CHAPTER
[07]
Understanding Population Health and Sustainability
Population analysis in Kora provides systematic assessment of breeding programme demographics. Evaluates genetic health. Assesses long-term sustainability. You analyse population size. Review breeding ratios. Track growth trends. Calculate genetic metrics. Evaluate viability. Analysis transforms scattered studbook data into comprehensive population health reports. These support programme management decisions. Identify sustainability risks. Guide breeding strategies for conservation, genetic improvement, or population stability.
This chapter explains how population analysis works. What metrics are tracked. How population assessment supports breeding programme success.
What is Population Analysis?
Population analysis is systematic evaluation of breeding programme health across multiple dimensions:
- Demographics: Population size, sex ratios, age distribution
- Breeding capacity: Number of breeding-age males and females
- Genetic health: Population-level genetic diversity and inbreeding
- Growth trends: Birth rates, mortality rates, population change over time
- Sustainability: Whether population is viable long-term
- Geographic distribution: Where animals are located across institutions or properties
Why population analysis matters:
- Identify risks early: Detect sustainability problems before crisis occurs
- Guide breeding decisions: Understand population needs informing breeding recommendations
- Track progress: Monitor whether breeding programme achieving goals
- Support planning: Project future population needs and resource requirements
- Enable reporting: Provide data for stakeholders, regulators, or funding organisations
- Coordinate efforts: Multi-institutional programmes see complete population picture
Example population analysis:
Population Analysis - Endangered Parrot Conservation Programme
Analysis Date: 2024-11-01
Analysis Period: 2024 breeding season
Population Demographics:
Total Population: 187 individuals
Adult Males: 82 (44%)
Adult Females: 89 (48%)
Juveniles (Male): 8 (4%)
Juveniles (Female): 6 (3%)
Unknown Sex: 2 (1%)
Breeding Population:
Breeding-Age Males: 65 (79% of adult males)
Breeding-Age Females: 71 (80% of adult females)
Sex Ratio (breeding): 0.92 males per female (well-balanced)
Genetic Metrics:
Population Inbreeding: 0.047 (low - acceptable)
Population Genetic Diversity: 0.768 (good)
Founder Genome Equivalents: 12.3 (moderate founder representation)
Growth Trends (Past Year):
Births: 23 offspring
Deaths: 15 individuals
Net Growth: +8 individuals (+4.5% population growth)
Birth Rate: 12.3% (healthy)
Mortality Rate: 8.0% (acceptable for species)
Sustainability Assessment: STABLE
- Population growing modestly but sustainably
- Breeding capacity adequate (136 breeding-age individuals)
- Genetic diversity maintained (no alarming inbreeding trends)
- Sex ratios favourable for breeding programme
Management Recommendations:
1. Continue current breeding strategy (working well)
2. Monitor 2 animals with unknown sex for breeding capacity planning
3. Focus breeding recommendations on maintaining genetic diversity
4. Consider expanding institutional participation to distribute risk
Status: Healthy breeding programme with stable demographics and good genetics
Population analysis provides comprehensive health check. Reveals programme strengths. Identifies areas requiring attention.
