lecture 11

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lecture 11

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1. 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

2. Population Genetics:marine dispersal (or not)? Cleaner goby (Elacatinus evelynae) Taylor & Hellberg 2003 Three color morphs Pelagic larvae (3 weeks)

3. Population Genetics:marine dispersal (or not) Cleaner goby (Elacatinus evelynae) High population differentiation Up to FST = 0.7 Surprising philopatry in larvae

4. Population Genetics:invisible walls Cuttlefish (Sepia officinalis) Perez-Losada et al 2002 Direct development Limited dispersal

5. 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?

6. Population GeneticsThe ghost of times gone past Reduction in genetic diversity Microsatellite heterozygosity MtDNA sequence diversity

7. 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?

9. 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?

10. Homing to very specific sites Sockeye salmon Little Togiak Lake Beach spawners Stream spawners Few meters apart Genetically differentiated

11. Identification of ESUs Definition Substantially reproductively isolated Important component of the evolutionary legacy of the species For example coho

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

14. Other applications Mixed Stock Analysis Estimation of mixture proportions from genetic data

15. 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

16. Yukon River chum salmon Exploited on North and South Bank of Lower Yukon Spearman & Miller 1997 Stocks differ in bank preference

17. Uniparentally inherited markers Uniparental inheritance mtDNA, cpDNA – maternal Y-chromosome – paternal Excellent marker for sex biased dispersal Inherited like surnames Can follow genealogies

18. 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 ?

19. 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 > protein genes > rRNA > tRNA Important for application Why?

20. Example:female philopatry in Bechstein’s 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

21. 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?

22. 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

23. Uniparentally inherited markers in humans General pattern Seielstad et al. 1998 More differentiation at Y chromosomes Tested in Thai communities Oota et al. 2001

24. 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

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