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Understanding Aging after Darwin
Published in Shamim I. Ahmad, Aging: Exploring a Complex Phenomenon, 2017
A second example involves the admixture of genetic material between two diverging species, a process referred to as reticulate evolution (Hoelzel 2016). There is DNA evidence that a low level of interbreeding occurred between Homo sapiens and two other human-lineage species, Neanderthal and Denisovan. In fact, the genetic underpinnings of the Tibetan population adaptation to high altitude are due to introgression of Denisovan genomic DNA (Fan et al. 2016). In addition, de Manuel et al. (2016) have documented gene flow between subspecies of chimpanzees as well as gene flow from bonobos to chimpanzees that occurred after divergence of these two species 1.5 to 2 million years ago. These examples indicate that natural hybridization may be an important contributor to speciation and evolution of existing species.
Tracing protein and proteome history with chronologies and networks: folding recapitulates evolution
Published in Expert Review of Proteomics, 2021
Gustavo Caetano-Anollés, M. Fayez Aziz, Fizza Mughal, Derek Caetano-Anollés
The comparative genomic analysis of structural domains in proteomes that began with Gerstein [100] informs about the lexicon, syntax and semantics of proteome vocabularies [101]. For example, Table 2 shows a decade-spanning series of analyses of SCOP FSF and FF distributions in the proteomes of superkingdoms and viruses [102–105]. The existence of ‘cores’ common to cellular life and viruses (Venn groups ABEV) and cellular life (ABE) (making up 20–26% of all domains) support both a last universal common ancestor (LUCA) and a last universal cellular ancestor (LUCellA) of life. A ‘periphery’ of domains specific or shared by groups suggest their late diversification, including vocabulary compression typical of microbial life [101]. Significant distribution biases, such as the supernumerary BE and BEV Venn groups, support a tripartite cellular world and an early origin of Archaea [106]. Groups that include viruses, while underrepresented, support wide structural exchange and very early viral origins [104,105]. Similar comparative genomic patterns can be extracted from Pfam domain data [107]. However, universal Pfam cores barely exceed 10%, showcasing the limitations of lower protein organization levels. Percent domain composition of each Venn group was quite constant despite significant increases in proteome and viral sampling (Table 2), suggesting comparative genomic patterns are robust. However, processes of reticulate evolution such as horizontal gene transfer complicate interpretations, prompting phylogenomic analyses.