I haven't come across a PCoA with this unusual shape before, and am wondering if anyone has any idea what could have gone wrong, or what it could mean?

The Data: I have around 7000 SNP loci (Filtered at a call rate>90%) from DArTseq for 188 eucalyptus individuals. This data is Bi-allelic, with some loci not present (00).

Using GenAlEx a covariance-standardized PCoA was produced for this data. Each color represents a different sampling population.

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