Env 121: Conservation of Biodiversity

Topics: Conservation genetics of small populations

Professor Sork: 15 May 2007

Conservation in the news:

• Ocean Blues, New York Times Magazine, May 13, 2007
• Flames Latest Threat to Catalina's Wildlife, NPR, May 11, 2007
  • http://www.npr.org/templates/story/story.php?storyId=10140375
• Cutting Greenhouse Emissions May Rest with China, NPR, May 14, 2007

I. Background on conservation genetics

A. What is conservaton genetics

1. Study of genetic processes within and among populations that underlie long-term sustainability of populations and species
2. Genetic processes that can increase extinction risk
3. Genetic processes associated with adaptation to local environment

B. What does it encompass?

1. Preservation of genetic biodiversity
2. Preservation of adaptive genetic variation
3. Genetic management of small populations
4. Definitions of management units

C. Key concepts

1. Genetic diversity
2. Effective population size
3. Inbreeding and inbreeding depression
4. Adapative variation
5. Evolutionary hotspots
6. Evolutonary management units

D. Evolutionary forces and conservation

Genetic drift

• Chance sampling of genotypes from one generation to the next
• Important in small populations
• Loss of advantageous alleles
• Fixation of deleterious alleles
• Estimated by measuring the "effective size of populations", N_e
  • defined as size of idealized population where all individuals are randomly mating
• Founder effects are special case

Natural selection

• Differential survival and reproduction of individuals with genotypes that are adapted to a specific environment.
• Loci affected by natural selection represent "adaptive variation".
• Affects fitness of populations

Gene flow

• Exchange of genes between populations
• Influences degree of divergence
• Source of genetic variation for local populations
• Reduces local adaptation
• Animals: movement of individuals
• Plants: movement of seeds and pollen

II. Genetic diversity

1. Genetic variation is the "stuff of evolution"

• Fisher made the point that evolutionary change occurs in proportion to the variance.
• Loss of adaptive genetic variation may affect population fitness.

2. Markers used to estimate genetic variation

a. visual traits

b. blood groups (enzymes)

c. allozyme variation (enzymes): common

d. molecular variation: more common now

• microsatellies DNA markers
  • nuclear, mitochondrial, and chloroplast
  • locus with short tanden repeat DNA sequence, such as AC sequence repeated different times
  • very informative genetic markers
  • ofter species, or genus specific
• gene sequences
  • useful for identifying evolutionary lineages
  • evolutionary management units
• single nucleotide polymorphisms (SNP)
  • a position in the DNA where 2 or more alternative base pairs can be found
  • used in model organisms

3. Statistical measures used to estimate genetic variation

Polymorphism (P): Percentage of total loci that are polymorphic at a specified criteria.

"Genetic diversity" -- a term often used to describe extent of variation in a population

• average heterozygosity across set of loci
• expected heterozygosity
• allelic diversity

III. Loss of Genetic diversity

A. Loss of diversity in small populations

• H=1 - 1/[2 Ne]
• When effective population size is small, heterogosity (and genetic diversity) is smaller.
  • See Figure below from http://www.for.gov.bc.ca/hre/forgen/projects/deployment.htm

B. Chance fixation of deleterious alleles

1. Potential problem for managed populations or species reintroduction
2. Example: white tiger in zoos

C. Effective population size

1. Definition: the effective number of randomly mating interbreeding individuals

2. Influenced by:

a. sex ratio--Ne is reduced if number of males and females is not equal



Example:
If 1 male and 99 females, Ne = 3.96
If 25 males and 75 females, Ne = 75
If 50 males and 50 females, Ne = 10

 

b. population size from generation to generation



 

Northern elephant seal Reduced to 20-30 individuals due to overhunting Recovered to 100,000 indiviudals Let's say pre-hunting population size was 100,000 for one generation Then, N1=100,000; N2=20, N3=100,000

Genetic bottleneck resulted in Ne ~ 50 individuals

==> ~1% of arithmetic mean

 

D. Effect of family size on Ne

1. For idealized populations size, variance in family size=2

2. Variation in family size can increase or decrease effective population size.

3. Different species of plants and animals have different mating systems

Even family size		Uneven family size
1		0
2		0
2		0
3		0
1		9
1.8	mean	1.8	mean
1.7	variance	16.2	variance

Species on left might be a monogamous bird species; species on right might be a mammal species with dominant male.