Population Demographics
Demographics describe population structure and composition:
Basic Population Counts:
- Total Population: All registered individuals (active studbook entries)
- Adult Males: Mature male animals
- Adult Females: Mature female animals
- Juveniles: Young animals not yet breeding age
- Unknown Sex: Animals not yet sexed or sex uncertain
Age Structure:
- Breeding Age: Animals physiologically capable of breeding
- Sub-Adult: Animals approaching breeding age but not yet mature
- Juvenile: Young animals dependent or recently independent
- Geriatric: Older animals past prime breeding years
Example demographic breakdown:
Cattle Breeding Programme Demographics:
Total Population: 450 animals
Age and Sex Distribution:
Adult Bulls (>24 months): 45 (10%)
Adult Cows (>24 months): 285 (63%)
Yearling Bulls (12-24 months): 28 (6%)
Yearling Heifers (12-24 months): 35 (8%)
Calves (<12 months, male): 30 (7%)
Calves (<12 months, female): 27 (6%)
Breeding Population:
Breeding Bulls: 42 (93% of adult bulls available for breeding)
Breeding Cows: 265 (93% of adult cows available for breeding)
Analysis:
- Strong breeding-age population (68% of total)
- Good replacement ratio (63 yearlings for 330 adults = 19% replacement)
- Balanced sex ratio in calves (30 males, 27 females)
- Minimal non-breeding adults (breeding capacity maximised)
Wildlife Conservation Programme Demographics:
Total Population: 78 rhinos
Age and Sex Distribution:
Adult Males (>7 years): 28 (36%)
Adult Females (>6 years): 35 (45%)
Sub-adult Males (3-7 years): 6 (8%)
Sub-adult Females (3-6 years): 5 (6%)
Juveniles (<3 years): 4 (5%)
Breeding Population:
Breeding Males: 22 (79% of adult males)
Breeding Females: 30 (86% of adult females)
Analysis:
- Healthy breeding-age population (67% breeding-capable adults)
- Sub-adult cohort provides future breeding stock (11 animals approaching maturity)
- Low juvenile population suggests recent breeding decline (requires investigation)
- Excellent adult breeding participation (>75% actively breeding)
Demographics reveal population structure. Support breeding programme assessment. Enable planning across livestock and conservation contexts.
Breeding Population Assessment
Breeding population metrics focus on reproductive capacity:
Breeding Capacity Metrics:
- Breeding Males: Number of males capable and available for breeding
- Breeding Females: Number of females capable and available for breeding
- Sex Ratio: Ratio of breeding males to breeding females
- Breeding Participation: Percentage of breeding-age animals actively breeding
Sex Ratio Interpretation:
- 1:1 ratio (1.0): Equal breeding males and females
- 1:2 ratio (0.5): More females than males (common in polygynous species)
- 2:1 ratio (2.0): More males than females (may indicate breeding constraints)
Example breeding assessment:
Elephant Breeding Programme - Breeding Population:
Breeding Males: 12 bulls (age 10-35 years)
Breeding Females: 28 cows (age 10-40 years)
Sex Ratio: 0.43 (12 males : 28 females)
Assessment:
- Breeding male to female ratio appropriate for elephants
- Bulls distributed across 8 institutions (genetic diversity support)
- 23 of 28 cows (82%) actively participating in breeding programme
- 5 cows (18%) not breeding due to health concerns or breeding rest
- 10 of 12 bulls (83%) actively used for breeding
- 2 bulls (17%) in breeding rest (recently bred multiple females)
Breeding Capacity: GOOD
- Sufficient breeding males for current female population
- Strong female participation (82% breeding)
- Good geographic distribution preventing over-reliance on single location
Recommendations:
- Continue monitoring 5 non-breeding cows for health clearance
- Rotate bull breeding assignments to prevent fatigue
- No urgent need for additional breeding males
Sheep Breeding Programme - Breeding Population (Farm):
Breeding Males: 8 rams (age 1-5 years)
Breeding Females: 120 ewes (age 1-7 years)
Sex Ratio: 0.07 (8 males : 120 females)
Assessment:
- Ram to ewe ratio appropriate for sheep (1:15 typical)
- All 8 rams actively used for breeding (100% participation)
- 115 of 120 ewes (96%) actively breeding
- 5 ewes (4%) not breeding due to age or health
Breeding Capacity: EXCELLENT
- Sufficient rams for current ewe population
- Outstanding breeding participation (96% of ewes)
- Age distribution ensures breeding capacity maintained (rams ages 1-5)
Recommendations:
- Maintain current ram numbers
- Consider replacing 2 oldest rams within 2 years
- Monitor non-breeding ewes for culling decisions
Breeding population assessment reveals reproductive capacity. Identifies potential constraints across different species and management contexts.
Genetic Population Metrics
Population-level genetic metrics assess overall genetic health:
Population Inbreeding Coefficient
What it measures: Average inbreeding across entire population. Shows how inbred the population is as a whole.
