, the genus can be abbreviated: H. sapiens. This avoids confusion between common names.

WORKED EXAMPLE 4 Writing names (basic)

Write the name of the domestic dog correctly.

Solution

Canis familiaris (italics; or Canis lupus familiaris)A1

Quick check

1. Why are common names unsuitable for scientific communication?

Answers: 1. they differ between languages and regions; one name may refer to several species

12 Chromosome number and karyotypes

Diversity in genomes.

Species differ in chromosome number: humans 46, chimpanzees 48, dogs 78, Ophioglossum fern over 1200. A karyotype displays chromosomes arranged in pairs by size and centromere position, used to determine sex and detect chromosome abnormalities.

WORKED EXAMPLE 5 Karyotype (standard)

State two uses of karyotyping.

Solution

Determine sex (XX or XY)A1

Detect abnormalities such as trisomy 21A1

In the real world

Human chromosome 2 appears to be a fusion of two ancestral ape chromosomes, explaining why humans have 46 chromosomes and other great apes 48.

Quick check

1. How many chromosomes does a human gamete contain?

Answers: 1. 23

13 Genome size and diversity

Bigger is not always more complex.

Genome size varies enormously: E. coli about 4.6 million base pairs, humans about 3.2 billion, the plant Paris japonica about 150 billion. Genome size does not correlate simply with complexity because much DNA is non-coding.

WORKED EXAMPLE 6 Comparison (standard)

Why does genome size not reflect organism complexity?

Solution

Large amounts of non-coding and repetitive DNAR1

Polyploidy in some plantsR1

14 Dichotomous keys

Identifying organisms.

A dichotomous key uses a series of paired choices based on observable features to identify organisms. Good keys use clear, measurable features that are present in all individuals (not size alone, which varies).

WORKED EXAMPLE 7 Designing a key (exam level)

Suggest two features that would be suitable to separate insects from spiders in a key.

Solution

Number of legs: 6 versus 8A1

Antennae present versus absent; body segments 3 versus 2A1

Quick check

1. Why is colour sometimes a poor feature for a key?

Answers: 1. it can vary between individuals, ages or seasons

15 Biodiversity: definitions and levels

Genetic, species, ecosystem.

Biodiversity includes: genetic diversity (variation of alleles within a species), species diversity (number and relative abundance of species), and ecosystem diversity (range of habitats). Richness is the number of species; evenness is how equally individuals are distributed.

WORKED EXAMPLE 8 Evenness (standard)

Two woods each contain 4 species. In wood A each species has 25 individuals; in wood B one species has 97 and the others 1 each. Which is more diverse?

Solution

Same richnessR1

Wood A: greater evenness, so higher diversityR1

16 Simpson's reciprocal index

Quantifying diversity.

Simpson's reciprocal index D = N(N − 1)/Σn(n − 1), where N is the total number of organisms and n the number of each species. Higher values mean greater diversity.

WORKED EXAMPLE 9 Calculation (exam level)

Calculate D for a site with species counts 10, 6 and 4.

Solution

N = 20; N(N − 1) = 380A1

Σn(n − 1) = 90 + 30 + 12 = 132A1

D = 2.88A1

Quick check

1. Calculate D for counts 5, 5, 5, 5.

Answers: 1. N = 20: 380/80 = 4.75

17 Classification hierarchy (introduction)

From domain to species.

Organisms are classified in a nested hierarchy: domain, kingdom, phylum, class, order, family, genus, species. Each level includes organisms sharing more features. (Classification and cladistics are developed in A3.2.)

WORKED EXAMPLE 10 Hierarchy (basic)

List the taxa from kingdom to species for humans.

Solution

Animalia, Chordata, Mammalia, Primates, Hominidae, Homo, sapiensA2

18 Estimating the number of species

How many species are there?

About 1.8 million species have been described, but estimates of the total range from about 8 to 10 million eukaryotes, plus vast numbers of bacteria. Most undiscovered species are insects, fungi and microorganisms in tropical and marine habitats.

WORKED EXAMPLE 11 Uncertainty (standard)

Suggest why the total number of species is so uncertain.

Solution

Many habitats poorly explored (deep sea, rainforest canopy, soil)R1

Microorganisms hard to culture and classifyR1

19 Using DNA to identify species

Barcoding and eDNA.

DNA barcoding compares short standard gene sequences (such as mitochondrial COI in animals) to identify species. Environmental DNA (eDNA) collected from water or soil reveals which species live in an area without seeing them.

WORKED EXAMPLE 12 eDNA (standard)

Give one advantage of eDNA surveys.

Solution

Detects rare or elusive species without disturbing themR1

In the real world

eDNA from river water has been used to detect rare species such as great crested newts and invasive fish without having to catch them.

20 Mixed review: worked problems

Bringing the ideas together.

WORKED EXAMPLE 13 Mixed problem (exam level)

Explain the difficulties in applying the biological species concept to bacteria.

Solution

Bacteria reproduce asexually (binary fission)R1

Horizontal gene transfer blurs boundariesR1

21 Additional exam-style practice

Paper 1 and Paper 2.

WORKED EXAMPLE 14 Paper 1 question (standard)

Which is the correct binomial name format? A. homo Sapiens B. Homo sapiens C. Homo Sapiens D. HOMO SAPIENS

Solution

BA1

WORKED EXAMPLE 15 Paper 2 question (exam level)

Outline how a karyotype is prepared and one use.

Solution

Cells arrested in metaphase; chromosomes stained and photographedR1

Arranged in homologous pairs by size and banding; detects abnormalitiesR1

22 Polyploidy and diversity

Extra chromosome sets.

