Biology • Year 12 • Module 5 • Lesson 16
Frequency Data and SNP Analysis
Apply allele-frequency arithmetic, frequency trend analysis, and SNP comparison to real-style population data sets.
1. Calculate and compare allele frequencies across populations
Researchers genotyped a single SNP (the T/C variant at locus rs4988235, near the LCT lactase gene) in four sampled human populations. Each population sample consisted of 100 unrelated individuals (200 alleles per population). 8 marks
| Population | TT | TC | CC | Total individuals |
|---|---|---|---|---|
| Northern European | 49 | 42 | 9 | 100 |
| Southern European | 16 | 48 | 36 | 100 |
| East Asian | 1 | 10 | 89 | 100 |
| West African | 4 | 30 | 66 | 100 |
Use the rule: p(T) = (2 × TT + TC) ÷ (2 × total individuals). Then q(C) = 1 − p.
1.1 Calculate the frequency of the T allele p in each of the four populations. Show working for at least one. 4 marks
1.2 Describe the trend in T-allele frequency across the four populations using cautious scientific language. 2 marks
1.3 Each sample is only 100 individuals. State two limitations of using these frequencies to characterise each whole population. 2 marks
2. Bar chart, observed allele frequencies at one SNP
The chart below plots the T-allele frequency from your calculations in Q1 across the four populations. 6 marks
Figure 2.1. T-allele frequency at SNP rs4988235 in four sampled populations. Stylised data after Bersaglieri et al. (2004), Am. J. Hum. Genet. 74:1111–1120.
2.1 Which population has the highest T-allele frequency, and which has the lowest? State the values. 2 marks
2.2 Calculate the difference in T-allele frequency between the Northern European and East Asian samples. 1 mark
2.3 A student concludes: "These four groups must be different species because the bar heights are so different." Explain, using lesson terms, what is wrong with that conclusion. 3 marks
3. Sample quality, evaluating data reliability
Use the allele-frequency data from Question 1 (the four-population SNP table) and the lesson's framework for evaluating data quality to answer the following. 7 marks
3.1 Each population in Question 1 was sampled with only 100 individuals. State two reasons why this limits the strength of any conclusion about the true population-wide allele frequency. 2 marks
3.2 A researcher collects all 400 individuals from a single clinic in one city. Explain how this could introduce bias even though 400 is a larger sample than 100. 2 marks
3.3 A newspaper headline reads: "New data shows East Asian populations have almost no T allele, this SNP definitively separates them from Northern Europeans." Using lesson terms (trend, sample, bias), explain why this headline is not scientifically cautious. 3 marks
4. Four-step data interpretation, worked example practice
Lesson 16 Card 5 describes a four-step approach to answering a data interpretation question (state the trend, compare groups explicitly, state a limitation, keep the conclusion proportional). Apply all four steps to the SNP frequency data in Section 2 (the bar chart showing T-allele frequency). 6 marks
4.1 Step 1, State the visible trend. In one sentence, describe the overall pattern in T-allele frequency shown in the bar chart. 1 mark
4.2 Step 2, Compare groups using actual values. Write one comparison sentence that names the highest and lowest populations and quotes their values. 1 mark
4.3 Step 3, State at least one limitation. Identify one reason why the conclusion from this single SNP should not be extended to a claim about overall genetic difference between the populations. 2 marks
4.4 Step 4, Keep the conclusion proportional. Write a one-sentence conclusion that uses cautious language (such as "in this sample", "suggests a trend", "more common") rather than absolute claims. 2 marks
5. Apply, interpret a SNP-based relatedness claim
A press release reports: "DNA testing has shown that Population P and Population Q share 99.8% of their genome, but a single SNP at locus X differs between them. Therefore the two populations are essentially identical." Population P (n = 240) carries the A allele at frequency 0.05; Population Q (n = 260) carries the A allele at frequency 0.94 at locus X. 6 marks
5.1 Calculate the difference in A-allele frequency at locus X between the two populations. 1 mark
5.2 Explain why the press release's overall conclusion is too strong, despite the genome-wide similarity figure being high. Use the words marker, variation and sample. 3 marks
5.3 Suggest one way the team could strengthen their evidence for the claim about relatedness. 2 marks
Q1.1, Allele frequencies (4 marks)
Using p(T) = (2 × TT + TC) ÷ 200:
- Northern European: (2 × 49 + 42) ÷ 200 = 140 ÷ 200 = 0.70 [1]
- Southern European: (2 × 16 + 48) ÷ 200 = 80 ÷ 200 = 0.40 [1]
- East Asian: (2 × 1 + 10) ÷ 200 = 12 ÷ 200 = 0.06 [1]
- West African: (2 × 4 + 30) ÷ 200 = 38 ÷ 200 = 0.19 [1]
Q1.2, Trend (2 marks)
The T-allele frequency is highest in the Northern European sample (~0.70) and falls progressively through the Southern European (~0.40) and West African (~0.19) samples to the lowest in the East Asian sample (~0.06) [1]. The trend should be described as "in the sampled groups" rather than "in every member of these populations" [1].
