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  • incorporating outgroup in a SNP phylogeny

    I'm looking for advice on incorporating information from the genome of outgroups in a phylogeny based on SNPs called by aligning ingroup short-read sequences to the ingroup reference genome.

    The focus is on intraspecific genetic relationships but I would like to be able to root my tree with two closely-related outgroups (genomes available for both) and to estimate divergence times between populations in the ingroup. I'll be using a variety of phylogenetic reconstruction methods that can handle SNPs but at the moment am trying to figure out how to add the outgroup information.

    Is it appropriate to just find the corresponding position of SNPs in the outgroup genomes and simply add the nucleotide information for the outgroup to my ingroup alignment? I'm worried about missing critical sites that are fixed in the ingroup but that would speak to divergence between the ingroup and outgroup taxa. What solutions have others used?

    Also should mention that genome is >200Mb and a eukaryote.

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