Lecture 19 Long term selection handout - University of...

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Lecture 19Lecture 19Long Term Selection:Long Term Selection:

TopicsTopicsSelection limits Selection limits Avoidance of inbreeding

New Mutations

Lecture 19 2

Roberson (1960) Limits of Roberson (1960) Limits of SelectionSelection

• 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 3

VerificationVerification

Lecture 19 4

VerificationVerification

Lecture 19 5

Effect of Selection Intensity on Effect of Selection Intensity on N, the effective population sizeN, 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 6


• 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 7

Selection Limits as a function of Percent SavedSelection Limits as a function of Percent SavedGen 1Gen 1--1010

N=2048u=.0001

Lecture 19 8

Selection Limits as a function of Percent SavedSelection Limits as a function of Percent SavedGenerations 1Generations 1--100100

N=2048

u=.0001N=2048u=.0001

Lecture 19 9

Selection Limits as a function of Percent SavedSelection Limits as a function of Percent SavedGenerations 1Generations 1--200200

N=2048

u=.0001N=2048u=.0001

Lecture 19 10


• 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 11

Experimental EvidenceExperimental 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 12

Experimental Results Experimental Results (Wilson, 1974)(Wilson, 1974)

I=individual Mass SelectionI=individual

Mass Selection

Lecture 19 13


I=individual Mass Selection

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Wilson (1974) Wilson (1974) ConcludedConcluded

““There Is No Obvious There Is No Obvious Explanation for the Explanation for the

Discrepancies That Exist Discrepancies That Exist Between These Experimental Between These Experimental Results and the Theoretical Results and the Theoretical

Expectations”.Expectations”.

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Possible Possible ExplanationExplanation

InbreedingInbreeding

Lecture 19 16INT 5 7 8 10 20 50

RESP

ONSE

-10

0

10

20

30

40

50

60

70

80

GENERATIONS1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

BLUP Selection Additive Effects

50%

20%

5%

Lecture 19 17

INT 5 7 8 10 20 50

RESP

ONSE

0

10

20

30

40

50

60

GENERATIONS1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

BLUP Selection Dominance Effects

50%

20%

5%

Lecture 19 18INT 5 7 8 10 20 50

INBRE

EDING

0.0

0.1

0.2

0.3

0.4

0.5

0.6

GENERATIONS1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

5%

20%

50%

Selection Intensity and Inbreeding with BLUP

Lecture 19 19

Inbreeding ImpactsInbreeding 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

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Comparison Between Comparison Between BLUP and MASSBLUP and MASS

Same Selection IntensitySame Selection Intensity

Lecture 19 21LINE 1 2 3 4 5 6

7 8 9 10 11 12

RESP

ONSE

-10

0

10

20

30

40

50

60

70

80

GENERATIONS1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

Additive Effects

BLUP

MASS

50%5%

20%

Lecture 19 22LINE 1 2 3 4 5 6

7 8 9 10 11 12

RESP

ONSE

0

10

20

30

40

50

60

GENERATIONS1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

Dominance Effects

5%

7%

20%

50%

BLUP

MASS

Lecture 19 23


Lecture 19 24

Avoid InbreedingAvoid Inbreeding• Selection Program

–Maximize Selection Intensity–Minimize Inbreeding–Cannot do both

• Optimal Breeding Program–Depends on Time Horizon

Short term-Maximize selection intensityLong Term-select upper 50% and equal

number of males and femalesWithin Family Selection

Lecture 19 25

Methods to Control Inbreeding and Methods to Control Inbreeding and Maximize Response: Fixed GenerationsMaximize 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 26

Methods to Control Inbreeding and Methods to Control Inbreeding and Maximize Response:Maximize Response: Overlapping Overlapping

GenerationsGenerations

• 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

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Long Term SelectionLong Term Selection

LimitsLimitsCausesCauses

New MutationsNew Mutations

Lecture 19 28

Case StudyCase StudyTribolium Tribolium castaneum:castaneum:TheThe red flour red flour

beetlebeetle

Lecture 19 29

Tribolium Life HistoryTribolium Life History

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Large LinesLarge 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 31

