Executive Summary

787
G5 animals with EBV
16
Unique sires used
86
Unique dams used
150
Full-sib groups
54
Ne (G5 production)
Critical finding: Only 16 sires were used to produce all 787 G5 animals. With a mean of 49 offspring per sire , the male side is a severe bottleneck . This limits the maximum achievable Ne for Generation 6. Immediate action is needed to use more sires in future matings.

1 G5 Population Structure — Who Are the Parents?

1.1 Key Definitions (for Beginners)

Before diving into the numbers, here are the three family units used in this analysis — explained in plain language:

Term Plain meaning In this programme
Sire The father of a group of offspring A G4 male that was mated to produce G5 chicks
Dam The mother of a group of offspring A G4 female that was mated to produce G5 chicks
Sire family All offspring sharing the same father (paternal half-sibs) All G5 chicks fathered by the same sire — they share ~50% genes from the father's side
Dam family All offspring sharing the same mother All G5 chicks born from the same dam — they share ~50% genes from the mother's side
Full-sib group (FSG) Offspring sharing BOTH father AND mother G5 chicks from the same sire x dam mating — they share ~50% of all genes (like human brothers and sisters)

Why does this matter? When we select parents for G6, if we pick two full siblings, their offspring will be more inbred. By selecting at most one animal per full-sib group , we keep the next generation genetically diverse and healthy.

1.2 How G5 Was Produced — The Big Picture

Reading the chart: Each bar is one G4 sire. The height = total G5 offspring from that sire. Sire 813 produced 114 offspring — 14.5% of the entire G5 generation by itself. This extreme imbalance is the main driver of low Ne.

1.3 Complete Per-Sire Breakdown

This table shows, for each of the 16 sires that fathered G5 animals, exactly how many dams they were mated with, how many full-sib groups (litters) were produced, and how many sons and daughters resulted.

Per-sire contribution to G5 ( 16 sires total)
Sire ID Dams mated with Full-sib groups Male offspring Female offspring Total G5 offspring % of G5
813 12 12 48 66 114 14.5%
891 10 10 37 29 66 8.4%
4654 11 11 24 35 59 7.5%
620 10 10 22 33 55 7%
1794 9 9 25 29 54 6.9%
257 10 10 25 26 51 6.5%
562 9 9 26 23 49 6.2%
1800 8 8 18 28 46 5.8%
545 10 10 18 26 44 5.6%
1609 8 8 21 22 43 5.5%
792 9 9 21 19 40 5.1%
561 9 9 21 18 39 5%
1419 10 10 22 15 37 4.7%
1615 10 10 14 23 37 4.7%
919 6 6 11 16 27 3.4%
853 9 9 9 17 26 3.3%
How to read this table:
  • Dams mated with = how many different mothers this sire was paired with. More dams = more diverse full-sib groups.
  • Full-sib groups = the number of distinct sire x dam pairs. Each group is a 'litter' of siblings.
  • Total G5 offspring = total chicks this sire fathered with a Week 16 weight and known sex.
  • % of G5 = share of the entire G5 generation that came from this one sire.

1.4 Complete Per-Dam Breakdown

Dam family summary — how many offspring per mother
Category Value
Total unique dams in G5 86.0
Dams with 1 offspring recorded 3.0
Dams with 2–5 offspring 15.0
Dams with 6–10 offspring 36.0
Dams with more than 10 offspring 32.0
Average offspring per dam 9.2
Most prolific dam (max offspring) 18.0

1.5 Full-Sib Group (FSG) Structure

A full-sib group = all chicks from the same father AND same mother. They are the closest relatives possible in the flock (brothers and sisters).

