Lecture 36 - Genetic Management of Threatened Species

Genetic Diversity and Adaptive Potential

• Genetic diversity is crucial. Its importance stems from:
  • Providing the raw material for adaptation to changing environments.

Genetic Diversity Loss

• Occurs through several mechanisms:
  • Genetic bottleneck: A sharp reduction in population size leading to loss of alleles.
  • Inbreeding: Mating between closely related individuals, increasing homozygosity and potentially expressing recessive deleterious alleles.
  • Genetic drift: Random fluctuations in allele frequencies, especially impactful in small populations.
• Effects of Inbreeding:
  • Illustrated using allele examples: A (dominant) and a (recessive deleterious).
  • Mating scenarios:
    • Aa x Aa can result in AA, Aa, or aa genotypes.
    • Inbreeding increases the likelihood of aa (expression of recessive alleles).
    • Outbreeding (mating with unrelated individuals) maintains heterozygosity (Aa).

Genetic Management for Translocations

• Translocations involve moving individuals to new locations to:
  • Supplement existing populations.
  • Establish new populations.

Regaining Genetic Diversity

• Genetic admixture: Combining individuals from different populations can restore genetic diversity.
• Process:
  • Population 1 and Population 2 interbreed.
  • Resulting in Population 3 with a mix of genetic material.
• Examples of Genetic Admixture:
  • Bighorn sheep (Piorier et al. 2018, Evolutionary Applications).
  • Mountain pygmy possum (Weeks et al. 2017, Nature Communications).
  • Burrowing bettong and Western barred bandicoot (White et al. 2018, Biological Conservation).

Planning Translocations and Captive Breeding

1. Assess Source Populations:
   • Evaluate several factors:
     • Population differentiation (genetic differences between populations).
     • Diversity within populations.
     • Inbreeding and relatedness between individuals.
   • Metrics to Consider:
     • Heterozygosity (H).
       -Standardized Heterozygosity: A measure of genetic diversity, often compared across populations or time points.
     • Mean Kinship: Average relatedness of an individual to all others in the population. Higher mean kinship indicates lower overall genetic diversity and potentially increased inbreeding depression.
2. Decide Sourcing Strategy:
   • Key considerations:
     • Founder group size (number of individuals used to establish a new population).
     • Single vs. multiple source populations.
     • One-way or reciprocal translocations (movement of individuals in one or both directions).
   • Goal: Optimize genetic diversity and minimize kinship among founders.
3. Undertake Translocation:
   • Release Strategies:
     • Mixing individuals from different populations.
     • Soft vs. hard release (gradual acclimatization vs. immediate release).
   • Maximize breeding opportunities and juvenile survival:
     • Establishment breeding (e.g., small pen before release).
     • Release with pouch young, cross-fostering.
     • Headstarting (raising young in a protected environment).
4. Post-Translocation Monitoring:
   • Short-term (1-2 generations):
     • Confirm successful breeding and mixing, equal founder contribution.
     • Maintenance or increase in genetic diversity.
     • Decrease in inbreeding and/or relatedness.
   • Medium (2-3 generations) and Long-term (5+ generations):
     • Success criteria (e.g., conservation of 90-95% genetic diversity).
     • Ongoing management (e.g., supplementation).
     • Viability as future source population.
5. Rectify Genetic Problems:
   • Address issues such as:
     • Reproductive skew (unequal contribution to reproduction).
     • Inbreeding.
     • Genetic bottleneck.
     • Population divergence (e.g., in fenced reserves or islands).
   • Periodic genetic assessment is vital.
   • Prevention is better than cure.

Tasmanian Devil Case Study

• Focus: Genetic management in ex situ (captive) and in situ (wild) populations.

Molecular Pedigree Reconstruction

• Using genetic markers to determine relationships between individuals.
• Applications:
  • Determining relatedness.
  • Assessing reproductive success and skew.
  • Evaluating post-release survival.
• Integration with other data:
  • Mate choice.
  • Drivers of successful reproduction.

Relatedness and Inbreeding

• Standard programs often assume founders are unrelated (inbreeding = 0).
• Molecular data reveals actual relationships and inbreeding levels:
  • Example: Population average inbreeding changes from 0 to 0.037 when molecular relationships are included.
  • Demonstrates how inbreeding coefficient (F) changes across generations (F0, F1, F2) with specific values (e.g., F = 0.0625, F = 0.25).

Plight of the Tasmanian Devil

• Devil Facial Tumour Disease (DFTD) has severely impacted populations.
• Distribution Map (2018) shows confirmed locations of DFTD.

Founder Relationships

• Analysis of founder intake of Tasmanian Devils (2005-2015).
• Studies by Hogg et al. (2015, Conservation Genetics; 2019, Animal Conservation) reveal:
  • Founder relationships and their impact on genetic diversity.
  • Increase of pF (Founder relationships) over time from 2006 to 2017.

Reproductive Success and Skew

• Unequal contribution to reproduction among individuals.
• Example:
  • 8 females (Melanie, Wilhelmina, Willow, Ruby, Jean, Genie, Fudge, Ashes, Alex).
  • 12 males (Ziggy Starman, Aladdin, Blue, Jean, Joey, Sharpay, Mars, Surprise, Major Tom, Geronimo, Honky Tonk, Tonto, Studley).
  • Offspring examples: Jon Snow, Tyrion, Khal, Catelyn, Shae, Joffrey (Farquharson et al. 2019, Conservation Genetics).
• Calculation of offspring per female (6 offspring / 8 females = 0.75).
• Calculation of offspring per male (6 offspring / 12 males = 0.5).
• High reproductive skew: over half of wild-born founders did not breed.

Releases to Maria Island

• Multiple releases to Maria Island:
  • 2012 (N = 15), 2013 (N = 13), 2017 (N = 6), 2019 (N = 8).

Genetic Measures on Maria Island

• Devils have poor connectivity and low diversity compared to other species (Long-nosed potoroo, Western quoll).
• Studies:
  • Wright et al. 2019, BMC Genomics.
  • Grueber et al. 2019, Evolutionary Applications.
  • Frankham et al. 2016, Journal of Biogeography.
  • Spencer et al. 2007, Molecular Ecology.

Genetic Admixture on Maria Island

• Genetic admixture occurring on Maria Island.
• Data from McLennan et al. 2020, Animal Conservation.

Reproductive Success on Maria Island

• Reproductive success varies between introduced and island-born females.
• Data from McLennan et al. 2020, Animal Conservation, showing differences in average offspring/female.

Maria Island Pedigree

• Distribution of offspring number among individuals.
• Example: 53% of individuals have 1 offspring vs. 33% (McLennan et al. 2022 Ecological Applications).

Maria Island Inbreeding

• Average inbreeding coefficient over time (2012-2015).
• Data from McLennan et al. 2018, Conservation Genetics.

Genetic Management of Maria Island

• Summary of releases and removals:
  • 2012-2023 showing number of devils released and removed each year.
• Impact of removals on IR (Inbreeding risk) spread.
  • High, Medium, Low.
• Hogg et al. 2020 Biological Conservation

Genetic Diversity and Mean Kinship over Time

• Trends in standardized heterozygosity and mean kinship from 2012-2023.