Phylodynamics of G4P[8] and G2P[4] strains of rotavirus A isolated in Russia in 2017 based on full-genome analyses

Domestication Explains Two-Thirds of Differential-Gene-Expression Variance between Domestic and Wild Animals; The Remaining One-Third Reflects Intraspecific and Interspecific Variation

“…Furthermore, columns viii and ix of Table 8 translate a log2 value of a gene in an animal into either low or excessive expression of this gene during divergence of both domestic and wild forms of this animal from their most recent common ancestor. Recently [ 57 , 58 ], an RNA-Seq data analysis was based on this oldest phylogeny concept [ 59 ] widely used elsewhere [ 60 , 61 , 62 , 63 ]. Let us look at these orthologous genes one by one and discuss effects of their expression changes on reproductive potential in humans as well as during divergence of domestic and wild animals from their most recent com-mon ancestor [ 24 , 25 , 28 , 29 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 , 72 , 73 , 74 , 75 , 76 , 77 , 78 , 79 , 80 , 81 , 82 , 83 , 84 , 85 , 86 ] ( Table 8 ).…”

A Bioinformatics Model of Human Diseases on the Basis of Differentially Expressed Genes (of Domestic Versus Wild Animals) That Are Orthologs of Human Genes Associated with Reproductive-Potential Changes

“…Then, by means of PubMed [43], we compiled independent publicly available experimental in vivo RNA-Seq data sets on domestic versus wild animals [26,28,29], as depicted in Figure 1 (Step-2) and presented in Table 1. For the RNA-Seq data analysis, here, we, for the first time, resumed the use of one of the eldest [44] commonly accepted (e.g., see [45]) and widely used (e.g., see [46]) concepts of "divergence from the nearest common ancestor (NCA)" within the framework of the microevolution theory in relation to domesticated and wild animals, whose differentially expressed genes (DEGs) were compared with orthologous human genes under this study, as depicted in Figure 1. After that, we found 28 pairs of orthologous genes in humans and animals among all genes analyzed in this work, as depicted by a Venn diagram in Figure 1 (Step-3).…”

“…The only novelty of this work is that for the RNA-Seq data analysis, we, for the first time, resumed the use of one of the most ancient [44] conventional (e.g., see [45]) and actual (e.g., see [46]) microevolutional concepts of "divergence from the nearest common ancestor (NCA)" in the case of domestic and wild animals, whose differentially expressed genes (DEGs) were compared with orthologous human genes under this study (Figure 1: Step-3). This allows us to compare the effects of co-directional changes in the expression of orthologous genes on human reproductive potential and on the divergence of domestic and wild animals from their NCA, as shown in Tables 2 and 4, as well as in Figure 1 (Step-4).…”

A bioinformatic search for correspondence between differentially expressed genes of domestic versus wild animals and orthologous human genes altering reproductive potential

“…A total of 3080 DEGs of domestic versus wild animals were analyzed here, which are freely available in the PubMed database (Lu, 2011), as described in Table 2 and characterized by examples in Table 3. At the same time, according to (Klimova et al, 2021;Vasiliev et al, 2021), here, RNA-Seq data were examined in accordance with one of the oldest (Samet, 1985), widely used (Sun et al, 2008;Morozova et al, 2020;Hakizimana et al, 2021), and fundamental (Zhang et al, 2021) concepts of phylogenetic analysis -"most recent common ancestor" (Samet, 1985). In this regard, domestic animals and their wild relatives were studied by means of oppositely directed equivalent changes in gene expression in comparison with their unknown most recent common ancestor.…”