Computer Lab1-Jan27-2010

Computer Lab1-Jan27-2010 - Computer Lab#1 Ecological...

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Computer Lab #1 Ecological Genetics / ECL242_PHR242 Wed, January 27, 2010 Proofing and preliminary analysis of population genetic data to assess population structure and genetic diversity Course announcements Term project paragraph was due to Smartsite today – if not handed in yet, do soon. For Mon Feb 1, read text Ch 1 and Mullens et al 2009 paper Homework #4 - Will be posted on SmartSite Friday and Due Wed Feb 3 at 1pm Questions that we are starting to address in this and future computer labs: Does our data represent one or more populations? Is this set of samples representative of a single or more than one sexually reproducing population? What is the genetic diversity of the population(s)? Answering these questions are also prerequisite to other objectives including analyzing data for relatedness/parentage/kinship and individual ID (trace or noninvasive sampling, etc). Goals today Reviewing your data – by eye - Proof-reading, screening, and pruning the data, catching problem loci, finding interesting patterns, archiving raw data in a safe place Introduction to software – preparing input files for software Working with genotype data and generating basic “summary statistics” If time today (if not next week): Hardy-Weinberg (HWE) and Linkage equilibria (LE) tests o Effects on summary statistics HWE and LE of THE PROCESS Think of it like the game SNAKES AND LADDERS Sometimes you fly forward up the DNA analysis ladders, but sometimes you hit a snake and get sent way back! 1.
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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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Computer Lab1-Jan27-2010 - Computer Lab#1 Ecological...

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