Polyploid organisms have more than two sets of chromosomes. Polyploidy is common in plants (wheat is hexaploid) and can create new species in one generation because polyploids cannot breed successfully with the parent species.

Quick check

1. Why can polyploidy lead to instant speciation?

Answers: 1. offspring of a cross with the parent species have unpaired chromosomes and are infertile

23 Ring species and gradual divergence

Where species boundaries blur.

In ring species (such as Ensatina salamanders around California's Central Valley), neighbouring populations interbreed, but populations at the ends of the ring cannot. This shows speciation as a gradual process and challenges sharp species definitions.

Quick check

1. Why are ring species a problem for the biological species concept?

Answers: 1. populations are connected by gene flow yet the end populations are reproductively isolated

24 Practical: measuring variation

Collecting and displaying data.

Measure a continuous variable (leaf length, hand span) in a large sample, record in a frequency table, plot a histogram, and calculate the mean and standard deviation. Repeat for two populations to compare.

WORKED EXAMPLE 16 Sampling (standard)

Why should leaves be selected randomly?

Solution

To avoid bias and obtain a representative sampleR1

Try this

Measure the lengths of 30 leaves from a sunny and a shaded part of the same plant species. Compare the means and standard deviations.

25 Common misconceptions and links

Students often think…	Actually…
all individuals of a species look alike	morphology varies; the biological concept is based on interbreeding
bigger genome means more complex organism	genome size does not correlate with complexity
diploid means two chromosomes	diploid means two sets of chromosomes
Homo Sapiens	Homo sapiens: species name lower case

How A3.1 connects to the rest of the course

Topic	Connection
A3.2 Classification (HL)	cladistics and DNA evidence
A4.1 Evolution and speciation	how species form
D2.1 Cell division	meiosis halves chromosome number
D3.2 Inheritance	alleles and genes
A4.2 Conservation	biodiversity

26 Exam-style question with markscheme

Try this under exam conditions (about 15 minutes) before reading the markscheme.

Figure 3. A human karyogram.

(a) State the number of autosomes in a human body cell. [1]

(b) Explain how a karyogram can be used to diagnose Down syndrome. [2]

(d) Explain why the biological species concept defines horses and donkeys as different species. [2]

(e) Suggest why genome size is not a reliable indicator of complexity. [2]

(f) Explain how DNA barcoding could be used to identify fish sold as tuna. [3]

Markscheme

Part	Answer	Marks
(a)	44	A1
(b)	chromosomes arranged in homologous pairs	R1
	three copies of chromosome 21 seen	R1
(c)	diploid: two sets of chromosomes	A1
	haploid: one set	A1
(d)	they can interbreed	R1
	but offspring (mules) are sterile	R1
(e)	much non-coding DNA	R1
	polyploidy increases size	R1
(f)	sequence a standard gene region (COI)	R1
	compare with reference database	R1
	match identifies species; mislabelling detected	R1

Examiner's comments. In (a), many candidates answered 46: autosomes exclude the two sex chromosomes. In (d), the word 'fertile' is essential.

27 Check your understanding

Section A: multiple choice

1. The biological species concept is based on

A. the ability to interbreed and produce fertile offspring B. appearance C. habitat D. diet

2. A diploid human cell contains

A. 23 chromosomes B. 44 chromosomes C. 46 chromosomes D. 92 chromosomes

3. Homologous chromosomes carry

A. identical alleles B. the same genes at the same loci C. different genes D. no genes

4. A karyogram shows chromosomes

A. randomly B. as DNA sequences C. in haploid sets only D. in pairs ordered by size

5. The correct way to write a binomial name is

A. panthera Tigris B. Panthera tigris C. Panthera Tigris D. PANTHERA tigris

6. The genome is

A. all the genetic information of an organism B. one chromosome C. one gene D. the proteins of a cell

7. DNA barcoding in animals usually uses

A. ribosomal proteins B. the whole genome C. chloroplast genes D. the mitochondrial COI gene

Section B: structured

8. Compare the morphological and biological species concepts. [4]

9. Explain how a karyogram is produced and used. [4]

10. Explain why chromosome number differs between humans and chimpanzees. [2]

11. Construct a dichotomous key for four organisms of your choice. [4]

Answers

1. A 2. C 3. B 4. D 5. B 6. A 7. D

8. Morphological: shared appearance, usable for fossils; biological: interbreeding, fertile offspring; problems of each.

9. Chromosomes photographed in dividing cells; arranged in pairs by size; used to determine sex and abnormalities.

10. Fusion of two ancestral chromosomes formed human chromosome 2.

11. Couplets with observable, non-variable features leading to each name.

28 Summary and topic map

Idea	Remember
Variation	genetic (mutation, meiosis, fertilization) and environmental
Species concepts	morphological; biological (fertile offspring)
Binomial	Genus species, italic
Chromosomes	diploid 2n, haploid n; homologous pairs
Karyogram	pairs by size; sex; trisomy 21
Genome	all DNA; size varies; sequencing
HL	species concept problems; keys; DNA barcoding; eDNA

Before the exam, make sure you…

•include 'fertile' in the species definition
•write binomial names correctly
•distinguish chromosome sets from chromosomes
•remember genome size does not equal complexity

Diversity of Organisms on one page

Cover this page with a sheet of paper and try to rebuild it from memory. Whatever you can't recall is what to revise next.

Figure 4. Topic map for Diversity of Organisms.

revisionprep.comIB-style notes · question bank · mock papers