Full-sib group size distribution ( 150 groups across 787 animals)
FSG.size..siblings. Number.of.groups Animals.in.category
1 animal (singleton) 11 11
2 animals 17 34
3–5 animals 65 263
6–10 animals 48 359
11–15 animals 9 120
Top 15 largest full-sib groups — sorted by family size
Sire (Father) Dam (Mother) Male chicks Female chicks Total siblings Best EBV (g) Lowest EBV (g)
813 1601 11 4 15 38.4 -65.1
813 1879 5 10 15 93.4 -30.3
813 1899 8 7 15 52.8 -31.4
813 1397 8 6 14 5.4 -72.4
562 1159 5 8 13 186.7 82.7
813 1946 3 10 13 117.2 30.6
813 337 1 12 13 37.4 -49.1
1794 1056 6 5 11 174.9 96.6
792 1173 4 7 11 228.1 90.3
1800 1522 4 6 10 155.1 109.6
813 1750 6 4 10 45.9 -46.2
891 272 5 5 10 161.9 96.3
1609 1577 5 4 9 206.9 123.1
1609 642 3 6 9 131.8 74.8
257 1111 3 6 9 211.8 154.8
Key insight from the FSG table: Within large families (e.g., 15 siblings), the range of EBVs can be very wide (best vs lowest). This confirms that family-based selection — picking the best individual from each group — captures most of the genetic gain while avoiding inbreeding. Simply picking the top animals across the whole population would mean selecting many siblings from a few families and ignoring other families entirely.

1.6 Population Structure — Visual Summary

1.7 Summary Table — G5 Population Structure at a Glance

Complete G5 population structure summary
Metric Value Interpretation
G4 sires (fathers) that produced G5 16.0 Only 16 unique fathers — very small male base
G4 dams (mothers) that produced G5 86.0 86 unique mothers — much better female diversity
Unique sire x dam matings (full-sib groups) 150.0 150 distinct family groups (litters)
G5 animals with Week 16 weight AND known sex 787.0 These are the animals used in this selection analysis
G5 females 425.0 54% of the measured G5 population
G5 males 362.0 46% of the measured G5 population
Average G5 offspring per sire (father) 49.2 Each sire fathered ~49 chicks on average — very high
Average G5 offspring per dam (mother) 9.2 Each dam mothered ~9 chicks on average — reasonable
Average size of a full-sib group (litter) 5.2 About 5 siblings share both parents on average
Largest single sire family (most offspring) 114.0 Sire 813 fathered 114 G5 chicks (14.5% of G5)
Largest full-sib group (most siblings) 15.0 One mating pair produced up to 15 siblings
Effective population size (Ne) of G5 production 54.0 Ne = 54 — near FAO threshold of Ne >= 50
FAO minimum threshold: The Food and Agriculture Organization (FAO) recommends a minimum effective population size of Ne ≥ 50 to avoid significant inbreeding accumulation per generation. The current G5 Ne of 54 is just above this threshold, but only because the dam numbers are relatively high. If sire numbers drop further, Ne will fall below the danger zone.

2 Background: Why Family-Based Selection?

2.1 The Problem with Simple Top-Ranking

If we simply select the top 50 G5 animals by EBV regardless of family, we risk choosing many full siblings from the same high-performing family. This:

  • Reduces Ne (fewer distinct genetic lineages contributing)
  • Increases inbreeding in G6 and beyond
  • Concentrates genetic risk — if that family carries hidden deleterious alleles, we lose diversity to purge them

2.2 The Principle of One-per-Family Selection

The core rule applied here:

Select at most one male and one female from each full-sib group (same sire AND same dam). Additionally, select at most one male across each entire sire family (all offspring of the same sire).

This ensures: 1. No full-sib matings in G6 (the selected M × F are from different families) 2. No half-sib concentration on the sire side 3. Maximum Ne for the given number of sires 4. Genetic gain is still captured — we pick the BEST individual from each family

2.3 The Ne Formula

\[N_e = \frac{4 \, N_m \, N_f}{N_m + N_f}\]

where \(N_m\) = number of breeding males and \(N_f\) = number of breeding females selected.

