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Under the neutral evolutionary scenario, over evolutionary time, orthologous transcription factors have accumulated so many mutations, albeit neutral ones, that though their functions may remain the same they are no longer identifiable as orthologs by computational means.
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In contrast, the neutral evolutionary rates using synonymous sites were similar across all the timescales.
Nucleotide conservation was estimated using the Genomic Evolutionary Rate Profiling (GERP) (scores: −12.3 = least conserved to 6.17 = most conserved) (Cooper et al., 2005) and PhyloP, which compares the probability of observed substitutions under the hypothesis of neutral evolutionary rate: positive scores suggest constraint (conservation) (Pollard et al., 2010).
In the absence of natural selection (i.e., under a strictly neutral evolutionary process), the genetic diversity measure obtained reflects the change in effective number of infections over time (N et, where t is the average generation time).
We have elaborated on our usage of this term in the Materials and methods section as follows: "In the absence of natural selection (i.e. under a strictly neutral evolutionary process) the genetic diversity measure obtained reflects the change in effective number of infections over time (Net, where t is the average generation time).
Given the high likelihood of gene duplication under neutral evolutionary processes, however, as the size of molecular data sets gets larger (in number of genes and taxa used) the amplification of duplicated genes may happen inadvertently even in the course of targeting genes that appear at first glance to be single copy (See below).
Analyses under neutral evolutionary scenarios, on the other hand, have argued for the spontaneous gain and loss of binding sites [ 17].
Under a neutral evolutionary scenario, longer sequences are more likely to accumulate deleterious mutations than shorter ones.
Across the whole genome, most CNV have evolved under neutral evolutionary pressures and their frequency and sequence context have been shaped by demographic events, mutation, and genetic drift [ 14, 15, 17].
The presented results must be interpreted in relation to the reported expected rate of morphological change for mammals under neutral evolutionary expectations, which ranges from 0.0001 to 0.01 [18].
Genome-wide, most CNVs evolved under neutral evolutionary pressures.
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