Lecture 19 Long Term Selection: Topics Selection limits Avoidance of inbreeding New Mutations 1
Roberson (1960) Limits of Selection For a single gene selective advantage s, the chance of fixation is a function only of Ns, where N is the effective population size. In artificial selection based on the individual measurements, the expected limit is a function of Ni i is the selection intensity Lecture 19 2
Verification Lecture 19 3
Verification Lecture 19 4
Effect of Selection Intensity on N, the effective population size As Selection Intensity Increases Number of breeders decreases For the same total number of breeders Effective population size is less for Randomly Selected parents than directionally selected If the heritability is greater than 0, then relatives are more similar for that trait than non-relatives Directional Selection tends to select relatives because they have similar performance Lecture 19 5
Roberson (1960) Limits of Selection In a selection program of individual selection of equal intensity in both sexes, the furthest limit should be attained when half the population is selected each generation. This is especially true if additive variance predominates and within family selection is utilized, i.e. the best male and female in each family is chosen. In which case the limit may be increased by almost 50% above that of simple mass selection saving the best 50% (Dempfle, 1975) Lecture 19 6
Selection Limits as a function of Percent Saved Gen 1-101 10 N=2048 u=.0001 Lecture 19 7
Selection Limits as a function of Percent Saved Generations 1-1001 100 N=2048 u=.0001 N=2048 u=.0001 Lecture 19 8
Selection Limits as a function of Percent Saved Generations 1-2001 N=2048 u=.0001 N=2048 u=.0001 Lecture 19 9
Roberson (1960) Limits of Selection The use of information on relatives is always a sacrifice on the eventual limit for the sake of immediate gain in the early generation. The loss may be small in large populations Lecture 19 10
Experimental Evidence Theoretical Advantages of Index (family) Selection Over Mass Selection Not Attained Kinney Et Al., 1970 Doolittle, Et Al. 1972 Garwood and Lowe, 1979; Garwood Et Al., 1980 Wilson, 1974; Campo and Tagarro, 1977 Perez and Toro 1992 Lecture 19 11
Experimental Results (Wilson, 1974) I=individual I=individual Mass Selection Mass Selection Lecture 19 12
Experimental Results (Wilson, 1974) I=individual Mass Selection Lecture 19 13
Wilson (1974) Concluded There Is No Obvious Explanation for the Discrepancies That Exist Between These Experimental Results and the Theoretical Expectations. 14
Possible Explanation Inbreeding 15
80 70 BLUP Selection Additive Effects 60 RESPONSE 50 40 30 5% 20% 50% 20 10 0-10 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 GENERATIONS INT 5 7 Lecture 8 19 10 20 5016
60 50 BLUP Selection Dominance Effects RESPONSE 40 30 20% 20 5% 10 0 50% 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 GENERATIONS Lecture 19 17 INT 5 7 8 10 20 50
Selection Intensity and Inbreeding with BLUP 0.6 0.5 0.4 5% INBREEDING 0.3 20% 0.2 0.1 50% 0.0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 GENERATIONS INT 5 7 8 10 20 50 Lecture 19 18
Inbreeding Impacts Random Genetic Drift With Additive Systems Inbreeding Causes Loss of Favorable Alleles Lowers Selection Limits Effects Seen in the Long Term Directional Dominance Causes a Further Depression in The Mean Due to Loss of Heterozygosity Effect Seen in the Short Term Lecture 19 19
Comparison Between BLUP and MASS Same Selection Intensity 20
80 70 Additive Effects 60 BLUP 50 MASS 20% RESPONSE 40 30 20 5% 50% 10 0-10 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 GENERATIONS Lecture 19 21 LINE 1 2 3 4 5 6 7 8 9 10 11 12
60 50 BLUP Dominance Effects 20% 40 MASS RESPONSE 30 20 7% 5% 10 0 50% 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 GENERATIONS Lecture 19 22 LINE 1 2 3 4 5 6 7 8 9 10 11 12
Experimental Results (Wilson, 1974) Lecture 19 23
Avoid Inbreeding Selection Program Maximize Selection Intensity Minimize Inbreeding Cannot do both Optimal Breeding Program Depends on Time Horizon Short term-maximize selection intensity Long Term-select upper 50% and equal number of males and females Within Family Selection Lecture 19 24
Methods to Control Inbreeding and Maximize Response: Fixed Generations Meuwissen (1997) Maximizing the response of selection with a predefined rate of inbreeding J ANIM SCI 75 (4): 934-940 maximizes genetic gain constraining their average coancestry to a predefined value. At equal rates of inbreeding, genetic gains were 21 to 60% greater than that with selection just for BLUP-EBV Lecture 19 25
Methods to Control Inbreeding and Maximize Response: Overlapping Generations Meuwissen and Sonesson AK (1998). Maximizing the response of selection with a predefined rate of inbreeding: Overlapping generations. J ANIM SCI. 76 : 2575-2583 dynamic selection rule developed maximizes selection response in populations with overlapping generations. At the same rates of inbreeding, the dynamic selection rule obtained up to 44% more genetic gain than direct selection for BLUP breeding values. advantage of the dynamic rule over pure BLUP selection decreased with increasing population sizes Lecture 19 26