To maximise Ne for any given total \(N = N_m + N_f\): choose \(N_m = N_f\). However, since the sire bottleneck limits \(N_m \leq 16\), the practical strategy is to use all available sire families and maximise \(N_f\).

3 G5 Family Structure

3.1 Sire Families

Sire families in G5 — sorted by offspring count
SireID Total_offspring Males Females Mean_EBV_Males Mean_EBV_Females Max_EBV N_FSG
813 114 48 66 10.3 37.9 135.3 12
891 66 37 29 144.6 140.4 249.9 10
4654 59 24 35 141.3 155.6 276.9 11
620 55 22 33 195.7 164.4 249.3 10
1794 54 25 29 85.4 90.2 174.9 9
257 51 25 26 189.1 172.6 251.6 10
562 49 26 23 155.5 148.6 237.6 9
1800 46 18 28 61.4 59.6 155.1 8
545 44 18 26 103.5 79.0 206.6 10
1609 43 21 22 113.3 102.6 206.9 8
792 40 21 19 122.9 117.7 228.1 9
561 39 21 18 85.5 114.9 216.7 9
1419 37 22 15 90.6 86.3 149.9 10
1615 37 14 23 35.2 56.2 150.9 10
919 27 11 16 89.1 94.9 160.6 6
853 26 9 17 26.3 11.0 98.0 9
Sire 813 dominates: With 114 offspring , sire 813 contributed 14.5% of all G5 animals. While this sire may be genetically superior, such heavy use concentrates inbreeding risk. Future mating plans should limit the maximum offspring contribution per sire.

3.2 Dam Families

Dam family summary
Category Value
Unique dams 86.0
Dams with 1 offspring 3.0
Dams with 2–5 offspring 15.0
Dams with 6–10 offspring 36.0
Dams with 10+ offspring 32.0
Mean offspring per dam 9.2
Max offspring per dam 18.0

3.3 Full-Sib Groups (FSG)

Distribution of full-sib group sizes
FSG.size Count Animals.in.group
1 animal 11 11
2 animals 17 34
3–5 animals 65 263
6–10 animals 48 359
11–15 animals 9 120

4 Selection Strategy & Scenarios

4.1 Strategy Applied

Three progressive constraints are applied in order:

Priority Constraint Purpose
1st One male per sire family Prevents half-sib concentration on paternal side; uses all 16 sire lineages
2nd One female per full-sib group Prevents full-sib pairs among selected dams
3rd Balance Nm ≈ Nf Maximises Ne = 4NmNf/(Nm+Nf)

Within each allowed slot, the individual with the highest EBV is chosen (truncation selection).

4.2 Ne Under Different Selection Intensities

Effective population size (Ne) under different selection scenarios
Scenario Selected Males (Nm) Selected Females (Nf) Ne Notes
Current G5 production (all 16 sires, 86 dams) 16 86 54.0 Historical reference
Select all: 1M/sire-family × 1F/FSG 16 136 57.3 Maximum Ne with family constraint
Balanced top-50: 25M + 25F (best EBV within family constraint) 25 25 50.0 Balanced, moderate intensity
Balanced top-40: 20M + 20F 20 20 40.0 Balanced, higher intensity
Balanced top-32: 16M + 16F (1M per sire family × 16 best F) 16 16 32.0 Minimum size — all sire families represented

Reading the curve: With 16 sires fixed, increasing the number of dams beyond ~50 gives diminishing Ne returns. The curve flattens because Ne is bounded above by 64 (= 4 × Nm) regardless of how many dams are used. This is why increasing the number of sires is the most impactful action for future cycles.

