conservation genetics readings: freeman chapter 55

CONSERVATION GENETICS

READINGS:FREEMAN

Chapter 55

GENETIC DIVERSITYThe diversity of life is fundamentally genetic. A

variety of genetic methods have been used to investigate diversity both within and between species. Here are a few:

1. Morphological variation -- a good clue, but does not correlate perfectly with genetics;

2. Chromosomal variation -- inversions, translocations and polyploidy;

3. Soluble proteins -- blood groups, soluble enzyme polymorphism’s;

4. DNA markers -- microsatellites, “fingerprint” loci.

CONSERVATION OF GENETIC VARIATION

• The foundation of diversity is the process of natural selection shaping genetic variation.

• When genetic variation is absent (zero heterozygosity), the population (or species) has limited evolutionary potential and the risk of extinction is high.

• The conservation of genetic variation provides a hedge against extinction.

An Endangered Species: Red Wolf

• This canine family member was once found in the southeast. It disappeared in the wild by the late 1970s.

• Reintroduced into Great Smoky Mountains National Park in 1990’s.

An Endangered Species: Red Wolf

• Examination of DNA demonstrated that the red wolf is a hybrid between gray wolf and coyote.

• Expansion of coyote range and shrinking of gray wolf range resulted in gene swamping of red wolf genes by coyote genes.

An Endangered Species: Cheetah• A species that shows a

very low level of genetic variation.

• May have experienced a genetic bottleneck near the end of the last ice age (10,000 - 12,000 years ago) when many other mammal species became extinct.

• Low genetic variation in “fingerprint” loci compared to other cat species.

Population Size and Extinction Risk

• Populations are subject to chance or sampling error in getting alleles from one generation to the next (genetic drift, genetic bottlenecks, founder effects).

• Populations are subject reduction in gene flow and gene swamping.

• Small populations are particularly vulnerable to extinction due to reduction in genetic variation (heterozygosity).

CONSERVATION GENETICS (I)

• Conservation genetics is an area of study that determines genetic variation and the processes that diminish it.

• Heterozygosity is a measure of genetic variation.

• Processes that diminish heterozygosity, especially in small populations, are: 1) genetic drift; 2) genetic bottlenecks; 3) inbreeding.

CONSERVATION GENETICS (II)

• The movement of alleles from one population to another is called gene flow.

• Gene flow promotes heterozygosity by increasing the chances of outbreeding.

• Fragmentation often results in a reduction of gene flow into isolated populations.

• Gene swamping occurs when small populations are genetically assimilated by much larger populations.

Effective Population Size (Ne)

• Effective population size gives a crude estimate of the average number of contributors to the next generation (Ne).

• Always a fraction of the total population.• Some individuals will not produce

offspring due to age, sterility, etc. • Of those that do, the number of progeny

many vary.

Effective Population Size (Ne)

• A variety of ways of estimating (Ne) have been formulated.

• One that accounts for unequal sex ratios among breeding adults is:

Ne = 4(NM * NF)

NM + NF

where NM = number of males

NF = number of females

Effective Population Size (Ne)

• What is the effective population size (Ne) of one with 100 females and 10 males?

• Remember:

Ne = 4(NM * NF)

NM + NF

where NM = number of males

NF = number of females

Effective Population Size (Ne)

• What is the effective population size (Ne) of one with 100 females and 10 males?

Ne = 4(100 * 10) = 4000 = 36 100 + 10 110• Remember:

Ne = 4(NM * NF)

NM + NF

where NM = number of males

NF = number of females

Genetic Drift

• Random change in allele frequency due to sampling only a small portion of gametes from the previous generation.

• Most likely in small populations (<100 individuals).

• Least likely in large populations (< 1,000 individuals.

Genetic Drift

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Genetic Drift

The proportion of genetic variation retained in a population of constant size after t generations is approximately:

Proportion = (1 -1/(2N))t

where N = number of individuals

t = number of generations

Genetic Drift

What proportion of genetic variation is retained in a population of 10 individuals after 10 generations?

Proportion = (1 - 1/20)10 = 0.9510

= .5987 or about 60% Proportion = ((1 -1/(2N))t

where N = number of individuals

t = number of generations

Genetic Bottleneck

• The loss of genetic variation when a population drops in size.

