A few examples: applications of molecular markers to

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Lecture 11

• A few examples applications of molecular markers
  to
• Dispersal patterns
• Gobies
• Cuttlefish
• Demographic history
• Elephant seal
• Resource management
• European anchovy
• Pacific salmon

• Sex specific markers
• Features and detection
• An example

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Population Geneticsmarine dispersal (or not)?

• Cleaner goby (Elacatinus evelynae)
• Taylor Hellberg 2003
• Three color morphs
• Pelagic larvae (3 weeks)

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Population Geneticsmarine dispersal (or not)

• Cleaner goby (Elacatinus evelynae)
• High population differentiation
• Up to FST 0.7
• Surprising philopatry in larvae

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Population Geneticsinvisible walls

• Cuttlefish (Sepia officinalis)
• Perez-Losada et al 2002
• Direct development
• Limited dispersal

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Population GeneticsThe ghost of times gone past

• Elephant Seal
• Hoelzel et al. 2002
• Northern and Southern subspecies
• Northern almost hunted to extinction
• mid 19th century
• 10-30 ind. left
• Any genetic effects?
• Loss of molecular diversity?
• Fitness effects?

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Population GeneticsThe ghost of times gone past

• Reduction in genetic diversity
• Microsatellite heterozygosity
• MtDNA sequence diversity

• Increase in asymmetry
• Skull measurement

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Population geneticsmanagement units

• Interdependence of fishery
• Do fisheries in the UK affect fisheries in Spain?
• European anchovy
• Bembo et al 1996
• Fished mainly in Mediterranean
• Several stocks?

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Molecular markers resource management

• Pacific salmon
• Spawn in freshwater
• Grow in the sea
• Natal homing
• Morphological and life-history variation among
  rivers
• How accurate?
• Conservation problem
• Fished at sea
• Habitat degradation
• dams
• How can population genetics help?

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Homing to very specific sites

• Sockeye salmon
• Little Togiak Lake
• Beach spawners
• Stream spawners
• Few meters apart
• Genetically differentiated

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Identification of ESUs

• Definition
• Substantially reproductively isolated
• Important component of the evolutionary legacy of
  the species
• For example
• coho

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Mixed Fisheries

• Salmon fisheries
• during spawning migration
• Mixed populations
• Problem to conserve some and exploit others
• Mixture proportions?

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Other applications Mixed Stock Analysis

• Estimation of mixture proportions from genetic
  data

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Mixed stock analysis

• Fraser River coho salmon
• Beacham et al. 2001
• Exploited by fish wheel in lower Frazer river
• Protection of upper Fraser river stocks
• Estimate proportions in total catch
• Close fishery when necessary

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Yukon River chum salmon

• Exploited on North and South Bank of Lower Yukon
• Spearman Miller 1997
• Stocks differ in bank preference

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Uniparentally inherited markers

• Uniparental inheritance
• mtDNA, cpDNA maternal
• Y-chromosome paternal
• Excellent marker for sex biased dispersal
• Inherited like surnames
• Can follow genealogies

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Mitochondrial DNA

• Exclusively maternally inherited
• No recombination
• haploid
• Contained in mitochondria
• Cell organelles
• Cell respiration
• Probably derived from bacteria
• Each cell
• 10s to 100s of mitochondria
• Each mitochondrion has several copies of DNA
• Usually all the same
• Only one haplotype
• Effective population size ?

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Mitochondrial DNA

• Circular molecule
• About 15 20 kbp
• Conserved gene order (in animals)
• 2 rRNA
• 22 tRNA
• 13 protein encoding genes
• 6 for one enzyme (NADH dehydrogenase)
• One non-coding region
• D-loop or control region
• Origin of replication
• May contain repeats (microsatellites)
• Different regions have different variability
• Very slow in plants
• D-loop gt protein genes gt rRNA gt tRNA
• Important for application
• Why?

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Examplefemale philopatry in Bechsteins bats

• Kerth et al. 2002
• Live in colonies in forests
• Females stay in natal colony
• Males?
• High relatedness among some individuals, but also
  unrelated
• Male gene flow?
• MtDNA and nuclear microsatellites
• Combination most powerful

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Chloroplast DNA

• Chloroplasts
• Cell organelles for photosynthesis
• DNA also circular
• Larger 20 250 kbp
• Very slow mutation rate
• Usually maternally inherited
• Biparental
• Paternal (some gymnosperms)
• Not as widely used
• Plant mtDNA
• Larger 20-2400 kbp
• Variable gene order
• Several circles
• Recombination
• Slow mutation rate
• Less often used
• Why?

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Y chromosome

• Present in
• Mammals
• Some fish, amphibians and reptiles
• Not birds
• ZW system
• No recombination
• May contain microsatellites
• Used a lot in human research

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Uniparentally inherited markers in humans

• General pattern
• Seielstad et al. 1998
• More differentiation at Y chromosomes
• Tested in Thai communities
• Oota et al. 2001

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Key Concepts

• Application of population genetics
• Dispersal patterns
• Expected vs. observed
• invisible walls
• Demographic history
• Genetic diversity inbreeding
• Resource management
• Population identification
• Data collection
• Mixed stock management

• Uniparentally inherited markers
• mtDNA
• Animals maternal, small, conserved gene order,
  fast evolution
• Plants maternal, large, slowly evolving
• cpDNA (chloroplasts)
• Maternal, biparental, paternal
• very slow
• Y-chromosome
• Paternal
• Used for human population biology and genetics
• And others