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