Long Term Selection Limits Causes New Mutations 27
Case Study Tribolium castaneum:the red flour beetle Lecture 19 28
Tribolium Life History Lecture 19 29
Large Lines Replications I and II (Large I and II) Initiated 1954 8 heterogeneous randomly mated populations (Purdue +) Rep III initiated in 1961 Purdue + foundation Lecture 19 30
Initiated in 1963 Small Lines Used Same Line as Large (Purdue +) Lecture 19 31
Procedure Large I, II, III and Small Closed Populations Selection Pupae Weight (100/400) 200 Pupa Of Each Sex Were Weighed Largest or Smallest 50 of Each Sex Chosen Randomly Mated in Mass Lecture 19 32
Relaxed Selection Varying Periods Of Length Combat The Loss Of Reproductive Fitness Lecture 19 33
Results 30 years and 360 Generations Later About 150 Generations of Selection 34
Large and Small Adults Lecture 19 35
Large and Small Pupae Lecture 19 36
Large I Over All Fit b=11.85 mg/gen b=1.28 dug/gen b=4.74 dug/gen Lecture 19 37
Large I Gen 260-360 b=1.28 dug/gen b=4.74 dug/gen Lecture 19 38
Large II Overall Fit b=1.70 dug/gen b=9.26 dug/gen Lecture 19 39
Large II Generations 260-360 b=1.70 dug/gen b=9.26 dug/gen Lecture 19 40
Large III Overall Fit b=1.6 dug/gen b=11.6 dug/gen Lecture 19 41
Large III Generations 250-320 b=1.6 dug/gen Lecture 19 42
Small: Overall Fit b= -0.85 dug/gen b= -5.47 dug/gen b= +0.05 dug/gen Lecture 19 43
Small: Generations 240-360 b= -0.85 dug/gen b= +0.05 dug/gen Lecture 19 44
Possible Causes Plateaus Loss of Genetic Variability Physiological Limits Loss of Selection Differential Loss of Fitness Lecture 19 45
Test of Alternative Hypothesis Loss of Genetic Variability Reverse Selection Observe Response Physiological Limit Loss of Selection Differential Examine Change In Selection Differential Loss of Fitness Measure Fitness Related Traits in Direct and Reverse Selected Lines Lecture 19 46
Loss of Genetic Variability? Reverse Selection Applied Generations 340-360 Same Selection Intensity As In The Positive Selection Measured Response Lecture 19 47
Up-Down Selection Large Line b=0.09 dug/gen (ns) b= - 53.1 dug/gen (p <.01) Lecture 19 48
Up-Down Selection Small Line b= 0.41 dug/gen (ns) b= -0.00 dug/gen (ns) Lecture 19 49
Up-Down Selection Control Line b=13.8 dug/gen (p <.01) b= -9.2 dug/gen (p <.01) Lecture 19 50
Conclusions Plateau in Small Line Due to Loss of Genetic Variability Plateau in Small Line May Also Be Due to Physiological Limit Plateau in Large Line Due to Physiological Limit Lecture 19 51
Physiological Limit Loss of Selection Differential Examine Change In Selection Differential As Selection Advances Selection Differentials Measured Generations 200-360 Generations of Sustained Selection Lecture 19 52
Selection Differential b= 0.39 dug/gen b= -0.08 dug/gen Lecture 19 53
Relative Selection Differential RSD=100xSD/Generation Mean b= -0.01%/gen (ns) b= +0.00 %/gen (ns) Lecture 19 54
Conclusion Selection Differential Unaffected by Selection Not Cause For Limit Lecture 19 55
Physiological Limit Loss of Fitness In Direction of Selection? 56
Physiological Limits Last Generation (360) Large I and Small Assortatively Mated 1,200 Single Pairs Measured Parental Pupae Weight Offspring Pupae Weight Offspring Pupae Number Regressed Offspring Number on Parental Weight (Genetic Regression) Lecture 19 57
Relationship Between Pupae Number and Parental Weight b=+21 Pupae/mg b= -4.4 Pupae/mg Lecture 19 58
Fitness Conclusion Positively Correlated With Pupae Wt In Small Line Negatively Correlated With Pupae Wt In Large Line Effective Selection Differential Diminishes in Direction of Selection Physiological Limits Constrain Further Progress in Either Line Lecture 19 59
Conclusion Causes For Selection Limit Loss of Effective Selection Differential Due to Negative Correlation with Fitness In Both Lines Loss of Genetic Variability in Small Line Verified via DNA Finger Prints No Variability Lecture 19 60
Remaining Questions 1. True Physiological Limit? Refuted by Goliath Single Gene Mutation For Large Homozygote Same Size as Large Cross With Large Additive Effect Doubles Body Size Is Fertile Lecture 19 61
Remaining Questions 2. Mechanism For Relationship Between Pupae Number and Parental Weight Unknown 3. Mutations What Happened To Mutational Heritability Particularly w.r.t. Small Line Possibility Rate of Inbreeding? F > 85% by Termination of Experiment But Same as For Large Line Lecture 19 62
Nature of Selection Limits in Other Laboratory Experiments (WL( ch16) Lecture 19 63
Nature of Selection Limits in Other Laboratory Experiments (WL( ch16) Lecture 19 64
New Mutations and Selection Limits 50% of population selected Only helpful if population size large Lecture 19 65
Lab Problem Chose one of the commodity groups below Design an optimal breeding program What traits to select on What method of selection would you utilize How many animals be utilized How many breeders would be chosen (How many of each sex would you save) What mating system would be employed (how would you determine who mates to whom and how many offspring would be kept per mating? Lecture 19 66