5 Selected G5 Parents

5.2 Selected Males — 16 Sires (One per Sire Family)

Selected G5 sires — one per sire family, sorted by EBV
Animal ID Father (Sire) Mother (Dam) EBV (g) SE Inbr. (%) Wk16 BW (g)
8967 4654 1881 276.9 88.9 0.000 1,925
8819 257 420 251.6 92.2 0.000 1,760
9390 891 1192 249.9 87.7 0.000 2,000
9300 620 420 249.3 91.2 0.000 1,955
9222 562 1359 237.6 89.2 0.000 1,780
8568 792 1173 228.1 87.6 0.000 2,210
8749 1609 1577 206.9 88.6 0.000 1,735
8677 545 1881 192.2 89.5 0.000 1,490
8870 1794 1056 174.9 88.0 0.000 1,655
9002 919 1577 160.6 90.4 0.000 1,560
8632 561 1605 156.5 90.4 0.000 1,640
9144 1800 1522 155.1 88.3 0.000 1,565
8761 1419 1947 149.9 89.8 0.000 1,420
9164 813 1517 135.3 89.0 0.000 1,735
8713 1615 1522 115.7 89.5 0.000 1,100
8990 853 1902 98.0 90.2 3.125 1,735

Summary — Selected Males:

  • N selected: 16 (one from each of the 16 sire families)
  • Mean EBV: 189.9 g
  • Range: 98 to 276.9 g
  • Mean inbreeding: 0.2%

5.3 Selected Females — 50 Dams (Best EBV, One per Full-Sib Group)

Top 50 selected G5 dams — best EBV per full-sib group
Animal ID Father (Sire) Mother (Dam) EBV (g) SE Inbr. (%) Wk16 BW (g)
9252 4654 1881 242.1 88.9 0.000 1,330
9412 891 1923 238.4 88.4 0.000 1,475
9231 4654 631 234.3 88.7 0.000 1,365
8883 562 1359 228.7 89.2 0.000 1,510
9269 4654 867 223.5 89.2 0.000 1,720
8460 257 870 219.9 89.3 0.000 1,460
8446 257 1147 218.5 88.1 0.000 1,400
8510 561 1056 216.7 90.3 0.000 1,730
8570 792 1173 212.3 87.6 0.000 1,830
9351 620 1673 211.9 89.6 0.000 1,395
8536 545 631 206.6 89.3 0.000 1,750
9332 620 1147 206.0 87.8 3.125 1,230
9074 891 1192 205.0 87.7 0.000 1,420
8800 257 1111 204.4 88.3 0.000 1,245
9327 620 865 202.8 88.5 3.125 1,540
8539 792 1192 202.1 88.3 0.000 1,855
9096 891 1173 196.7 87.4 0.000 1,235
8823 257 324 194.5 88.7 0.000 1,110
9258 4654 1162 193.6 88.1 0.000 1,315
8682 792 1923 186.3 88.8 0.000 1,260
8910 562 1159 176.0 88.3 0.000 1,325
8934 4654 1770 174.5 88.3 0.000 1,505
9017 620 661 174.3 88.6 0.000 1,300
9021 620 1111 173.0 88.4 3.125 1,240
8816 257 865 172.1 88.9 0.000 1,060
9344 620 303 171.3 87.5 0.000 1,240
8886 562 1621 171.0 89.8 0.000 1,415
9239 4654 449 166.4 89.3 0.000 1,245
8556 545 1881 166.3 89.6 0.000 1,300
8463 257 661 165.5 89.3 0.000 1,235
9304 620 420 163.9 91.2 0.000 975
8789 257 303 163.7 87.5 0.000 960
8562 1609 1577 163.6 88.6 0.000 1,395
9347 620 604 162.6 93.4 0.000 1,330
9397 891 272 161.9 90.7 0.000 1,520
9285 4654 799 160.9 89.3 0.000 1,300
9322 620 324 160.3 88.9 3.125 1,030
8871 1794 1056 158.0 88.0 0.000 1,265
9226 4654 1623 154.5 87.0 0.000 1,235
8473 561 1293 153.5 90.3 0.000 1,765
8714 1615 1522 150.9 89.5 0.000 1,160
8524 561 1894 148.0 89.9 0.000 1,480
9138 1800 1522 146.1 88.3 0.000 1,295
9402 891 1624 145.9 87.1 0.000 1,290
9189 1794 1894 145.7 88.7 0.000 1,450
9331 620 870 144.2 89.3 3.125 745
9206 562 1249 142.8 90.9 0.000 1,315
9214 562 737 141.3 90.4 0.000 1,165
9384 891 1789 133.6 88.5 0.000 1,080
8726 792 1880 133.3 90.7 0.000 1,045