Interpretation (high-level):
- Below 0.05: Low population inbreeding (healthy)
- 0.05 to 0.10: Moderate inbreeding (monitor carefully)
- Above 0.10: High inbreeding (significant concern, breeding strategy needed)
Why it matters: High population inbreeding indicates limited genetic diversity. Increases genetic health risks. Reduces population viability. Breeding programmes aim to minimise population inbreeding. This happens through careful breeding pair selection.
Population Genetic Diversity
What it measures: Overall genetic variation present in entire population. Measures heterozygosity and genetic richness.
Interpretation (high-level):
- Above 0.70: Excellent population diversity
- 0.60 to 0.70: Good diversity
- 0.50 to 0.60: Moderate diversity (improvement needed)
- Below 0.50: Low diversity (significant concern)
Why it matters: Genetic diversity supports population health. Enhances disease resistance. Improves adaptability. Conservation programmes prioritise maintaining or increasing population genetic diversity.
Founder Genome Equivalents
What it measures: How many equally contributing founders would produce current population genetic diversity. Higher numbers indicate better founder representation.
Example:
Founder Genome Equivalents: 8.5
Interpretation: The genetic diversity in this population is equivalent to what
you would have if 8.5 unrelated founders contributed equally to
the gene pool. Since the actual population descended from 15
founders, some founders are over-represented while others are
underrepresented.
Breeding Strategy: Prioritise breeding animals descended from underrepresented
founders to balance founder contributions and increase
founder genome equivalents toward actual founder count (15).
Why it matters: Founder genome equivalents reveal effectiveness. Show how well breeding programme preserves original genetic diversity from founding animals.
Example genetic assessment:
Conservation Breeding Programme - Genetic Population Metrics:
Population Inbreeding Coefficient: 0.062 (6.2%)
Status: MODERATE - Inbreeding elevated but manageable
Trend: Increased from 0.045 (4.5%) last year
Concern: Inbreeding rising; breeding strategy adjustments recommended
Population Genetic Diversity: 0.712 (71.2%)
Status: GOOD - Healthy genetic variation maintained
Trend: Stable from 0.718 last year
Note: Diversity holding steady despite modest inbreeding increase
Founder Genome Equivalents: 11.8
Actual Founders: 18
Founder Retention: 65.6% (11.8/18)
Status: MODERATE - Some founder genetics lost or underrepresented
Analysis:
Population retains good genetic diversity overall, but inbreeding creeping
upward. Breeding recommendations should prioritise reducing inbreeding while
maintaining diversity. Focus on underrepresented founders to improve founder
genome equivalents.
Recommendations:
1. Prioritise breeding pairs with low relatedness
2. Increase breeding from underrepresented founder lineages
3. Consider introducing unrelated animals if available
4. Avoid breeding closely related animals for next 2-3 generations
Genetic population metrics guide breeding strategy adjustments. Maintain population health across conservation and livestock programmes.
Growth Trends and Vital Rates
Population growth analysis tracks change over time:
Vital Rate Metrics:
- Birth Rate: Percentage of population born in period (births divided by population)
- Mortality Rate: Percentage of population that died in period (deaths divided by population)
- Net Growth Rate: Population change (births minus deaths, adjusted for additions or removals)
- Doubling Time: How long population takes to double at current growth rate
Example growth analysis:
Annual Population Trends - Zoo Breeding Cooperative:
Analysis Period: January 2024 to December 2024
Population Change:
Starting Population: 89 individuals (Jan 1, 2024)
Births: 12 offspring
Deaths: 8 individuals
Transfers In: 3 animals (from other institutions)
Transfers Out: 5 animals (to other institutions)
Ending Population: 91 individuals (Dec 31, 2024)
Vital Rates (Annual):
Birth Rate: 13.5% (12 births divided by 89 starting population)
Mortality Rate: 9.0% (8 deaths divided by 89 starting population)
Natural Growth: +4.5% (birth rate minus mortality rate)
Net Change: +2.2% (including transfers)
Growth Trend: STABLE GROWTH
- Births exceeding deaths (healthy reproduction)
- Modest net growth (+2 individuals equals +2.2%)
- Sustainable growth trajectory (not overpopulation risk)
Five-Year Trend:
2020: 78 animals
2021: 82 animals (+5.1%)
2022: 85 animals (+3.7%)
2023: 89 animals (+4.7%)
2024: 91 animals (+2.2%)
Average Annual Growth: +3.9%
Projection:
At current growth (3.9% annually), population will reach:
- 2025: approximately 94 animals
- 2026: approximately 98 animals
- 2027: approximately 102 animals
Assessment: Healthy, sustainable population growth suitable for long-term
breeding programme. Current trajectory appropriate for institutional
capacity across cooperative (no overpopulation concerns).