• Effective population size (Ne) after a fluctuation in population size is estimated by:

Ne = t/ sum of (1/Ni)

where Ni = size of population in generation i t = number of generations

Genetic Bottleneck

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Genetic BottleneckWhat is the effective population size (Ne) of one

that goes from 1,000 (t1) to 10 (t2) and recovers to 2,000 (t3)?

Ne = t/ sum of (1/Ni)

where Ni = size of population in generation i t = number of generations

Genetic BottleneckWhat is the effective population size (Ne) of one

that goes from 1,000 (t1) to 10 (t2) and recovers to 2,000 (t3)?

Ne = _________ 3 ________ = 3/0.1015 1/1000 + 1/10 + 1/2000 = 29 individuals

Ne = t/ sum of (1/Ni)

where Ni = size of population in generation i t = number of generations

Inbreeding

• Inbreeding occurs more frequently in isolated and small populations.

• It acts to reduce Ne. It is estimated bY;

Ne. = ____N_____

1 + F

where F is the inbreeding coefficient

or probability of inheriting 2 alleles

from the same ancestor.

Inbreeding vs Outbreeding

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Inbreeding Depression

• Prairie chickens in Illinois declined due to decreased hatching success.

• Individuals from Iowa were introduced to the breeding population and hatching success improved.

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Metapopulations Reduce Extinction Risk (I)

• Studies of the Granville fritillary show how subpopulations stabilize overall population size.

• In addition, provide opportunity for gene flow.

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Metapopulations Reduce Extinction Risk (I)

• Oerall population size remains relatively stable even when local populations go extinct.

• The metapopulation provided for increased opportunity for gene flow between local populations.

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Population Viability Analysis (I)

• PVA provides a means for estimating the likelihood that a population will avoid extinction for a given period of time.

• Freeman (2005) describes a study of how migration rates are likely to influence population viability of an endangered marsupial.

Population Viability Analysis (II)

• This endangered marsupial lives in an old-growth forest in southeastern Australia and relies on dead trees for nest sites.

• PVA was used to predict the consequences of habitat loss and forest fragmentation on this endangered species.

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Population Viability Analysis (III)

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Population Viability Analysis

• Freeman describes demographic studies of a European lizard species that is declining in some areas.

• He explains how migration maintains some local populations in spite of local extinction.

• He presents a model of how migration rates are likely to influence population viability of an endangered marsupial.

Life History Characteristics, Population Size and Extinction

Risk

• Extinction risk is related to the life history characteristics of the species in question.

• Small populations with “long-lived” life history characteristics are particularly vulnerable to extinction .

LIFE HISTORY CHARACTERISTICS

• Population attributes such as lifespan, mortality and natality patterns, biotic potentials, and patterns of population dynamics are called life history characteristics.

• Life history characteristics have important consequences for wildlife management and extinction risk.

FOUR IMPORTANT ASPECTS OF LIFE

HISTORIES • 1. Lifespan --- the upper age limit for the

species.• 2. Mortality --- the pattern of survivorship (I,

II, or III).• 3. Natality --- the age to reproductive

maturity and number of offspring produced.• 4. Biotic potential --- maximum rate of

natural increase (rmax = births - deaths).

LIFE HISTORY EXTREMES

• Short-lived.• Type III survivorship

high juvenile mortality; relatively secure old age.

• Many offspring from young adults.

• High maximum rate of population growth.

• Long-lived.• Type I survivorship:

low juvenile mortality; high mortality at old age.

• Few offspring from older adults.

• Low maximum rate of population growth.

LIFE HISTORY TRAITS FORM A CONTINUUM (I)

• Every species can be placed somewhere on a continuum with respect to the life history extremes.

• Comparisons of life histories are best done between species that show similar evolutionary histories.

LIFE HISTORY TRAITS FORM A CONTINUUM (II)

• Field mice and muskrats are rodents in closely related taxonomic families.

• Field mice (short-lived) show a Type III survivorship and produce many offspring.

• Muskrats (long-lived) have a Type I survivorship and produce few young.

LIFE HISTORY TRAITS FORM A CONTINUUM (III)

• See Freeman (2005) page 1195 for full discussion.

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Some Long Lived Species

• These have moderate juvenile mortality, low adult mortality, and low fecundity.

• They are endangered.

Whooping Crane Spotted Owl

Some Short Lived Species

• These have high juvenile mortality, moderate adult mortality, and high fecundity.

• They are thriving.

Starling House Finch

CONSERVATION GENETICS

READINGS:FREEMAN

Chapter 55