User:Molly Schumer/Notebook/Analysis of X. birchmanni - X. malinche hybrid zones

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Project Description/Abstract

  • We are working on several projects that involve analyzing admixture between X. birchmanni and X. malinche

Notes

  • All analyses on this page use Multiplexed Shotgun Genotyping data (or MSG: http://www.ncbi.nlm.nih.gov/pubmed/21233398) to genotype hybrids
  • MSG has some limits on its ability to genotype natural hybrids, see the simMSG page for more details

28 May 2014

  • Individuals from PERI look best in terms of block sizes and admixture proportions
  • The PERI site is also near JITO and BATS on the river so concentrating collecting in these areas is probably our best bet, though fish are not abundant and the site is difficult to get to
  • Here are some plots (site names in the individual ids)

Image:IndivBATS-01 GCCTGG-hmmprob.pdf Image:IndivBATS-02 AATGTG-hmmprob.pdf Image:IndivPERI-01 GGAAGT-hmmprob.pdf Image:IndivPERI-05 GGGTTG-hmmprob.pdf

27 May 2014

  • I'm working on analysis of a few new samples from several hybrid populations
  • JITO
  • BATS
  • ROCA
  • TOTO
  • ACUA
  • PERI
  • So far I've run individuals from TOTO, JITO and ROCA through the pipeline. Unfortunately it looks like TOTO will be unusable which is a pain because we collected a bunch of individuals from there in March. They are >85% birchmanni. Both JITO and ROCA look like usable populations, JITO looks like ~65% birchmanni while ROCA is 68% malinche. I think both of these sites were difficult to get to. I will do a full analysis when MSG is operational on della

Image:IndivJITO-04 TATAGT-hmmprob.pdf

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