Farm Breeding Programme - Cattle Herd Trends:
Analysis Period: January 2024 to December 2024
Population Change:
Starting Population: 450 cattle (Jan 1, 2024)
Births: 98 calves
Deaths: 12 animals
Sales: 85 animals (market sales)
Purchases: 5 animals (replacement genetics)
Ending Population: 456 cattle (Dec 31, 2024)
Vital Rates (Annual):
Birth Rate: 21.8% (98 births divided by 450 starting population)
Mortality Rate: 2.7% (12 deaths divided by 450 starting population)
Natural Growth: +19.1% (birth rate minus mortality rate)
Net Change: +1.3% (including sales and purchases)
Growth Trend: CONTROLLED GROWTH
- High birth rate (21.8%) typical for well-managed cattle herd
- Low mortality rate (2.7%) indicates excellent herd health
- Sales offset natural growth maintaining stable herd size
- Intentional population management balancing growth with capacity
Assessment: Excellent herd productivity (21.8% birth rate, 2.7% mortality).
Sales strategy successfully maintains target herd size around 450-460
animals matching property carrying capacity. Sustainable long-term model.
Growth trends reveal whether population sustainable, expanding, or declining. Apply across conservation, zoo, and farm contexts.
Sustainability Assessment
Sustainability analysis evaluates long-term population viability:
Sustainability Indicators:
- Population size: Is population large enough for genetic viability?
- Growth trajectory: Is population growing, stable, or declining?
- Breeding capacity: Sufficient breeding-age animals for reproduction?
- Genetic health: Acceptable inbreeding and diversity levels?
- Age structure: Balanced distribution across age classes?
Sustainability Categories:
- Thriving: Healthy growth, excellent genetics, strong demographics
- Stable: Sustainable population without growth or decline
- Vulnerable: Some concerns requiring attention or intervention
- At Risk: Significant concerns threatening long-term viability
- Critical: Urgent action needed to prevent population collapse
Example sustainability assessment:
Breeding Programme Sustainability Assessment:
Programme: Endangered Amphibian Conservation Programme
Assessment Date: November 2024
Sustainability Category: VULNERABLE
Population Size: 45 individuals
Concern: Small population size increases genetic drift and inbreeding risk
Status: VULNERABLE - Below ideal minimum (recommended: 50+ individuals)
Growth Trajectory: Declining (-3.5% annually)
Concern: More deaths than births over past 3 years
Status: AT RISK - Population shrinking, not sustainable long-term
Breeding Capacity: 18 breeding pairs available
Status: ADEQUATE - Sufficient breeding animals if mortality addressed
Note: Breeding capacity exists; reproduction not the limiting factor
Genetic Health: Population Inbreeding 0.089 (8.9%)
Concern: Moderate inbreeding in small population
Status: VULNERABLE - Inbreeding manageable but increasing
Age Structure: Skewed toward older animals (62% over 8 years old)
Concern: Ageing population without sufficient juvenile recruitment
Status: AT RISK - Limited reproductive years remaining for many animals
Overall Assessment: VULNERABLE - Population at risk without intervention
Critical Issues:
1. Mortality exceeding births (population declining)
2. Small population size compounds genetic risks
3. Ageing population limits future breeding potential
Recommended Actions (Priority Order):
1. URGENT: Investigate and address mortality causes (health, husbandry)
2. HIGH: Intensive breeding programme to increase juvenile recruitment
3. HIGH: Consider introducing unrelated individuals to increase population size
4. MEDIUM: Breeding recommendations prioritising genetic diversity
5. MEDIUM: Enhanced husbandry protocols to improve survival
Timeline: Actions needed within 6-12 months to prevent further decline
Outcome: Without intervention, population likely to continue declining toward
non-viability. With aggressive management, population can stabilise
and recover within 3-5 years.
