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Morphometric analyses
This protocol is extracted from research article:
Morphology of the Denisovan phalanx closer to modern humans than to Neanderthals
Sci Adv, Sep 4, 2019;

Procedure

For the morphometric comparative analysis, DPs from published and unpublished Neanderthals, Pleistocene modern humans, and three samples of recent modern humans from France and Belgium dated from the Neolithic to the Middle Ages (including a modern human and a Neanderthal DP5 undergoing epiphyseal fusion) were assigned to a specific digit based on their respective length and robustness [DP3 ≥ DP4 > DP2 > DP5; (25)] and the morphology of their extremities (table S1) (26, 27, 35). When uncertain, the DPs were pooled in two additional ranks: DP2–4 or DP2–5. The measurements used were those defined by Musgrave (36) for phalanges. The dimensions of Denisova 3 used were those taken on the original specimen for all measurements except the maximum length, which was taken on the virtual reconstruction of the two fragments (Table 2).

We used univariate and multivariate analyses to explore the morphometric characteristics of the DP5 Denisova 3. To compare the dimensions of Denisova 3 to the means and SDs of the Neanderthal and modern human comparative groups, we calculated the scaled Z-score with the distribution variance estimated by the sample variance. The scaled Z-score was chosen such that at Z = 1, it will correspond to a 5% P value for two tails. This was achieved by introducing a scaling factor for the Z-score, which effectively uses a normal distribution with zero mean and variance 1/1.9599. The scaled Z-score was estimated modeling a student’s distribution and correcting for sample size using the following formula (37, 38)$Z*=∣X−m∣t0.975;n−1*s2(1+1n)$where Z* is the scaled Z-score, X is the Denisova 3 measurement, m is the mean of the corresponding measurement in the Neanderthal or AMH population, s is the SD, and n is the sample size. Last, t0.975;n-1 is the 97.5% unilateral quantile of the Student’s distribution for n − 1 degree of freedom. The multivariate analysis of the various DPs was performed using principal components analyses (PCAs) on dimensions that were size adjusted through the normalization of each dimension by the geometric mean of all dimensions (39, 40).

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