I have difficulty with the implications of the PcoA analysis. Please help me?

[Kimhyeongsu]

I analyzed PcoA targeting the mealybug mitochondrial CO1 region. Why are they grouped into one cluster?

[colinbrislawn (Colin J Brislawn)]

Hello Kim,

Welcome to the forums!

Thank you for sharing that plot! Are you able to share the .qzv or .qza file used to make it?
(If not, that's okay, I know data can be important to keep private.)

I ask because there are a few things that can 'break' PCoA plots, resulting in grouping like that.

PCoA plots place similar samples close together, so this graph implies that GG, GB, and JB samples are all identical.

Identical samples can result from problems in denoising or filtering.
(This could be related to the CO1 region, or not!)