Small LinesSmall Lines• Initiated in 1963

– Used Same Line as Large (Purdue +)

Lecture 19 32

Procedure 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 33

Relaxed SelectionRelaxed Selection• Varying Periods Of Length• Combat The Loss Of Reproductive

Fitness

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ResultsResults30 years and 360 Generations 30 years and 360 Generations

LaterLaterAbout 150 Generations of About 150 Generations of

SelectionSelection

Lecture 19 35

Large and Small AdultsLarge and Small Adults

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Large and Small PupaeLarge and Small Pupae

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Large ILarge IOver All FitOver All Fit

b=11.85 mg/Gen

b=4.74 dug/Gen

b=1.28 dug/Gen

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Large I Large I Gen 260Gen 260--360360

b=1.28 dug/Gen

b=4.74 dug/Gen

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Large IILarge IIOverall FitOverall Fit

b=9.26 dug/Gen

b=1.70 dug/Gen

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Large II Large II Generations Generations

260260--360360

b=9.26 dug/Gen

b=1.70 dug/Gen

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Large III Overall FitLarge III Overall Fit

b=11.6 dug/Gen

b=1.6 dug/Gen

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Large IIILarge IIIGenerations Generations

250250--320320

b=1.6 dug/Gen

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Small: Overall Small: Overall FitFit

b= -5.47 dug/Gen

b= -0.85 dug/Gen

b= +0.05 dug/Gen

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Small: Small: Generations 240Generations 240--

360360

b= -0.85 dug/Gen

b= +0.05 dug/Gen

Lecture 19 45

Plateaus Plateaus • Possible Causes

–Loss of Genetic Variability–Physiological Limits

• Loss of Selection Differential• Loss of Fitness

Lecture 19 46

Test of Alternative Test of Alternative HypothesisHypothesis

–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 47

Loss of Genetic Variability?Loss of Genetic Variability?• Reverse Selection

–Applied Generations 340-360 –Same Selection Intensity As In The

Positive Selection –Measured Response

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UpUp--Down Down SelectionSelection

Large LineLarge Line

b=0.09 dug/Gen (ns)

b= - 53.1 dug/Gen (p <.01)

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UpUp--Down Down SelectionSelectionSmall LineSmall Line

b= 0.41 dug/Gen (ns)

b= -0.00 dug/Gen (ns)

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UpUp--Down SelectionDown SelectionControl LineControl Line

b=13.8 dug/Gen (p <.01)

b= -9.2 dug/Gen (p <.01)

Lecture 19 51

ConclusionsConclusions• 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 52

Physiological LimitPhysiological 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 53

Selection DifferentialSelection Differential

b= 0.39 dug/gen

b= -0.08 dug/gen

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Relative Selection DifferentialRelative Selection DifferentialRSD=100xSD/Generation RSD=100xSD/Generation

MeanMean

b= +0.00 %/gen (ns)

b= -0.01%/gen (ns)

Lecture 19 55

ConclusionConclusion• Selection Differential Unaffected by

Selection• Not Cause For Limit

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Physiological LimitPhysiological Limit

Loss of Fitness In Loss of Fitness In Direction of Selection?Direction of Selection?

Lecture 19 57

Physiological LimitsPhysiological 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 58

Relationship Between Pupae Relationship Between Pupae Number and Parental WeightNumber and Parental Weight

b=+21 Pupae/mg

b= -4.4 Pupae/mg

Lecture 19 59

ConclusionConclusion

• Fitness–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 60

ConclusionConclusion• 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 61

Remaining QuestionsRemaining Questions1. 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 62

Remaining QuestionsRemaining Questions2. 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 63

Nature of Selection Limits in Other Nature of Selection Limits in Other Laboratory Experiments (Laboratory Experiments (WLWL ch16)ch16)

Lecture 19 64

Nature of Selection Limits in Other Nature of Selection Limits in Other Laboratory Experiments (Laboratory Experiments (WLWL ch16)ch16)

Lecture 19 65

New Mutations and Selection LimitsNew Mutations and Selection Limits

Only helpful if population size large

50% of population selected

Lecture 19 66

Lab ProblemLab 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 Long term selection handout - University of...

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