Sustainability assessment provides honest evaluation. Drives strategic decisions for conservation and breeding programmes.
Geographic Distribution
Multi-institutional programmes track animal distribution across locations:
Distribution Metrics:
- Number of Institutions: How many facilities participate
- Animals per Institution: Distribution across facilities
- Geographic Redundancy: Spread across regions reducing single-location risk
- Breeding Pairs by Institution: Reproductive capacity distribution
Example geographic analysis:
Geographic Distribution - International Elephant Breeding Programme:
Participating Institutions: 18 zoos across 8 countries
Population Distribution:
Zoo A (Country 1): 12 elephants (6 breeding-age)
Zoo B (Country 1): 8 elephants (4 breeding-age)
Zoo C (Country 2): 15 elephants (9 breeding-age)
Zoo D (Country 2): 7 elephants (3 breeding-age)
Zoo E (Country 3): 11 elephants (7 breeding-age)
... (13 additional institutions)
Total: 187 elephants across 18 institutions
Average: 10.4 elephants per institution
Range: 4 elephants (smallest) to 15 elephants (largest)
Regional Distribution:
Europe: 145 elephants (77.5%) across 14 institutions
North America: 28 elephants (15.0%) across 3 institutions
Asia: 14 elephants (7.5%) across 1 institution
Distribution Assessment: GOOD REDUNDANCY
- Animals spread across 18 institutions (no single point of failure)
- Geographic diversity across continents
- Largest concentration (15 animals) is 8% of population (not excessive)
- Smallest institution (4 animals) still contributing breeding capacity
Breeding Pair Distribution:
Institutions with breeding capacity: 16 of 18 (89%)
Institutions with only males or females: 2 (breeding potential if transfers)
Cross-institutional breeding pairs: 23 potential pairings across locations
Coordination Benefits:
- Multi-institutional spread protects against single-facility disasters
- Geographic diversity enables cross-continental genetic exchange
- Multiple breeding locations reduce inbreeding risk
- Coordinated breeding recommendations leverage full population diversity
Geographic distribution reveals programme resilience. Shows coordination effectiveness across international conservation efforts.
Target Population Comparisons
Programmes can set target population goals. Compare actual versus desired state.
Example target comparison:
Breeding Programme Targets vs Actuals:
Programme: Commercial Breed Registry - Purebred Hereford Cattle
Target Population (Set 2020): 500 registered breeding animals by 2025
Actual Population (Nov 2024): 478 registered animals
Progress: 95.6% of target (22 animals short of goal)
Demographic Targets vs Actuals:
Target Breeding Bulls: 50 | Actual: 48 (96% of target)
Target Breeding Cows: 350 | Actual: 342 (98% of target)
Target Replacement Stock: 100 | Actual: 88 (88% of target)
Genetic Targets vs Actuals:
Target Population Diversity: over 0.75 | Actual: 0.782 (ACHIEVED)
Target Inbreeding: under 0.05 | Actual: 0.043 (ACHIEVED)
Growth Targets vs Actuals:
Target Annual Growth: +5% | Actual: +4.2% (close to target)
Assessment: ON TRACK
- Population nearly at target (95.6% achieved)
- Genetic health targets exceeded (excellent diversity, low inbreeding)
- Growth slightly below target but within acceptable range
- Replacement stock lower than ideal (breeding priority for next year)
Recommendations:
- Focus breeding recommendations on increasing replacement stock
- Maintain genetic diversity achievements in upcoming breeding season
- Expect to meet 500 animal target by mid-2025 at current growth
Target comparisons track programme progress. Measure performance toward explicit goals.