Summary — Selected Females:

  • N selected: 50 (from 50 full-sib groups, 12 sire families)
  • Mean EBV: 179.8 g
  • Range: 133.3 to 242.1 g
  • Mean inbreeding: 0.31%

6 Ne Comparison: Before and After Selection

Ne at each stage
Stage Breeding Males (Nm) Breeding Females (Nf) Ne
G4 → G5 production (historical Ne) 16 86 54.0
G5 pool (all available animals) 16 425 61.7
Selected G6 parents (Recommended: 16M + 50F) 16 50 48.5
Maximum possible (1M/sire-family + 1F/FSG) 16 136 57.3

7 Mating Plan Recommendations

7.1 How to Mate the Selected Animals

Rule 1 — Avoid sire x daughter: Confirm no selected female is a daughter of any selected male (check pedigree before mating).

Rule 2 — Avoid full-sib mating: No selected male should mate with a female from the same FSG as himself.

Rule 3 — Rotate sires: Assign each of the 16 selected sires to mate with approximately 4 dams , ideally from different dam families per sire.

Rule 4 — Limit repeat matings: If a sire-dam combination produced G5 animals, avoid the same pairing for G6 (avoids inflating inbreeding in G7).

7.2 Suggested Sire Allocation

Suggested mating allocation — dams per sire
SireID Sire_EBV Dams_assigned
8967 276.9 4
8819 251.6 4
9390 249.9 4
9300 249.3 4
9222 237.6 4
8568 228.1 4
8749 206.9 4
8677 192.2 4
8870 174.9 4
9002 160.6 4
8632 156.5 4
9144 155.1 4
8761 149.9 4
9164 135.3 4
8713 115.7 4
8990 98.0 -10

7.3 Long-Term Ne Projection

Long-term Ne projection
Generation Breeding Males Breeding Females Note Ne
G5 (current) 16 86 Based on observed pedigree 54.0
G6 (recommended) 16 50 This selection plan 48.5
G7 (projected) 20 60 If sire numbers increase to 20 60.0
G7 (if no action) 10 40 If sire bottleneck worsens 32.0

8 Critical Recommendation: Increase Number of Sires

The single most impactful action to improve Ne is to increase the number of sires.

With only 16 sires, no amount of female selection can push Ne above 64 (= 4 × 16). This is the theoretical ceiling with the current sire base.

For G7 planning:

  • Target at least 20-25 sires selected from G6
  • Each G6 sire should come from a different G5 sire family (using this selection plan ensures this)
  • Limit each sire to a maximum of 25-30 daughters kept for further selection

This selection plan uses all 16 available G5 sire families as a foundation. If each selected male has at least 1 son retained for G7, the sire pool can grow to 16 → 20+ in two generations.

9 Output Files Saved

File Contents N animals
G5_Selected_Sires.csv Selected G5 males (one per sire family) 16
G5_Selected_Dams.csv Selected G5 females (top 50 by EBV, 1/FSG) 50
G5_All_Candidates.csv All G5 candidates with selection status 787

Session Information

Report generated: 2026-03-02 09:19:32 
R version: R version 4.5.1 (2025-06-13 ucrt) 
EBV source: Tilili_v2/Model1_Animal_YearMonth/RnSoln_animal.dat
Trait: Week 16 body weight | h2 = 0.208