Lec6_Jan25-2010_Ernest_PopGen2

Lec6_Jan25-2010_Ernest_PopGen2 - Population Genetics 2 Text...

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Population Genetics 2 Text ch. 5 ECL242_PHR242 January 25, 2010 Ernest
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For Next Class Wed Jan 27, 2010 Computer LAB 1 Location: 2020 Science Lab Building (SLB) Map in following slide Read Excoffier and Heckel (2006) for computer lab Jan 27 Computer programs for population genetics data analysis: a survival guide. Nature Reviews. Genetics volume:7 issue: 10 page: 745. On SmartSite – Resources – Assigned Readings Focus on concepts rather than intricate details of programs. Review concepts of linkage disequilibrium, selective neutrality, Bayesian inference, Max Likelihood, "descriptive stats" (what are they?), etc. In tables scan for "special features" and what basic analyses the various software can do. Gain more exposure to the vocabulary of ecol. genetics data analysis.
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Computer lab 2020 Science Lab Bldg (SLB)
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Effective population size Pop. bottlenecks, founder effects, expansions Population structure Bayesian stats Genetic Distance and Differentiation Gene Flow and Migration (F ST ) Topics for today If we do not get through them all today, make sure to review these topics in text and assigned papers
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Effective population size, N e “The number of individuals in an idealized randomly mating pop. with equal sex ratios, that would exhibit the same rate of heterozygosity loss as an actual pop with a particular census size (total adult number of individuals)” Genetic diversity correlated with N e ≈ average # individuals that successfully reproduce in each generation Rare alleles lost faster in small than large pop Genetic drift = chance loss of alleles in small pop Mutation-drift dynamics Where we left off Last week
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N e , Effective Population Size N e vs. N c N e /N c ratio What affects N e ? Why does just a few generations of low N e cause dramatic lowering of long-term N e ? What is the term for transient low N e ? How can genetic data be used to infer N e ? Refer to text, chapter 5 page 146-147 Examples African Buffalo Brown Trout in Denmark mtDNA in leatherback turtles
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Genetic bottlenecks Significant declines in effective pop. size Why is rapid fall in Ne potentially more dangerous for a population than slow and gradual? Lowered Ne for short term followed by rapid increase vs. long term low Ne. Disequilibrium in expectations of heterozygotes relative to allele numbers. Why? Rare alleles lost more rapidly than common Most heterozygosity is contributed by common alleles Refer to text, chapter 5 page 150-154
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Significant declines in effective pop. Size Bottleneck tests Heterozygosity excess relative to allele numbers M ratio (ratio of microsatellite allele numbers to range in allele sizes) What about rapid population expansion? What happens then? Refer to text, chapter 5 page 150-154
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This note was uploaded on 03/02/2010 for the course ECL 242 taught by Professor Holly during the Winter '10 term at UC Davis.

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Lec6_Jan25-2010_Ernest_PopGen2 - Population Genetics 2 Text...

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