salit kark department of evolution, systematics and ecology
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Conservation Biology (Ecology) Lecture 4 November 2009. Salit Kark Department of Evolution, Systematics and Ecology The Silberman Institute of Life Sciences The Hebrew University of Jerusalem. Loss of genetic variability has multiple aspects. - PowerPoint PPT PresentationTRANSCRIPT
Salit Kark
Department of Evolution, Systematics and Ecology
The Silberman Institute of Life Sciences
The Hebrew University of Jerusalem
Conservation Biology (Ecology)
Lecture 4
November 2009
Loss of genetic variability has multiple aspects
• specific alleles will either be lost or retained (maintained)
• genetic variance (or heterozygosity) will be lost
Probability that alleles are lost in a “founder” population can be described
by the following equation:
E = m - (1 - Pj)
# of alleles leftat a locusafter foundation
2N
# of original allelesat a given locus
# of founders
frequency ofeach allele
Loss of Alleles
4
E = 4 - (.0081 + .6561 + .6561 + .6561) = 2.0236 alleles left
E = m - (1 - Pj)2N# of original allelesat a given locus
# of alleles leftat a locus
Let m be 4allele freq =p1= 0.70 p2 = p3 = p4 =0.10 N = 2 (two founders)
E = 4 - (1- .10) = .6561 (1- .10) = .6561 (1- .10) = .6561
(1- .70) = .0081- little influence- large influence- large influence- large influence
2N
2N
2N
2N
AVERAGE # OF ALLELES RETAINED# INDIVIDUALSIN SAMPLE (N) P1=.70, P1=.94, P2=P3=P4=.10 P2=P3=P4=.02
1 1.48 1.12 2 2.02 1.23 6 3.15 1.64 10 3.63 2.00 50 3.99 3.60 >>50 4.00 4.00
Two things are clear from this example:
1. More alleles are lost in populations founded by small numbers of individuals
2. Alleles with a high frequency have relatively little influence, while alleles with low frequencies have considerable influence
Heterozygosity (H)
Approximation of the proportion of
heterozygosity remaining following the
sudden reduction of a large population can
be described by the following equation:
Hf = (1 - ) Hor 12N
# foundersHeterozygosityremaining
Originalheterozygosity
# % of original percentagefounders heterozygosity lost remaining 1 50% 50% 2 75 25 6 91.7 8.3 10 95 5 20 97.5 2.5 50 99 1 100 99.5 0.5
For any size of HOriginal
The expected proportion of variation remaining after t
generations can be calculated by:
Ht = (1 - ) Hor 12N
t
Heterozygosityretained aftert generations
# generations
# individuals
originalheterozygosity
% Genetic Variance H remaining after t generationsPopSize (N) 1 5 10 100
2 75 24 6 <<<1 6 91.7 65 42 <<1 10 95 77 60 <1 20 97.5 88 78 8 50 99 95 90 36100 99.5 97.5 95 60
So, the following conclusions can be drawn:
• Small populations of constant size will lose heterozygosity through time
• The smaller the population is, the more rapidly heterozygosity will decline
• The higher the number of generations a population of small size is bred the more heterozygosity is lost
During Bottlenecks… the loss of
alleles, especially rare ones, is much
greater than the loss of heterozygosity
Rare allele freq. is 10%
q2 = .012pq = .18
Rare allele freq. is 1%
q2 = .00012pq = .02
Changes following the foundation (or reduction in size)
When population sizes are low, a population is, in effect, going through a serious bottleneck every generation,
and the effects are cumulative…
Factors affecting population genetic diversity
Population structure, size, sex ratio etc…
Dispersal and gene flow in or out of the population
Rates of various processes, (e.g., mutation)
Recombination (creates new combinations of existing diversity)
Selection
Genetic Drift
more…
Various genetic variability estimates Various genetic variability estimates and markers can be used, such as:and markers can be used, such as:
AllozymesAllozymes
Sequencing (genes and others)Sequencing (genes and others)
mDNA, nuclear DNAmDNA, nuclear DNA
MicrosatellitlesMicrosatellitles
and many more…and many more…
……which show different patterns of which show different patterns of diversity…diversity…
Clegg, S.M., S.M. Degnan, J. Kikkawa, Clegg, S.M., S.M. Degnan, J. Kikkawa, et al. 2002. Genetic consequences of et al. 2002. Genetic consequences of sequential founder events by an island-sequential founder events by an island-colonizing bird. PNAS 99:8127-8132colonizing bird. PNAS 99:8127-8132
FOUNDER EFFECTS
silvereye (Zosterops lateralis)
They chose to work with allelic variation at six microsatellite loci
They found that allelic diversity gradually declined with repeated colonizations of new islands.
The individual reductions are small, but the cumulative changes are large.
From first to last in the sequence of recent colonizations, the mean number of alleles per locus dropped by almost half.
Because the last population in the sequence is the youngest, one cannot explain this result by long-term genetic drift.
Instead, the pattern seems to reflect a small loss of alleles at each colonization, although hardly on the scale envisaged in the original formulation of the founder effects model.
More in paper…..
Effective Population Size
UP to now – we made the assumption that the number of males and females contributing to each subsequent
generation is the same
If the sex ratio is not 1:1 for each generation then the population loses
genetic variability more rapidly
This is because the “effective number” of individuals is smaller than the actual
number of individuals in the population
Effective Number can be calculated as follows:
Ne = 4Nm * NfNe = 4Nm * Nf Nm + NfNm + Nf
# breeding # breeding femalesfemales
# breeding males# breeding males
Effective NumberEffective Number
For a sex ratio of 1 male : 9 females in a population of
100 animals
4(10 X 90)4(10 X 90) 10 + 9010 + 90
= 36= 36Ne =Ne =
Which means that a population of 100 individuals, consisting of 10 breeding males and 90 breeding females would lose genetic variability as rapidly as a population consisting of only 18 males
and 18 females or 36 individuals
When do we want to include population genetics in
conservation considerations?
Many possible inferences from population genetic studies that are
important for conservation:
Effective population size Inbreeding/selfing Mating success Bottlenecks Time of isolation Migration/dispersal