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Still, we found that the most abundant lineage, the 'modern' Euro-American, was associated with a higher acute phase response as well as a higher leukocyte count.
It would statistically favour the fixation of the already most abundant lineage ' italica' in Southern Italy as we actually observed in our study.
For example, a newly discovered phage HMO-20111) capable of infecting the most abundant lineage of marine bacteria, the SAR116 clade, can account for up to 25% of all viral genome reads in the ocean (Kang et al., 2013).
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Our results show that tests using the unweighted and weighted UniFrac distances are less powerful in detecting abundance change in moderately abundant lineages.
On the other hand, weighted UniFrac distance is most sensitive to detect change in abundant lineages since it uses absolute abundance difference in its definition.
Since d U and d W reflect the abundance change in either rare lineages or abundant lineages, combining d U and d W may potentially increase the overall power.
Apart from being abundant, lineage-specific genes have also been thought to be important for lineage specific traits and adaptations [ 54].
We investigate six scenarios, where the environmental factor affects the community membership, species evenness, species richness, most abundant lineages moderately abundant lineages and rare lineages (Fig. 1B G).
In contrast, d 0.5) is the most powerful for detecting change in moderately abundant lineages (Panel 5).
The results are consistent with the 2D circle-based simulation: d W is most powerful in detecting the environmental effect on most abundant lineages, d 0.5) is most powerful for moderately abundant lineages and d U is most powerful for rare lineages.
However, these two measures assign too much weight either to rare lineages or to most abundant lineages, which can lead to loss of power when the important composition change occurs in moderately abundant lineages.
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