 

Table. Illustration of effect of variation in family size on Ne.

variance	Nc	Ne	Ne/Nc
0	100	200	2.0
1	100	133	1.3
2	100	57	.1.0
5	100	57	.57
10	100	33	.33

 

Example 1: Darwin's Cactus finch variance in family size: 6.74 Ne/Nc = 4/(6.74+4) = .46
Example 2: Asiatic Lions Average family size: 1.64 Variance in family size: 32.65 Ne is 8% of census population!

 

IV. Conservation genetics in managed zoological populations

A. Fitness and inbreeding

• Fitness is the relative survivorship and fertility of individuals
• Inbreeding is mating among relatives
• When populations have a history of outcrossing, inbreeding often results in reduced fitness (known as inbreeding depression)

B. Inbreeding depression

• Definition: reduction in viablility, birth weight, and fertility due to breeding among relatives
• Causes: expression of deleterious alleles at one or several genes
• Recommendation for captive animals: breeding programs must be designed to reduce or avoid ID

 

Example: Przewalski's horse Providing early evidence for inbreeding in zoos original wild horse inbred in zoos now re-introduced. http://www.treemail.nl/takh/horse/index.htm

C. Evidence of Inbreeding in zoos

1. Study by Katharine Ralls and Jonathon Ballou

• Surveys of 16 ungulates, 12 small mammals, 16 primates
• Methods: Compare juvenile mortality of inbred versus non-inbred progeny
• Results: 41 of 44 species showed significantly higher mortality of inbred progeny

Success story: Dorca's Gazelle American Association of Zoological Parks and Aquariums presented National Zoological Park an award for sustained captive breeding in 1978 Analysis of breeding herd indicated deleterious inbreeding effects: high juvenile mortality in inbred calves delayed sexual maturity in inbred female miscellaneous veterinary problems Demonstrates benefits for cooperative breeding programs

Example of Solution: Speke's Gazelle Alan Templeton and Bruce Read at St. Louis Zoo Problem: highly inbred population founding population was 3 females and 1 male Breeding program goal: eliminate inbreeding depression Solution: inbreed offspring and select healthy progeny

D. Breeding design to eliminate inbreeding depression in Speke's gazelle

1. Increase size of herd
2. Rules for selection of parents:
   • Select parents that will maximize genetic variability in the herds’ gene pool
   • Select parents that are in good health (even though inbred)
3. Rules for offspring attributes
   • Choose mates that result in offpsring with maximal genetic variability
   • Choose mates that result in inbreed offspring

RESULTS:

1. Survival of selected inbred animals was greater than previously observed.
2. Severity of inbreeding depression as expressed in birth weight was reduced.

E. SSP program for Siberian tiger

Carrying capacity has been established as 250 animals Current population is 250 animals but age and sex ratios need adjustment All animals over 15 yrs should be removed Litters should be produced at 7 or 8 yrs so that viability of offspring can be evaluated Population as 17 founders but representation among population needs improvement Equalization of family size will permit each animal to produce two litters but young animals will be removed to maintain 2 offspring average.

F. General components of genetic management of captive zoo populations

1. Acquire an adequate number of founders
2. Expand population as rapidly as possible from founders
3. Subdivide populations
• maximize effective population size
• equalize founder representation
• manage inbreeding coefficients (F)
• (minimize F is best unless inbreeding is unavoidable)

V. Management of genetic populations for reintroduction

A. Extent of captive breeding

• 245 threatened vertebrate species

• Few invertebrate

• Many threatened plants

  • Kew Gardens 2.7K species

  • Center for Plant Conservation, USA 600 spp

B. Genetic deterioration in captivity

• Inbreeding depression
• Loss of genetic diversity
• Mutation accumulation
• Genetic adaptation to captivity

VI. Evolutionary conservation science

A. Phylogenies and management units

B. Evolutionary process

C. Example in tree population: valley oak

1. Study of the distribution of cp markers to look at areas of evolutionary history

2. Sampled throughout range of valley oak

3. Result: similar areas of high genetic gradients as seen my mammals

(in map, dark areas show high gradients)

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