Q1.3, Limitations (2 marks)
Any two of: (a) sample of only 100 is small relative to the size of each population [1]; (b) one geographic sample may not be representative of the diversity within a population (e.g. one city only) [1]; (c) data describes only one SNP locus, not the whole genome; (d) sampling/recruitment may be biased toward certain groups.
Q2.1, Highest / lowest (2 marks)
Highest: Northern European at 0.70 [1]. Lowest: East Asian at 0.06 [1].
Q2.2, Difference (1 mark)
0.70 − 0.06 = 0.64 (or 64 percentage points) [1].
Q2.3, Why the species claim is wrong (3 marks)
A SNP is a single position out of millions in the genome, one position cannot define species identity [1]. Frequency differences at one locus typically reflect normal genetic variation within a species, not separation between species [1]. All four populations are Homo sapiens; differences in this SNP's frequency reflect population history (e.g. selection for lactase persistence in dairy-cultured groups) and not speciation [1].
Q3.1, Limitations of small sample (2 marks)
Any two of: (a) 100 individuals is small relative to any national population, the observed frequency may not accurately represent the wider group [1]; (b) a small sample is more likely to produce a biased or unrepresentative result by chance [1]; (c) rare alleles that are present in the population may not appear at all in a small sample [1].
Q3.2, Bias despite larger sample (2 marks)
All 400 individuals come from one clinic in one city, this is a single location, not a representative cross-section of the population [1]. Bias is introduced because the sample may over-represent people from that region, socioeconomic group, or ancestry background, even though the raw number is large. A larger unrepresentative sample can be more misleading than a smaller representative one [1].
Q3.3, Why the headline is not cautious (3 marks)
The headline uses absolute language ("definitively separates"), which goes beyond what data from one sample at one SNP can show [1]. The correct framing is a trend: the T-allele frequency is much lower in the East Asian sample than the Northern European sample in this data set, but this is a single marker out of millions in the genome [1]. Frequency differences at one SNP reflect normal genetic variation and do not define species or "definitive" separation, they suggest a pattern worth investigating further with more SNPs and larger, more representative samples [1].
Q4.1, Step 1: state the trend (1 mark)
The T-allele frequency in this SNP is highest in the Northern European sample and decreases across the other sampled populations, with the East Asian sample showing the lowest value [1].
Q4.2, Step 2: compare with values (1 mark)
The Northern European sample shows the highest T-allele frequency (0.70) and the East Asian sample shows the lowest (0.06), a difference of 0.64 [1].
Q4.3, Step 3: state a limitation (2 marks)
This is a single SNP out of millions in the human genome, one marker alone cannot describe overall genetic difference between populations [1]. Additionally, each sample is only 100 individuals from one geographic location, so the data may not represent the full diversity within any of the named populations [1].
Q4.4, Step 4: proportional conclusion (2 marks)
In these sampled groups, the T allele at this SNP locus is more common in Northern and Southern European samples than in East Asian and West African samples, suggesting a trend in allele frequency across these populations; however, this pattern is based on one marker and small samples, so broader claims about genetic difference would require more data [2].
Q5.1, Allele-frequency difference (1 mark)
0.94 − 0.05 = 0.89 (an extremely large per-locus difference). [1]
Q5.2, Why the press release overreaches (3 marks)
Genome-wide 99.8% similarity refers to the average across the whole genome, but most of the variation that distinguishes populations is concentrated in specific SNPs, one such marker can differ in frequency by nearly 90 percentage points [1]. So "essentially identical" is misleading: the populations show substantial variation at this locus, which may have biological or evolutionary significance [1]. Conclusions should reference the sample measured and be proportional to it, the press release converts a per-locus frequency difference into a sweeping identity claim and ignores the meaning of marker-level variation [1].
Q5.3, Strengthening the evidence (2 marks)
Any one of: examine many SNPs across the genome rather than a single locus and report the pattern of differences [1]; increase and diversify sample sizes (more individuals across more locations) so the samples better represent each population [1]; report both genome-wide similarity and per-locus variation rather than mixing them.