Gamma values > 1.0 and negative Z scores

[burbrink]

Hello,

I have concatenated a Rad dataset for 100 individuals between two populations with an outgroup for >200,000 bps (not just snps). I placed all individuals with ancestral coefficients from ADMIXTURE between 0.15-0.85 into a category labeled hybrids. These hybrids occur at the geographic interface between two populations and do likely represent some hybrids or introgressed individuals.

When I ran dat.test_triple("p1", "hybrids", "p2") It does not detect the population as hybrids: Zscore': 1.1033779680260525, 'Pvalue': 0.13493157539518108, 'Gamma': 0.3994434282279553

Similarly when I run dat.test_individuals it finds no significant hybrids. Some of these are likely hybrids. But some of the results yield gammas close to 0.5 and are not significant. Others have yielded negative z scores with gammas >1.0. Here are some examples: Zscore': 0.633475935023594, 'Pvalue': 0.26321138714970815, 'Gamma': 0.3780456480258329 'Zscore': -0.29460033809760533, 'Pvalue': 0.6158503303969829, 'Gamma': 1.1279513034923758

I realize that the Z scores are not high enough to be significant, but I am wondering how the gammas could be this high and not significant.

I read the new paper by Kong and Kubatko comparing performance of HyDe with structure based methods, but it would be hard to believe that so many instances of admixture are not detected with HyDe. Might this to do with missing data, which here could be upwards of 30% for some individuals.

Thanks so much for taking the time to look this over and answer me.

Frank

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