If we use RAD-seq to investigate speciation between cryptic (?) insect species, what would we expect the output to look like? We don´t know beforehand what species the sample originate from so they need to be separated from each other during data processing. They have high genetic divergence so they should be easy to separate during alignment.
So, given a scenario where we have 24 pooled samples of which 8 orginate from species 1 and 16 from species 2. After demultiplexing, I guess that we need to align all samples to two different reference genomes. Would that mean that when using reference genome for species 1, we would only find alignment for 8 samples and the remaining 16 will look like crap with low/no matches (and the other way around)?
So, given a scenario where we have 24 pooled samples of which 8 orginate from species 1 and 16 from species 2. After demultiplexing, I guess that we need to align all samples to two different reference genomes. Would that mean that when using reference genome for species 1, we would only find alignment for 8 samples and the remaining 16 will look like crap with low/no matches (and the other way around)?