Post date: Aug 03, 2017 2:54:36 PM
I am collaborating with Axel Meyer and others on an analysis of artificial Xiphophorus fish hybrids. Basically, this system has many natural hybrid lineages and Axel et al. have fish from 100 generations of natural hybridization with back-crossing (and with or without selection). My goal is to help with some of the ancestry analyses. I have two initial analyses planned:
1. reconstruction of ancestry frequencies using popanc
2. some simulations (leading to ABC) of null expectations for ancestry frequencies (I have some information on rearing conditions, bottom line is that N has been tiny).
The data are in /uufs/chpc.utah.edu/common/home/u6000989/projects/xip/data_notes/. There are two vcf files, one for the artificial hybrids (lab-cross.vcf) and one for natural hybrids (wild-sample.vcf). For now I plan to focus on the lab hybrids. The supplemental xlsx file explains the IDs, there are parents, first generation BC and ~100 generation BC without and without selection.The data for the wild individuals are described in Jones_et_al-2013-Molecular_Ecology.pdf.