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Communities with greater human disturbance were not more functionally homogeneous; they did not harbor communities with more generalists.
We have observed that the more recurrent the edge clusters are, the more functionally homogeneous they are.
For example, Devictor et al. [ 9] showed that the mean habitat specialization of birds declined with human disturbance, concluding that communities were more functionally homogeneous with disturbance.
The result indicates that our method can identify more functionally homogeneous modules with more diverse GO terms (see Section S7 of Supplementary material).
In some communities with expanded human land use, generalists may replace specialists, dominance by fewer species may increase, and communities may become more functionally homogeneous [ 6- 9].
To focus on only canonical TFs, which should be more functionally homogeneous and increase our specificity for HOT regions, we removed from the analysis four classes of proteins with different behaviors that confounded our goal of HOT region analysis.
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We find in particular that communities with a high mean clustering coefficient are far more likely to be functionally homogeneous than those with a lower one.
For instance, due to the larger niche availability, species that coexist in heterogeneous environments experience a less severe effect of clustering in their functional traits giving rise to assemblages that are more functionally diverse than in more homogeneous areas.
We also find that proteins involved in some processes are much more likely to be in functionally homogeneous communities than others.
Figure 3 illustrates for the A network these percentages for four particular processes.. Proteins of some types are far more likely to be found in functionally homogeneous communities than others.
For example, for both the A and P networks, proteins involved in chromosome organisation are far more likely to be found in functionally homogeneous communities than proteins involved in lipid metabolism.
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