Questions: Conservation Genetics: Effective Population Size and Inbreeding

Question 1

A lion population in a reserve has 500 individuals, but genetic analysis reveals that only 10 males sire essentially all offspring while 490 females reproduce equally. Using the sex-ratio formula Ne = 4NmNf/(Nm + Nf), what is the approximate effective population size?

• A. ~500 — the census size is the relevant number for conservation management
• B. ~250 — the average of the breeding male and female counts
• C. ~40 — determined by the bottleneck of the small number of breeding males
• D. ~10 — because only the 10 breeding males contribute novel genetic material

Answer: (C)

Ne = 4 × 10 × 490 / (10 + 490) = 19,600 / 500 ≈ 39. The bottleneck imposed by the rare sex (here, the small number of breeding males) dramatically reduces Ne below the census size of 500. This is not an obscure formula edge case — it captures a fundamental biological reality. Every allele in the next generation must pass through one of those 10 males (or one of the 490 females). The genetic bottleneck is the rarer sex, regardless of how large the total population appears.

Question 2

A species' population sizes over four generations were: 2000, 1000, 20, 800. Which calculation best estimates the long-term effective population size?

• A. The arithmetic mean ≈ 955 — reflecting the average population experience
• B. The most recent population size of 800 — since current size determines current drift
• C. The harmonic mean ≈ 70 — because bottleneck generations dominate long-term genetic diversity
• D. The minimum of 20 — because all diversity was lost in the crash generation

Answer: (C)

Long-term Ne is the harmonic mean: 4 / (1/2000 + 1/1000 + 1/20 + 1/800) = 4 / (0.0005 + 0.001 + 0.05 + 0.00125) ≈ 4 / 0.053 ≈ 75. The harmonic mean is dominated by the smallest value because the 1/Ne term for the bottleneck year (1/20 = 0.05) is nearly as large as all other terms combined. This is why a single severe bottleneck leaves a lasting genetic signature even after recovery — the harmonic mean remains depressed for generations. The arithmetic mean (955) dramatically overestimates genetic resilience.

Question 3

A population with a current census size of 10,000 individuals could have an effective population size of only a few hundred due to historical bottlenecks and reproductive skew.

• T. True
• F. False

Answer: True

Effective population size reflects the genetic history of a lineage, not just its current census. Two mechanisms explain this: first, a historical bottleneck permanently depresses long-term Ne via the harmonic mean effect, even after the population recovers numerically. Second, ongoing reproductive skew — a few dominant individuals siring most offspring — continuously reduces Ne below census size in each generation. The Florida panther, cheetah, and Northern elephant seal all show genetic signatures of small Ne despite having census sizes in the hundreds or thousands.

Question 4

Inbreeding depression occurs because close relative mating causes new harmful mutations to arise more frequently.

• T. True
• F. False

Answer: False

Inbreeding depression does not create new mutations — it exposes pre-existing ones. Most organisms carry deleterious recessive alleles that are harmlessly 'hidden' in heterozygous form (one functional copy masks one defective copy). When closely related individuals mate, their offspring have a much higher probability of being homozygous for the same recessive allele — both copies defective, with no functional copy to compensate. The harmful alleles were always there; inbreeding merely increases the probability they are expressed. This distinction matters for management: purging deleterious alleles requires exposure, not prevention, which creates a careful tradeoff in small-population conservation.

Question 5

Why does a population bottleneck that occurred 50 generations ago continue to affect the genetic diversity of the current population, even after the population has recovered to large numbers?

Model answer: Alleles that were lost during the bottleneck cannot be recovered by population growth alone. If an allele was at low frequency and was lost by genetic drift during the crash, no amount of reproduction by the survivors will recreate it — the only sources are new mutation (extremely rare) or gene flow from other populations. The harmonic mean effect means the bottleneck generation continues to suppress long-term Ne estimates. Additionally, the genetic drift during the bottleneck may have fixed deleterious alleles and eliminated beneficial ones, leaving a population that is less adaptable to future environmental challenges even though it appears numerically robust.

This is the key practical insight for conservation genetics: counting animals is not enough. A population that crashed to 30 individuals three generations ago and recovered to 3,000 has the genetic diversity of a population that never exceeded ~100 individuals, because the harmonic mean of 30 and 3,000 is dominated by the 30. Managing only current census size misses the genetic legacy of the bottleneck — hence the conservation target of Ne > 500, which requires far larger census sizes (typically 5–10× Ne) to achieve.