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Lec3_Jan-11-2010_Ernest-GeneticID

Lec3_Jan-11-2010_Ernest-GeneticID - Genetic Identification...

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Today’s Session Genetic Identification: individual, sex, species Trace DNA Molecular Marker highlight: microsatellites Rudnick paper – Eagle feathers/genetic identification Announcements for Wednesday Jan 13 Read Jones and Ardren paper for class discussion Scan ch 4 – see next slide for details Homework-2 due Wed Jan 13 at 1pm Today’s Plan Genetic Identification ECL242 / PHR 242 Ecological Genetics Jan 11 2010
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Chapter 4 What to focus on for Jan 13 Spend more time on the Jones and Ardren paper than chapter 4. Mostly scan it, with a little more focus on: P 102-107 starting with “Monogramy…” section Box 4.2 and 4.3 (CERVUS and KINSHIP) Scan and focus on broad concepts for rest of chapter (no intricate details of the example systems necessary, just use them to learn concepts) Ignore minisatellite box 4.1
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Jones and Ardren paper What to focus on for Jan 13 Read through and learn the basics of methods for parentage analysis We’ll be discussing the paper after the Lecture on Jan 13. Look through “Information Box” and Table 1 No need to memorize the equations in the Box, but if you are able, see if you can make sense of them Exclusion, categorical allocation, parental reconstruction. Just basic concept behind fractional allocation – not need to focus on equation No need to focus on specifics of particular software programs – scan those sections. Focus on the Tech. /Biol hurtles section starting on page 2518 (null alleles, linked loci, linkage diseq., etc) Review the basics of AFLP, SNP, Microsat from previous reading and lectures.
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A few highlights from first 2 sessions
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Molecular Markers Optimal characteristics THERE IS NO COMPLETELY IDEAL MARKER however here are some characteristics that allow utility depending on specific question Alternate alleles readily identifiable and differ from each other in DNA sequence Assayable by polymerase chain reaction (PCR) Comparability DNA rather than protein Produces frequency data Single-locus (mSat, SNP, etc) as opposed to multilocus markers (minisat) Codominant (but not always required) homo- and heterozygotes can be distinguished Works in variety of source tissues Present in all life stages of organism Neutrality important for some purposes (pop gen, etc) However genes signaling a selected / adaptive trait useful in others.
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Key points to take home MtDNA Unique and common characteristics of: mtDNA relative to nuclear DNA MtDNA Numts (Nuclear inserts in mtDNA) What they are, how they impact analyses General patterns of variation – that mtDNA varies in size, gene content across and within taxonomic groups. From your reading: Plasmids – what they are & how they’re used Mutation rate and evolution
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Key points to take home Immune Genes Very high genetic variation Mechanisms for generating variation differ from much of nuclear DNA Balancing selection Codominant expression of MHC Thousands other immune genes beside MHC Innate immunity (mucous membrane integrity,…)
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