Population Analysis Reports
Analysis generates comprehensive reports supporting stakeholder communication:
Report Components:
- Executive Summary: High-level population status
- Detailed Demographics: Complete population breakdown
- Genetic Assessment: Population genetic health metrics
- Growth Trends: Historical and projected population change
- Sustainability Evaluation: Long-term viability assessment
- Management Recommendations: Specific actions based on analysis
- Supporting Data: Charts, tables, historical comparisons
Report Uses:
- Programme coordination: Share population status with participating institutions
- Funding justification: Demonstrate programme success or resource needs
- Regulatory compliance: Document population management for authorities
- Scientific publication: Support conservation research and reporting
- Annual reporting: Communicate programme progress to stakeholders
- Strategic planning: Inform long-term breeding programme strategy
Population reports transform raw data into actionable intelligence. Drive programme success across conservation, livestock, and zoo contexts.
Integration with Other Studbook Features
Population analysis connects to complete breeding programme ecosystem:
Integration Points:
- Studbook Entries: Population counts derived from active or inactive entries
- Pedigrees: Demographic analysis identifies family structures and relationships
- Genetic Profiles: Genetic metrics calculated from individual testing results
- Breeding Recommendations: Analysis informs recommendation priorities and strategies
- Reproductive Records: Birth and mortality rates calculated from breeding outcomes
- Population Goals: Targets compared against actual analysis results
Example integrated workflow:
Annual Breeding Programme Cycle:
November: Population Analysis Conducted
- Demographics assessed (187 animals, 136 breeding-age)
- Genetic metrics calculated (inbreeding 0.047, diversity 0.768)
- Growth trends reviewed (+4.5% annual growth, stable)
- Sustainability assessed (stable, healthy programme)
December: Breeding Recommendations Generated
- Analysis informs recommendation priorities
- Genetic diversity goals set based on population metrics
- Breeding targets established (aim for 20-25 offspring next season)
- High-priority pairings identified for underrepresented genetics
January-March: Breeding Season Preparation
- Institutions receive breeding assignments
- Pedigrees reviewed ensuring no close relatives breed
- Genetic profiles consulted for compatibility assessment
April-August: Breeding Season
- Breeding attempts based on recommendations
- Reproductive records document breeding events and pregnancies
September: Offspring Registration
- New births registered as studbook entries
- Pedigree relationships created linking parents to offspring
- Population demographics updated with new individuals
October: Outcome Assessment
- Breeding success evaluated (18 offspring born from 23 attempts)
- Mortality documented (15 deaths during year)
- Updated population analysis shows +8 net growth (+4.5%)
November: Next Year's Analysis
- Process repeats with updated population data
- Breeding recommendations refined based on previous year outcomes
- Long-term trends tracked year-over-year
Integration creates continuous improvement cycle. Analysis informs breeding. Breeding creates outcomes. Outcomes update analysis.
Common Population Analysis Scenarios
Conservation Programme Annual Assessment
Scenario: Endangered species programme assessing yearly progress.
Workflow:
- Generate annual population analysis
- Review demographics, genetics, growth trends
- Assess progress toward recovery goals
- Identify sustainability risks or opportunities
- Generate recommendations for upcoming breeding season
- Share report with participating institutions and conservation authorities
Outcome: Systematic annual evaluation ensuring programme effectiveness and coordination.
Breed Registry Membership Reporting
Scenario: Cattle breed association reporting to members.
Workflow:
- Analyse registered breeding population
- Calculate growth rates and breeding participation
- Assess genetic diversity and inbreeding trends
- Compare to breed standards and targets
- Generate annual report for membership
- Highlight high-performing bloodlines or genetics
Outcome: Transparent reporting supporting breeder confidence and breed improvement.
Research Colony Sustainability Check
Scenario: Laboratory assessing mouse strain viability.
Workflow:
- Evaluate breeding colony demographics
- Assess genetic consistency and drift
- Calculate replacement rates and colony sustainability
- Identify breeding capacity or genetic concerns
- Adjust breeding strategy if needed
Outcome: Maintained research reproducibility through sustainable colony management.
Multi-Institutional Coordination
Scenario: Zoo consortium planning breeding across facilities.
Workflow:
- Analyse complete population across all participating zoos
- Identify breeding capacity at each institution
- Assess genetic distribution and diversity across locations
- Generate breeding recommendations considering institutional capacity
- Coordinate breeding assignments across consortium
- Track outcomes updating population analysis
Outcome: Coordinated multi-institutional breeding maximising genetic diversity and programme success.
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